| "+e[h].substring(0,4)+" | "),b.push(""+e[h].split("Title>")[1].split("");b.push(" |
");
+if (ptPre >= 0) this.line = this.line.substring(ptPre + 5);
+var intTableNo = this.parseIntStr(this.line);
+if (intTableNo == 0) {
+this.setSpaceGroupName(this.line.substring(2));
+} else {
+while (intTableNo < 0 && this.rdLine() != null) intTableNo = this.parseIntStr(this.line);
+
+this.setSpaceGroupName("" + intTableNo);
+}var data = Clazz.newFloatArray (6, 0);
+this.fillFloatArray(this.rdLine(), 0, data);
+for (var i = 0; i < 6; i++) this.setUnitCellItem(i, data[i]);
+
+this.i0 = this.asc.ac;
+this.nAtoms = this.parseIntStr(this.rdLine());
+for (var i = this.nAtoms; --i >= 0; ) {
+var tokens = JU.PT.getTokens(this.rdLine());
+if (!this.getSym && tokens[1].contains("_")) continue;
+if (tokens.length == 3) this.addAtomXYZSymName(tokens, 0, "Be", "Be1");
+ else this.addAtomXYZSymName(tokens, 3, tokens[0], tokens[0] + tokens[1]);
+}
+if (Float.isNaN(fAmp)) {
+if (ptPre >= 0) this.applySymmetryAndSetTrajectory();
+return;
+}this.line = null;
+this.readDisplacements(fAmp);
+}, "~S,~N");
+Clazz.defineMethod(c$, "setSpaceGroupName",
+function(name){
+if (!this.ignoreFileSpaceGroupName) {
+name = "bilbao:" + name;
+} else if (this.sgName.startsWith(":")) {
+var pt = name.indexOf(':');
+if (pt < 0) pt = name.length;
+name = name.substring(0, pt);
+var s = this.htParams.get("loadScript");
+if (s != null) {
+pt = s.indexOf("spacegroup \":");
+if (pt > 0) s.insert(pt + 12, name);
+}name += this.sgName;
+this.ignoreFileSpaceGroupName = false;
+}Clazz.superCall(this, J.adapter.readers.xtal.BilbaoReader, "setSpaceGroupName", [name]);
+}, "~S");
+Clazz.defineMethod(c$, "readDisplacements",
+function(fAmp){
+for (var i = 0; i < this.nAtoms; i++) {
+if (this.line == null) this.rdLine();
+var tokens = JU.PT.split(this.line, "x|x");
+if (this.getSym || !tokens[0].contains("_")) this.asc.atoms[this.i0 + i].vib = JU.V3.new3(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+this.line = null;
+}
+this.applySymmetryAndSetTrajectory();
+for (var i = this.asc.ac; --i >= this.i0; ) {
+var a = this.asc.atoms[i];
+if (a.vib != null) {
+var v = new JU.Vibration();
+v.setT(a.vib);
+a.vib = v;
+this.asc.getSymmetry().toCartesian(v, true);
+v.scale(1 / fAmp);
+}}
+this.appendLoadNote((this.asc.ac - this.i0) + " displacements");
+}, "~N");
+Clazz.defineMethod(c$, "setTitle",
+function(title){
+if (title != null) {
+this.asc.setAtomSetName(title);
+this.appendLoadNote(title);
+}}, "~S");
+Clazz.defineMethod(c$, "rdLine",
+function(){
+while (this.rd() != null && (this.line.trim().length == 0 || this.checkComment())) {
+}
+return this.line;
+});
+Clazz.defineMethod(c$, "readVirtual",
+function(){
+if (this.line.contains("K-vector:")) this.kvec = this.line.substring(this.line.indexOf("("), this.line.indexOf(")") + 1);
+var s = this.getLinesUntil("\"BCS\"");
+var pt = s.indexOf("The amplitude");
+pt = s.indexOf("=", pt);
+var amp = s.substring(pt + 2, s.indexOf(" ", pt + 2));
+var fAmp = (this.normDispl ? this.parseFloatStr(amp) : 1);
+var irrep = this.getAttr(s, "irrep");
+if (irrep.indexOf(":") >= 0) irrep = irrep.substring(0, irrep.indexOf(":"));
+this.line = this.line.substring(this.line.indexOf("value=") + 7);
+this.readBilbaoFormat(this.kvec + " " + irrep + " (" + amp + " Ang.)", fAmp);
+});
+Clazz.defineMethod(c$, "getAttr",
+function(s, key){
+var pt = s.indexOf("value", s.indexOf("\"" + key + "\""));
+s = JU.PT.getQuotedStringAt(s, pt);
+s = JU.PT.rep(s, "", "");
+s = JU.PT.rep(s, "", "");
+return s.trim();
+}, "~S,~S");
+Clazz.defineMethod(c$, "getLinesUntil",
+function(key){
+var sb = new JU.SB();
+do {
+sb.append(this.line);
+} while (!this.rd().contains(key));
+return sb.toString();
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CastepReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CastepReader.js
new file mode 100755
index 000000000000..aecc1ef6369e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CastepReader.js
@@ -0,0 +1,520 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.CastepReader", ["JU.DF", "$.Lst", "$.M4", "$.P3", "$.PT", "$.V3", "J.adapter.smarter.Atom", "JU.Escape", "$.Logger", "$.Tensor"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.tokens = null;
+this.isPhonon = false;
+this.isTS = false;
+this.isOutput = false;
+this.isCell = false;
+this.a = 0;
+this.b = 0;
+this.c = 0;
+this.alpha = 0;
+this.beta = 0;
+this.gamma = 0;
+this.abc = null;
+this.ac = 0;
+this.atomPts = null;
+this.havePhonons = false;
+this.lastQPt = null;
+this.qpt2 = 0;
+this.desiredQpt = null;
+this.desiredQ = null;
+this.chargeType = "MULL";
+this.isAllQ = false;
+this.haveCharges = false;
+this.tsType = null;
+this.matSupercell = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "CastepReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.abc = new Array(3);
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+if (this.filter != null) {
+this.chargeType = this.getFilter("CHARGE=");
+if (this.chargeType != null && this.chargeType.length > 4) this.chargeType = this.chargeType.substring(0, 4);
+this.filter = this.filter.$replace('(', '{').$replace(')', '}');
+this.filter = JU.PT.rep(this.filter, " ", " ");
+this.isAllQ = this.checkFilterKey("Q=ALL");
+this.tsType = this.getFilter("TSTYPE=");
+if (!this.isAllQ && this.filter.indexOf("{") >= 0) this.setDesiredQpt(this.filter.substring(this.filter.indexOf("{")));
+this.filter = JU.PT.rep(this.filter, "-PT", "");
+}this.continuing = this.readFileData();
+});
+Clazz.defineMethod(c$, "setDesiredQpt",
+function(s){
+this.desiredQpt = new JU.V3();
+this.desiredQ = "";
+var num = 1;
+var denom = 1;
+var ipt = 0;
+var xyz = 0;
+var useSpace = (s.indexOf(',') < 0);
+for (var i = 0; i < s.length; i++) {
+var c = s.charAt(i);
+switch ((c).charCodeAt(0)) {
+case 123:
+ipt = i + 1;
+num = 1;
+denom = 1;
+break;
+case 47:
+num = this.parseFloatStr(s.substring(ipt, i));
+ipt = i + 1;
+denom = 0;
+break;
+case 44:
+case 32:
+case 125:
+if (c == '}') this.desiredQ = s.substring(0, i + 1);
+ else if ((c == ' ') != useSpace) break;
+if (denom == 0) {
+denom = this.parseFloatStr(s.substring(ipt, i));
+} else {
+num = this.parseFloatStr(s.substring(ipt, i));
+}num /= denom;
+switch (xyz++) {
+case 0:
+this.desiredQpt.x = num;
+break;
+case 1:
+this.desiredQpt.y = num;
+break;
+case 2:
+this.desiredQpt.z = num;
+break;
+}
+denom = 1;
+if (c == '}') i = s.length;
+ipt = i + 1;
+break;
+}
+}
+JU.Logger.info("Looking for q-pt=" + this.desiredQpt);
+}, "~S");
+Clazz.defineMethod(c$, "readFileData",
+function(){
+while (this.tokenizeCastepCell() > 0) if (this.tokens.length >= 2 && this.tokens[0].equalsIgnoreCase("%BLOCK")) {
+JU.Logger.info(this.line);
+if (this.tokens[1].equalsIgnoreCase("LATTICE_ABC")) {
+this.readLatticeAbc();
+continue;
+}if (this.tokens[1].equalsIgnoreCase("LATTICE_CART")) {
+this.readLatticeCart();
+continue;
+}if (this.tokens[1].equalsIgnoreCase("POSITIONS_FRAC")) {
+this.setFractionalCoordinates(true);
+this.readPositionsFrac();
+continue;
+}if (this.tokens[1].equalsIgnoreCase("POSITIONS_ABS")) {
+this.setFractionalCoordinates(false);
+this.readPositionsAbs();
+continue;
+}}
+if (this.isPhonon || this.isOutput || this.isTS) {
+if (this.isPhonon) {
+this.isTrajectory = (this.desiredVibrationNumber <= 0);
+this.asc.allowMultiple = false;
+}return true;
+}return false;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.isOutput) {
+if (this.line.contains("Real Lattice(A)")) {
+this.readOutputUnitCell();
+} else if (this.line.contains("Fractional coordinates of atoms")) {
+if (this.doGetModel(++this.modelNumber, null)) {
+this.readOutputAtoms();
+}} else if (this.doProcessLines && (this.line.contains("Atomic Populations (Mulliken)") || this.line.contains("Hirshfield Charge (e)"))) {
+this.readOutputCharges();
+} else if (this.doProcessLines && this.line.contains("Born Effective Charges")) {
+this.readOutputBornChargeTensors();
+} else if (this.line.contains("Final energy ")) {
+this.readEnergy(3, null);
+} else if (this.line.contains("Dispersion corrected final energy*")) {
+this.readEnergy(5, null);
+} else if (this.line.contains("Total energy corrected")) {
+this.readEnergy(8, null);
+}return true;
+}if (this.line.contains("<-- E")) {
+this.readPhononTrajectories();
+return true;
+}if (this.line.indexOf("Unit cell vectors") == 1) {
+this.readPhononUnitCell();
+return true;
+}if (this.line.indexOf("Fractional Co-ordinates") >= 0) {
+this.readPhononFractionalCoord();
+return true;
+}if (this.line.indexOf("q-pt") >= 0) {
+this.readPhononFrequencies();
+return true;
+}return true;
+});
+Clazz.defineMethod(c$, "readOutputUnitCell",
+function(){
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSetClear(false);
+this.setFractionalCoordinates(true);
+this.abc = this.read3Vectors(false);
+this.setLatticeVectors();
+});
+Clazz.defineMethod(c$, "readOutputAtoms",
+function(){
+this.readLines(2);
+while (this.rd().indexOf("xxx") < 0) {
+var atom = new J.adapter.smarter.Atom();
+this.tokens = this.getTokens();
+atom.elementSymbol = this.tokens[1];
+atom.atomName = this.tokens[1] + this.tokens[2];
+this.asc.addAtomWithMappedName(atom);
+this.setAtomCoordTokens(atom, this.tokens, 3);
+}
+});
+Clazz.defineMethod(c$, "readEnergy",
+function(pt, prefix){
+if (this.isTrajectory) this.applySymmetryAndSetTrajectory();
+this.tokens = this.getTokens();
+try {
+var energy = Double.$valueOf(Double.parseDouble(this.tokens[pt]));
+this.asc.setAtomSetName(prefix + "Energy = " + energy + " eV");
+this.asc.setAtomSetEnergy("" + energy, energy.floatValue());
+this.asc.setCurrentModelInfo("Energy", energy);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+this.appendLoadNote("CASTEP Energy could not be read: " + this.line);
+} else {
+throw e;
+}
+}
+}, "~N,~S");
+Clazz.defineMethod(c$, "readPhononTrajectories",
+function(){
+if (!this.isTS) this.isTrajectory = (this.desiredVibrationNumber <= 0);
+if (this.isTrajectory) this.asc.setTrajectory();
+this.doApplySymmetry = true;
+while (this.line != null && this.line.contains("<-- E")) {
+var skip = (this.isTS && this.tsType != null && this.prevline.indexOf(this.tsType) < 0);
+if (!skip) {
+this.asc.newAtomSetClear(false);
+if (this.isTS) this.readEnergy(0, JU.PT.getTokens(this.prevline + " -")[0] + " ");
+this.discardLinesUntilContains("<-- h");
+this.setSpaceGroupName("P1");
+this.abc = this.read3Vectors(true);
+this.setLatticeVectors();
+this.setFractionalCoordinates(false);
+this.discardLinesUntilContains("<-- R");
+while (this.line != null && this.line.contains("<-- R")) {
+this.tokens = this.getTokens();
+this.setAtomCoordScaled(null, this.tokens, 2, 0.5291772).elementSymbol = this.tokens[0];
+this.rd();
+}
+this.applySymmetryAndSetTrajectory();
+}this.discardLinesUntilContains("<-- E");
+}
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+if (this.isPhonon || this.isOutput || this.isTS) {
+this.isTrajectory = false;
+} else {
+this.doApplySymmetry = true;
+this.setLatticeVectors();
+var nAtoms = this.asc.ac;
+for (var i = 0; i < nAtoms; i++) this.setAtomCoord(this.asc.atoms[i]);
+
+}this.finalizeReaderASCR();
+});
+Clazz.defineMethod(c$, "setLatticeVectors",
+function(){
+if (this.abc[0] == null) {
+this.setUnitCell(this.a, this.b, this.c, this.alpha, this.beta, this.gamma);
+return;
+}var lv = Clazz.newFloatArray (3, 0);
+for (var i = 0; i < 3; i++) {
+lv[0] = this.abc[i].x;
+lv[1] = this.abc[i].y;
+lv[2] = this.abc[i].z;
+this.addExplicitLatticeVector(i, lv, 0);
+}
+});
+Clazz.defineMethod(c$, "readLatticeAbc",
+function(){
+if (this.tokenizeCastepCell() == 0) return;
+var factor = this.readLengthUnit(this.tokens[0]);
+if (this.tokens.length >= 3) {
+this.a = this.parseFloatStr(this.tokens[0]) * factor;
+this.b = this.parseFloatStr(this.tokens[1]) * factor;
+this.c = this.parseFloatStr(this.tokens[2]) * factor;
+} else {
+JU.Logger.warn("error reading a,b,c in %BLOCK LATTICE_ABC in CASTEP .cell file");
+return;
+}if (this.tokenizeCastepCell() == 0) return;
+if (this.tokens.length >= 3) {
+this.alpha = this.parseFloatStr(this.tokens[0]);
+this.beta = this.parseFloatStr(this.tokens[1]);
+this.gamma = this.parseFloatStr(this.tokens[2]);
+} else {
+JU.Logger.warn("error reading alpha,beta,gamma in %BLOCK LATTICE_ABC in CASTEP .cell file");
+}});
+Clazz.defineMethod(c$, "readLatticeCart",
+function(){
+if (this.tokenizeCastepCell() == 0) return;
+var factor = this.readLengthUnit(this.tokens[0]);
+var x;
+var y;
+var z;
+for (var i = 0; i < 3; i++) {
+if (this.tokens.length >= 3) {
+x = this.parseFloatStr(this.tokens[0]) * factor;
+y = this.parseFloatStr(this.tokens[1]) * factor;
+z = this.parseFloatStr(this.tokens[2]) * factor;
+this.abc[i] = JU.V3.new3(x, y, z);
+} else {
+JU.Logger.warn("error reading coordinates of lattice vector " + Integer.toString(i + 1) + " in %BLOCK LATTICE_CART in CASTEP .cell file");
+return;
+}if (this.tokenizeCastepCell() == 0) return;
+}
+this.a = this.abc[0].length();
+this.b = this.abc[1].length();
+this.c = this.abc[2].length();
+this.alpha = (this.abc[1].angle(this.abc[2]) * 57.29577951308232);
+this.beta = (this.abc[2].angle(this.abc[0]) * 57.29577951308232);
+this.gamma = (this.abc[0].angle(this.abc[1]) * 57.29577951308232);
+});
+Clazz.defineMethod(c$, "readPositionsFrac",
+function(){
+if (this.tokenizeCastepCell() == 0) return;
+this.readAtomData(1.0);
+});
+Clazz.defineMethod(c$, "readPositionsAbs",
+function(){
+if (this.tokenizeCastepCell() == 0) return;
+var factor = this.readLengthUnit(this.tokens[0]);
+this.readAtomData(factor);
+});
+Clazz.defineMethod(c$, "readLengthUnit",
+function(units){
+var factor = 1.0;
+for (var i = 0; i < J.adapter.readers.xtal.CastepReader.lengthUnitIds.length; i++) if (units.equalsIgnoreCase(J.adapter.readers.xtal.CastepReader.lengthUnitIds[i])) {
+factor = J.adapter.readers.xtal.CastepReader.lengthUnitFactors[i];
+this.tokenizeCastepCell();
+break;
+}
+return factor;
+}, "~S");
+Clazz.defineMethod(c$, "readAtomData",
+function(factor){
+do {
+if (this.tokens.length >= 4) {
+var atom = this.asc.addNewAtom();
+var pt = this.tokens[0].indexOf(":");
+if (pt >= 0) {
+atom.elementSymbol = this.tokens[0].substring(0, pt);
+atom.atomName = this.tokens[0];
+} else {
+atom.elementSymbol = this.tokens[0];
+}atom.set(this.parseFloatStr(this.tokens[1]), this.parseFloatStr(this.tokens[2]), this.parseFloatStr(this.tokens[3]));
+atom.scale(factor);
+} else {
+JU.Logger.warn("cannot read line with CASTEP atom data: " + this.line);
+}} while (this.tokenizeCastepCell() > 0 && !this.tokens[0].equalsIgnoreCase("%ENDBLOCK"));
+}, "~N");
+Clazz.defineMethod(c$, "tokenizeCastepCell",
+function(){
+while (this.rd() != null) {
+if ((this.line = this.line.trim()).length == 0 || this.line.startsWith("#") || this.line.startsWith("!")) continue;
+if (!this.isCell) {
+if (this.line.startsWith("%")) {
+this.isCell = true;
+break;
+}if (this.line.startsWith("LST")) {
+this.isTS = true;
+JU.Logger.info("reading CASTEP .ts file");
+return -1;
+}if (this.line.startsWith("BEGIN header")) {
+this.isPhonon = true;
+JU.Logger.info("reading CASTEP .phonon file");
+return -1;
+}if (this.line.contains("CASTEP")) {
+this.isOutput = true;
+JU.Logger.info("reading CASTEP .castep file");
+return -1;
+}}break;
+}
+return (this.line == null ? 0 : (this.tokens = this.getTokens()).length);
+});
+Clazz.defineMethod(c$, "readOutputBornChargeTensors",
+function(){
+if (this.rd().indexOf("--------") < 0) return;
+var atoms = this.asc.atoms;
+this.appendLoadNote("Ellipsoids: Born Charge Tensors");
+while (this.rd().indexOf('=') < 0) this.getTensor(atoms[this.readOutputAtomIndex()], this.line.substring(12));
+
+});
+Clazz.defineMethod(c$, "readOutputAtomIndex",
+function(){
+this.tokens = this.getTokens();
+return this.asc.getAtomIndex(this.tokens[0] + this.tokens[1]);
+});
+Clazz.defineMethod(c$, "getTensor",
+function(atom, line0){
+var data = Clazz.newFloatArray (9, 0);
+var a = Clazz.newDoubleArray (3, 3, 0);
+this.fillFloatArray(line0, 0, data);
+JU.Logger.info("tensor " + atom.atomName + "\t" + JU.Escape.eAF(data));
+for (var p = 0, i = 0; i < 3; i++) for (var j = 0; j < 3; j++) a[i][j] = data[p++];
+
+
+atom.addTensor(( new JU.Tensor()).setFromAsymmetricTensor(a, "charge", atom.atomName + " " + line0), null, false);
+if (!this.haveCharges) this.appendLoadNote("Ellipsoids set \"charge\": Born Effective Charges");
+this.haveCharges = true;
+}, "J.adapter.smarter.Atom,~S");
+Clazz.defineMethod(c$, "readOutputCharges",
+function(){
+if (this.line.toUpperCase().indexOf(this.chargeType) < 0) return;
+JU.Logger.info("reading charges: " + this.line);
+this.readLines(2);
+var haveSpin = (this.line.indexOf("Spin") >= 0);
+this.rd();
+var atoms = this.asc.atoms;
+var spins = (haveSpin ? Clazz.newFloatArray (atoms.length, 0) : null);
+if (spins != null) for (var i = 0; i < spins.length; i++) spins[i] = 0;
+
+while (this.rd() != null && this.line.indexOf('=') < 0) {
+var index = this.readOutputAtomIndex();
+var charge = this.parseFloatStr(this.tokens[haveSpin ? this.tokens.length - 2 : this.tokens.length - 1]);
+atoms[index].partialCharge = charge;
+if (haveSpin) spins[index] = this.parseFloatStr(this.tokens[this.tokens.length - 1]);
+}
+if (haveSpin) this.asc.setAtomProperties("spin", spins, -1, false);
+});
+Clazz.defineMethod(c$, "readPhononUnitCell",
+function(){
+this.abc = this.read3Vectors(this.line.indexOf("bohr") >= 0);
+this.setSpaceGroupName("P1");
+this.setLatticeVectors();
+});
+Clazz.defineMethod(c$, "readPhononFractionalCoord",
+function(){
+this.setFractionalCoordinates(true);
+while (this.rd() != null && this.line.indexOf("END") < 0) {
+this.tokens = this.getTokens();
+this.addAtomXYZSymName(this.tokens, 1, this.tokens[4], null).bfactor = this.parseFloatStr(this.tokens[5]);
+}
+this.ac = this.asc.ac;
+this.atomPts = new Array(this.ac);
+var atoms = this.asc.atoms;
+for (var i = 0; i < this.ac; i++) this.atomPts[i] = JU.P3.newP(atoms[i]);
+
+});
+Clazz.defineMethod(c$, "readPhononFrequencies",
+function(){
+this.tokens = this.getTokens();
+var v = new JU.V3();
+var qvec = JU.V3.new3(this.parseFloatStr(this.tokens[2]), this.parseFloatStr(this.tokens[3]), this.parseFloatStr(this.tokens[4]));
+var fcoord = this.getFractionalCoord(qvec);
+var qtoks = "{" + this.tokens[2] + " " + this.tokens[3] + " " + this.tokens[4] + "}";
+if (fcoord == null) fcoord = qtoks;
+ else fcoord = "{" + fcoord + "}";
+var isOK = this.isAllQ;
+var isSecond = (this.tokens[1].equals(this.lastQPt));
+this.qpt2 = (isSecond ? this.qpt2 + 1 : 1);
+this.lastQPt = this.tokens[1];
+if (!isOK && this.checkFilterKey("Q=")) {
+if (this.desiredQpt != null) {
+v.sub2(this.desiredQpt, qvec);
+if (v.length() < 0.001) fcoord = this.desiredQ;
+}isOK = (this.checkFilterKey("Q=" + fcoord + "." + this.qpt2 + ";") || this.checkFilterKey("Q=" + this.lastQPt + "." + this.qpt2 + ";") || !isSecond && this.checkFilterKey("Q=" + fcoord + ";") || !isSecond && this.checkFilterKey("Q=" + this.lastQPt + ";"));
+if (!isOK) return;
+}var isGammaPoint = (qvec.length() == 0);
+var nx = 1;
+var ny = 1;
+var nz = 1;
+if (this.ptSupercell != null && !isOK && !isSecond) {
+this.matSupercell = new JU.M4();
+this.matSupercell.m00 = this.ptSupercell.x;
+this.matSupercell.m11 = this.ptSupercell.y;
+this.matSupercell.m22 = this.ptSupercell.z;
+this.matSupercell.m33 = 1;
+JU.Logger.info("Using supercell \n" + this.matSupercell);
+nx = this.ptSupercell.x;
+ny = this.ptSupercell.y;
+nz = this.ptSupercell.z;
+var dx = (qvec.x == 0 ? 1 : qvec.x) * nx;
+var dy = (qvec.y == 0 ? 1 : qvec.y) * ny;
+var dz = (qvec.z == 0 ? 1 : qvec.z) * nz;
+if ((nx != 1 || ny != 1 || nz != 1) && isGammaPoint || !J.adapter.readers.xtal.CastepReader.isInt(dx) || !J.adapter.readers.xtal.CastepReader.isInt(dy) || !J.adapter.readers.xtal.CastepReader.isInt(dz)) return;
+isOK = true;
+}if (this.ptSupercell == null || !this.havePhonons) this.appendLoadNote(this.line);
+if (!isOK && isSecond) return;
+if (!isOK && (this.ptSupercell == null) == !isGammaPoint) return;
+if (this.havePhonons && !this.isAllQ) return;
+this.havePhonons = true;
+var qname = "q=" + this.lastQPt + " " + fcoord;
+this.applySymmetryAndSetTrajectory();
+if (isGammaPoint) qvec = null;
+var freqs = new JU.Lst();
+while (this.rd() != null && this.line.indexOf("Phonon") < 0) {
+this.tokens = this.getTokens();
+freqs.addLast(Float.$valueOf(this.parseFloatStr(this.tokens[1])));
+}
+this.rd();
+var frequencyCount = freqs.size();
+var data = Clazz.newFloatArray (8, 0);
+var t = new JU.V3();
+this.asc.setCollectionName(qname);
+for (var i = 0; i < frequencyCount; i++) {
+if (!this.doGetVibration(++this.vibrationNumber)) {
+for (var j = 0; j < this.ac; j++) this.rd();
+
+continue;
+}if (this.desiredVibrationNumber <= 0) {
+if (!this.isTrajectory) {
+this.cloneLastAtomSet(this.ac, this.atomPts);
+this.applySymmetryAndSetTrajectory();
+}}this.symmetry = this.asc.getSymmetry();
+var iatom = this.asc.getLastAtomSetAtomIndex();
+var freq = freqs.get(i).floatValue();
+var atoms = this.asc.atoms;
+var aCount = this.asc.ac;
+for (var j = 0; j < this.ac; j++) {
+this.fillFloatArray(null, 0, data);
+for (var k = iatom++; k < aCount; k++) if (atoms[k].atomSite == j) {
+t.sub2(atoms[k], atoms[atoms[k].atomSite]);
+if (this.matSupercell != null) this.matSupercell.rotTrans(t);
+this.setPhononVector(data, atoms[k], t, qvec, v);
+this.asc.addVibrationVectorWithSymmetry(k, v.x, v.y, v.z, true);
+}
+}
+if (this.isTrajectory) this.asc.setTrajectory();
+this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, "" + freq, null);
+this.asc.setAtomSetName(JU.DF.formatDecimal(freq, 2) + " cm-1 " + qname);
+}
+});
+Clazz.defineMethod(c$, "getFractionalCoord",
+function(qvec){
+return (this.symmetry != null && J.adapter.readers.xtal.CastepReader.isInt(qvec.x * 12) && J.adapter.readers.xtal.CastepReader.isInt(qvec.y * 12) && J.adapter.readers.xtal.CastepReader.isInt(qvec.z * 12) ? this.symmetry.fcoord(qvec) : null);
+}, "JU.V3");
+c$.isInt = Clazz.defineMethod(c$, "isInt",
+function(f){
+return (Math.abs(f - Math.round(f)) < 0.001);
+}, "~N");
+Clazz.defineMethod(c$, "setPhononVector",
+function(data, atom, rTrans, qvec, v){
+if (qvec == null) {
+v.set(data[2], data[4], data[6]);
+} else {
+var phase = qvec.dot(rTrans);
+var cosph = Math.cos(6.283185307179586 * phase);
+var sinph = Math.sin(6.283185307179586 * phase);
+v.x = (cosph * data[2] - sinph * data[3]);
+v.y = (cosph * data[4] - sinph * data[5]);
+v.z = (cosph * data[6] - sinph * data[7]);
+}v.scale(Math.sqrt(1 / atom.bfactor));
+}, "~A,J.adapter.smarter.Atom,JU.V3,JU.V3,JU.V3");
+c$.lengthUnitIds = Clazz.newArray(-1, ["bohr", "m", "cm", "nm", "ang", "a0"]);
+c$.lengthUnitFactors = Clazz.newFloatArray(-1, [0.5291772, 1E10, 1E8, 1E1, 1.0, 0.5291772]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CgdReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CgdReader.js
new file mode 100755
index 000000000000..41f3478a2f83
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CgdReader.js
@@ -0,0 +1,163 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "JU.V3"], "J.adapter.readers.xtal.CgdReader", ["java.util.Hashtable", "JU.Lst", "$.M3", "$.P3", "$.PT", "J.adapter.smarter.Bond", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.noBondSym = false;
+this.tokens = null;
+this.htEdges = null;
+this.lastName = null;
+this.edgeData = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "CgdReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setFractionalCoordinates(true);
+this.asc.setNoAutoBond();
+this.asc.vibScale = 1;
+this.forceSymmetry(!this.noPack);
+this.noBondSym = this.checkFilterKey("NOBONDSYM");
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+this.line = this.line.trim();
+if (this.line.length == 0 || this.line.startsWith("#")) return true;
+if (!Character.isLetter(this.line.charAt(0))) this.line = this.lastName + " " + this.line;
+this.tokens = this.getTokens();
+if (this.tokens.length > 0) {
+this.lastName = this.tokens[0].toUpperCase();
+var pt = "NAME |CELL |GROUP|ATOM |EDGE |".indexOf(this.lastName);
+if (this.tokens.length > 1 && (pt == 0 || this.doProcessLines)) switch (pt) {
+case 0:
+if (!this.doGetModel(++this.modelNumber, null)) return this.checkLastModel();
+this.applySymmetryAndSetTrajectory();
+this.setFractionalCoordinates(true);
+this.asc.newAtomSet();
+this.asc.setAtomSetName(this.line.substring(6).trim());
+this.htEdges = null;
+this.edgeData = null;
+break;
+case 6:
+for (var i = 0; i < 6; i++) this.setUnitCellItem(i, (i < 3 ? 10 : 1) * this.parseFloatStr(this.tokens[i + 1]));
+
+break;
+case 12:
+this.setSpaceGroupName("bilbao:" + this.group(this.tokens[1]));
+break;
+case 18:
+this.atom();
+break;
+case 24:
+if (!this.doApplySymmetry) break;
+if (this.edgeData == null) this.edgeData = new JU.Lst();
+this.edgeData.addLast(this.line);
+break;
+}
+}return true;
+});
+Clazz.defineMethod(c$, "group",
+function(name){
+var name0 = null;
+if (name.charAt(0) == '"') name = name.substring(1, name.length - 1);
+var pt = ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf(";" + name + "=");
+if (pt >= 0) {
+name0 = name;
+name = ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".substring(";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf("=", pt) + 1, ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf(";", pt + 1));
+}JU.Logger.info("CgdReader using GROUP " + name + (name0 == null ? "" : " alias of " + name0));
+return name;
+}, "~S");
+Clazz.defineMethod(c$, "atom",
+function(){
+var name = this.getName(this.tokens[1]);
+var edgeCount = this.parseIntStr(this.tokens[2]);
+for (var i = 3; i < 6; i++) if (this.tokens[i].indexOf("/") >= 0) this.tokens[i] = "" + JU.PT.parseFloatFraction(this.tokens[i]);
+
+var a = this.addAtomXYZSymName(this.tokens, 3, null, name);
+if (!this.doApplySymmetry) return;
+this.asc.atomSymbolicMap.put(name, a);
+this.asc.addVibrationVector(a.index, 1, 3, 7);
+if (this.htEdges == null) this.htEdges = new java.util.Hashtable();
+this.htEdges.put(a, new Array(edgeCount));
+});
+Clazz.defineMethod(c$, "getName",
+function(name){
+return (name.charAt(0) == '"' ? name.substring(1, name.length - 1) : Character.isDigit(name.charAt(0)) ? "C" + name : name);
+}, "~S");
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+this.finalizeReaderASCR();
+if (this.doApplySymmetry) this.finalizeNet();
+});
+Clazz.defineMethod(c$, "finalizeEdges",
+function(){
+var p;
+var name;
+var a;
+var atomEdges;
+for (var j = 0; j < this.edgeData.size(); j++) {
+this.tokens = JU.PT.getTokens(this.line = this.edgeData.get(j));
+switch (this.tokens.length) {
+case 3:
+name = this.getName(this.tokens[1]);
+a = this.asc.getAtomFromName(name);
+atomEdges = this.htEdges.get(a);
+p = this.asc.getAtomFromName(this.getName(this.tokens[2]));
+break;
+case 5:
+name = this.getName(this.tokens[1]);
+a = this.asc.getAtomFromName(name);
+atomEdges = this.htEdges.get(a);
+p = this.getCoord(2);
+break;
+case 7:
+atomEdges = this.htEdges.get(this.findAtom(this.getCoord(1)));
+p = this.getCoord(4);
+break;
+default:
+JU.Logger.error("EDGE record skipped: " + this.line);
+continue;
+}
+for (var i = 0, n = atomEdges.length; i < n; i++) if (atomEdges[i] == null) {
+atomEdges[i] = JU.V3.newV(p);
+break;
+}
+}
+});
+Clazz.defineMethod(c$, "getCoord",
+function(i){
+return JU.P3.new3(JU.PT.parseFloatFraction(this.tokens[i++]), JU.PT.parseFloatFraction(this.tokens[i++]), JU.PT.parseFloatFraction(this.tokens[i++]));
+}, "~N");
+Clazz.defineMethod(c$, "finalizeNet",
+function(){
+this.finalizeEdges();
+var m = new JU.M3();
+var pt = new JU.P3();
+for (var i = 0, n = this.asc.ac; i < n; i++) {
+var a = this.asc.atoms[i];
+var a0 = this.asc.atoms[a.atomSite];
+if (this.noBondSym && a !== a0) continue;
+var edges = this.htEdges.get(a0);
+if (edges == null) continue;
+var ix = Clazz.floatToInt(a.vib.x) + 7;
+var iy = Clazz.floatToInt(a.vib.y) + 7;
+var iz = Clazz.floatToInt(a.vib.z) + 7;
+m.setRowV(0, J.adapter.readers.xtal.CgdReader.vecs[ix]);
+m.setRowV(1, J.adapter.readers.xtal.CgdReader.vecs[iy]);
+m.setRowV(2, J.adapter.readers.xtal.CgdReader.vecs[iz]);
+for (var j = 0, n1 = edges.length; j < n1; j++) {
+pt.sub2(edges[j], a0);
+m.rotate(pt);
+pt.add(a);
+var b = this.findAtom(pt);
+if (b != null) this.asc.addBond( new J.adapter.smarter.Bond(a.index, b.index, 1));
+ else if (pt.x >= 0 && pt.x <= 1 && pt.y >= 0 && pt.y <= 1 && pt.z >= 0 && pt.z <= 1) JU.Logger.error(" not found: i=" + i + " pt=" + pt + " for a=" + a + "\n a0=" + a0 + " edge[" + j + "]=" + edges[j] + "\n a.vib=" + a.vib + "\n m=" + m);
+}
+a.vib = null;
+}
+});
+Clazz.defineMethod(c$, "findAtom",
+function(pt){
+for (var i = this.asc.ac; --i >= 0; ) if (this.asc.atoms[i].distanceSquared(pt) < 0.00001) return this.asc.atoms[i];
+
+return null;
+}, "JU.P3");
+c$.vecs = Clazz.newArray(-1, [JU.V3.new3(0, 0, -1), JU.V3.new3(1, 0, -1), null, JU.V3.new3(0, 1, -1), JU.V3.new3(0, -1, 0), JU.V3.new3(1, -1, 0), JU.V3.new3(-1, 0, 0), null, JU.V3.new3(1, 0, 0), JU.V3.new3(-1, 1, 0), JU.V3.new3(0, 1, 0), JU.V3.new3(0, -1, 1), null, JU.V3.new3(-1, 0, 1), JU.V3.new3(0, 0, 1)]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CmdfReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CmdfReader.js
new file mode 100755
index 000000000000..6ec8510a6392
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CmdfReader.js
@@ -0,0 +1,121 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.CmdfReader", ["J.adapter.smarter.Atom", "J.api.JmolAdapter"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.buf = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "CmdfReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.buf = Clazz.newByteArray (100, 0);
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setFractionalCoordinates(true);
+});
+Clazz.overrideMethod(c$, "processBinaryDocument",
+function(){
+this.binaryDoc.setStream(null, false);
+this.binaryDoc.seek(28);
+var len = this.binaryDoc.readInt();
+System.out.println("file length: " + len + " " + Integer.toHexString(len));
+this.seek("CELL", 32);
+var uc = Clazz.newFloatArray (6, 0);
+for (var i = 0; i < 6; i++) {
+uc[i] = this.binaryDoc.readFloat();
+}
+this.setUnitCell(uc[0], uc[1], uc[2], uc[3], uc[4], uc[5]);
+this.seek("SYMM", -1);
+var sg = J.adapter.readers.xtal.CmdfReader.fixSpaceGroup(this.binaryDoc.readString(20));
+this.setSpaceGroupName(sg);
+System.out.println("Space group is " + sg);
+this.readAtoms();
+System.out.println("done");
+});
+c$.fixSpaceGroup = Clazz.defineMethod(c$, "fixSpaceGroup",
+function(sg){
+var pt = sg.indexOf('\0');
+if (pt == 0) System.out.println("SYMM: empty;NO space group??");
+return (pt < 0 ? sg : sg.substring(0, pt)).trim();
+}, "~S");
+Clazz.defineMethod(c$, "readAtoms",
+function(){
+this.seek("AUN7", 32);
+var nSites = this.binaryDoc.readInt();
+System.out.println(nSites + " sites");
+for (var i = 0; i < nSites; i++) this.readSite();
+
+});
+Clazz.defineMethod(c$, "readSite",
+function(){
+var nOccupants = this.binaryDoc.readByte();
+var atoms = new Array(nOccupants);
+for (var i = 0; i < nOccupants; i++) {
+var a = atoms[i] = new J.adapter.smarter.Atom();
+var ch2 = String.fromCharCode(this.binaryDoc.readByte());
+var ch1 = String.fromCharCode(this.binaryDoc.readByte());
+a.elementSymbol = J.adapter.readers.xtal.CmdfReader.getSymbol("" + ch1 + ch2);
+if (J.api.JmolAdapter.getElementNumber(a.elementSymbol) == 0) {
+System.out.println("ELEMENT error " + a.elementSymbol + " " + this.fileName);
+}a.foccupancy = this.binaryDoc.readFloat();
+this.asc.addAtom(a);
+}
+this.binaryDoc.readInt();
+var sym0 = atoms[0].elementSymbol;
+var name = this.readString();
+var valence = this.binaryDoc.readInt();
+for (var i = 0; i < nOccupants; i++) {
+atoms[i].atomName = (i == 0 || sym0.length > name.length ? name : atoms[i].elementSymbol + name.substring(sym0.length));
+}
+var unk3s = this.binaryDoc.readShort() & 0xFFFF;
+var x = this.binaryDoc.readFloat();
+var y = this.binaryDoc.readFloat();
+var z = this.binaryDoc.readFloat();
+for (var i = 0; i < nOccupants; i++) {
+this.setAtomCoordXYZ(atoms[i], x, y, z);
+}
+var index2 = this.binaryDoc.readInt() / 32;
+var unk4b = this.binaryDoc.readByte() & 0xFF;
+var siteNumber = this.binaryDoc.readShort();
+var unk5b = this.binaryDoc.readByte() & 0xFF;
+var wyn = this.binaryDoc.readInt();
+var wyabc = this.binaryDoc.readByte();
+var wyckoff = "" + wyn + String.fromCharCode(0x60 + wyabc);
+System.out.println("SITE " + siteNumber + " occ=" + nOccupants + " " + atoms[0].elementSymbol + " " + atoms[0].atomName + " " + wyckoff + " " + atoms[0] + (nOccupants > 1 ? atoms[1].atomName : "") + " valence=" + valence + " " + index2 + " " + Integer.toHexString(unk3s) + " " + Integer.toHexString(unk4b) + " " + Integer.toHexString(unk5b));
+return;
+});
+Clazz.defineMethod(c$, "readString",
+function(){
+var n = this.binaryDoc.readByte();
+this.binaryDoc.readByteArray(this.buf, 0, n);
+return String.instantialize(this.buf, 0, n);
+});
+Clazz.defineMethod(c$, "seek",
+function(label, where){
+var bytes = label.getBytes();
+if (where > 0) this.binaryDoc.seek(where);
+var p = (where >= 0 ? where : this.binaryDoc.getPosition());
+System.out.println("looking for " + label + " @" + p);
+var off = 0;
+var n = bytes.length;
+var p0 = p;
+while (off < n) {
+var b = this.binaryDoc.readByte();
+p++;
+if (b == bytes[off]) {
+off++;
+} else if (off > 0) {
+this.binaryDoc.seek(p = p0 = p0 + 1);
+off = 0;
+}}
+System.out.println(label + " found at " + (p - n));
+return p;
+}, "~S,~N");
+c$.getSymbol = Clazz.defineMethod(c$, "getSymbol",
+function(sym){
+if (sym == null) return "Xx";
+var len = sym.length;
+if (len < 2) return sym;
+var ch1 = sym.charAt(1);
+if (ch1 >= 'a' && ch1 <= 'z') return sym.substring(0, 2);
+return "" + sym.charAt(0);
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CrystalReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CrystalReader.js
new file mode 100755
index 000000000000..deb01b20b2d5
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/CrystalReader.js
@@ -0,0 +1,812 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "JU.Lst", "$.P3"], "J.adapter.readers.xtal.CrystalReader", ["java.util.Arrays", "$.Hashtable", "JU.DF", "$.M3", "$.M4", "$.PT", "$.Quat", "$.SB", "$.V3", "JS.SymmetryOperation", "JU.Logger", "$.Tensor"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isVersion3 = false;
+this.isPolymer = false;
+this.isSlab = false;
+this.haveCharges = false;
+this.inputOnly = false;
+this.isLongMode = false;
+this.getLastConventional = false;
+this.havePrimitiveMapping = false;
+this.isProperties = false;
+this.state = 0;
+this.ac = 0;
+this.atomIndexLast = 0;
+this.atomFrag = null;
+this.primitiveToIndex = null;
+this.nuclearCharges = null;
+this.lstCoords = null;
+this.energy = null;
+this.ptOriginShift = null;
+this.directLatticeVectors = null;
+this.spaceGroupName = null;
+this.checkModelTrigger = false;
+this.fullSymmetry = false;
+this.htCriticalPoints = null;
+this.directLatticeVectorsFirst = false;
+this.cpno = -1;
+this.symops = null;
+this.f14 = null;
+this.f16 = null;
+this.primitiveVolume = 0;
+this.primitiveDensity = 0;
+this.firstLine = null;
+this.type = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "CrystalReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.ptOriginShift = new JU.P3();
+this.symops = new JU.Lst();
+this.f14 = Clazz.newFloatArray (14, 0);
+this.f16 = Clazz.newFloatArray (16, 0);
+});
+Clazz.defineMethod(c$, "rd",
+function(){
+while (Clazz.superCall(this, J.adapter.readers.xtal.CrystalReader, "rd", []) != null && (this.line.startsWith(" PROCESS") || this.line.startsWith(" INFORMATION") || this.line.startsWith(" WARNING"))) {
+}
+return this.line;
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.doProcessLines = false;
+this.inputOnly = this.checkFilterKey("INPUT");
+this.isPrimitive = !this.inputOnly && !this.checkFilterKey("CONV");
+this.addVibrations = new Boolean (this.addVibrations & (!this.inputOnly && this.desiredModelNumber < 0)).valueOf();
+this.getLastConventional = (!this.isPrimitive && this.desiredModelNumber == 0);
+this.fullSymmetry = this.checkFilterKey("FULLSYM");
+this.setFractionalCoordinates(this.readHeader());
+this.asc.crystalReaderLatticeOpsOnly = !this.inputOnly;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.firstLine != null) {
+this.line = this.firstLine;
+this.firstLine = null;
+}if (this.line.startsWith(" TYPE OF CALCULATION")) {
+this.calculationType = this.line.substring(this.line.indexOf(":") + 1).trim();
+return true;
+}if (this.line.indexOf("DIMENSIONALITY OF THE SYSTEM") >= 0) {
+this.isMolecular = this.isSlab = this.isPolymer = false;
+if (this.line.indexOf("2") >= 0) this.isSlab = true;
+ else if (this.line.indexOf("1") >= 0) this.isPolymer = true;
+ else if (this.line.indexOf("0") >= 0) this.isMolecular = true;
+return true;
+}if (!this.isPolymer && this.line.indexOf("CONSTRUCTION OF A NANOTUBE FROM A SLAB") >= 0) {
+this.isPolymer = true;
+this.isSlab = false;
+return true;
+}if (!this.isMolecular && this.line.indexOf("* CLUSTER CALCULATION") >= 0) {
+this.isMolecular = true;
+this.isSlab = false;
+this.isPolymer = false;
+return true;
+}if (this.line.startsWith(" INPUT COORDINATES")) {
+this.state = 1;
+if (this.inputOnly) {
+this.newAtomSet();
+this.readCoordLines();
+this.continuing = false;
+}return true;
+}if (this.line.startsWith(" GEOMETRY INPUT FROM EXTERNAL")) {
+this.state = 2;
+if (this.inputOnly) this.continuing = false;
+return true;
+}if (this.line.startsWith(" GEOMETRY FOR WAVE FUNCTION")) {
+this.state = 3;
+return true;
+}if (this.line.startsWith(" COORDINATE OPTIMIZATION - POINT")) {
+this.state = 4;
+return true;
+}if (this.line.startsWith(" FINAL OPTIMIZED GEOMETRY")) {
+this.getLastConventional = false;
+this.state = 5;
+return true;
+}if (this.addVibrations && this.line.contains(this.isVersion3 ? "EIGENVALUES (EV) OF THE MASS" : "EIGENVALUES (EIGV) OF THE MASS") || this.line.indexOf("LONGITUDINAL OPTICAL (LO)") >= 0) {
+this.state = 6;
+this.isLongMode = (this.line.indexOf("LONGITUDINAL OPTICAL (LO)") >= 0);
+this.readFrequencies();
+return true;
+}if (this.line.startsWith(" TRANSFORMATION MATRIX")) {
+this.readPrimitiveLatticeVectors();
+return true;
+}if (this.line.startsWith(" COORDINATES OF THE EQUIVALENT ATOMS") || this.line.startsWith(" INPUT LIST - ATOM N.")) {
+return true;
+}if (this.line.indexOf("SYMMOPS - ") >= 0) {
+this.readSymmetryOperators();
+return true;
+}if (this.line.startsWith(" LATTICE PARAMETER")) {
+this.newLattice(this.line.indexOf("- CONVENTIONAL") >= 0);
+return true;
+}if (this.line.startsWith(" CRYSTALLOGRAPHIC CELL")) {
+if (!this.isPrimitive) {
+this.newLattice(true);
+}return true;
+}if (this.line.startsWith(" DIRECT LATTICE VECTOR")) {
+this.getDirect();
+return true;
+}if (this.line.startsWith(" COORDINATES IN THE CRYSTALLOGRAPHIC CELL")) {
+this.checkModelTrigger = !this.isPrimitive;
+if (this.checkModelTrigger) {
+this.readCoordLines();
+}return true;
+}if (this.addVibrations && this.line.startsWith(" FREQUENCIES COMPUTED ON A FRAGMENT")) {
+this.readFreqFragments();
+return true;
+}if (this.checkModelTrigger) {
+if (this.line.indexOf("CARTESIAN COORDINATES") >= 0 || this.line.indexOf("TOTAL ENERGY") >= 0 || this.line.indexOf("REFERENCE GEOMETRY DEFINED") >= 0 || this.line.indexOf("FUNCTIONS") >= 0) {
+this.checkModelTrigger = false;
+if (!this.addModel()) return true;
+}}if (this.line.startsWith(" ATOMS IN THE ASYMMETRIC UNIT")) {
+if (this.isMolecular) return (this.doGetModel(++this.modelNumber, null) ? this.readAtoms() : this.checkLastModel());
+this.readCoordLines();
+this.checkModelTrigger = true;
+}if (this.isProperties && this.line.startsWith(" ATOM N.AT.")) {
+if (this.doGetModel(++this.modelNumber, null)) this.readAtoms();
+ else this.checkLastModel();
+}if (!this.doProcessLines) return true;
+if (this.line.startsWith(" TOTAL ENERGY(")) {
+this.line = JU.PT.rep(this.line, "( ", "(");
+var tokens = this.getTokens();
+this.energy = Double.$valueOf(Double.parseDouble(tokens[2]));
+this.setEnergy();
+this.rd();
+if (this.line.startsWith(" ********")) this.discardLinesUntilContains("SYMMETRY ALLOWED");
+ else if (this.line.startsWith(" TTTTTTTT")) this.discardLinesUntilContains(" *******");
+return true;
+}if (this.line.startsWith(" MULLIKEN POPULATION ANALYSIS")) return this.readPartialCharges();
+if (this.line.startsWith(" TOTAL ATOMIC CHARGES")) return this.readTotalAtomicCharges();
+if (this.line.startsWith(" MAX GRADIENT")) return this.readGradient();
+if (this.line.startsWith(" ATOMIC SPINS SET")) return this.readData("spin", 3);
+if (this.line.startsWith(" TOTAL ATOMIC SPINS :")) return this.readData("magneticMoment", 1);
+if (this.line.startsWith(" BORN CHARGE TENSOR.")) return this.readBornChargeTensors();
+if (!this.isProperties) return true;
+if (this.line.startsWith(" DEFINITION OF TRACELESS")) return this.getQuadrupoleTensors();
+if (this.line.startsWith(" MULTIPOLE ANALYSIS BY ATOMS")) {
+this.appendLoadNote("Multipole Analysis");
+return true;
+}if (this.line.startsWith(" CP N. ")) {
+this.cpno = this.parseIntAt(this.line, 6);
+return true;
+}if (this.line.startsWith(" CP TYPE ")) {
+this.processNextCriticalPoint();
+return true;
+}return true;
+});
+Clazz.defineMethod(c$, "processNextCriticalPoint",
+function(){
+if (this.htCriticalPoints == null) {
+this.htCriticalPoints = new java.util.Hashtable();
+this.asc.setModelInfoForSet("criticalPoints", this.htCriticalPoints, 0);
+}var nblank = 0;
+var id = null;
+var entry = null;
+var f = 0.5291772;
+var m = null;
+var v = NaN;
+var g = NaN;
+var rho = NaN;
+var evalues = null;
+var type = null;
+while (this.line != null || this.rd().length > 0 || ++nblank < 2) {
+if (this.line.indexOf("CLUSTER") >= 0) {
+break;
+}if (this.line.length > 0) nblank = 0;
+var pt = this.line.indexOf(":");
+if (pt > 0) {
+var key = this.line.substring(0, pt).trim();
+var value = this.line.substring(pt + 1);
+if (key.equals("CP TYPE")) {
+type = J.adapter.readers.xtal.CrystalReader.crtypes[Clazz.doubleToInt("??,-3,-1,+1,+3".indexOf(value.substring(5, 7)) / 3)];
+entry = this.htCriticalPoints.get(type);
+if (entry == null) {
+this.htCriticalPoints.put(type, entry = new JU.Lst());
+}m = new java.util.Hashtable();
+entry.addLast(m);
+var i = entry.size();
+id = "cp_" + i;
+m.put("cpno", Integer.$valueOf(this.cpno));
+m.put("id", id);
+m.put("type", type);
+m.put("index", Integer.$valueOf(i));
+} else if (key.equals("COORD(AU) (X Y Z)")) {
+var xyz = JU.P3.new3(f * this.parseFloatStr(value.substring(0, 12)), f * this.parseFloatStr(value.substring(12, 24)), f * this.parseFloatStr(value.substring(24, 36)));
+m.put("point", xyz);
+JU.Logger.info("CRYSTAL TOPOND critical point " + type + " " + xyz);
+} else if (key.equals("PROPERTIES (RHO,GRHO,LAP)")) {
+rho = this.parseFloatStr(value.substring(0, 12));
+m.put("rho", Float.$valueOf(rho));
+m.put("lap", Float.$valueOf(this.parseFloatStr(value.substring(24, 36))));
+} else if (key.equals("PROPERTIES (-LAP,GLAP,RHO)")) {
+m.put("lap", Float.$valueOf(-this.parseFloatStr(value.substring(0, 12))));
+rho = this.parseFloatStr(value.substring(24, 36));
+m.put("rho", Float.$valueOf(rho));
+} else if (key.equals("KINETIC ENERGY DENSITIES (G,K)")) {
+g = this.parseFloatStr(value.substring(0, 12));
+m.put("kineticEnergyG", Float.$valueOf(g));
+} else if (key.equals("VIRIAL DENSITY")) {
+v = this.parseFloatStr(value.substring(0, 12));
+m.put("virialDensityV", Float.$valueOf(v));
+m.put("ratioVG", Float.$valueOf(Math.abs(v) / g));
+m.put("energyDensityH", Float.$valueOf(g + v));
+m.put("ratioHRho", Float.$valueOf((g + v) / rho));
+} else if (key.equals("EIGENVALUES (L1 L2 L3)")) {
+var e1 = this.parseFloatStr(value.substring(0, 12));
+var e2 = this.parseFloatStr(value.substring(12, 24));
+var e3 = this.parseFloatStr(value.substring(24, 36));
+evalues = Clazz.newFloatArray(-1, [e1, e2, e3]);
+m.put("eigenvalues", evalues);
+m.put("ellipticity", Float.$valueOf(e1 / e2 - 1));
+m.put("anisotropy", Float.$valueOf(e3 - Math.abs(e1 + e2) / 2));
+} else if (key.equals("EIGENVECTORS")) {
+value = value + this.rd().substring(33) + this.rd().substring(33);
+var ev = Clazz.newDoubleArray (3, 3, 0);
+for (var ei = 0, p = 0; ei < 3; ei++) {
+for (var ej = 0; ej < 3; ej++, p += 12) {
+ev[ej][ei] = this.parseFloatStr(value.substring(p, p + 12));
+}
+}
+var evectors = new Array(3);
+evectors[0] = JU.P3.new3(ev[0][0], ev[0][1], ev[0][2]);
+evectors[1] = JU.P3.new3(ev[1][0], ev[1][1], ev[1][2]);
+evectors[2] = JU.P3.new3(ev[2][0], ev[2][1], ev[2][2]);
+System.out.println("evpts " + evectors[0] + " " + evectors[1] + " " + evectors[2]);
+m.put("eigenvectors", evectors);
+var t = new JU.Tensor().setFromEigenVectors(evectors, evalues, "cp", id, null);
+m.put("tensor", t);
+}}this.line = null;
+}
+});
+Clazz.defineMethod(c$, "newLattice",
+function(isConv){
+this.lstCoords = null;
+this.readLatticeParams(!isConv);
+this.symops.clear();
+if (!isConv) this.primitiveToCrystal = null;
+if (!this.directLatticeVectorsFirst) this.directLatticeVectors = null;
+}, "~B");
+Clazz.defineMethod(c$, "addModel",
+function(){
+if (this.getLastConventional) {
+return true;
+}if (!this.doGetModel(++this.modelNumber, null)) {
+this.lstCoords = null;
+this.checkLastModel();
+if (this.asc.iSet >= 0) this.asc.removeAtomSet(this.asc.iSet);
+return false;
+}this.processCoordLines();
+return true;
+});
+Clazz.defineMethod(c$, "readSymmetryOperators",
+function(){
+this.symops.clear();
+this.rd();
+this.f16[15] = 1;
+while (this.rd() != null && this.line.length > 0 && this.line.indexOf("END") < 0) {
+if (this.line.indexOf("V INV") >= 0) continue;
+this.fillFloatArray(this.line, 0, this.f14);
+if (Float.isNaN(this.f14[0])) break;
+for (var i = 0; i < 12; i++) this.f16[i] = this.f14[J.adapter.readers.xtal.CrystalReader.smap[i]];
+
+JU.Logger.info("CrystalReader: " + this.line);
+if (this.isSlab || this.isPolymer) continue;
+var m4 = JU.M4.newA16(this.f16);
+var xyz = JS.SymmetryOperation.getXYZFromMatrix(m4, false, false, false);
+if (xyz.indexOf("0y") >= 0 || xyz.indexOf("0z") >= 0) {
+JU.Logger.error("CrystalReader: Symmetry operator could not be created for " + xyz);
+} else {
+this.symops.addLast(xyz);
+JU.Logger.info("CrystalReader: state=" + this.state + " Symmop " + this.symops.size() + ": " + xyz);
+}}
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+this.asc.setInfo("symmetryType", (this.isSlab ? "2D - SLAB" : this.isPolymer ? "1D - POLYMER" : this.type));
+this.processCoordLines();
+if (this.energy != null) this.setEnergy();
+this.finalizeReaderASCR();
+this.asc.checkNoEmptyModel();
+if (this.htCriticalPoints != null) {
+var note = "";
+var list;
+list = this.htCriticalPoints.get("nuclei");
+if (list != null) note += "\n _M.criticalPoints.nuclei.length = " + list.size();
+list = this.htCriticalPoints.get("bonds");
+if (list != null) note += "\n _M.criticalPoints.bonds.length = " + list.size();
+list = this.htCriticalPoints.get("rings");
+if (list != null) note += "\n _M.criticalPoints.rings.length = " + list.size();
+list = this.htCriticalPoints.get("cages");
+if (list != null) note += "\n _M.criticalPoints.cages.length = " + list.size();
+note += "\n Use MACRO TOPOND for TOPOND functions.";
+this.addJmolScript("set drawHover");
+this.appendLoadNote(note);
+this.setLoadNote();
+}});
+Clazz.defineMethod(c$, "getDirect",
+function(){
+this.directLatticeVectors = this.read3Vectors(this.line.indexOf("(BOHR") >= 0);
+if (!this.iHaveUnitCell) this.directLatticeVectorsFirst = true;
+});
+Clazz.defineMethod(c$, "setUnitCellOrientation",
+function(){
+if (this.directLatticeVectors == null) return;
+var a = new JU.V3();
+var b = new JU.V3();
+if (this.isPrimitive) {
+a = this.directLatticeVectors[0];
+b = this.directLatticeVectors[1];
+} else {
+if (this.primitiveToCrystal == null) return;
+var mp = new JU.M3();
+mp.setColumnV(0, this.directLatticeVectors[0]);
+mp.setColumnV(1, this.directLatticeVectors[1]);
+mp.setColumnV(2, this.directLatticeVectors[2]);
+mp.mul(this.primitiveToCrystal);
+a = new JU.V3();
+b = new JU.V3();
+mp.getColumnV(0, a);
+mp.getColumnV(1, b);
+}this.matUnitCellOrientation = JU.Quat.getQuaternionFrame( new JU.P3(), a, b).getMatrix();
+JU.Logger.info("oriented unit cell is in model " + this.asc.atomSetCount);
+});
+Clazz.defineMethod(c$, "readPrimitiveLatticeVectors",
+function(){
+this.primitiveToCrystal = JU.M3.newA9(this.fillFloatArray(null, 0, Clazz.newFloatArray (9, 0)));
+});
+Clazz.defineMethod(c$, "readHeader",
+function(){
+this.havePrimitiveMapping = true;
+this.discardLinesUntilContains("*******************************************************************************");
+this.readLines(2);
+this.isVersion3 = (this.line.indexOf("CRYSTAL03") >= 0);
+this.discardLinesUntilContains("EEEEEEEEEE");
+this.rd();
+var name;
+if (this.line.length == 0) {
+this.discardLinesUntilContains("*********");
+name = this.rd().trim();
+} else {
+name = this.line.trim();
+this.rd();
+}this.type = this.rd().trim();
+var pt = this.type.indexOf("- PROPERTIES");
+if (pt >= 0) {
+this.isProperties = true;
+this.type = this.type.substring(0, pt).trim();
+}this.asc.setCollectionName(name + (!this.isProperties && this.desiredModelNumber == 0 ? " (optimized)" : ""));
+if (this.type.indexOf("GEOMETRY INPUT FROM EXTERNAL FILE") >= 0) {
+this.firstLine = this.line;
+this.type = this.rd().trim();
+}this.isPolymer = (this.type.equals("1D - POLYMER") || this.type.equals("POLYMER CALCULATION"));
+this.isSlab = (this.type.equals("2D - SLAB") || this.type.equals("SLAB CALCULATION"));
+if ((this.isPolymer || this.isSlab) && !this.isPrimitive) {
+JU.Logger.error("Cannot use FILTER \"conventional\" with POLYMER or SLAB");
+this.isPrimitive = true;
+}this.asc.setInfo("unitCellType", (this.isPrimitive ? "primitive" : "conventional"));
+if (this.type.indexOf("MOLECULAR") >= 0) {
+this.isMolecular = this.doProcessLines = true;
+this.rd();
+this.asc.setInfo("molecularCalculationPointGroup", this.line.substring(this.line.indexOf(" OR ") + 4).trim());
+return false;
+}this.discardLinesUntilContains2("SPACE GROUP", "****");
+pt = this.line.indexOf(":");
+if (pt >= 0 && !this.isPrimitive) this.spaceGroupName = this.line.substring(pt + 1).trim();
+this.doApplySymmetry = this.isProperties;
+return !this.isProperties;
+});
+Clazz.defineMethod(c$, "readLatticeParams",
+function(isPrimitive){
+var f = (this.line.indexOf("(BOHR") >= 0 ? 0.5291772 : 1);
+if (isPrimitive) this.newAtomSet();
+this.primitiveVolume = 0;
+this.primitiveDensity = 0;
+if (this.isPolymer && !isPrimitive && this.line.indexOf("BOHR =") < 0) {
+this.setUnitCell(this.parseFloatStr(this.line.substring(this.line.indexOf("CELL") + 4)) * f, -1, -1, 90, 90, 90);
+} else {
+while (this.rd().indexOf("GAMMA") < 0) if (this.line.indexOf("VOLUME=") >= 0) {
+this.primitiveVolume = this.parseFloatStr(this.line.substring(43));
+this.primitiveDensity = this.parseFloatStr(this.line.substring(66));
+}
+var tokens = JU.PT.getTokens(this.rd());
+var a = this.parseFloatStr(tokens[0]);
+var b = this.parseFloatStr(tokens[1]);
+if (!this.isSlab && !this.isPolymer && tokens.length == 7) {
+this.primitiveVolume = this.parseFloatStr(tokens[6]);
+if (Math.abs(this.primitiveVolume - a * b) < 0.1) {
+this.isSlab = true;
+}}if (this.isSlab) {
+if (isPrimitive) this.setUnitCell(a * f, b * f, -1, this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[4]), this.parseFloatStr(tokens[5]));
+ else this.setUnitCell(a * f, b * f, -1, 90, 90, this.parseFloatStr(tokens[2]));
+} else if (this.isPolymer) {
+this.setUnitCell(a, -1, -1, this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[4]), this.parseFloatStr(tokens[5]));
+} else {
+this.setUnitCell(a * f, b * f, this.parseFloatStr(tokens[2]) * f, this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[4]), this.parseFloatStr(tokens[5]));
+}}}, "~B");
+Clazz.defineMethod(c$, "getAtomIndexFromPrimitiveIndex",
+function(iPrim){
+return (this.primitiveToIndex == null ? iPrim : this.primitiveToIndex[iPrim]);
+}, "~N");
+Clazz.defineMethod(c$, "readAtoms",
+function(){
+if (this.isMolecular) this.newAtomSet();
+this.lstCoords = null;
+while (this.rd() != null && this.line.indexOf("*") < 0) {
+if (this.line.indexOf("X(ANGSTROM") >= 0) {
+this.setFractionalCoordinates(false);
+this.isMolecular = true;
+}}
+var i = this.atomIndexLast;
+var doNormalizePrimitive = false;
+this.atomIndexLast = this.asc.ac;
+var isFractional = this.iHaveFractionalCoordinates;
+if (!isFractional) {
+this.setUnitCellOrientation();
+if (this.matUnitCellOrientation != null) this.getSymmetry().initializeOrientation(this.matUnitCellOrientation);
+}while (this.rd() != null && this.line.length > 0 && this.line.indexOf(this.isPrimitive ? "*" : "=") < 0) {
+var atom = this.asc.addNewAtom();
+var tokens = this.getTokens();
+var pt = (this.isProperties ? 1 : 2);
+atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(this.getAtomicNumber(tokens[pt++]));
+atom.atomName = J.adapter.readers.xtal.CrystalReader.fixAtomName(tokens[pt++]);
+if (this.isProperties) pt++;
+var x = this.parseFloatStr(tokens[pt++]);
+var y = this.parseFloatStr(tokens[pt++]);
+var z = this.parseFloatStr(tokens[pt]);
+if (this.haveCharges) atom.partialCharge = this.asc.atoms[i++].partialCharge;
+if (isFractional && !this.isProperties) {
+if (x < 0 && (this.isPolymer || this.isSlab || doNormalizePrimitive)) x += 1;
+if (y < 0 && (this.isSlab || doNormalizePrimitive)) y += 1;
+if (z < 0 && doNormalizePrimitive) z += 1;
+}this.setAtomCoordXYZ(atom, x, y, z);
+}
+this.ac = this.asc.ac - this.atomIndexLast;
+return true;
+});
+c$.fixAtomName = Clazz.defineMethod(c$, "fixAtomName",
+function(s){
+return (s.length > 1 && JU.PT.isLetter(s.charAt(1)) ? s.substring(0, 1) + Character.toLowerCase(s.charAt(1)) + s.substring(2) : s);
+}, "~S");
+Clazz.defineMethod(c$, "getAtomicNumber",
+function(token){
+return this.parseIntStr(token) % 100;
+}, "~S");
+Clazz.defineMethod(c$, "readCoordLines",
+function(){
+var atom = (this.inputOnly ? " ATOM" : " ATOM");
+if (this.line.indexOf(atom) < 0) this.discardLinesUntilContains(atom);
+this.lstCoords = new JU.Lst();
+while (this.rd() != null && this.line.length > 0) if (this.line.indexOf("****") < 0) this.lstCoords.addLast(this.line);
+
+});
+Clazz.defineMethod(c$, "processCoordLines",
+function(){
+if (this.lstCoords == null) return;
+this.ac = this.lstCoords.size();
+var irreducible = null;
+for (var i = 0; i < this.ac; i++) {
+var atom = this.asc.addNewAtom();
+var tokens = JU.PT.getTokens(this.lstCoords.get(i));
+atom.atomSerial = this.parseIntStr(tokens[0]);
+var atomicNumber;
+var offset;
+switch (tokens.length) {
+case 8:
+case 7:
+atomicNumber = this.getAtomicNumber(tokens[2]);
+offset = 4;
+if (i == 0) irreducible = Clazz.newFloatArray (this.ac, 0);
+if (tokens[1].equals("T")) irreducible[i] = 1;
+break;
+default:
+atomicNumber = this.getAtomicNumber(tokens[1]);
+offset = 2;
+break;
+}
+var x = this.parseFloatStr(tokens[offset++]) + this.ptOriginShift.x;
+var y = this.parseFloatStr(tokens[offset++]) + this.ptOriginShift.y;
+var z = this.parseFloatStr(tokens[offset]) + this.ptOriginShift.z;
+this.setAtomCoordXYZ(atom, x, y, z);
+atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(atomicNumber);
+}
+this.lstCoords = null;
+if (irreducible != null) {
+this.asc.setAtomProperties("irreducible", irreducible, -1, false);
+}if (this.primitiveVolume > 0) {
+this.asc.setAtomSetModelProperty("volumePrimitive", JU.DF.formatDecimal(this.primitiveVolume, 3));
+this.asc.setModelInfoForSet("primitiveVolume", Float.$valueOf(this.primitiveVolume), this.asc.iSet);
+}if (this.primitiveDensity > 0) {
+this.asc.setAtomSetModelProperty("densityPrimitive", JU.DF.formatDecimal(this.primitiveDensity, 3));
+this.asc.setModelInfoForSet("primitiveDensity", Float.$valueOf(this.primitiveDensity), this.asc.iSet);
+}});
+Clazz.overrideMethod(c$, "applySymmetryAndSetTrajectory",
+function(){
+this.setUnitCellOrientation();
+var m4p2c;
+var m4c2p;
+if (this.primitiveToCrystal != null) {
+this.asc.setModelInfoForSet("primitiveToCrystal", this.primitiveToCrystal, this.asc.iSet);
+m4p2c = new JU.M4();
+m4p2c.setRotationScale(this.primitiveToCrystal);
+m4p2c.m33 = 1;
+this.asc.setModelInfoForSet("mat4PrimitiveToCrystal", m4p2c, this.asc.iSet);
+m4c2p = JU.M4.newM4(m4p2c);
+m4c2p.invert();
+this.asc.setModelInfoForSet("mat4CrystalToPrimitive", m4c2p, this.asc.iSet);
+if (this.symops.size() > 0) {
+this.asc.setModelInfoForSet("fileSymmetryOperations", this.symops.clone(), this.asc.iSet);
+}}this.iHaveSymmetryOperators = false;
+this.applySymTrajASCR();
+});
+Clazz.defineMethod(c$, "newAtomSet",
+function(){
+if (this.ac > 0 && this.asc.ac > 0) {
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSet();
+}if (this.spaceGroupName != null) {
+this.setSpaceGroupName(this.spaceGroupName);
+}this.ac = 0;
+});
+Clazz.defineMethod(c$, "setEnergy",
+function(){
+this.asc.setAtomSetEnergy("" + this.energy, this.energy.floatValue());
+this.asc.setCurrentModelInfo("Energy", this.energy);
+this.asc.setInfo("Energy", this.energy);
+this.asc.setAtomSetName("Energy = " + this.energy + " Hartree");
+});
+Clazz.defineMethod(c$, "readPartialCharges",
+function(){
+if (this.haveCharges || this.asc.ac == 0) return true;
+this.haveCharges = true;
+this.readLines(3);
+var atoms = this.asc.atoms;
+var i0 = this.asc.getLastAtomSetAtomIndex();
+var iPrim = 0;
+while (this.rd() != null && this.line.length > 3) if (this.line.charAt(3) != ' ') {
+var iConv = this.getAtomIndexFromPrimitiveIndex(iPrim);
+if (iConv >= 0) atoms[i0 + iConv].partialCharge = this.parseFloatRange(this.line, 9, 11) - this.parseFloatRange(this.line, 12, 18);
+iPrim++;
+}
+return true;
+});
+Clazz.defineMethod(c$, "readTotalAtomicCharges",
+function(){
+var data = new JU.SB();
+while (this.rd() != null && this.line.indexOf("T") < 0) data.append(this.line);
+
+var tokens = JU.PT.getTokens(data.toString());
+var charges = Clazz.newFloatArray (tokens.length, 0);
+if (this.nuclearCharges == null || this.nuclearCharges.length != charges.length) this.nuclearCharges = charges;
+if (this.asc.ac == 0) return true;
+var atoms = this.asc.atoms;
+var i0 = this.asc.getLastAtomSetAtomIndex();
+for (var i = 0; i < charges.length; i++) {
+var iConv = this.getAtomIndexFromPrimitiveIndex(i);
+if (iConv >= 0) {
+charges[i] = this.parseFloatStr(tokens[i]);
+atoms[i0 + iConv].partialCharge = this.nuclearCharges[i] - charges[i];
+}}
+return true;
+});
+Clazz.defineMethod(c$, "readFreqFragments",
+function(){
+var numAtomsFrag = this.parseIntRange(this.line, 39, 44);
+if (numAtomsFrag < 0) return;
+this.atomFrag = Clazz.newIntArray (numAtomsFrag, 0);
+var Sfrag = "";
+while (this.rd() != null && this.line.indexOf("(") >= 0) Sfrag += this.line;
+
+Sfrag = JU.PT.rep(Sfrag, "(", " ");
+Sfrag = JU.PT.rep(Sfrag, ")", " ");
+var tokens = JU.PT.getTokens(Sfrag);
+for (var i = 0, pos = 0; i < numAtomsFrag; i++, pos += 3) this.atomFrag[i] = this.getAtomIndexFromPrimitiveIndex(this.parseIntStr(tokens[pos]) - 1);
+
+java.util.Arrays.sort(this.atomFrag);
+});
+Clazz.defineMethod(c$, "readFrequencies",
+function(){
+this.getLastConventional = false;
+this.addModel();
+this.energy = null;
+this.discardLinesUntilContains("MODES");
+var haveIntensities = (this.line.indexOf("INTENS") >= 0);
+this.rd();
+var vData = new JU.Lst();
+var freqAtomCount = (this.atomFrag == null ? this.ac : 0);
+while (this.rd() != null && this.line.length > 0) {
+var i0 = this.parseIntRange(this.line, 1, 5);
+var i1 = this.parseIntRange(this.line, 6, 10);
+var irrep = (this.isLongMode ? this.line.substring(48, 51) : this.line.substring(49, 52)).trim();
+var intens = (!haveIntensities ? "not available" : (this.isLongMode ? this.line.substring(53, 61) : this.line.substring(59, 69).$replace(')', ' ')).trim());
+var irActivity = (this.isLongMode ? "A" : this.line.substring(55, 58).trim());
+var ramanActivity = (this.isLongMode ? "I" : this.line.substring(71, 73).trim());
+var data = Clazz.newArray(-1, [irrep, intens, irActivity, ramanActivity]);
+for (var i = i0; i <= i1; i++) vData.addLast(data);
+
+}
+var test = (this.isLongMode ? "LO MODES FOR IRREP" : this.isVersion3 ? "THE CORRESPONDING MODES" : "NORMAL MODES NORMALIZED TO CLASSICAL AMPLITUDES");
+this.rd();
+var ramanData = null;
+if (this.line.indexOf("") >= 0) ramanData = this.readRaman(null);
+if (!this.line.contains(test)) this.discardLinesUntilContains(test);
+this.rd();
+var modelAtomCount = -1;
+while (this.rd() != null && this.line.startsWith(" FREQ(CM**-1)")) {
+var tokens = JU.PT.getTokens(this.line.substring(15));
+var frequencies = Clazz.newFloatArray (tokens.length, 0);
+var frequencyCount = frequencies.length;
+for (var i = 0; i < frequencyCount; i++) {
+frequencies[i] = this.parseFloatStr(tokens[i]);
+if (this.debugging) JU.Logger.debug((this.vibrationNumber + i) + " frequency=" + frequencies[i]);
+}
+var ignore = Clazz.newBooleanArray(frequencyCount, false);
+var iAtom0 = 0;
+var nData = vData.size();
+var isFirst = true;
+for (var i = 0; i < frequencyCount; i++) {
+tokens = vData.get(this.vibrationNumber % nData);
+ignore[i] = (!this.doGetVibration(++this.vibrationNumber) || tokens == null);
+if (ignore[i]) continue;
+this.applySymmetryAndSetTrajectory();
+if (isFirst) {
+modelAtomCount = this.asc.getLastAtomSetAtomCount();
+}this.cloneLastAtomSet(this.ac, null);
+if (isFirst) {
+iAtom0 = this.asc.getLastAtomSetAtomIndex();
+isFirst = false;
+}this.setFreqValue(frequencies[i], tokens);
+}
+this.rd();
+this.fillFrequencyData(iAtom0, freqAtomCount, modelAtomCount, ignore, false, 14, 10, this.atomFrag, 0, null);
+this.rd();
+}
+if (ramanData != null) this.readRaman(ramanData);
+});
+Clazz.defineMethod(c$, "setFreqValue",
+function(freq, data){
+var activity = "IR: " + data[2] + ", Ram.: " + data[3];
+this.asc.setAtomSetFrequency(this.vibrationNumber, null, activity, "" + freq, null);
+this.asc.setAtomSetModelProperty("IRintensity", data[1] + " km/Mole");
+this.asc.setAtomSetModelProperty("vibrationalSymmetry", data[0]);
+this.asc.setAtomSetModelProperty("IRactivity", data[2]);
+this.asc.setAtomSetModelProperty("Ramanactivity", data[3]);
+this.asc.setAtomSetName((this.isLongMode ? "LO " : "") + data[0] + " " + JU.DF.formatDecimal(freq, 2) + " cm-1 (" + JU.DF.formatDecimal(Float.parseFloat(data[1]), 0) + " km/Mole), " + activity);
+}, "~N,~A");
+Clazz.defineMethod(c$, "readRaman",
+function(ramanData){
+if (ramanData == null) {
+ramanData = new JU.Lst();
+this.rd();
+while (this.rd() != null && !this.line.contains("")) ramanData.addLast(this.line);
+
+return ramanData;
+}var info;
+var i = 0;
+var n = ramanData.size();
+for (; i < n; i++) {
+this.line = ramanData.get(i);
+if (this.line.contains("---")) break;
+}
+for (++i; i < n; i++) {
+this.line = ramanData.get(i);
+if (this.line.length == 0) break;
+var mode1 = this.parseIntRange(this.line, 1, 5);
+var mode2 = this.parseIntRange(this.line, 6, 10);
+var i_tot = this.parseFloatRange(this.line, 30, 40);
+var i_par = this.parseFloatRange(this.line, 40, 50);
+var i_perp = this.parseFloatRange(this.line, 50, 60);
+for (var i0 = 0, mode = mode1; mode <= mode2; mode++) {
+var imodel = this.getModelForMode(i0, mode);
+if (imodel < 0) continue;
+i0 = imodel + 1;
+info = this.asc.getAtomSetAuxiliaryInfoValue(imodel, "ramanInfo");
+if (info == null) this.asc.setModelInfoForSet("ramanInfo", info = new java.util.Hashtable(), imodel);
+info.put("isotropicIntensities", Clazz.newFloatArray(-1, [i_tot, i_par, i_perp]));
+}
+}
+for (; i < n; i++) {
+this.line = ramanData.get(i);
+if (this.line.contains("---")) break;
+}
+for (++i; i < n; i++) {
+this.line = ramanData.get(i);
+if (this.line.length == 0) break;
+var mode1 = this.parseIntRange(this.line, 1, 5);
+var mode2 = this.parseIntRange(this.line, 6, 10);
+var i_xx = this.parseFloatRange(this.line, 30, 38);
+var i_xy = this.parseFloatRange(this.line, 38, 46);
+var i_xz = this.parseFloatRange(this.line, 46, 54);
+var i_yy = this.parseFloatRange(this.line, 54, 62);
+var i_yz = this.parseFloatRange(this.line, 62, 70);
+var i_zz = this.parseFloatRange(this.line, 70, 78);
+for (var i0 = 0, mode = mode1; mode <= mode2; mode++) {
+var imodel = this.getModelForMode(i0, mode);
+if (imodel < 0) continue;
+i0 = imodel + 1;
+var a = Clazz.newArray(-1, [ Clazz.newDoubleArray(-1, [i_xx, i_xy, i_xz]), Clazz.newDoubleArray(-1, [i_xy, i_yy, i_yz]), Clazz.newDoubleArray(-1, [i_xz, i_yz, i_zz])]);
+this.asc.atoms[this.asc.getAtomSetAtomIndex(imodel)].addTensor( new JU.Tensor().setFromAsymmetricTensor(a, "raman", "mode" + mode), "raman", false);
+}
+}
+this.appendLoadNote("Ellipsoids set \"raman\": Raman tensors");
+return null;
+}, "JU.Lst");
+Clazz.defineMethod(c$, "getModelForMode",
+function(i0, mode){
+var n = this.asc.atomSetCount;
+for (var i = i0; i < n; i++) {
+var imode = this.asc.getAtomSetAuxiliaryInfoValue(i, "vibrationalMode");
+var m = (imode == null ? 0 : imode.intValue());
+if (m == mode) return i;
+}
+return -1;
+}, "~N,~N");
+Clazz.defineMethod(c$, "readGradient",
+function(){
+var key = null;
+while (this.line != null) {
+var tokens = this.getTokens();
+if (this.line.indexOf("MAX GRAD") >= 0) key = "maxGradient";
+ else if (this.line.indexOf("RMS GRAD") >= 0) key = "rmsGradient";
+ else if (this.line.indexOf("MAX DISP") >= 0) key = "maxDisplacement";
+ else if (this.line.indexOf("RMS DISP") >= 0) key = "rmsDisplacement";
+ else break;
+if (this.asc.ac > 0) this.asc.setAtomSetModelProperty(key, tokens[2]);
+this.rd();
+}
+return true;
+});
+Clazz.defineMethod(c$, "readData",
+function(name, nfields){
+this.processCoordLines();
+var f = Clazz.newFloatArray (this.ac, 0);
+for (var i = 0; i < this.ac; i++) f[i] = 0;
+
+var data = "";
+while (this.rd() != null && (this.line.length < 4 || JU.PT.isDigit(this.line.charAt(3)))) data += this.line;
+
+data = JU.PT.rep(data, "-", " -");
+var tokens = JU.PT.getTokens(data);
+for (var i = 0, pt = nfields - 1; i < this.ac; i++, pt += nfields) {
+var iConv = this.getAtomIndexFromPrimitiveIndex(i);
+if (iConv >= 0) f[iConv] = this.parseFloatStr(tokens[pt]);
+}
+this.asc.setAtomProperties(name, f, -1, false);
+return true;
+}, "~S,~N");
+Clazz.defineMethod(c$, "getQuadrupoleTensors",
+function(){
+this.readLines(6);
+var atoms = this.asc.atoms;
+var vectors = new Array(3);
+if (this.directLatticeVectors == null) vectors = Clazz.newArray(-1, [JU.V3.new3(1, 0, 0), JU.V3.new3(0, 1, 0), JU.V3.new3(0, 0, 1)]);
+ else for (var i = 0; i < 3; i++) {
+vectors[i] = JU.V3.newV(this.directLatticeVectors[i]);
+vectors[i].normalize();
+}
+while (this.rd() != null && this.line.startsWith(" *** ATOM")) {
+var tokens = this.getTokens();
+var index = this.parseIntStr(tokens[3]) - 1;
+tokens = JU.PT.getTokens(this.readLines(3));
+atoms[index].addTensor( new JU.Tensor().setFromEigenVectors(vectors, Clazz.newFloatArray(-1, [this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[5])]), "quadrupole", atoms[index].atomName, null), null, false);
+this.rd();
+}
+this.appendLoadNote("Ellipsoids set \"quadrupole\": Quadrupole tensors");
+return true;
+});
+Clazz.defineMethod(c$, "readBornChargeTensors",
+function(){
+this.processCoordLines();
+this.rd();
+var atoms = this.asc.atoms;
+while (this.rd().startsWith(" ATOM")) {
+var index = this.parseIntAt(this.line, 5) - 1;
+var atom = atoms[index];
+this.readLines(2);
+atom.addTensor( new JU.Tensor().setFromAsymmetricTensor(this.fill3x3(null, -3), "charge", atom.elementSymbol + (index + 1)), null, false);
+this.rd();
+}
+this.appendLoadNote("Ellipsoids set \"charge\": Born charge tensors");
+return false;
+});
+c$.crtypes = Clazz.newArray(-1, ["??", "nuclei", "bonds", "rings", "cages"]);
+c$.smap = Clazz.newIntArray(-1, [2, 3, 4, 11, 5, 6, 7, 12, 8, 9, 10, 13]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/DmolReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/DmolReader.js
new file mode 100755
index 000000000000..81be3a55e7a6
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/DmolReader.js
@@ -0,0 +1,103 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.DmolReader", ["JU.DF", "$.PT", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.unitCellData = null;
+this.totE = null;
+this.geomOpt = false;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "DmolReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.contains("** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES **")) {
+this.geomOpt = true;
+} else if (this.line.contains("INCOOR, atomic coordinates")) {
+this.geomOpt = false;
+} else if (!this.geomOpt ? this.line.contains("$cell vectors") : this.line.contains("Lattice:")) {
+this.readCellParam();
+} else if (!this.geomOpt ? this.line.contains("$coordinates") : this.line.contains("Input Coordinates")) {
+this.readCoord();
+} else if (this.line.contains(" Total Energy")) {
+this.readEnergy();
+} else if (this.line.contains("Frequencies (cm-1)")) {
+this.readFreq();
+}return true;
+});
+Clazz.defineMethod(c$, "readCellParam",
+function(){
+this.unitCellData = Clazz.newFloatArray (9, 0);
+for (var n = 0, i = 0; n < 3; n++) {
+var tokens = JU.PT.getTokens(this.rd());
+this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[0] : tokens[4]) * 0.5291772;
+this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[1] : tokens[5]) * 0.5291772;
+this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[2] : tokens[6]) * 0.5291772;
+}
+});
+Clazz.defineMethod(c$, "newAtomSet",
+function(){
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSet();
+if (this.totE != null) this.setEnergy();
+this.doApplySymmetry = true;
+if (this.unitCellData != null) {
+this.addExplicitLatticeVector(0, this.unitCellData, 0);
+this.addExplicitLatticeVector(1, this.unitCellData, 3);
+this.addExplicitLatticeVector(2, this.unitCellData, 6);
+this.setSpaceGroupName("P1");
+}this.setFractionalCoordinates(false);
+});
+Clazz.defineMethod(c$, "readCoord",
+function(){
+this.newAtomSet();
+if (this.geomOpt) this.readLines(2);
+while (this.rd() != null && !this.geomOpt ? !this.line.contains("$end") : !this.line.contains("-----")) {
+var tokens = this.getTokens();
+var atom = this.asc.addNewAtom();
+atom.atomName = !this.geomOpt ? tokens[0] : tokens[1];
+var factor = (!this.geomOpt ? 0.5291772 : 1.00);
+var x = this.parseFloatStr(!this.geomOpt ? tokens[1] : tokens[2]) * factor;
+var y = this.parseFloatStr(!this.geomOpt ? tokens[2] : tokens[3]) * factor;
+var z = this.parseFloatStr(!this.geomOpt ? tokens[3] : tokens[4]) * factor;
+atom.set(x, y, z);
+this.setAtomCoord(atom);
+}
+});
+Clazz.defineMethod(c$, "readEnergy",
+function(){
+this.rd();
+if (this.line.contains("Ef")) this.totE = Double.$valueOf(Double.parseDouble(JU.PT.getTokens(this.line.substring(this.line.indexOf("Ef") + 1, this.line.indexOf("Ha")))[1]));
+});
+Clazz.defineMethod(c$, "setEnergy",
+function(){
+this.asc.setAtomSetEnergy("" + this.totE, this.totE.floatValue());
+this.asc.setInfo("Energy", this.totE);
+this.asc.setAtomSetName("E = " + this.totE + " Hartree");
+});
+Clazz.defineMethod(c$, "readFreq",
+function(){
+var lastAtomCount = 0;
+var ac = this.asc.getLastAtomSetAtomCount();
+while (this.rd() != null && this.line.charAt(1) == ' ') {
+var tokens = this.getTokens();
+var frequencyCount = Clazz.doubleToInt(tokens.length / 2);
+var frequencies = Clazz.newFloatArray (frequencyCount, 0);
+for (var i = 1, n = 0; i < tokens.length; i += 2, n++) {
+frequencies[n] = this.parseFloatStr(tokens[i]);
+if (this.debugging) JU.Logger.debug((this.vibrationNumber + n) + " frequency=" + frequencies[n]);
+}
+var ignore = Clazz.newBooleanArray(frequencyCount, false);
+var iAtom0 = 0;
+for (var i = 0; i < frequencyCount; i++) {
+ignore[i] = (!this.doGetVibration(++this.vibrationNumber));
+if (ignore[i]) continue;
+this.applySymmetryAndSetTrajectory();
+lastAtomCount = this.cloneLastAtomSet(ac, null);
+if (i == 0) iAtom0 = this.asc.getLastAtomSetAtomIndex();
+this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, String.valueOf(frequencies[i]), null);
+this.asc.setAtomSetName(JU.DF.formatDecimal(frequencies[i], 2) + " cm-1");
+}
+this.rd();
+this.fillFrequencyData(iAtom0, ac, lastAtomCount, ignore, false, 5, 13, null, 0, null);
+this.readLines(2);
+}
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/EspressoReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/EspressoReader.js
new file mode 100755
index 000000000000..ff0cfae55eda
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/EspressoReader.js
@@ -0,0 +1,102 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.EspressoReader", ["JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.cellParams = null;
+this.totEnergy = null;
+this.endFlag = false;
+this.aPar = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "EspressoReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setSpaceGroupName("P1");
+this.doApplySymmetry = true;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.contains("lattice parameter (a_0)") || this.line.contains("lattice parameter (alat)")) {
+this.readAparam();
+} else if (this.line.contains("crystal axes:")) {
+this.readCellParam(false);
+} else if (this.line.contains("CELL_PARAMETERS (")) {
+this.readCellParam(true);
+} else if (this.line.contains("Cartesian axes")) {
+this.discardLinesUntilContains("positions (");
+if (this.doGetModel(++this.modelNumber, null)) this.readAtoms();
+} else if (this.line.contains("POSITIONS (")) {
+if (this.doGetModel(++this.modelNumber, null)) this.readAtoms();
+} else if (this.line.contains("! total energy")) {
+this.readEnergy();
+} else if (this.line.contains("A final scf")) {
+this.endFlag = true;
+}return true;
+});
+Clazz.defineMethod(c$, "readAparam",
+function(){
+this.aPar = this.parseFloatStr(this.getTokens()[4]) * 0.5291772;
+});
+Clazz.defineMethod(c$, "readCellParam",
+function(andAPar){
+var i0 = (andAPar ? 0 : 3);
+if (this.line.contains("bohr")) this.aPar = 0.5291772;
+if (andAPar && this.line.contains("=")) this.aPar = this.parseFloatStr(this.line.substring(this.line.indexOf("=") + 1)) * 0.5291772;
+this.cellParams = Clazz.newFloatArray (9, 0);
+for (var n = 0, i = 0; n < 3; n++) {
+var tokens = JU.PT.getTokens(this.rd());
+this.cellParams[i++] = this.parseFloatStr(tokens[i0]) * this.aPar;
+this.cellParams[i++] = this.parseFloatStr(tokens[i0 + 1]) * this.aPar;
+this.cellParams[i++] = this.parseFloatStr(tokens[i0 + 2]) * this.aPar;
+}
+}, "~B");
+Clazz.defineMethod(c$, "newAtomSet",
+function(){
+this.asc.newAtomSet();
+if (this.totEnergy != null) this.setEnergy();
+});
+Clazz.defineMethod(c$, "setCellParams",
+function(){
+if (this.cellParams != null) {
+this.addExplicitLatticeVector(0, this.cellParams, 0);
+this.addExplicitLatticeVector(1, this.cellParams, 3);
+this.addExplicitLatticeVector(2, this.cellParams, 6);
+this.setSpaceGroupName("P1");
+}});
+Clazz.defineMethod(c$, "readAtoms",
+function(){
+this.newAtomSet();
+var isAlat = (this.line.contains("alat") || this.line.contains("a_0"));
+var firstStr = (this.line.contains("site n."));
+var isFractional = this.line.contains("crystal");
+var isBohr = this.line.contains("bohr");
+var isAngstrom = this.line.contains("angstrom");
+if (isAlat || isFractional || isAngstrom) this.setCellParams();
+this.setFractionalCoordinates(isFractional);
+while (this.rd() != null && this.line.length > 45) {
+var tokens = this.getTokens();
+var atom = this.asc.addNewAtom();
+atom.atomName = tokens[(isBohr || tokens.length == 4 || !firstStr ? 0 : 1)];
+var i1 = (isBohr || tokens.length == 4 || !firstStr ? 1 : tokens.length - 4);
+var x = this.parseFloatStr(tokens[i1++]);
+var y = this.parseFloatStr(tokens[i1++]);
+var z = this.parseFloatStr(tokens[i1++]);
+atom.set(x, y, z);
+if (isBohr) {
+atom.scale(0.5291772);
+} else if (isAlat) {
+atom.scale(this.aPar);
+}this.setAtomCoord(atom);
+}
+this.applySymmetryAndSetTrajectory();
+if (this.endFlag) this.discardLinesUntilContains("Harris-Foulkes estimate");
+});
+Clazz.defineMethod(c$, "readEnergy",
+function(){
+this.totEnergy = Double.$valueOf(Double.parseDouble(JU.PT.getTokens(this.line.substring(this.line.indexOf("=") + 1))[0]));
+});
+Clazz.defineMethod(c$, "setEnergy",
+function(){
+this.asc.setAtomSetEnergy("" + this.totEnergy, this.totEnergy.floatValue());
+this.asc.setInfo("Energy", this.totEnergy);
+this.asc.setAtomSetName("E = " + this.totEnergy + " Ry");
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/GulpReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/GulpReader.js
new file mode 100755
index 000000000000..9c565bdb199f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/GulpReader.js
@@ -0,0 +1,247 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.GulpReader", ["java.util.Hashtable", "JU.PT", "$.V3"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isSlab = false;
+this.isPolymer = false;
+this.$isPrimitive = false;
+this.sep = "-------";
+this.coordinatesArePrimitive = false;
+this.atomCharges = null;
+this.bTest = false;
+this.a = 0;
+this.b = 0;
+this.c = 0;
+this.alpha = 0;
+this.beta = 0;
+this.gamma = 0;
+this.primitiveData = null;
+this.totEnergy = null;
+this.energyUnits = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "GulpReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.$isPrimitive = !this.checkFilterKey("CONV");
+this.coordinatesArePrimitive = true;
+this.setFractionalCoordinates(this.readDimensionality());
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+if (this.atomCharges == null) return;
+var atoms = this.asc.atoms;
+var f;
+for (var i = this.asc.ac; --i >= 0; ) if ((f = this.atomCharges.get(atoms[i].atomName)) != null || (f = this.atomCharges.get(atoms[i].getElementSymbol())) != null) atoms[i].partialCharge = f.floatValue();
+
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.contains("Space group ")) {
+this.readSpaceGroup();
+return true;
+}if (this.isSlab ? this.line.contains("Surface cell parameters") : this.isPolymer ? this.line.contains("Polymer cell parameter") : (this.bTest = this.line.contains("Cartesian lattice vectors")) || this.line.contains("Cell parameters (Angstroms/Degrees)") || this.line.contains("Primitive cell parameters")) {
+this.readCellParameters(this.bTest);
+return true;
+}if (this.line.contains("Monopole - monopole (total)")) {
+this.readEnergy();
+return true;
+}if (this.line.contains("Fractional coordinates of asymmetric unit :") || (this.bTest = this.line.contains("Final asymmetric unit coordinates")) || (this.bTest = this.line.contains("Final fractional coordinates ")) || this.line.contains("Mixed fractional/Cartesian coordinates") || this.line.contains("Cartesian coordinates of cluster ") || this.line.contains("Final cartesian coordinates of atoms :") && this.isMolecular) {
+if (this.doGetModel(++this.modelNumber, null)) this.readAtomicPos(!this.bTest);
+return true;
+}if (this.line.contains("Species output for all configurations")) {
+this.readPartialCharges();
+return true;
+}if (!this.doProcessLines) return true;
+if (this.line.contains("Final cell parameters and derivatives")) {
+this.readFinalCell();
+return true;
+}return true;
+});
+Clazz.defineMethod(c$, "readDimensionality",
+function(){
+this.discardLinesUntilContains("Dimensionality");
+var tokens = this.getTokens();
+switch (this.parseIntStr(tokens[2])) {
+case 0:
+this.isMolecular = true;
+this.$isPrimitive = false;
+return false;
+case 1:
+this.isPolymer = true;
+this.$isPrimitive = false;
+break;
+case 2:
+this.isSlab = true;
+this.$isPrimitive = false;
+break;
+}
+return true;
+});
+Clazz.defineMethod(c$, "readSpaceGroup",
+function(){
+this.sgName = this.line.substring(this.line.indexOf(":") + 1).trim();
+});
+c$.parameterIndex = Clazz.defineMethod(c$, "parameterIndex",
+function(key){
+for (var i = J.adapter.readers.xtal.GulpReader.tags.length; --i >= 0; ) if (J.adapter.readers.xtal.GulpReader.tags[i].equals(key)) return i;
+
+return -1;
+}, "~S");
+Clazz.defineMethod(c$, "setParameter",
+function(key, value){
+switch (J.adapter.readers.xtal.GulpReader.parameterIndex(key)) {
+case 0:
+this.a = value;
+break;
+case 1:
+this.b = value;
+break;
+case 2:
+this.c = value;
+break;
+case 3:
+this.alpha = value;
+break;
+case 4:
+this.beta = value;
+break;
+case 5:
+this.gamma = value;
+break;
+}
+}, "~S,~N");
+Clazz.defineMethod(c$, "newAtomSet",
+function(doSetUnitCell){
+this.asc.newAtomSet();
+if (doSetUnitCell) {
+this.setModelParameters(this.coordinatesArePrimitive);
+if (this.totEnergy != null) this.setEnergy();
+}}, "~B");
+Clazz.defineMethod(c$, "setModelParameters",
+function(isPrimitive){
+if (this.sgName != null) this.setSpaceGroupName(isPrimitive ? "P1" : this.sgName);
+if (isPrimitive && this.primitiveData != null) {
+this.addExplicitLatticeVector(0, this.primitiveData, 0);
+this.addExplicitLatticeVector(1, this.primitiveData, 3);
+this.addExplicitLatticeVector(2, this.primitiveData, 6);
+} else if (this.a != 0) {
+if (this.isSlab) {
+this.c = -1;
+this.beta = this.gamma = 90;
+} else if (this.isPolymer) {
+this.b = this.c = -1;
+this.alpha = this.beta = this.gamma = 90;
+}this.setUnitCell(this.a, this.b, this.c, this.alpha, this.beta, this.gamma);
+}}, "~B");
+Clazz.defineMethod(c$, "readCellParameters",
+function(isLatticeVectors){
+if (isLatticeVectors) {
+this.rd();
+this.primitiveData = this.fillFloatArray(null, 0, Clazz.newFloatArray (9, 0));
+this.a = 0;
+return;
+}var i0 = (this.line.indexOf("Full cell") < 0 ? 0 : 4);
+this.coordinatesArePrimitive = (i0 == 0);
+this.rd();
+while (this.rd() != null && this.line.contains("=")) {
+var tokens = JU.PT.getTokens(this.line.$replace('=', ' '));
+for (var i = i0; i < i0 + 4; i += 2) if (tokens.length > i + 1) this.setParameter(tokens[i], this.parseFloatStr(tokens[i + 1]));
+
+}
+}, "~B");
+Clazz.defineMethod(c$, "readFinalCell",
+function(){
+this.discardLinesUntilContains(this.sep);
+var tokens;
+while (this.rd() != null && (tokens = this.getTokens()).length >= 2) this.setParameter(tokens[0], this.parseFloatStr(tokens[1]));
+
+if (this.primitiveData != null) {
+this.scalePrimitiveData(0, this.a);
+this.scalePrimitiveData(3, this.b);
+this.scalePrimitiveData(6, this.c);
+if (!this.coordinatesArePrimitive) while (this.rd() != null && this.line.indexOf("Final") < 0) if (this.line.indexOf("Non-primitive lattice parameters") > 0) {
+this.rd();
+for (var i = 0; i < 2; i++) {
+tokens = JU.PT.getTokens(this.rd().$replace('=', ' '));
+this.setParameter(tokens[0], this.parseFloatStr(tokens[1]));
+this.setParameter(tokens[2], this.parseFloatStr(tokens[3]));
+this.setParameter(tokens[4], this.parseFloatStr(tokens[5]));
+}
+break;
+}
+}this.setModelParameters(this.coordinatesArePrimitive);
+this.applySymmetryAndSetTrajectory();
+if (this.totEnergy != null) this.setEnergy();
+});
+Clazz.defineMethod(c$, "scalePrimitiveData",
+function(i, value){
+var v = JU.V3.new3(this.primitiveData[i], this.primitiveData[i + 1], this.primitiveData[i + 2]);
+v.normalize();
+v.scale(value);
+this.primitiveData[i++] = v.x;
+this.primitiveData[i++] = v.y;
+this.primitiveData[i++] = v.z;
+}, "~N,~N");
+Clazz.overrideMethod(c$, "applySymmetryAndSetTrajectory",
+function(){
+if (this.coordinatesArePrimitive && this.iHaveUnitCell && this.doCheckUnitCell && this.primitiveData != null && !this.$isPrimitive) {
+this.setModelParameters(false);
+var symFull = this.symmetry;
+this.setModelParameters(true);
+var atoms = this.asc.atoms;
+var i0 = this.asc.getLastAtomSetAtomIndex();
+var i1 = this.asc.ac;
+for (var i = i0; i < i1; i++) {
+var atom = atoms[i];
+this.symmetry.toCartesian(atom, true);
+symFull.toFractional(atom, true);
+this.fixFloatPt(atom, 100000.0);
+}
+this.setModelParameters(false);
+}this.applySymTrajASCR();
+});
+Clazz.defineMethod(c$, "readAtomicPos",
+function(finalizeSymmetry){
+this.newAtomSet(finalizeSymmetry);
+this.discardLinesUntilContains(this.sep);
+this.discardLinesUntilContains(this.sep);
+while (this.rd() != null) {
+if (this.line.indexOf(this.sep) >= 0 && this.rd().indexOf("Region") < 0) break;
+if (this.line.indexOf("Region") >= 0) {
+this.rd();
+continue;
+}this.line = this.line.$replace('*', ' ');
+var tokens = this.getTokens();
+if (tokens[2].equals("c")) this.addAtomXYZSymName(tokens, 3, null, tokens[1]);
+}
+if (finalizeSymmetry) this.applySymmetryAndSetTrajectory();
+}, "~B");
+Clazz.defineMethod(c$, "readPartialCharges",
+function(){
+this.atomCharges = new java.util.Hashtable();
+this.discardLinesUntilContains(this.sep);
+this.discardLinesUntilContains(this.sep);
+var tokens;
+while ((tokens = JU.PT.getTokens(this.rd())).length > 5) {
+var species = tokens[0];
+var charge = this.atomCharges.get(species);
+var f = (charge == null ? 0 : charge.floatValue());
+this.atomCharges.put(species, Float.$valueOf((f + this.parseFloatStr(tokens[4]))));
+}
+});
+Clazz.defineMethod(c$, "readEnergy",
+function(){
+if (this.line.indexOf("=") < 0) this.discardLinesUntilContains("=");
+var tokens = JU.PT.getTokens(this.line.substring(this.line.indexOf("=")));
+this.totEnergy = Double.$valueOf(Double.parseDouble(tokens[1]));
+this.energyUnits = tokens[2];
+this.discardLinesUntilContains(this.sep);
+});
+Clazz.defineMethod(c$, "setEnergy",
+function(){
+this.asc.setAtomSetEnergy("" + this.totEnergy, this.totEnergy.floatValue());
+this.asc.setInfo("Energy", this.totEnergy);
+this.asc.setAtomSetName("E = " + this.totEnergy + " " + this.energyUnits);
+this.totEnergy = null;
+});
+c$.tags = Clazz.newArray(-1, ["a", "b", "c", "alpha", "beta", "gamma"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/JanaReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/JanaReader.js
new file mode 100755
index 000000000000..ba33c09fa562
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/JanaReader.js
@@ -0,0 +1,562 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.JanaReader", ["java.util.Hashtable", "JU.A4", "$.BS", "$.Lst", "$.Matrix", "$.P3", "$.PT", "$.Quat", "$.Rdr", "$.V3", "J.adapter.smarter.Atom", "J.api.Interface", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.lattvecs = null;
+this.thisSub = 0;
+this.modAxes = null;
+this.haveM40Data = false;
+this.qicount = 0;
+this.molName = null;
+this.molAtoms = null;
+this.molTtypes = null;
+this.modelMolecule = null;
+this.molHasTLS = false;
+this.matR = null;
+this.rho = null;
+this.firstPosition = false;
+this.vR = null;
+this.v0Cart = null;
+this.isLegendre = false;
+this.floats = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "JanaReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.floats = Clazz.newFloatArray (6, 0);
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.modAxes = this.getFilter("MODAXES=");
+this.setFractionalCoordinates(true);
+this.asc.newAtomSet();
+this.asc.setCurrentModelInfo("autoBondUsingOccupation", Boolean.TRUE);
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.length < 3) return true;
+JU.Logger.info(this.line);
+this.parseTokenStr(this.line);
+switch ("tit cell ndim qi lat sym spg end wma".indexOf(this.line.substring(0, 3))) {
+case 0:
+this.asc.setAtomSetName(this.line.substring(5).trim());
+break;
+case 5:
+this.cell();
+this.setSymmetryOperator("x,y,z");
+break;
+case 10:
+this.ndim();
+break;
+case 20:
+if (this.lattvecs == null) this.lattvecs = new JU.Lst();
+if (!this.ms.addLatticeVector(this.lattvecs, this.line.substring(8))) this.appendLoadNote(this.line + " not supported");
+break;
+case 30:
+this.setSpaceGroupName(this.getTokens()[1]);
+break;
+case 25:
+this.symmetry();
+break;
+case 15:
+this.qi();
+break;
+case 35:
+while (this.rd() != null) {
+if (this.line.startsWith("command") || this.parseIntStr(this.line) >= 0) {
+this.readM40Data(true);
+break;
+}}
+this.continuing = false;
+break;
+case 40:
+var n = 3 + this.modDim;
+var m;
+if (this.thisSub++ == 0) {
+m = JU.Matrix.identity(n, n);
+this.ms.addSubsystem("" + this.thisSub++, m);
+}m = new JU.Matrix(null, n, n);
+var a = m.getArray();
+var data = Clazz.newFloatArray (n * n, 0);
+this.fillFloatArray(null, 0, data);
+for (var i = 0, pt = 0; i < n; i++) for (var j = 0; j < n; j++, pt++) a[i][j] = data[pt];
+
+
+this.ms.addSubsystem("" + this.thisSub, m);
+}
+return true;
+});
+Clazz.overrideMethod(c$, "doPreSymmetry",
+function(){
+if (this.ms != null) this.ms.setModulation(false, null);
+if (this.vibsFractional) this.asc.getXSymmetry().scaleFractionalVibs();
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+if (!this.haveM40Data) this.readM40Data(false);
+if (this.lattvecs != null && this.lattvecs.size() > 0) this.asc.getSymmetry().addLatticeVectors(this.lattvecs);
+this.applySymmetryAndSetTrajectory();
+this.finalizeReaderASCR();
+});
+Clazz.overrideMethod(c$, "finalizeSubclassSymmetry",
+function(haveSymmetry){
+this.adjustM40Occupancies();
+if (this.ms != null && haveSymmetry) {
+this.ms.setModulation(true, this.asc.getXSymmetry().getBaseSymmetry());
+this.ms.finalizeModulation();
+}}, "~B");
+Clazz.defineMethod(c$, "cell",
+function(){
+for (var ipt = 0; ipt < 6; ipt++) this.setUnitCellItem(ipt, this.parseFloat());
+
+});
+Clazz.defineMethod(c$, "ndim",
+function(){
+this.ms = J.api.Interface.getOption("adapter.readers.cif.MSRdr", this.vwr, "file");
+this.modDim = this.ms.initialize(this, (this.parseIntStr(this.getTokens()[1]) - 3));
+});
+Clazz.defineMethod(c$, "qi",
+function(){
+var pt = Clazz.newDoubleArray (this.modDim, 0);
+pt[this.qicount] = 1;
+var a = Clazz.newDoubleArray(-1, [this.parseFloat(), this.parseFloat(), this.parseFloat()]);
+this.parseTokenStr(this.rd());
+for (var i = 0; i < 3; i++) a[i] += this.parseFloat();
+
+this.ms.addModulation(null, "W_" + (++this.qicount), a, -1);
+this.ms.addModulation(null, "F_" + this.qicount + "_coefs_", pt, -1);
+});
+Clazz.defineMethod(c$, "symmetry",
+function(){
+this.setSymmetryOperator(JU.PT.rep(this.line.substring(9).trim(), " ", ","));
+});
+Clazz.defineMethod(c$, "readM40Data",
+function(haveReader){
+if (haveReader) {
+this.parseM40Floats();
+} else {
+var m40File = this.filePath;
+var ipt = m40File.lastIndexOf(".");
+if (ipt < 0) return;
+m40File = m40File.substring(0, ipt + 2) + "40";
+var id = m40File.substring(0, ipt);
+this.reader.close();
+this.reader = JU.Rdr.getBR(this.vwr.getLigandModel(id, m40File, "_file", "----"));
+if (this.out != null) this.out.append("******************************* M40 DATA *******************************\n");
+this.readM40Floats();
+}this.haveM40Data = true;
+if (this.line.startsWith("command")) this.readM40WaveVectors();
+var nFree = 0;
+var nGroups = 0;
+var isAxial = false;
+var newSub = (this.thisSub == 0 ? null : new JU.BS());
+var iSub = (this.thisSub == 0 ? 1 : this.thisSub);
+for (var i = 0, n = 0, pt = 0; i < iSub; i++, pt += 10) {
+nFree = this.getInt(pt, pt + 5);
+nGroups = this.getInt(pt + 5, pt + 10);
+isAxial = (this.getInt(pt + 15, pt + 20) == 1);
+if (nGroups != 0 && i > 0) {
+throw new Exception("Jmol cannot read rigid body M40 files for composites");
+}if (newSub != null) newSub.set(n = n + nFree);
+}
+iSub = (newSub == null ? 0 : 1);
+var nAtoms = -1;
+var refAtomName = null;
+this.rho = null;
+if (nGroups > 0) {
+JU.Logger.info("JanaReader found " + nFree + " free atoms and " + nGroups + " groups");
+this.molName = null;
+this.molAtoms = new JU.Lst();
+this.molTtypes = new JU.Lst();
+}while (this.skipToNextAtom() != null) {
+nAtoms++;
+var atom = new J.adapter.smarter.Atom();
+JU.Logger.info(this.line);
+var name = this.line.substring(0, 9).trim();
+atom.atomName = name;
+var isRefAtom = name.equals(refAtomName);
+atom.foccupancy = this.floats[2];
+var isJanaMolecule = Float.isNaN(atom.foccupancy);
+if (isJanaMolecule) {
+var pointGroup = this.getStr(12, 18);
+if (pointGroup.length > 0 && !pointGroup.equals("1")) {
+throw new Exception("Jmol cannot process M40 files with molecule positions based on point-group symmetry.");
+}refAtomName = null;
+if (Float.isNaN(this.floats[4])) refAtomName = this.getStr(28, 37);
+ else this.rho = JU.P3.new3(this.floats[3], this.floats[4], this.floats[5]);
+this.molName = name;
+this.molAtoms.clear();
+this.molTtypes.clear();
+this.molHasTLS = false;
+this.firstPosition = true;
+this.modelMolecule = new JU.Lst();
+continue;
+}var isExcluded = false;
+var posName = (name.startsWith("pos#") ? name : null);
+if (posName == null) {
+if (!this.filterAtom(atom, 0)) {
+if (!isRefAtom) continue;
+isExcluded = true;
+}this.setAtomCoordXYZ(atom, this.floats[3], this.floats[4], this.floats[5]);
+if (isRefAtom) {
+this.rho = JU.P3.newP(atom);
+if (isExcluded) continue;
+}this.asc.addAtom(atom);
+if (iSub > 0) {
+if (newSub.get(nAtoms)) iSub++;
+atom.altLoc = ("" + iSub).charAt(0);
+}this.readAtomRecord(atom, null, null, false);
+if (this.molAtoms != null) this.molAtoms.addLast(atom);
+} else {
+if (this.molAtoms.size() == 0) continue;
+this.processPosition(posName, atom, isAxial);
+}}
+}, "~B");
+Clazz.defineMethod(c$, "getInt",
+function(col1, col2){
+var n = this.line.length;
+return (n > col1 ? this.parseIntStr(this.getStr(col1, col2)) : 0);
+}, "~N,~N");
+Clazz.defineMethod(c$, "getStr",
+function(col1, col2){
+var n = this.line.length;
+return (n > col1 ? this.line.substring(col1, Math.min(n, col2)).trim() : "");
+}, "~N,~N");
+Clazz.defineMethod(c$, "getFlag",
+function(i){
+return (this.getInt(i, i + 1) > 0);
+}, "~N");
+Clazz.defineMethod(c$, "skipToNextAtom",
+function(){
+while (this.readM40Floats() != null && (this.line.length == 0 || this.line.charAt(0) == ' ' || this.line.charAt(0) == '-')) {
+}
+return this.line;
+});
+Clazz.defineMethod(c$, "readM40WaveVectors",
+function(){
+while (!this.readM40Floats().contains("end")) if (this.line.startsWith("wave")) {
+var tokens = this.getTokens();
+var pt = Clazz.newDoubleArray (this.modDim, 0);
+for (var i = 0; i < this.modDim; i++) pt[i] = this.parseFloatStr(tokens[i + 2]);
+
+this.ms.addModulation(null, "F_" + this.parseIntStr(tokens[1]) + "_coefs_", pt, -1);
+}
+this.readM40Floats();
+});
+Clazz.defineMethod(c$, "processPosition",
+function(posName, pos, isAxial){
+pos.atomName = this.molName + "_" + posName;
+var isImproper = (this.getInt(9, 11) == -1);
+var systType = this.getInt(13, 14);
+var rm = (systType == 0 ? null : new JU.P3());
+var rp = (systType == 0 ? null : new JU.P3());
+if (systType != 0) {
+throw new Exception("Jmol can only read rigid body groups with basic crystallographic settings.");
+}var rotData = this.readAtomRecord(pos, rm, rp, true);
+var name = pos.atomName;
+var n = this.molAtoms.size();
+JU.Logger.info(name + " Molecular group " + this.molName + " has " + n + " atoms");
+var ext = "_" + posName.substring(4);
+var vTrans = JU.V3.new3(pos.anisoBorU[3], pos.anisoBorU[4], pos.anisoBorU[5]);
+var phi = JU.Quat.newAA(JU.A4.newVA(JU.V3.new3(0, 0, 1), (pos.anisoBorU[0] / 180 * 3.141592653589793)));
+var chi = JU.Quat.newAA(JU.A4.newVA(isAxial ? JU.V3.new3(0, 1, 0) : JU.V3.new3(1, 0, 0), (pos.anisoBorU[1] / 180 * 3.141592653589793)));
+var psi = JU.Quat.newAA(JU.A4.newVA(isAxial ? JU.V3.new3(1, 0, 0) : JU.V3.new3(0, 0, 1), (pos.anisoBorU[2] / 180 * 3.141592653589793)));
+this.matR = phi.mulQ(chi).mulQ(psi).getMatrix();
+if (isImproper) this.matR.scale(-1);
+var script = "";
+for (var i = 0; i < n; i++) {
+var a = this.molAtoms.get(i);
+var newName = a.atomName;
+script += ", " + newName;
+if (this.firstPosition) {
+newName += ext;
+this.modelMolecule.addLast(JU.P3.newP(a));
+} else {
+a = this.asc.newCloneAtom(a);
+newName = newName.substring(0, newName.lastIndexOf("_")) + ext;
+}a.atomName = newName;
+var v0 = JU.V3.newVsub(this.modelMolecule.get(i), this.rho);
+this.getSymmetry().toCartesian(this.v0Cart = JU.V3.newV(v0), true);
+this.vR = JU.V3.newV(v0);
+this.cartesianProduct(this.vR, null);
+a.setT(this.rho);
+a.add(vTrans);
+a.add(this.vR);
+this.copyModulations(";" + pos.atomName, ";" + newName);
+if (rotData != null) this.setRigidBodyRotations(";" + newName, rotData);
+}
+this.firstPosition = false;
+script = "@" + this.molName + ext + script.substring(1);
+this.addJmolScript(script);
+this.appendLoadNote(script);
+}, "~S,J.adapter.smarter.Atom,~B");
+Clazz.defineMethod(c$, "cartesianProduct",
+function(vA, vB){
+this.symmetry.toCartesian(vA, true);
+if (vB == null) this.matR.rotate2(vA, vA);
+ else vA.cross(vA, vB);
+this.symmetry.toFractional(vA, true);
+}, "JU.T3,JU.T3");
+Clazz.defineMethod(c$, "readAtomRecord",
+function(atom, rm, rp, isPos){
+var label = ";" + atom.atomName;
+var tType = (isPos ? -1 : this.getInt(13, 14));
+if (!isPos && this.molTtypes != null) this.molTtypes.addLast(Integer.$valueOf(tType));
+var haveSpecialOcc = this.getFlag(60);
+var haveSpecialDisp = this.getFlag(61);
+var haveSpecialUij = this.getFlag(62);
+var nOcc = this.getInt(65, 68);
+var nDisp = this.getInt(68, 71);
+var nUij = this.getInt(71, 74);
+if (rm != null) {
+this.readM40Floats();
+rm.set(this.floats[0], this.floats[1], this.floats[2]);
+rp.set(this.floats[3], this.floats[4], this.floats[5]);
+}if (tType > 2) this.readM40Floats();
+this.readM40Floats();
+switch (tType) {
+case 6:
+case 5:
+case 4:
+case 3:
+this.readLines(tType - 1);
+this.appendLoadNote("Skipping temperature factors with order > 2");
+case 2:
+case -1:
+for (var j = 0; j < 6; j++) this.asc.setU(atom, j, this.floats[j]);
+
+break;
+case 1:
+if (this.floats[0] != 0) this.asc.setU(atom, 7, this.floats[0]);
+break;
+case 0:
+this.molHasTLS = true;
+this.appendLoadNote("Jmol cannot process molecular TLS parameters");
+break;
+}
+if (this.modDim == 0) return null;
+if (isPos && this.molHasTLS) this.readLines(4);
+var pt;
+var o_0 = (nOcc > 0 && !haveSpecialOcc ? this.parseFloatStr(this.rd()) : 1);
+if (o_0 != 1) this.ms.addModulation(null, "J_O#0" + label, Clazz.newDoubleArray(-1, [atom.foccupancy, o_0, 0]), -1);
+atom.foccupancy *= o_0;
+var wv = 0;
+var a1;
+var a2;
+this.isLegendre = false;
+for (var j = 0; j < nOcc; j++) {
+if (haveSpecialOcc) {
+var data = this.readM40FloatLines(2, 1);
+a2 = data[0][0];
+a1 = data[1][0];
+} else {
+wv = j + 1;
+this.readM40Floats();
+a1 = this.floats[0];
+a2 = this.floats[1];
+}pt = Clazz.newDoubleArray(-1, [a1, a2, 0]);
+if (a1 != 0 || a2 != 0) this.ms.addModulation(null, "O_" + wv + "#0" + label, pt, -1);
+}
+for (var j = 0; j < nDisp; j++) {
+if (haveSpecialDisp) {
+this.readM40Floats();
+var c = this.floats[3];
+var w = this.floats[4];
+for (var k = 0; k < 3; k++) if (this.floats[k] != 0) this.ms.addModulation(null, "D_S#" + J.adapter.readers.xtal.JanaReader.XYZ[k] + label, Clazz.newDoubleArray(-1, [c, w, this.floats[k]]), -1);
+
+} else {
+this.addSinCos(j, "D_", label, isPos);
+}}
+var rotData = (isPos && nDisp > 0 ? this.readM40FloatLines(nDisp, 6) : null);
+if (!isPos) {
+if (this.isLegendre) nUij *= 2;
+for (var j = 0; j < nUij; j++) {
+if (tType == 1) {
+this.addSinCos(j, "U_", label, false);
+} else {
+if (haveSpecialUij) {
+JU.Logger.error("JanaReader -- not interpreting SpecialUij flag: " + this.line);
+} else if (this.isLegendre) {
+var data = this.readM40FloatLines(1, 6);
+var order = j + 1;
+var coeff = 0;
+for (var k = 0, p = 0; k < 6; k++, p += 3) {
+if ((coeff = data[0][k]) != 0) this.ms.addModulation(null, "U_L" + order + "#" + "U11U22U33U12U13U23UISO".substring(p, p + 3) + label, Clazz.newDoubleArray(-1, [coeff, order, 0]), -1);
+}
+} else {
+var data = this.readM40FloatLines(2, 6);
+for (var k = 0, p = 0; k < 6; k++, p += 3) {
+var csin = data[1][k];
+var ccos = data[0][k];
+this.ms.addModulation(null, "U_" + (j + 1) + "#" + "U11U22U33U12U13U23UISO".substring(p, p + 3) + label, Clazz.newDoubleArray(-1, [csin, ccos, 0]), -1);
+}
+}}}
+}return rotData;
+}, "J.adapter.smarter.Atom,JU.P3,JU.P3,~B");
+Clazz.defineMethod(c$, "addSinCos",
+function(j, key, label, isPos){
+this.readM40Floats();
+if (this.isLegendre) {
+for (var i = 0; i < 2; i++) {
+var order = (j * 2 + i + 1);
+for (var k = 0; k < 3; ++k) {
+var coeff = this.floats[3 * i + k];
+if (coeff == 0) {
+continue;
+}var axis = J.adapter.readers.xtal.JanaReader.XYZ[k % 3];
+if (this.modAxes != null && this.modAxes.indexOf(axis.toUpperCase()) < 0) continue;
+var id = key + "L#" + axis + order + label;
+this.ms.addModulation(null, id, Clazz.newDoubleArray(-1, [coeff, order, 0]), -1);
+}
+}
+return;
+}this.ensureFourier(j);
+for (var k = 0; k < 3; ++k) {
+var csin = this.floats[k];
+var ccos = this.floats[k + 3];
+if (csin == 0 && ccos == 0) {
+if (!isPos) continue;
+csin = 1e-10;
+}var axis = J.adapter.readers.xtal.JanaReader.XYZ[k % 3];
+if (this.modAxes != null && this.modAxes.indexOf(axis.toUpperCase()) < 0) continue;
+var id = key + (j + 1) + "#" + axis + label;
+this.ms.addModulation(null, id, Clazz.newDoubleArray(-1, [csin, ccos, 0]), -1);
+}
+}, "~N,~S,~S,~B");
+Clazz.defineMethod(c$, "ensureFourier",
+function(j){
+var pt;
+if (j > 0 && this.ms.getMod("F_" + (++j) + "_coefs_") == null && (pt = this.ms.getMod("F_1_coefs_")) != null) {
+var p = Clazz.newDoubleArray (this.modDim, 0);
+for (var i = this.modDim; --i >= 0; ) p[i] = pt[i] * j;
+
+this.ms.addModulation(null, "F_" + j + "_coefs_", p, -1);
+}}, "~N");
+Clazz.defineMethod(c$, "readM40Floats",
+function(){
+if ((this.line = this.rd()) == null || this.line.indexOf("-------") >= 0) return (this.line = null);
+if (this.debugging) JU.Logger.debug(this.line);
+this.parseM40Floats();
+return this.line;
+});
+Clazz.defineMethod(c$, "parseM40Floats",
+function(){
+var ptLast = this.line.length - 9;
+for (var i = 0, pt = 0; i < 6; i++, pt += 9) {
+this.floats[i] = (pt <= ptLast ? this.parseFloatStr(this.line.substring(pt, pt + 9)) : NaN);
+}
+});
+Clazz.defineMethod(c$, "readM40FloatLines",
+function(nLines, nFloats){
+var data = Clazz.newFloatArray (nLines, nFloats, 0);
+for (var i = 0; i < nLines; i++) {
+this.readM40Floats();
+if (this.line.indexOf("Legendre") == 19) this.isLegendre = true;
+for (var j = 0; j < nFloats; j++) data[i][j] = this.floats[j];
+
+}
+return data;
+}, "~N,~N");
+Clazz.defineMethod(c$, "adjustM40Occupancies",
+function(){
+var htSiteMult = new java.util.Hashtable();
+var atoms = this.asc.atoms;
+var symmetry = this.asc.getSymmetry();
+for (var i = this.asc.ac; --i >= 0; ) {
+var a = atoms[i];
+var ii = htSiteMult.get(a.atomName);
+if (ii == null) htSiteMult.put(a.atomName, ii = Integer.$valueOf(symmetry.getSiteMultiplicity(a)));
+a.foccupancy *= ii.intValue();
+}
+});
+Clazz.defineMethod(c$, "copyModulations",
+function(label, newLabel){
+var mapTemp = new java.util.Hashtable();
+for (var e, $e = this.ms.getModulationMap().entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var key = e.getKey();
+if (!key.contains(label)) continue;
+key = JU.PT.rep(key, label, newLabel);
+var val = e.getValue();
+switch ((key.charAt(0)).charCodeAt(0)) {
+case 79:
+this.setRigidBodyPhase(key, val = Clazz.newDoubleArray(-1, [val[0], val[1], 0]));
+break;
+case 68:
+break;
+case 85:
+continue;
+}
+mapTemp.put(key, val);
+}
+for (var e, $e = mapTemp.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) this.ms.addModulation(null, e.getKey(), e.getValue(), -1);
+
+}, "~S,~S");
+Clazz.defineMethod(c$, "setRigidBodyPhase",
+function(key, v){
+var isCenter = false;
+switch ((this.ms.getModType(key)).charCodeAt(0)) {
+case 111:
+case 102:
+case 117:
+break;
+case 99:
+case 115:
+isCenter = true;
+break;
+}
+var nqDotD = 0;
+var n = -1;
+var qcoefs = this.ms.getQCoefs(key);
+for (var i = this.modDim; --i >= 0; ) {
+if (qcoefs[i] != 0) {
+n = qcoefs[i];
+var q = this.ms.getMod("W_" + (i + 1));
+nqDotD = n * (q[0] * this.vR.x + q[1] * this.vR.y + q[2] * this.vR.z);
+break;
+}}
+if (isCenter) {
+v[0] += nqDotD;
+} else {
+var sA = v[0];
+var cA = v[1];
+var sX = Math.sin(2 * 3.141592653589793 * nqDotD);
+var cX = Math.cos(2 * 3.141592653589793 * nqDotD);
+v[0] = sA * cX + cA * sX;
+v[1] = -sA * sX + cA * cX;
+}return v;
+}, "~S,~A");
+Clazz.defineMethod(c$, "setRigidBodyRotations",
+function(label, params){
+var n = params.length;
+for (var i = 0; i < n; i++) {
+this.ensureFourier(i);
+var key = "D_" + (i + 1);
+var data = params[i];
+var vsin = JU.V3.new3(data[0], data[1], data[2]);
+var vcos = JU.V3.new3(data[3], data[4], data[5]);
+this.cartesianProduct(vcos, this.v0Cart);
+this.cartesianProduct(vsin, this.v0Cart);
+var keyx = key + "#x" + label;
+var keyy = key + "#y" + label;
+var keyz = key + "#z" + label;
+var vx = this.combineModulation(keyx, vsin.x, vcos.x);
+var vy = this.combineModulation(keyy, vsin.y, vcos.y);
+var vz = this.combineModulation(keyz, vsin.z, vcos.z);
+vsin.set(vx[0], vy[0], vz[0]);
+vcos.set(vx[1], vy[1], vz[1]);
+this.cartesianProduct(vsin, null);
+this.cartesianProduct(vcos, null);
+this.setMolecularModulation(keyx, vsin.x, vcos.x);
+this.setMolecularModulation(keyy, vsin.y, vcos.y);
+this.setMolecularModulation(keyz, vsin.z, vcos.z);
+}
+}, "~S,~A");
+Clazz.defineMethod(c$, "combineModulation",
+function(key, csin, ccos){
+var v = this.ms.getMod(key);
+return Clazz.newDoubleArray(-1, [v[0] + csin, v[1] + ccos, 0]);
+}, "~S,~N,~N");
+Clazz.defineMethod(c$, "setMolecularModulation",
+function(key, csin, ccos){
+this.ms.addModulation(null, key, this.setRigidBodyPhase(key, Clazz.newDoubleArray(-1, [csin, ccos, 0])), -1);
+}, "~S,~N,~N");
+c$.XYZ = Clazz.newArray(-1, ["x", "y", "z"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/MagresReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/MagresReader.js
new file mode 100755
index 000000000000..ad44ea811a89
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/MagresReader.js
@@ -0,0 +1,178 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "java.util.Hashtable", "JU.Lst", "$.SB"], "J.adapter.readers.xtal.MagresReader", ["JU.PT", "J.adapter.smarter.Atom", "JU.Escape", "$.Logger", "$.Tensor"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.currentBlock = -1;
+this.cellParams = null;
+this.magresUnits = null;
+this.interactionTensors = null;
+this.header = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "MagresReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.magresUnits = new java.util.Hashtable();
+this.interactionTensors = new JU.Lst();
+this.header = new JU.SB();
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setFractionalCoordinates(false);
+this.ignoreFileSpaceGroupName = true;
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+this.asc.setInfo("fileHeader", this.header.toString());
+this.finalizeReaderASCR();
+if (this.interactionTensors.size() > 0) this.asc.setCurrentModelInfo("interactionTensors", this.interactionTensors);
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (!this.trimLine()) return true;
+switch (this.checkBlock()) {
+case 0:
+this.header.append(this.line).append("\n");
+this.appendLoadNote(this.line);
+break;
+case 1:
+if (this.cellParams == null && this.line.startsWith("lattice")) return this.readCellParams();
+if (this.line.startsWith("symmetry")) return this.readSymmetry();
+if (this.line.startsWith("units")) return this.setUnits(false);
+if (this.line.startsWith("atom")) return this.readAtom();
+break;
+case 2:
+if (this.line.startsWith("units")) return this.setUnits(true);
+return this.readTensor();
+}
+return true;
+});
+Clazz.defineMethod(c$, "trimLine",
+function(){
+var pt = this.line.indexOf("#");
+if (pt >= 0) this.line = this.line.substring(0, pt);
+this.line = this.line.trim();
+return (this.line.length > 0);
+});
+Clazz.defineMethod(c$, "checkBlock",
+function(){
+if (!(this.line.startsWith("<") && this.line.endsWith(">")) && !(this.line.startsWith("[") && this.line.endsWith("]"))) return this.currentBlock;
+this.line = JU.PT.rep(this.line, "<", "[");
+this.line = JU.PT.rep(this.line, ">", "]");
+switch (Clazz.doubleToInt(("...............[calculation]..[/calculation].[atoms]........[/atoms].......[magres].......[/magres]......").indexOf(this.line + ".") / 15)) {
+case 0:
+JU.Logger.info("block indicator ignored: " + this.line);
+break;
+case 1:
+if (this.currentBlock == -1) this.currentBlock = 0;
+break;
+case 2:
+if (this.currentBlock == 0) this.currentBlock = -1;
+break;
+case 3:
+if (this.currentBlock == -1) {
+this.currentBlock = 1;
+this.asc.newAtomSet();
+this.magresUnits = new java.util.Hashtable();
+}break;
+case 4:
+if (this.currentBlock == 1) this.currentBlock = -1;
+break;
+case 5:
+if (this.currentBlock == -1) {
+this.currentBlock = 2;
+this.magresUnits = new java.util.Hashtable();
+this.asc.setCurrentModelInfo("magresUnits", this.magresUnits);
+}break;
+case 6:
+if (this.currentBlock == 2) this.currentBlock = -1;
+break;
+}
+return -2;
+});
+Clazz.defineMethod(c$, "setUnits",
+function(isMagresBlock){
+var tokens = this.getTokens();
+var id = tokens[1];
+if (isMagresBlock) this.appendLoadNote("Ellipsoid set " + JU.PT.esc(id) + ": " + (id.startsWith("ms") ? "Magnetic Shielding" : id.startsWith("efg") ? "Electric Field Gradient" : id.startsWith("isc") ? "J-Coupling" : "?"));
+this.magresUnits.put(id, tokens[2]);
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "readSymmetry",
+function(){
+this.setSymmetryOperator(this.getTokens()[1]);
+return true;
+});
+Clazz.defineMethod(c$, "readCellParams",
+function(){
+var tokens = this.getTokens();
+this.cellParams = Clazz.newFloatArray (9, 0);
+for (var i = 0; i < 9; i++) this.cellParams[i] = this.parseFloatStr(tokens[i + 1]);
+
+this.addExplicitLatticeVector(0, this.cellParams, 0);
+this.addExplicitLatticeVector(1, this.cellParams, 3);
+this.addExplicitLatticeVector(2, this.cellParams, 6);
+this.setSpaceGroupName("P1");
+return true;
+});
+Clazz.defineMethod(c$, "readAtom",
+function(){
+var units = this.magresUnits.get("atom");
+if (units == null) return true;
+var f = (units.startsWith("A") ? 1 : 0.5291772);
+var tokens = this.getTokens();
+var atom = new J.adapter.smarter.Atom();
+var pt = 1;
+atom.elementSymbol = tokens[pt++];
+atom.atomName = J.adapter.readers.xtal.MagresReader.getAtomName(tokens[pt++], tokens[pt++]);
+this.asc.addAtomWithMappedName(atom);
+var x = this.parseFloatStr(tokens[pt++]) * f;
+var y = this.parseFloatStr(tokens[pt++]) * f;
+var z = this.parseFloatStr(tokens[pt++]) * f;
+atom.set(x, y, z);
+this.setAtomCoord(atom);
+return true;
+});
+c$.getAtomName = Clazz.defineMethod(c$, "getAtomName",
+function(name, index){
+return name + "_" + index;
+}, "~S,~S");
+Clazz.defineMethod(c$, "readTensor",
+function(){
+var tokens = this.getTokens();
+var type = tokens[0];
+var units = this.magresUnits.get(type);
+if (units == null) {
+JU.Logger.warn(type + " ignored; no units defined; line: " + this.line);
+return true;
+}var isIsc = type.startsWith("isc");
+if (tokens.length == 10) {
+this.magresUnits.remove(type);
+var data = Clazz.newFloatArray (9, 0);
+for (var i = 0; i < 9; ) data[i] = this.parseFloatStr(tokens[++i]);
+
+JU.Logger.info("Magres reader creating magres_" + type + ": " + JU.Escape.eAF(data));
+this.asc.setCurrentModelInfo("magres_" + type, data);
+}var atomName1 = J.adapter.readers.xtal.MagresReader.getAtomName(tokens[1], tokens[2]);
+var pt = 3;
+var atomName2 = (isIsc ? J.adapter.readers.xtal.MagresReader.getAtomName(tokens[pt++], tokens[pt++]) : null);
+if (atomName1.equals(atomName2)) {
+JU.Logger.warn(type + " ignored; atom1 == atom2 for " + atomName1 + " line: " + this.line);
+return true;
+}var id = atomName1;
+if (atomName2 != null) id += "//" + atomName2;
+var a = Clazz.newDoubleArray (3, 3, 0);
+for (var i = 0; i < 3; i++) for (var j = 0; j < 3; j++) a[i][j] = Double.$valueOf(tokens[pt++]).doubleValue();
+
+
+var a1 = this.asc.getAtomFromName(atomName1);
+if (a1 == null) return true;
+var a2 = null;
+var t = new JU.Tensor().setFromAsymmetricTensor(a, type, id);
+if (atomName2 == null) {
+a1.addTensor(t, null, false);
+} else {
+a2 = this.asc.getAtomFromName(atomName2);
+if (a2 == null) return true;
+this.interactionTensors.addLast(t);
+}t.setAtomIndexes(a1.index, (a2 == null ? -1 : a2.index));
+return true;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/OptimadeReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/OptimadeReader.js
new file mode 100755
index 000000000000..ba32584c7d70
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/OptimadeReader.js
@@ -0,0 +1,181 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.OptimadeReader", ["java.util.HashMap", "JU.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.modelNo = 0;
+this.iHaveDesiredModel = false;
+this.permutation = 0;
+this.isPolymer = false;
+this.isSlab = false;
+this.noSlab = false;
+this.xyz = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "OptimadeReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.xyz = Clazz.newFloatArray (3, 0);
+});
+Clazz.defineMethod(c$, "initializeReader",
+function(){
+Clazz.superCall(this, J.adapter.readers.xtal.OptimadeReader, "initializeReader", []);
+this.noSlab = this.checkFilterKey("NOSLAB");
+try {
+var strJSON = this.htParams.get("fileData");
+if (strJSON == null) {
+var sb = new JU.SB();
+while (this.rd() != null) sb.append(this.line);
+
+strJSON = sb.toString();
+this.line = null;
+}var aData = null;
+if (strJSON.startsWith("[")) {
+var data = this.vwr.parseJSONArray(strJSON);
+for (var i = 0; i < data.size(); i++) {
+if (Clazz.instanceOf(data.get(i),"java.util.Map")) {
+aData = (data.get(i)).get("data");
+if (aData != null) {
+break;
+}}}
+} else {
+aData = this.vwr.parseJSONMap(strJSON).get("data");
+}if (aData != null) {
+for (var i = 0; !this.iHaveDesiredModel && i < aData.size(); i++) {
+var data = aData.get(i);
+if ("structures".equals(data.get("type"))) {
+this.readModel(data.get("attributes"));
+}}
+}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+}
+this.continuing = false;
+});
+Clazz.defineMethod(c$, "readModel",
+function(map){
+if (!this.doGetModel(this.modelNumber = ++this.modelNo, null)) return;
+this.iHaveDesiredModel = this.isLastModel(this.modelNumber);
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSet();
+this.setFractionalCoordinates(false);
+var dimensionType = Clazz.newFloatArray (3, 0);
+if (J.adapter.readers.xtal.OptimadeReader.toFloatArray(map.get("dimension_types"), dimensionType)) {
+this.checkDimensionType(dimensionType);
+}if (!this.isMolecular) {
+this.setSpaceGroupName("P1");
+this.asc.setInfo("symmetryType", (this.isSlab ? "2D - SLAB" : this.isPolymer ? "1D - POLYMER" : "3D"));
+}this.asc.setAtomSetName(map.get("chemical_formula_descriptive"));
+this.doConvertToFractional = (!this.isMolecular && this.readLattice(map.get("lattice_vectors")));
+this.readAtoms(map.get("species"), map.get("species_at_sites"), map.get("cartesian_site_positions"));
+}, "java.util.Map");
+Clazz.defineMethod(c$, "checkDimensionType",
+function(dt){
+this.isPolymer = this.isSlab = this.isMolecular = false;
+if (this.noSlab) return;
+this.permutation = 0;
+switch (Clazz.floatToInt(dt[2] + dt[1] * 2 + dt[0] * 4)) {
+default:
+case 0:
+this.isMolecular = true;
+break;
+case 1:
+this.isPolymer = true;
+this.permutation = 1;
+break;
+case 2:
+this.isPolymer = true;
+this.permutation = 2;
+break;
+case 3:
+this.isSlab = true;
+this.permutation = 2;
+break;
+case 5:
+this.isSlab = true;
+this.permutation = 1;
+break;
+case 4:
+this.isPolymer = true;
+break;
+case 6:
+this.isSlab = true;
+break;
+case 7:
+break;
+}
+}, "~A");
+Clazz.defineMethod(c$, "readLattice",
+function(lattice){
+if (lattice == null) return false;
+var abc = Clazz.newFloatArray (3, 0);
+for (var i = 0; i < 3; i++) {
+if (!J.adapter.readers.xtal.OptimadeReader.toFloatArray(lattice.get(i), this.xyz)) {
+return false;
+}this.unitCellParams[0] = NaN;
+if (this.isSlab || this.isPolymer) {
+abc[i] = Math.sqrt(this.xyz[0] * this.xyz[0] + this.xyz[1] * this.xyz[1] + this.xyz[2] * this.xyz[2]);
+if (abc[i] >= 500) {
+this.xyz[0] /= abc[i];
+this.xyz[1] /= abc[i];
+this.xyz[2] /= abc[i];
+}}if (this.isSlab || this.isPolymer) this.unitCellParams[0] = 0;
+if (i == 2) {
+if (this.isSlab || this.isPolymer) {
+this.unitCellParams[0] = abc[this.permutation];
+if (this.isSlab) this.unitCellParams[1] = abc[(this.permutation + 1) % 3];
+}}this.addExplicitLatticeVector((i + this.permutation) % 3, this.xyz, 0);
+}
+this.doApplySymmetry = true;
+return true;
+}, "java.util.List");
+Clazz.defineMethod(c$, "readAtoms",
+function(species, sites, coords){
+var natoms = sites.size();
+var speciesByName = null;
+if (species == null) {
+JU.Logger.error("OptimadeReader - no 'species' key");
+} else {
+speciesByName = new java.util.HashMap();
+for (var i = species.size(); --i >= 0; ) {
+var s = species.get(i);
+speciesByName.put(s.get("name"), s);
+}
+}for (var i = 0; i < natoms; i++) {
+var sname = sites.get(i);
+J.adapter.readers.xtal.OptimadeReader.toFloatArray(coords.get(i), this.xyz);
+if (species == null) {
+this.addAtom(this.xyz, sites.get(i), sname);
+} else {
+var sp = speciesByName.get(sname);
+var syms = sp.get("chemical_symbols");
+var nOcc = syms.size();
+if (nOcc > 1) {
+var conc = Clazz.newFloatArray (nOcc, 0);
+if (J.adapter.readers.xtal.OptimadeReader.toFloatArray(sp.get("concentration"), conc)) {
+for (var j = 0; j < conc.length; j++) {
+var a = this.addAtom(this.xyz, syms.get(j), sname);
+a.foccupancy = conc[j];
+}
+continue;
+}}this.addAtom(this.xyz, syms.get(0), sname);
+}}
+}, "java.util.List,java.util.List,java.util.List");
+Clazz.defineMethod(c$, "addAtom",
+function(xyz, sym, name){
+var atom = this.asc.addNewAtom();
+if (sym != null) atom.elementSymbol = sym;
+if (name != null) atom.atomName = name;
+this.setAtomCoordXYZ(atom, xyz[0], xyz[1], xyz[2]);
+return atom;
+}, "~A,~S,~S");
+c$.toFloatArray = Clazz.defineMethod(c$, "toFloatArray",
+function(list, a){
+if (list == null) return false;
+for (var i = a.length; --i >= 0; ) {
+var d = list.get(i);
+if (d == null) return false;
+a[i] = list.get(i).floatValue();
+}
+return true;
+}, "java.util.List,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/PWmatReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/PWmatReader.js
new file mode 100755
index 000000000000..04924dc04704
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/PWmatReader.js
@@ -0,0 +1,214 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.PWmatReader", ["java.util.Hashtable", "JU.Lst", "$.PT", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nAtoms = 0;
+this.haveLattice = false;
+this.havePositions = false;
+this.haveMagnetic = false;
+this.global3 = ";STRESS_MASK;STRESS_EXTERNAL;PTENSOR_EXTERNAL;";
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "PWmatReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.readers.xtal.PWmatReader, []);
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.doApplySymmetry = true;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.nAtoms == 0) {
+this.readComments();
+this.setSpaceGroupName("P1");
+this.nAtoms = JU.PT.parseInt(this.line);
+this.setFractionalCoordinates(true);
+return true;
+}this.removeComments();
+var lc = this.line.toLowerCase().trim();
+if (lc.length == 0) return true;
+if (!this.haveLattice) {
+if (lc.startsWith("lattice")) {
+this.readUnitCell();
+this.haveLattice = true;
+}return true;
+}if (!this.havePositions) {
+if (lc.startsWith("position")) {
+this.readCoordinates();
+this.havePositions = true;
+}return true;
+}if (!this.readDataBlock(lc)) {
+this.continuing = false;
+}return true;
+});
+Clazz.defineMethod(c$, "readComments",
+function(){
+});
+Clazz.defineMethod(c$, "readUnitCell",
+function(){
+var unitCellData = Clazz.newFloatArray (3, 0);
+this.addExplicitLatticeVector(0, this.fillFloatArray(this.getLine(), 0, unitCellData), 0);
+this.addExplicitLatticeVector(1, this.fillFloatArray(this.getLine(), 0, unitCellData), 0);
+this.addExplicitLatticeVector(2, this.fillFloatArray(this.getLine(), 0, unitCellData), 0);
+});
+Clazz.defineMethod(c$, "readCoordinates",
+function(){
+var constraints = new JU.Lst();
+var haveConstraints = true;
+var i = 0;
+while (i++ < this.nAtoms && this.getLine() != null) {
+var tokens = this.getTokens();
+var z = Integer.parseInt(tokens[0]);
+this.addAtomXYZSymName(tokens, 1, J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(z), null).elementNumber = z;
+haveConstraints = (tokens.length >= 7) && haveConstraints;
+if (haveConstraints) constraints.addLast( Clazz.newFloatArray(-1, [Float.parseFloat(tokens[4]), Float.parseFloat(tokens[5]), Float.parseFloat(tokens[6])]));
+}
+var cx = Clazz.newFloatArray (this.nAtoms, 0);
+var cy = Clazz.newFloatArray (this.nAtoms, 0);
+var cz = Clazz.newFloatArray (this.nAtoms, 0);
+var c = Clazz.newFloatArray(-1, [1, 1, 1]);
+for (i = this.nAtoms; --i >= 0; ) {
+if (haveConstraints) c = constraints.get(i);
+cx[i] = c[0];
+cy[i] = c[1];
+cz[i] = c[2];
+}
+this.setVectors("constraints", cx, cy, cz, this.nAtoms);
+});
+Clazz.defineMethod(c$, "readDataBlock",
+function(name){
+name = this.trimPWPropertyNameTo(name, " ([,");
+this.getLine();
+if (this.line == null) return false;
+var tokens = this.getTokens();
+switch (tokens.length) {
+case 1:
+case 2:
+case 3:
+this.readItems(name, tokens.length - 1, null);
+return true;
+case 4:
+this.readVectors(name, 1, true);
+return true;
+default:
+JU.Logger.error("PWmatReader block " + name.toUpperCase() + " ignored");
+return false;
+}
+}, "~S");
+Clazz.defineMethod(c$, "trimPWPropertyNameTo",
+function(name, chars){
+for (var i = chars.length; --i >= 0; ) {
+var pt = name.indexOf(chars.charAt(i));
+if (pt > 0) name = name.substring(0, pt);
+}
+return name;
+}, "~S,~S");
+Clazz.defineMethod(c$, "readItems",
+function(name, offset, values){
+if (name.equalsIgnoreCase("magnetic")) this.haveMagnetic = true;
+var isGlobal = JU.PT.isOneOf(name.toUpperCase(), this.global3);
+if (isGlobal) {
+var lines = new Array(3);
+lines[0] = this.line;
+lines[1] = this.getLine();
+lines[2] = this.getLine();
+var info = this.asc.getAtomSetAuxiliaryInfo(0);
+var data = info.get("globalPWmatData");
+if (data == null) info.put("globalPWmatData", data = new java.util.Hashtable());
+data.put(name, lines);
+} else {
+name = "pwm_" + name;
+if (values == null) {
+values = Clazz.newFloatArray (this.nAtoms, 0);
+} else {
+this.getLine();
+}var n = 0;
+for (var i = 0; ; ) {
+var tokens = this.getTokens();
+if ((values[i] = Float.parseFloat(tokens[offset])) != 0) n++;
+if (++i == this.nAtoms) break;
+this.getLine();
+}
+this.setProperties(name, values, n);
+}}, "~S,~N,~A");
+Clazz.defineMethod(c$, "setProperties",
+function(name, values, n){
+this.asc.setAtomProperties(name, values, this.asc.iSet, false);
+JU.Logger.info("PWmatReader: " + name.toUpperCase() + " processed for " + n + " atoms");
+this.appendLoadNote("PWmatReader read property_" + name);
+}, "~S,~A,~N");
+Clazz.defineMethod(c$, "readVectors",
+function(name, offset, haveLine){
+if (!haveLine) this.getLine();
+var valuesX = Clazz.newFloatArray (this.nAtoms, 0);
+var valuesY = Clazz.newFloatArray (this.nAtoms, 0);
+var valuesZ = Clazz.newFloatArray (this.nAtoms, 0);
+var n = 0;
+for (var i = 0; ; ) {
+var tokens = this.getTokens();
+if ((((valuesX[i] = Float.parseFloat(tokens[offset])) == 0 ? 0 : 1) | ((valuesY[i] = Float.parseFloat(tokens[offset + 1])) == 0 ? 0 : 1) | ((valuesZ[i] = Float.parseFloat(tokens[offset + 2])) == 0 ? 0 : 1)) != 0) n++;
+if (++i == this.nAtoms) break;
+this.getLine();
+}
+this.setVectors(name, valuesX, valuesY, valuesZ, n);
+}, "~S,~N,~B");
+Clazz.defineMethod(c$, "getLine",
+function(){
+this.rd();
+return this.removeComments();
+});
+Clazz.defineMethod(c$, "removeComments",
+function(){
+if (this.line != null) {
+var pt = this.line.indexOf("#");
+if (pt >= 0) {
+this.line = this.line.substring(0, pt).trim();
+}}return this.line;
+});
+Clazz.defineMethod(c$, "setVectors",
+function(name, valuesX, valuesY, valuesZ, n){
+name = "pwm_" + name;
+this.asc.setAtomProperties(name + "_x", valuesX, this.asc.iSet, false);
+this.asc.setAtomProperties(name + "_y", valuesY, this.asc.iSet, false);
+this.asc.setAtomProperties(name + "_z", valuesZ, this.asc.iSet, false);
+JU.Logger.info("PWmatReader: " + name.toUpperCase() + " processed for " + n + " atoms");
+this.appendLoadNote("PWmatReader read property_" + name + "_x");
+this.appendLoadNote("PWmatReader read property_" + name + "_y");
+this.appendLoadNote("PWmatReader read property_" + name + "_z");
+if (name.equals("pwm_magnetic_xyz")) {
+for (var i = 0; i < this.nAtoms; i++) {
+this.asc.addVibrationVector(i, valuesX[i], valuesY[i], valuesZ[i]);
+}
+this.addJmolScript("vectors 0.2;set vectorscentered");
+}}, "~S,~A,~A,~A,~N");
+Clazz.defineMethod(c$, "applySymmetryAndSetTrajectory",
+function(){
+Clazz.superCall(this, J.adapter.readers.xtal.PWmatReader, "applySymmetryAndSetTrajectory", []);
+if (this.nAtoms != this.asc.ac) {
+this.nAtoms = this.asc.ac;
+var p = this.asc.getAtomSetAuxiliaryInfoValue(this.asc.iSet, "atomProperties");
+if (p != null) {
+var atoms = this.asc.atoms;
+var n = (this.asc.bsAtoms == null ? this.nAtoms : this.asc.bsAtoms.cardinality());
+var map = (n == this.nAtoms ? null : Clazz.newIntArray (this.nAtoms, 0));
+if (map != null) {
+for (var j = 0, k = 0; j < this.nAtoms; j++) {
+if (this.asc.bsAtoms.get(j)) map[j] = k++;
+}
+}for (var e, $e = p.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var key = e.getKey();
+if (key.startsWith("pwm_")) {
+var af = e.getValue();
+var af2 = Clazz.newFloatArray (n, 0);
+for (var j = 0; j < this.nAtoms; j++) {
+af2[map == null ? j : map[j]] = af[atoms[j].atomSite];
+}
+e.setValue(af2);
+}}
+}}});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+if (!this.haveMagnetic && this.asc.ac > 0) {
+this.setProperties("pwm_magnetic", Clazz.newFloatArray (this.asc.ac, 0), this.nAtoms);
+}});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/ShelxReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/ShelxReader.js
new file mode 100755
index 000000000000..509eead87b4d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/ShelxReader.js
@@ -0,0 +1,226 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.ShelxReader", ["JU.AU", "$.PT", "J.adapter.smarter.Atom", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.sfacElementSymbols = null;
+this.isCmdf = false;
+this.tokens = null;
+this.altloc = '\0';
+this.isCentroSymmetric = false;
+this.haveXYZ = false;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "ShelxReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setFractionalCoordinates(true);
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+var lineLength;
+while ((lineLength = (this.line = this.line.trim()).length) > 0 && this.line.charAt(lineLength - 1) == '=') this.line = this.line.substring(0, lineLength - 1) + this.rd();
+
+this.tokens = this.getTokens();
+if (this.tokens.length == 0) return true;
+var command = this.tokens[0].toUpperCase();
+if (command.equals("TITL")) {
+if (!this.doGetModel(++this.modelNumber, null)) return this.checkLastModel();
+this.sfacElementSymbols = null;
+this.applySymmetryAndSetTrajectory();
+this.setFractionalCoordinates(true);
+this.asc.newAtomSet();
+this.asc.setAtomSetName(this.line.substring(4).trim());
+return true;
+}if (command.equals("NOTE")) {
+this.isCmdf = true;
+return true;
+}if (!this.doProcessLines || lineLength < 3) return true;
+if (";ZERR;DISP;UNIT;LAUE;REM;MORE;TIME;HKLF;OMIT;SHEL;BASF;TWIN;EXTI;SWAT;HOPE;MERG;SPEC;RESI;MOVE;ANIS;AFIX;HFIX;FRAG;FEND;EXYZ;EXTI;EADP;EQIV;CONN;BIND;FREE;DFIX;DANG;BUMP;SAME;SADI;CHIV;FLAT;DELU;SIMU;DEFS;ISOR;NCSY;SUMP;L.S.;CGLS;BLOC;DAMP;STIR;WGHT;FVAR;BOND;CONF;MPLA;RTAB;HTAB;LIST;ACTA;SIZE;TEMP;WPDB;FMAP;GRID;PLAN;MOLE;".indexOf(";" + command + ";") >= 0) return true;
+for (var i = J.adapter.readers.xtal.ShelxReader.supportedRecordTypes.length; --i >= 0; ) if (command.equals(J.adapter.readers.xtal.ShelxReader.supportedRecordTypes[i])) {
+this.processSupportedRecord(i);
+return true;
+}
+if (!this.isCmdf) this.assumeAtomRecord();
+return true;
+});
+Clazz.defineMethod(c$, "processSupportedRecord",
+function(recordIndex){
+switch (recordIndex) {
+case 0:
+case 9:
+break;
+case 1:
+this.cell();
+break;
+case 2:
+this.setSpaceGroupName(JU.PT.parseTrimmedAt(this.line, 4));
+break;
+case 3:
+this.parseSfacRecord();
+break;
+case 4:
+this.parseLattRecord();
+break;
+case 5:
+this.parseSymmRecord();
+break;
+case 6:
+this.isCmdf = true;
+break;
+case 7:
+this.isCmdf = true;
+this.processCmdfAtoms();
+break;
+case 8:
+this.processPartRecord();
+break;
+}
+}, "~N");
+Clazz.defineMethod(c$, "processPartRecord",
+function(){
+var part = this.parseIntStr(this.tokens[1]);
+this.altloc = String.fromCharCode(part == 0 ? 0 : 48 + part);
+});
+Clazz.defineMethod(c$, "parseLattRecord",
+function(){
+var latt = this.parseIntStr(this.tokens[1]);
+this.isCentroSymmetric = (latt > 0);
+if (latt == 1 || latt == -1) return;
+this.asc.getXSymmetry().setLatticeParameter(latt);
+});
+Clazz.defineMethod(c$, "parseSymmRecord",
+function(){
+if (!this.haveXYZ) {
+this.setSymmetryOperator("x,y,z");
+this.haveXYZ = true;
+}this.setSymmetryOperator(this.line.substring(4).trim());
+});
+Clazz.defineMethod(c$, "cell",
+function(){
+var ioff = this.tokens.length - 6;
+if (ioff == 2) this.asc.setInfo("wavelength", Float.$valueOf(this.parseFloatStr(this.tokens[1])));
+for (var ipt = 0; ipt < 6; ipt++) this.setUnitCellItem(ipt, this.parseFloatStr(this.tokens[ipt + ioff]));
+
+});
+Clazz.defineMethod(c$, "parseSfacRecord",
+function(){
+var allElementSymbols = true;
+for (var i = this.tokens.length; allElementSymbols && --i >= 1; ) {
+var token = this.tokens[i];
+allElementSymbols = J.adapter.readers.xtal.ShelxReader.isValidElementSymbolNoCaseSecondChar(token);
+}
+var sfacTokens = JU.PT.getTokens(this.line.substring(4));
+if (allElementSymbols) this.parseSfacElementSymbols(sfacTokens);
+ else this.parseSfacCoefficients(sfacTokens);
+});
+Clazz.defineMethod(c$, "parseSfacElementSymbols",
+function(sfacTokens){
+if (this.sfacElementSymbols == null) {
+this.sfacElementSymbols = sfacTokens;
+} else {
+var oldCount = this.sfacElementSymbols.length;
+var tokenCount = sfacTokens.length;
+this.sfacElementSymbols = JU.AU.arrayCopyS(this.sfacElementSymbols, oldCount + tokenCount);
+for (var i = tokenCount; --i >= 0; ) this.sfacElementSymbols[oldCount + i] = sfacTokens[i];
+
+}}, "~A");
+Clazz.defineMethod(c$, "parseSfacCoefficients",
+function(sfacTokens){
+var a1 = this.parseFloatStr(sfacTokens[1]);
+var a2 = this.parseFloatStr(sfacTokens[3]);
+var a3 = this.parseFloatStr(sfacTokens[5]);
+var a4 = this.parseFloatStr(sfacTokens[7]);
+var c = this.parseFloatStr(sfacTokens[9]);
+var z = Math.round(a1 + a2 + a3 + a4 + c);
+var elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(z);
+var oldCount = 0;
+if (this.sfacElementSymbols == null) {
+this.sfacElementSymbols = new Array(1);
+} else {
+oldCount = this.sfacElementSymbols.length;
+this.sfacElementSymbols = JU.AU.arrayCopyS(this.sfacElementSymbols, oldCount + 1);
+this.sfacElementSymbols[oldCount] = elementSymbol;
+}this.sfacElementSymbols[oldCount] = elementSymbol;
+}, "~A");
+Clazz.defineMethod(c$, "assumeAtomRecord",
+function(){
+var x = NaN;
+var y = NaN;
+var z = NaN;
+var occ = 1;
+var elementIndex = -1;
+var atomName = null;
+try {
+atomName = this.tokens[0];
+elementIndex = this.parseIntStr(this.tokens[1]) - 1;
+x = this.parseFloatStr(this.tokens[2]) % 10;
+y = this.parseFloatStr(this.tokens[3]) % 10;
+z = this.parseFloatStr(this.tokens[4]) % 10;
+occ = this.parseFloatStr(this.tokens[5]) % 10;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z)) {
+JU.Logger.error("skipping line " + this.line);
+return;
+}var atom = this.asc.addNewAtom();
+atom.atomName = atomName;
+atom.foccupancy = occ;
+var isQPeak = atomName.startsWith("Q");
+if (isQPeak) {
+atom.elementSymbol = "Xx";
+} else if (this.sfacElementSymbols != null && elementIndex >= 0 && elementIndex < this.sfacElementSymbols.length) {
+atom.elementSymbol = this.sfacElementSymbols[elementIndex];
+}this.setAtomCoordXYZ(atom, x, y, z);
+atom.altLoc = this.altloc;
+if (this.tokens.length == 12) {
+var data = Clazz.newFloatArray (8, 0);
+data[0] = this.parseFloatStr(this.tokens[6]);
+data[1] = this.parseFloatStr(this.tokens[7]);
+data[2] = this.parseFloatStr(this.tokens[8]);
+data[3] = this.parseFloatStr(this.tokens[11]);
+data[4] = this.parseFloatStr(this.tokens[10]);
+data[5] = this.parseFloatStr(this.tokens[9]);
+for (var i = 0; i < 6; i++) if (Float.isNaN(data[i])) {
+JU.Logger.error("Bad anisotropic Uij data: " + this.line);
+return;
+}
+this.asc.setAnisoBorU(atom, data, 8);
+}});
+Clazz.defineMethod(c$, "processCmdfAtoms",
+function(){
+while (this.rd() != null && this.line.length > 10) {
+this.tokens = this.getTokens();
+this.addAtomXYZSymName(this.tokens, 2, this.getSymbol(this.tokens[0]), this.tokens[1]);
+}
+});
+Clazz.defineMethod(c$, "getSymbol",
+function(sym){
+if (sym == null) return "Xx";
+var len = sym.length;
+if (len < 2) return sym;
+var ch1 = sym.charAt(1);
+if (ch1 >= 'a' && ch1 <= 'z') return sym.substring(0, 2);
+return "" + sym.charAt(0);
+}, "~S");
+c$.isValidElementSymbolNoCaseSecondChar = Clazz.defineMethod(c$, "isValidElementSymbolNoCaseSecondChar",
+function(str){
+if (str == null) return false;
+var length = str.length;
+if (length == 0) return false;
+var chFirst = str.charAt(0);
+if (length == 1) return J.adapter.smarter.Atom.isValidSym1(chFirst);
+if (length > 2) return false;
+var chSecond = str.charAt(1);
+return J.adapter.smarter.Atom.isValidSymNoCase(chFirst, chSecond);
+}, "~S");
+Clazz.overrideMethod(c$, "applySymmetryAndSetTrajectory",
+function(){
+if (this.isCentroSymmetric && !this.ignoreFileSymmetryOperators) {
+this.asc.getXSymmetry().getSymmetry().addInversion();
+this.isCentroSymmetric = false;
+}this.applySymTrajASCR();
+});
+c$.supportedRecordTypes = Clazz.newArray(-1, ["TITL", "CELL", "SPGR", "SFAC", "LATT", "SYMM", "NOTE", "ATOM", "PART", "END"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/SiestaReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/SiestaReader.js
new file mode 100755
index 000000000000..d8a14229508c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/SiestaReader.js
@@ -0,0 +1,206 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.SiestaReader", ["java.util.Hashtable", "JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.noAtoms = 0;
+this.acfUnits = "bohr";
+this.tokens = null;
+this.STATE_UNKNOWN = 0;
+this.STATE_INPUT = 1;
+this.STATE_OUTPUT = 2;
+this.state = 0;
+this.acfFactor = 0;
+this.htSpecies = null;
+this.unitCellVectors = null;
+this.unitCellParamsS = null;
+this.latticeConstant = 1;
+this.latticeUnits = null;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "SiestaReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.doApplySymmetry = true;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.length == 0 || this.line.charAt(0) == '#' || this.line.indexOf(' ') < 0 && this.line.indexOf('\t') < 0) return true;
+switch (this.state) {
+case 0:
+if (this.line.indexOf("Dump of input data file") >= 0) {
+this.state = 1;
+return true;
+}this.tokens = this.getTokens();
+if (this.fixToken(0).equals("numberofspecies")) {
+this.state = 1;
+return false;
+}return true;
+case 1:
+if (this.line.indexOf("End of input data file") >= 0) {
+this.state = 2;
+return true;
+}this.tokens = this.getTokens();
+if (this.tokens[0].equals("%block")) {
+this.readBlock(this.fixToken(1));
+} else {
+this.readValue(this.fixToken(0));
+}return true;
+}
+if (this.line.contains("outcoor: Atomic coordinates")) {
+if (this.doGetModel(++this.modelNumber, null)) this.readAtomsCartGeomThenCell();
+return true;
+}return true;
+});
+Clazz.defineMethod(c$, "readValue",
+function(key){
+if (key.equals("latticeconstant")) {
+this.setCell("latticeconstant");
+} else if (key.equals("atomiccoordinatesformat")) {
+this.readAtomicCoordinatesFormat();
+}}, "~S");
+Clazz.defineMethod(c$, "readBlock",
+function(key){
+if (key.equals("latticevectors") || key.equals("latticeparameters")) return this.setCell(key);
+if (key.equals("chemicalspecieslabel")) return this.readSpecies();
+if (key.equals("atomiccoordinatesandatomicspecies")) {
+if (!this.doGetModel(++this.modelNumber, null)) {
+this.skipModel();
+return false;
+}return this.readAtoms();
+}this.discardLinesUntilContains("%endblock");
+return true;
+}, "~S");
+Clazz.defineMethod(c$, "readSpecies",
+function(){
+this.htSpecies = new java.util.Hashtable();
+while (this.rdSiesta().indexOf("%") < 0) {
+this.tokens = this.getTokens();
+this.htSpecies.put(this.tokens[0], this.tokens);
+}
+return false;
+});
+Clazz.defineMethod(c$, "fixToken",
+function(i){
+return JU.PT.replaceAllCharacters(this.tokens[i], "_.-", "").toLowerCase();
+}, "~N");
+Clazz.defineMethod(c$, "rdSiesta",
+function(){
+var s = this.rd();
+var pt = s.indexOf("#");
+return (pt < 0 ? s : s.substring(pt)).trim();
+});
+Clazz.defineMethod(c$, "getACFValue",
+function(v){
+if (this.acfFactor == 0) {
+var isScaledCartesian = (this.acfUnits === "scaledcartesian");
+if (isScaledCartesian) this.acfUnits = this.latticeUnits;
+this.acfUnits = JU.PT.rep(this.acfUnits, "notscaledcartesian", "");
+switch ((this.acfUnits.charAt(0)).charCodeAt(0)) {
+default:
+case 98:
+this.setFractionalCoordinates(isScaledCartesian);
+this.acfFactor = (1.8897268777743552);
+break;
+case 109:
+this.setFractionalCoordinates(isScaledCartesian);
+this.acfFactor = (1.0E-10);
+break;
+case 110:
+this.setFractionalCoordinates(isScaledCartesian);
+this.acfFactor = (0.1);
+break;
+case 97:
+this.setFractionalCoordinates(isScaledCartesian);
+this.acfFactor = 1;
+break;
+case 102:
+case 115:
+this.setFractionalCoordinates(true);
+this.acfFactor = 1;
+break;
+}
+if (isScaledCartesian) {
+this.acfFactor /= this.latticeConstant;
+this.setFractionalCoordinates(true);
+}}return (this.acfFactor * v);
+}, "~N");
+Clazz.defineMethod(c$, "readAtomicCoordinatesFormat",
+function(){
+this.acfUnits = this.tokens[1].toLowerCase().intern();
+});
+Clazz.defineMethod(c$, "skipModel",
+function(){
+this.discardLinesUntilContains("%endblock AtomicCoordinatesAndAtomicSpecies");
+});
+Clazz.defineMethod(c$, "setCell",
+function(key){
+if (key.equals("latticevectors")) {
+this.unitCellVectors = Clazz.newFloatArray (9, 0);
+this.fillFloatArray(null, 0, this.unitCellVectors);
+} else if (key.equals("latticeconstant")) {
+var tokens = this.getTokens();
+this.latticeConstant = this.parseFloatStr(tokens[1]);
+this.latticeUnits = tokens[2].toLowerCase();
+} else if (key.equals("latticeparameters")) {
+this.unitCellParamsS = Clazz.newFloatArray (6, 0);
+this.fillFloatArray(this.line.substring(this.line.indexOf("ters") + 4), 0, this.unitCellParamsS);
+}return true;
+}, "~S");
+Clazz.defineMethod(c$, "readAtoms",
+function(){
+this.newAtomSet();
+if (this.unitCellVectors != null) {
+this.addExplicitLatticeVector(0, this.unitCellVectors, 0);
+this.addExplicitLatticeVector(1, this.unitCellVectors, 3);
+this.addExplicitLatticeVector(2, this.unitCellVectors, 6);
+} else if (this.unitCellParamsS != null) {
+this.setUnitCell(this.unitCellParamsS[0] * this.latticeConstant, this.unitCellParamsS[1] * this.latticeConstant, this.unitCellParamsS[2] * this.latticeConstant, this.unitCellParamsS[3], this.unitCellParamsS[4], this.unitCellParamsS[5]);
+}while (this.rdSiesta() != null && this.line.indexOf("%endblock Atomic") < 0) {
+var tokens = this.getTokens();
+var species = (this.htSpecies == null ? Clazz.newArray(-1, [null, null, tokens[4]]) : this.htSpecies.get(tokens[3]));
+var name = species[2];
+var sym = (species[1] == null ? name : J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(this.parseIntStr(species[1])));
+this.addAtomXYZSymName(tokens, 0, sym, name);
+}
+this.noAtoms = this.asc.ac;
+return true;
+});
+Clazz.defineMethod(c$, "setAtomCoordXYZ",
+function(atom, x, y, z){
+Clazz.superCall(this, J.adapter.readers.xtal.SiestaReader, "setAtomCoordXYZ", [atom, this.getACFValue(x), this.getACFValue(y), this.getACFValue(z)]);
+}, "J.adapter.smarter.Atom,~N,~N,~N");
+Clazz.defineMethod(c$, "newAtomSet",
+function(){
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSet();
+this.setSpaceGroupName("P1");
+this.setFractionalCoordinates(false);
+});
+Clazz.defineMethod(c$, "readAtomsCartGeomThenCell",
+function(){
+this.readLines(1);
+this.newAtomSet();
+var atom0 = this.asc.ac;
+for (var i = 0; i < this.noAtoms; i++) {
+var tokens = this.getTokens();
+var atom = this.asc.addNewAtom();
+atom.atomName = tokens[4];
+var x = this.parseFloatStr(tokens[0]);
+var y = this.parseFloatStr(tokens[1]);
+var z = this.parseFloatStr(tokens[2]);
+atom.set(x, y, z);
+this.rdSiesta();
+}
+this.discardLinesUntilContains("outcell: Unit cell vectors");
+this.setCell("vectors");
+var atoms = this.asc.atoms;
+var ac = this.asc.ac;
+for (var i = atom0; i < ac; i++) this.setAtomCoord(atoms[i]);
+
+this.discardLinesUntilContains("siesta: E_KS(eV) = ");
+var tokens = this.getTokens();
+var energy = Double.$valueOf(Double.parseDouble(tokens[3]));
+this.asc.setAtomSetEnergy("" + energy, energy.floatValue());
+this.asc.setCurrentModelInfo("Energy", energy);
+this.asc.setInfo("Energy", energy);
+this.asc.setAtomSetName("Energy = " + energy + " eV");
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspChgcarReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspChgcarReader.js
new file mode 100755
index 000000000000..0ea0663f05f0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspChgcarReader.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.readers.xtal.VaspPoscarReader"], "J.adapter.readers.xtal.VaspChgcarReader", null, function(){
+var c$ = Clazz.declareType(J.adapter.readers.xtal, "VaspChgcarReader", J.adapter.readers.xtal.VaspPoscarReader);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspOutcarReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspOutcarReader.js
new file mode 100755
index 000000000000..a19499a171e4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspOutcarReader.js
@@ -0,0 +1,188 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "JU.Lst"], "J.adapter.readers.xtal.VaspOutcarReader", ["JU.DF", "$.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.atomNames = null;
+this.ac = 0;
+this.inputOnly = false;
+this.mDsimulation = false;
+this.vaspVersion = 0;
+this.elementNames = null;
+this.gibbsEnergy = null;
+this.gibbsEntropy = null;
+this.electronEne = null;
+this.kinEne = null;
+this.totEne = null;
+this.temp = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "VaspOutcarReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.elementNames = new JU.Lst();
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.isPrimitive = true;
+this.setSpaceGroupName("P1");
+this.setFractionalCoordinates(true);
+this.inputOnly = this.checkFilterKey("INPUT");
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.vaspVersion == 0 && this.line.contains(" vasp.")) {
+this.readVersion();
+if (this.vaspVersion > 0) this.appendLoadNote("VASP version " + this.vaspVersion + " " + this.line);
+} else if (this.line.toUpperCase().startsWith(" POTCAR:")) {
+this.readElementNames();
+} else if (this.line.contains("ions per type")) {
+this.readAtomCountAndSetNames();
+} else if (this.line.contains("molecular dynamics for ions")) {
+this.mDsimulation = true;
+} else if (this.line.contains("direct lattice vectors")) {
+this.readUnitCellVectors();
+} else if (this.ac > 0 && this.line.contains("position of ions in fractional coordinates")) {
+this.readInitialCoordinates();
+if (this.inputOnly) this.continuing = false;
+} else if (this.line.contains("POSITION")) {
+this.readPOSITION();
+return true;
+} else if (this.line.startsWith(" FREE ENERGIE") && !this.mDsimulation) {
+this.readEnergy();
+} else if (this.line.contains("ENERGIE OF THE ELECTRON-ION-THERMOSTAT") && this.mDsimulation) {
+this.readMdyn();
+} else if (this.line.startsWith(" Eigenvectors and eigenvalues of the dynamical matrix")) {
+this.readFrequency();
+}return true;
+});
+Clazz.defineMethod(c$, "readVersion",
+function(){
+var tokens = JU.PT.split(this.line, ".");
+this.vaspVersion = JU.PT.parseInt(tokens[1]);
+});
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+this.setSymmetry();
+});
+Clazz.defineMethod(c$, "readElementNames",
+function(){
+this.line = JU.PT.rep(this.line, " _ ", "_");
+var tokens = this.getTokens();
+var pt = tokens[1].indexOf(":");
+var name = (pt >= 0 ? tokens[1].substring(0, pt) : tokens[2]);
+this.elementNames.addLast(name);
+});
+Clazz.defineMethod(c$, "readAtomCountAndSetNames",
+function(){
+var numofElement = Clazz.newIntArray (100, 0);
+var tokens = JU.PT.getTokens(this.line.substring(this.line.indexOf("=") + 1));
+this.ac = 0;
+for (var i = 0; i < tokens.length; i++) this.ac += (numofElement[i] = this.parseIntStr(tokens[i]));
+
+this.atomNames = new Array(this.ac);
+var nElements = this.elementNames.size();
+for (var pt = 0, i = 0; i < nElements; i++) for (var j = 0; j < numofElement[i] && pt < this.ac; j++) this.atomNames[pt++] = this.elementNames.get(i);
+
+
+});
+Clazz.defineMethod(c$, "readUnitCellVectors",
+function(){
+if (this.asc.ac > 0) {
+this.setSymmetry();
+this.asc.newAtomSet();
+this.setAtomSetInfo();
+}var f = Clazz.newFloatArray (3, 0);
+for (var i = 0; i < 3; i++) this.addExplicitLatticeVector(i, this.fillFloatArray(this.fixMinus(this.rd()), 0, f), 0);
+
+});
+Clazz.defineMethod(c$, "fixMinus",
+function(line){
+return JU.PT.rep(line, "-", " -");
+}, "~S");
+Clazz.defineMethod(c$, "setSymmetry",
+function(){
+this.applySymmetryAndSetTrajectory();
+this.setSpaceGroupName("P1");
+this.setFractionalCoordinates(false);
+});
+Clazz.defineMethod(c$, "readInitialCoordinates",
+function(){
+var counter = 0;
+while (this.rd() != null && this.line.length > 10) {
+this.addAtomXYZSymName(JU.PT.getTokens(this.fixMinus(this.line)), 0, null, this.atomNames[counter++]);
+}
+this.asc.setAtomSetName("Initial Coordinates");
+});
+Clazz.defineMethod(c$, "readPOSITION",
+function(){
+var counter = 0;
+this.readLines(1);
+while (this.rd() != null && this.line.indexOf("----------") < 0) this.addAtomXYZSymName(this.getTokens(), 0, null, this.atomNames[counter++]);
+
+});
+Clazz.defineMethod(c$, "readEnergy",
+function(){
+this.rd();
+var tokens = JU.PT.getTokens(this.rd());
+this.gibbsEnergy = Double.$valueOf(Double.parseDouble(tokens[4]));
+this.rd();
+tokens = JU.PT.getTokens(this.rd());
+var enthalpy = Double.parseDouble(tokens[3]);
+this.gibbsEntropy = Double.$valueOf(enthalpy - this.gibbsEnergy.doubleValue());
+});
+Clazz.defineMethod(c$, "setAtomSetInfo",
+function(){
+if (this.gibbsEnergy == null) return;
+this.asc.setAtomSetEnergy("" + this.gibbsEnergy, this.gibbsEnergy.floatValue());
+this.asc.setCurrentModelInfo("Energy", this.gibbsEnergy);
+this.asc.setCurrentModelInfo("Entropy", this.gibbsEntropy);
+this.asc.setInfo("Energy", this.gibbsEnergy);
+this.asc.setInfo("Entropy", this.gibbsEntropy);
+this.asc.setAtomSetName("G = " + this.gibbsEnergy + " eV, T*S = " + this.gibbsEntropy + " eV");
+});
+Clazz.defineMethod(c$, "readMdyn",
+function(){
+var tokens = this.getTokens();
+this.rd();
+tokens = JU.PT.getTokens(this.rd());
+this.electronEne = Double.$valueOf(Double.parseDouble(tokens[4]));
+tokens = JU.PT.getTokens(this.rd());
+this.kinEne = Double.$valueOf(Double.parseDouble(tokens[4]));
+this.temp = this.parseFloatStr(tokens[6]);
+this.readLines(3);
+tokens = JU.PT.getTokens(this.rd());
+this.totEne = Double.$valueOf(Double.parseDouble(tokens[4]));
+this.setAtomSetInfoMd();
+});
+Clazz.defineMethod(c$, "setAtomSetInfoMd",
+function(){
+this.asc.setAtomSetName("Temp. = " + JU.DF.formatDecimal((this.temp), 2) + " K, Energy = " + this.totEne + " eV");
+this.asc.setCurrentModelInfo("Energy", this.totEne);
+this.asc.setInfo("Energy", this.totEne);
+this.asc.setCurrentModelInfo("EleEnergy", this.kinEne);
+this.asc.setInfo("EleEnergy", this.electronEne);
+this.asc.setCurrentModelInfo("Kinetic", this.electronEne);
+this.asc.setInfo("Kinetic", this.kinEne);
+this.asc.setCurrentModelInfo("Temperature", JU.DF.formatDecimal((this.temp), 2));
+this.asc.setInfo("Temperature", JU.DF.formatDecimal((this.temp), 2));
+});
+Clazz.defineMethod(c$, "readFrequency",
+function(){
+var pt = this.asc.iSet;
+this.asc.baseSymmetryAtomCount = this.ac;
+if (this.vaspVersion >= 5) {
+this.readLines(3);
+} else {
+this.discardLinesUntilContains("Eigenvectors after division by SQRT(mass)");
+this.readLines(5);
+}var ignore = Clazz.newBooleanArray(1, false);
+while (this.rd() != null && (this.line.contains("f = ") || this.line.contains("f/i= "))) {
+this.applySymmetryAndSetTrajectory();
+var iAtom0 = this.asc.ac;
+this.cloneLastAtomSet(this.ac, null);
+if (!ignore[0]) {
+this.asc.iSet = ++pt;
+this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, this.line.substring(this.line.indexOf("2PiTHz") + 6, this.line.indexOf("c") - 1).trim(), null);
+}this.rd();
+this.fillFrequencyData(iAtom0, this.ac, this.ac, ignore, true, 35, 12, null, 0, null);
+this.rd();
+}
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspPoscarReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspPoscarReader.js
new file mode 100755
index 000000000000..4959c0e2672b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/VaspPoscarReader.js
@@ -0,0 +1,140 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.VaspPoscarReader", ["JU.Lst", "$.M3", "$.PT", "$.SB", "J.api.JmolAdapter", "JU.Logger", "$.Parser"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.atomLabels = null;
+this.haveAtomLabels = true;
+this.atomsLabeledInline = false;
+this.scaleFac = 0;
+this.ac = 0;
+this.title = null;
+this.quiet = false;
+this.defaultLabels = null;
+this.unitCellData = null;
+this.elementLabel = null;
+this.radiusPt = -2147483648;
+this.elementPt = -2147483648;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "VaspPoscarReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.isPrimitive = true;
+this.readStructure(null);
+this.continuing = false;
+});
+Clazz.defineMethod(c$, "readStructure",
+function(titleMsg){
+this.title = this.rd().trim();
+var pt = this.title.indexOf("--params");
+if ((pt = this.title.indexOf("& ", pt + 1)) >= 0) {
+this.latticeType = this.title.substring(pt + 2, pt + 3);
+JU.Logger.info("AFLOW lattice:" + this.latticeType + " title=" + this.title);
+}this.readUnitCellVectors();
+this.readMolecularFormula();
+this.readCoordinates();
+this.asc.setAtomSetName(this.title + (titleMsg == null ? "" : "[" + titleMsg + "]"));
+}, "~S");
+Clazz.overrideMethod(c$, "finalizeSubclassReader",
+function(){
+if (!this.iHaveFractionalCoordinates) this.fractionalizeCoordinates(true);
+if (!this.haveAtomLabels && !this.atomsLabeledInline) this.appendLoadNote("VASP POSCAR reader using pseudo atoms Al B C Db...");
+this.finalizeReaderASCR();
+});
+Clazz.defineMethod(c$, "readUnitCellVectors",
+function(){
+this.setSpaceGroupName("P1");
+this.setFractionalCoordinates(true);
+this.scaleFac = this.parseFloatStr(this.rdline().trim());
+var isVolume = (this.scaleFac < 0);
+if (isVolume) this.scaleFac = Math.pow(-this.scaleFac, 0.3333333333333333);
+this.unitCellData = Clazz.newFloatArray (9, 0);
+var s = this.rdline() + " " + this.rdline() + " " + this.rdline();
+JU.Parser.parseStringInfestedFloatArray(s, null, this.unitCellData);
+if (isVolume) {
+var m = JU.M3.newA9(this.unitCellData);
+this.scaleFac /= m.determinant3();
+}if (this.scaleFac != 1) for (var i = 0; i < this.unitCellData.length; i++) this.unitCellData[i] *= this.scaleFac;
+
+});
+Clazz.defineMethod(c$, "readMolecularFormula",
+function(){
+if (this.elementLabel == null) this.elementLabel = JU.PT.getTokens(this.discardLinesUntilNonBlank());
+var elementCounts;
+if (JU.PT.parseInt(this.elementLabel[0]) == -2147483648) {
+this.atomsLabeledInline = false;
+elementCounts = JU.PT.getTokens(this.rdline());
+while (this.line != null && (elementCounts.length == 0 || this.parseIntStr(elementCounts[0]) == -2147483648)) elementCounts = JU.PT.getTokens(this.rdline());
+
+} else {
+elementCounts = this.elementLabel;
+this.elementLabel = JU.PT.split(this.title, " ");
+if (this.elementLabel.length != elementCounts.length || this.elementLabel[0].length > 2) {
+this.elementLabel = JU.PT.split("Al B C Db Eu F Ga Hf I K Li Mn N O P Ru S Te U V W Xe Yb Zn", " ");
+this.haveAtomLabels = false;
+}}var labels = this.elementLabel;
+var mf = new JU.SB();
+this.atomLabels = new JU.Lst();
+this.ac = 0;
+for (var i = 0; i < elementCounts.length; i++) {
+var n = Integer.parseInt(elementCounts[i]);
+this.ac += n;
+var label = labels[i];
+mf.append(" ").append(label).appendI(n);
+for (var j = n; --j >= 0; ) this.atomLabels.addLast(label);
+
+}
+var s = mf.toString();
+if (!this.quiet) this.appendLoadNote(this.ac + " atoms identified for" + s);
+this.asc.newAtomSet();
+this.asc.setAtomSetName(s);
+});
+Clazz.defineMethod(c$, "readCoordinates",
+function(){
+var isSelective = this.discardLinesUntilNonBlank().toLowerCase().contains("selective");
+if (isSelective) this.rd();
+var isCartesian = (this.line.toLowerCase().contains("cartesian"));
+if (isCartesian) {
+this.setFractionalCoordinates(false);
+}this.addExplicitLatticeVector(0, this.unitCellData, 0);
+this.addExplicitLatticeVector(1, this.unitCellData, 3);
+this.addExplicitLatticeVector(2, this.unitCellData, 6);
+for (var i = 0; i < this.ac; i++) {
+var radius = NaN;
+var tokens = JU.PT.getTokens(this.rdline());
+if (this.radiusPt == -2147483648) {
+for (var j = tokens.length; --j > 2; ) {
+var t = tokens[j];
+if (t.equals("radius")) {
+this.radiusPt = j + 1;
+} else if (!t.equals("T") && !t.equals("F") && this.getElement(t) != null) {
+this.elementPt = j;
+this.atomsLabeledInline = true;
+}}
+}if (this.radiusPt >= 0) radius = this.parseFloatStr(tokens[this.radiusPt]);
+var label = (this.atomsLabeledInline ? tokens[this.elementPt] : this.atomLabels.get(i));
+if (isCartesian) for (var j = 0; j < 3; j++) tokens[j] = "" + this.parseFloatStr(tokens[j]) * this.scaleFac;
+
+var atom = this.addAtomXYZSymName(tokens, 0, null, label);
+if (!Float.isNaN(radius)) atom.radius = radius * this.scaleFac;
+if (this.asc.bsAtoms != null) this.asc.bsAtoms.set(atom.index);
+}
+});
+Clazz.defineMethod(c$, "getElement",
+function(token){
+var s = null;
+switch (token.length) {
+default:
+s = (token.length > 2 ? token.substring(0, 2) : null);
+if (s != null && J.api.JmolAdapter.getElementNumber(s) >= 0) return s;
+case 1:
+if (J.api.JmolAdapter.getElementNumber(s = token.substring(0)) >= 0) return s;
+case 0:
+return null;
+}
+}, "~S");
+Clazz.defineMethod(c$, "rdline",
+function(){
+this.rd();
+if (this.line != null && this.line.startsWith("[")) this.line = this.line.substring(this.line.indexOf("]") + 1).trim();
+return this.line;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/Wien2kReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/Wien2kReader.js
new file mode 100755
index 000000000000..b0d2dd59772d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/Wien2kReader.js
@@ -0,0 +1,115 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.Wien2kReader", ["JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isrhombohedral = false;
+this.latticeCode = '\0';
+this.doSymmetry = true;
+this.cxyz = " x y z";
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "Wien2kReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.doSymmetry = !this.sgName.equals("none");
+this.setFractionalCoordinates(true);
+this.asc.setCollectionName(this.rd());
+this.readUnitCell();
+this.readAtoms();
+this.readSymmetry();
+this.readEmbeddedScript();
+this.continuing = false;
+});
+Clazz.defineMethod(c$, "readUnitCell",
+function(){
+this.rd();
+this.isrhombohedral = ((this.latticeCode = this.line.charAt(0)) == 'R');
+if (this.line.startsWith("CYZ")) this.latticeCode = 'A';
+ else if (this.line.startsWith("CXZ")) this.latticeCode = 'B';
+ else if (this.line.startsWith("B")) this.latticeCode = 'I';
+if (this.latticeCode != 'R' && this.latticeCode != 'H') this.asc.getXSymmetry().setLatticeParameter(this.latticeCode.charCodeAt(0));
+if (this.line.length > 32) {
+var name = this.line.substring(32).trim();
+if (name.indexOf(" ") >= 0) name = name.substring(name.indexOf(" ") + 1);
+if (name.indexOf("_") >= 0) name = name.substring(name.indexOf("_") + 1);
+this.setSpaceGroupName(name);
+}var factor = (this.rd().toLowerCase().indexOf("ang") >= 0 ? 1 : 0.5291772);
+this.rd();
+var a = this.parseFloatRange(this.line, 0, 10) * factor;
+var b = this.parseFloatRange(this.line, 10, 20) * factor;
+var c = this.parseFloatRange(this.line, 20, 30) * factor;
+var l = this.line.length;
+var alpha = (l >= 40 ? this.parseFloatRange(this.line, 30, 40) : 0);
+var beta = (l >= 50 ? this.parseFloatRange(this.line, 40, 50) : 0);
+var gamma = (l >= 60 ? this.parseFloatRange(this.line, 50, 60) : 0);
+if (this.isrhombohedral) {
+var ar = Math.sqrt(a * a / 3 + c * c / 9);
+alpha = beta = gamma = (Math.acos((2 * c * c - 3 * a * a) / (2 * c * c + 6 * a * a)) * 180 / 3.141592653589793);
+a = b = c = ar;
+}if (Float.isNaN(alpha) || alpha == 0) alpha = 90;
+if (Float.isNaN(beta) || beta == 0) beta = 90;
+if (Float.isNaN(gamma) || gamma == 0) gamma = 90;
+this.setUnitCell(a, b, c, alpha, beta, gamma);
+});
+Clazz.defineMethod(c$, "readAtoms",
+function(){
+this.rd();
+while (this.line != null && (this.line.indexOf("ATOM") == 0 || !this.doSymmetry && this.line.indexOf(":") == 8)) {
+var thisAtom = this.asc.ac;
+this.addAtom();
+if (this.rd().indexOf("MULT=") == 10) for (var i = this.parseIntRange(this.line, 15, 18); --i >= 0; ) {
+this.rd();
+if (!this.doSymmetry) this.addAtom();
+}
+var atomName = this.line.substring(0, 10);
+var sym = atomName.substring(0, 2).trim();
+if (sym.length == 2 && JU.PT.isDigit(sym.charAt(1))) sym = sym.substring(0, 1);
+atomName = JU.PT.rep(atomName, " ", "");
+var n = 0;
+for (var i = this.asc.ac; --i >= thisAtom; ) {
+var atom = this.asc.atoms[i];
+atom.elementSymbol = sym;
+atom.atomName = atomName + "_" + (n++);
+}
+while (this.rd() != null && this.line.indexOf("ATOM") < 0 && this.line.indexOf("SYMMETRY") < 0) {
+}
+}
+});
+Clazz.defineMethod(c$, "addAtom",
+function(){
+var a = this.parseFloatRange(this.line, 12, 22);
+var b = this.parseFloatRange(this.line, 25, 35);
+var c = this.parseFloatRange(this.line, 38, 48);
+var atom = this.asc.addNewAtom();
+this.setAtomCoordXYZ(atom, a, b, c);
+});
+Clazz.defineMethod(c$, "readSymmetry",
+function(){
+if (this.line.indexOf("SYMMETRY") < 0) return;
+var n = this.parseIntRange(this.line, 0, 4);
+for (var i = n; --i >= 0; ) {
+var xyz = this.getJones() + "," + this.getJones() + "," + this.getJones();
+if (this.doSymmetry) this.setSymmetryOperator(xyz);
+this.rd();
+}
+});
+Clazz.defineMethod(c$, "getJones",
+function(){
+this.rd();
+var xyz = "";
+var trans = this.parseFloatStr(this.line.substring(6));
+for (var i = 0; i < 6; i++) {
+if (this.line.charAt(i) == '-') xyz += "-";
+if (this.line.charAt(++i) == '1') {
+xyz += " x y z".charAt(i);
+if (trans > 0) xyz += "+";
+if (trans != 0) xyz += trans;
+}}
+return xyz;
+});
+Clazz.defineMethod(c$, "readEmbeddedScript",
+function(){
+while (this.line != null) {
+this.checkCurrentLineForScript();
+this.rd();
+}
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/XcrysdenReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/XcrysdenReader.js
new file mode 100755
index 000000000000..3296b50e836a
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/readers/xtal/XcrysdenReader.js
@@ -0,0 +1,72 @@
+Clazz.declarePackage("J.adapter.readers.xtal");
+Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.XcrysdenReader", ["JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nAtoms = 0;
+this.animation = false;
+this.unitCellData = null;
+this.animationStep = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "XcrysdenReader", J.adapter.smarter.AtomSetCollectionReader);
+Clazz.prepareFields (c$, function(){
+this.unitCellData = Clazz.newFloatArray (9, 0);
+});
+Clazz.overrideMethod(c$, "initializeReader",
+function(){
+this.setFractionalCoordinates(false);
+this.doApplySymmetry = true;
+});
+Clazz.overrideMethod(c$, "checkLine",
+function(){
+if (this.line.startsWith("ATOMS")) {
+this.doApplySymmetry = false;
+return this.readCoordinates();
+}if (this.line.contains("ANIMSTEP")) {
+this.animation = true;
+} else if (this.line.contains("PRIMVEC")) {
+this.readUnitCell();
+} else if (this.line.contains("PRIMCOORD")) {
+return this.readCoordinates();
+}return true;
+});
+Clazz.defineMethod(c$, "readUnitCell",
+function(){
+this.setSymmetry();
+this.fillFloatArray(null, 0, this.unitCellData);
+this.setUnitCell();
+});
+Clazz.defineMethod(c$, "setUnitCell",
+function(){
+this.addExplicitLatticeVector(0, this.unitCellData, 0);
+this.addExplicitLatticeVector(1, this.unitCellData, 3);
+this.addExplicitLatticeVector(2, this.unitCellData, 6);
+});
+Clazz.defineMethod(c$, "setSymmetry",
+function(){
+this.applySymmetryAndSetTrajectory();
+this.asc.newAtomSet();
+this.setSpaceGroupName("P1");
+this.setFractionalCoordinates(false);
+});
+Clazz.defineMethod(c$, "readCoordinates",
+function(){
+if (this.doApplySymmetry) {
+var atomStr = JU.PT.getTokens(this.rd());
+this.nAtoms = Integer.parseInt(atomStr[0]);
+} else {
+this.nAtoms = 2147483647;
+}this.setFractionalCoordinates(false);
+var counter = 0;
+while (counter < this.nAtoms && this.rd() != null) {
+var tokens = this.getTokens();
+var an = JU.PT.parseInt(tokens[0]);
+if (an < 0) {
+break;
+}this.line = null;
+this.addAtomXYZSymName(tokens, 1, null, J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(an));
+counter++;
+}
+this.asc.setAtomSetName(this.animation ? "Structure " + (++this.animationStep) : "Initial coordinates");
+if (this.line != null) this.setSymmetry();
+return (this.line == null);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Atom.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Atom.js
new file mode 100755
index 000000000000..254dc949ce39
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Atom.js
@@ -0,0 +1,113 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["JU.P3"], "J.adapter.smarter.Atom", ["JU.AU", "$.Lst", "$.V3"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.atomSetIndex = 0;
+this.index = 0;
+this.bsSymmetry = null;
+this.atomSite = 0;
+this.elementSymbol = null;
+this.elementNumber = -1;
+this.atomName = null;
+this.formalCharge = -2147483648;
+this.partialCharge = NaN;
+this.vib = null;
+this.bfactor = NaN;
+this.foccupancy = 1;
+this.radius = NaN;
+this.isHetero = false;
+this.atomSerial = -2147483648;
+this.chainID = 0;
+this.bondingRadius = NaN;
+this.altLoc = '\0';
+this.group3 = null;
+this.sequenceNumber = -2147483648;
+this.insertionCode = '\0';
+this.anisoBorU = null;
+this.tensors = null;
+this.isNegDisorder = false;
+this.typeSymbol = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "Atom", JU.P3, Cloneable);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.smarter.Atom, []);
+this.set(NaN, NaN, NaN);
+});
+Clazz.defineMethod(c$, "addTensor",
+function(tensor, type, reset){
+if (tensor == null) return null;
+if (reset || this.tensors == null) this.tensors = new JU.Lst();
+this.tensors.addLast(tensor);
+if (type != null) tensor.setType(type);
+return tensor;
+}, "JU.Tensor,~S,~B");
+Clazz.defineMethod(c$, "getClone",
+function(){
+var a;
+try {
+a = this.clone();
+} catch (e) {
+if (Clazz.exceptionOf(e,"CloneNotSupportedException")){
+return null;
+} else {
+throw e;
+}
+}
+if (this.vib != null) {
+if (Clazz.instanceOf(this.vib,"JU.Vibration")) {
+a.vib = (this.vib).clone();
+} else {
+a.vib = JU.V3.newV(a.vib);
+}}if (this.anisoBorU != null) a.anisoBorU = JU.AU.arrayCopyF(this.anisoBorU, -1);
+if (this.tensors != null) {
+a.tensors = new JU.Lst();
+for (var i = this.tensors.size(); --i >= 0; ) a.tensors.addLast((this.tensors.get(i)).copyTensor());
+
+}return a;
+});
+Clazz.defineMethod(c$, "getElementSymbol",
+function(){
+if (this.elementSymbol == null && this.atomName != null) {
+var len = this.atomName.length;
+var ichFirst = 0;
+var chFirst = String.fromCharCode(0);
+while (ichFirst < len && !J.adapter.smarter.Atom.isValidSymChar1(chFirst = this.atomName.charAt(ichFirst))) ++ichFirst;
+
+switch (len - ichFirst) {
+case 0:
+break;
+default:
+var chSecond = this.atomName.charAt(ichFirst + 1);
+if (J.adapter.smarter.Atom.isValidSymNoCase(chFirst, chSecond)) {
+this.elementSymbol = "" + chFirst + chSecond;
+break;
+}case 1:
+if (J.adapter.smarter.Atom.isValidSym1(chFirst)) this.elementSymbol = "" + chFirst;
+break;
+}
+}return this.elementSymbol;
+});
+c$.isValidSym1 = Clazz.defineMethod(c$, "isValidSym1",
+function(ch){
+return (ch >= 'A' && ch <= 'Z' && J.adapter.smarter.Atom.elementCharMasks[ch.charCodeAt(0) - 65] < 0);
+}, "~S");
+c$.isValidSym2 = Clazz.defineMethod(c$, "isValidSym2",
+function(ch1, ch2){
+return (ch1 >= 'A' && ch1 <= 'Z' && ch2 >= 'a' && ch2 <= 'z' && ((J.adapter.smarter.Atom.elementCharMasks[ch1.charCodeAt(0) - 65] >> (ch2.charCodeAt(0) - 97)) & 1) != 0);
+}, "~S,~S");
+c$.isValidSymNoCase = Clazz.defineMethod(c$, "isValidSymNoCase",
+function(ch1, ch2){
+return J.adapter.smarter.Atom.isValidSym2(ch1, ch2 < 'a' ? String.fromCharCode(ch2.charCodeAt(0) + 32) : ch2);
+}, "~S,~S");
+c$.isValidSymChar1 = Clazz.defineMethod(c$, "isValidSymChar1",
+function(ch){
+return (ch >= 'A' && ch <= 'Z' && J.adapter.smarter.Atom.elementCharMasks[ch.charCodeAt(0) - 65] != 0);
+}, "~S");
+Clazz.defineMethod(c$, "copyTo",
+function(pt, asc){
+var a = asc.newCloneAtom(this);
+a.setT(pt);
+return a;
+}, "JU.P3,J.adapter.smarter.AtomSetCollection");
+c$.elementCharMasks = Clazz.newIntArray(-1, [1972292, -2147351151, -2146019271, -2130706430, 1441792, -2147348464, 25, -2147205008, -2147344384, 0, -2147352576, 1179905, 548936, -2147434213, -2147221504, -2145759221, 0, 1056947, -2147339946, -2147477097, -2147483648, -2147483648, -2147483648, 8388624, -2147483646, 139264]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomIterator.js
new file mode 100755
index 000000000000..d0629eba17fe
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomIterator.js
@@ -0,0 +1,126 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["J.api.JmolAdapterAtomIterator"], "J.adapter.smarter.AtomIterator", ["J.api.JmolAdapter"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.iatom = 0;
+this.atom = null;
+this.ac = 0;
+this.atoms = null;
+this.bsAtoms = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomIterator", null, J.api.JmolAdapterAtomIterator);
+Clazz.makeConstructor(c$,
+function(asc){
+this.ac = asc.ac;
+this.atoms = asc.atoms;
+this.bsAtoms = asc.bsAtoms;
+this.iatom = 0;
+}, "J.adapter.smarter.AtomSetCollection");
+Clazz.overrideMethod(c$, "hasNext",
+function(){
+if (this.iatom == this.ac) return false;
+while ((this.atom = this.atoms[this.iatom++]) == null || (this.bsAtoms != null && !this.bsAtoms.get(this.atom.index))) if (this.iatom == this.ac) return false;
+
+this.atoms[this.iatom - 1] = null;
+return true;
+});
+Clazz.overrideMethod(c$, "getAtomSetIndex",
+function(){
+return this.atom.atomSetIndex;
+});
+Clazz.overrideMethod(c$, "getSymmetry",
+function(){
+return this.atom.bsSymmetry;
+});
+Clazz.overrideMethod(c$, "getAtomSite",
+function(){
+return this.atom.atomSite + 1;
+});
+Clazz.overrideMethod(c$, "getUniqueID",
+function(){
+return Integer.$valueOf(this.atom.index);
+});
+Clazz.overrideMethod(c$, "getElementNumber",
+function(){
+return (this.atom.elementNumber > 0 ? this.atom.elementNumber : J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol()));
+});
+Clazz.overrideMethod(c$, "getAtomName",
+function(){
+return this.atom.atomName;
+});
+Clazz.overrideMethod(c$, "getFormalCharge",
+function(){
+return (this.atom.formalCharge == -2147483648 ? 0 : this.atom.formalCharge);
+});
+Clazz.overrideMethod(c$, "getPartialCharge",
+function(){
+return this.atom.partialCharge;
+});
+Clazz.overrideMethod(c$, "getTensors",
+function(){
+return this.atom.tensors;
+});
+Clazz.overrideMethod(c$, "getRadius",
+function(){
+return this.atom.radius;
+});
+Clazz.overrideMethod(c$, "getBondRadius",
+function(){
+return this.atom.bondingRadius;
+});
+Clazz.overrideMethod(c$, "getVib",
+function(){
+return (this.atom.vib == null || Float.isNaN(this.atom.vib.z) ? null : this.atom.vib);
+});
+Clazz.overrideMethod(c$, "getSeqID",
+function(){
+return (this.atom.vib == null || !Float.isNaN(this.atom.vib.y) || this.atom.vib.z != 1094713365 ? 0 : Clazz.floatToInt(this.atom.vib.x));
+});
+Clazz.overrideMethod(c$, "getBfactor",
+function(){
+return this.atom.bfactor;
+});
+Clazz.overrideMethod(c$, "getOccupancy",
+function(){
+return this.atom.foccupancy * 100;
+});
+Clazz.overrideMethod(c$, "getIsHetero",
+function(){
+return this.atom.isHetero;
+});
+Clazz.overrideMethod(c$, "getSerial",
+function(){
+return this.atom.atomSerial;
+});
+Clazz.overrideMethod(c$, "getChainID",
+function(){
+return this.atom.chainID;
+});
+Clazz.overrideMethod(c$, "getAltLoc",
+function(){
+return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc);
+});
+Clazz.overrideMethod(c$, "getGroup3",
+function(){
+return this.atom.group3;
+});
+Clazz.overrideMethod(c$, "getSequenceNumber",
+function(){
+return this.atom.sequenceNumber;
+});
+Clazz.overrideMethod(c$, "getInsertionCode",
+function(){
+return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode);
+});
+Clazz.overrideMethod(c$, "getXYZ",
+function(){
+return this.atom;
+});
+Clazz.overrideMethod(c$, "getElement",
+function(){
+return this.getElementNumber() & 0x7F;
+});
+Clazz.overrideMethod(c$, "getIsotope",
+function(){
+return this.getElementNumber() >> 7;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollection.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollection.js
new file mode 100755
index 000000000000..ac1829901019
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollection.js
@@ -0,0 +1,880 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["java.util.Hashtable"], "J.adapter.smarter.AtomSetCollection", ["java.util.Collections", "$.Properties", "JU.AU", "$.BS", "$.Lst", "$.P3", "$.V3", "J.adapter.smarter.Atom", "$.Bond", "$.SmarterJmolAdapter", "J.api.Interface", "JU.BSUtil", "$.Logger", "JV.JC"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.reader = null;
+this.bsAtoms = null;
+this.fileTypeName = null;
+this.collectionName = null;
+this.atomSetInfo = null;
+this.atoms = null;
+this.ac = 0;
+this.bonds = null;
+this.bondCount = 0;
+this.structures = null;
+this.structureCount = 0;
+this.atomSetCount = 0;
+this.iSet = -1;
+this.atomSetNumbers = null;
+this.atomSetAtomIndexes = null;
+this.atomSetAtomCounts = null;
+this.atomSetBondCounts = null;
+this.atomSetAuxiliaryInfo = null;
+this.errorMessage = null;
+this.coordinatesAreFractional = false;
+this.isTrajectory = false;
+this.trajectoryStepCount = 0;
+this.trajectorySteps = null;
+this.vibrationSteps = null;
+this.trajectoryNames = null;
+this.doFixPeriodic = false;
+this.allowMultiple = false;
+this.readerList = null;
+this.atomMapAnyCase = false;
+this.fixedSite = 0;
+this.bsStructuredModels = null;
+this.haveAnisou = false;
+this.baseSymmetryAtomCount = 0;
+this.crystalReaderLatticeOpsOnly = false;
+this.xtalSymmetry = null;
+this.bondIndex0 = 0;
+this.atomSymbolicMap = null;
+this.haveUnitCell = false;
+this.vibScale = 0;
+this.firstAtomToBond = -1;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomSetCollection", null);
+Clazz.prepareFields (c$, function(){
+this.atomSetInfo = new java.util.Hashtable();
+this.atoms = new Array(256);
+this.bonds = new Array(256);
+this.structures = new Array(16);
+this.atomSetNumbers = Clazz.newIntArray (16, 0);
+this.atomSetAtomIndexes = Clazz.newIntArray (16, 0);
+this.atomSetAtomCounts = Clazz.newIntArray (16, 0);
+this.atomSetBondCounts = Clazz.newIntArray (16, 0);
+this.atomSetAuxiliaryInfo = new Array(16);
+this.atomSymbolicMap = new java.util.Hashtable();
+});
+Clazz.makeConstructor(c$,
+function(fileTypeName, reader, array, list){
+this.fileTypeName = fileTypeName;
+this.reader = reader;
+this.allowMultiple = (reader == null || reader.desiredVibrationNumber < 0);
+var p = new java.util.Properties();
+p.put("PATH_KEY", ".PATH");
+p.put("PATH_SEPARATOR", J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);
+this.setInfo("properties", p);
+if (reader != null) {
+var ii = reader.htParams.get("appendToModelIndex");
+if (ii != null) this.setInfo("appendToModelIndex", ii);
+ii = reader.htParams.get("fixedSite");
+if (ii != null) this.fixedSite = ii.intValue();
+}if (array != null) {
+var n = 0;
+this.readerList = new JU.Lst();
+for (var i = 0; i < array.length; i++) if (array[i] != null && (array[i].ac > 0 || array[i].reader != null && array[i].reader.mustFinalizeModelSet)) this.appendAtomSetCollection(n++, array[i]);
+
+if (n > 1) this.setInfo("isMultiFile", Boolean.TRUE);
+} else if (list != null) {
+this.setInfo("isMultiFile", Boolean.TRUE);
+this.appendAtomSetCollectionList(list);
+}}, "~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");
+Clazz.defineMethod(c$, "setCollectionName",
+function(collectionName){
+if (collectionName != null && (collectionName = collectionName.trim()).length > 0) this.collectionName = collectionName;
+}, "~S");
+Clazz.defineMethod(c$, "clearGlobalBoolean",
+function(globalIndex){
+this.atomSetInfo.remove(JV.JC.getBoolName(globalIndex));
+}, "~N");
+Clazz.defineMethod(c$, "setGlobalBoolean",
+function(globalIndex){
+this.setInfo(JV.JC.getBoolName(globalIndex), Boolean.TRUE);
+}, "~N");
+Clazz.defineMethod(c$, "getGlobalBoolean",
+function(globalIndex){
+return (this.atomSetInfo.get(JV.JC.getBoolName(globalIndex)) === Boolean.TRUE);
+}, "~N");
+Clazz.defineMethod(c$, "appendAtomSetCollectionList",
+function(list){
+var n = list.size();
+if (n == 0) {
+this.errorMessage = "No file found!";
+return;
+}for (var i = 0; i < n; i++) {
+var o = list.get(i);
+if (Clazz.instanceOf(o,"JU.Lst")) this.appendAtomSetCollectionList(o);
+ else this.appendAtomSetCollection(i, o);
+}
+}, "JU.Lst");
+Clazz.defineMethod(c$, "setTrajectory",
+function(){
+if (!this.isTrajectory) this.trajectorySteps = new JU.Lst();
+this.isTrajectory = true;
+var n = (this.bsAtoms == null ? this.ac : this.bsAtoms.cardinality());
+if (n <= 1) return;
+var trajectoryStep = new Array(n);
+var haveVibrations = (n > 0 && this.atoms[0].vib != null && !Float.isNaN(this.atoms[0].vib.z));
+var vibrationStep = (haveVibrations ? new Array(n) : null);
+var prevSteps = (this.trajectoryStepCount == 0 ? null : this.trajectorySteps.get(this.trajectoryStepCount - 1));
+for (var i = 0, ii = 0; i < this.ac; i++) {
+if (this.bsAtoms != null && !this.bsAtoms.get(i)) continue;
+var pt = JU.P3.newP(this.atoms[i]);
+if (this.doFixPeriodic && prevSteps != null) pt = J.adapter.smarter.AtomSetCollection.fixPeriodic(pt, prevSteps[i]);
+trajectoryStep[ii] = pt;
+if (haveVibrations) vibrationStep[ii] = this.atoms[i].vib;
+ii++;
+}
+if (haveVibrations) {
+if (this.vibrationSteps == null) {
+this.vibrationSteps = new JU.Lst();
+for (var i = 0; i < this.trajectoryStepCount; i++) this.vibrationSteps.addLast(null);
+
+}this.vibrationSteps.addLast(vibrationStep);
+}this.trajectorySteps.addLast(trajectoryStep);
+this.trajectoryStepCount++;
+});
+Clazz.defineMethod(c$, "appendAtomSetCollection",
+function(collectionIndex, collection){
+if (collection.reader != null && collection.reader.mustFinalizeModelSet) this.readerList.addLast(collection.reader);
+var existingAtomsCount = this.ac;
+this.setInfo("loadState", collection.atomSetInfo.get("loadState"));
+if (collection.bsAtoms != null) {
+this.getBSAtoms(0);
+for (var i = collection.bsAtoms.nextSetBit(0); i >= 0; i = collection.bsAtoms.nextSetBit(i + 1)) this.bsAtoms.set(existingAtomsCount + i);
+
+}var clonedAtoms = 0;
+var atomSetCount0 = this.atomSetCount;
+for (var atomSetNum = 0; atomSetNum < collection.atomSetCount; atomSetNum++) {
+this.newAtomSet();
+var info = this.atomSetAuxiliaryInfo[this.iSet] = collection.atomSetAuxiliaryInfo[atomSetNum];
+var atomInfo = info.get("PDB_CONECT_firstAtom_count_max");
+if (atomInfo != null) atomInfo[0] += existingAtomsCount;
+this.setCurrentModelInfo("title", collection.collectionName);
+this.setAtomSetName(collection.getAtomSetName(atomSetNum));
+for (var atomNum = 0; atomNum < collection.atomSetAtomCounts[atomSetNum]; atomNum++) {
+if (this.bsAtoms != null) this.bsAtoms.set(this.ac);
+this.newCloneAtom(collection.atoms[clonedAtoms]);
+clonedAtoms++;
+}
+this.atomSetNumbers[this.iSet] = (collectionIndex < 0 ? this.iSet + 1 : ((collectionIndex + 1) * 1000000) + collection.atomSetNumbers[atomSetNum]);
+}
+for (var bondNum = 0; bondNum < collection.bondCount; bondNum++) {
+var bond = collection.bonds[bondNum];
+this.addNewBondWithOrder(bond.atomIndex1 + existingAtomsCount, bond.atomIndex2 + existingAtomsCount, bond.order);
+}
+for (var i = JV.JC.globalBooleans.length; --i >= 0; ) if (collection.getGlobalBoolean(i)) this.setGlobalBoolean(i);
+
+for (var i = 0; i < collection.structureCount; i++) {
+var s = collection.structures[i];
+this.addStructure(s);
+s.modelStartEnd[0] += atomSetCount0;
+s.modelStartEnd[1] += atomSetCount0;
+}
+}, "~N,J.adapter.smarter.AtomSetCollection");
+Clazz.defineMethod(c$, "setNoAutoBond",
+function(){
+this.setInfo("noAutoBond", Boolean.TRUE);
+});
+Clazz.defineMethod(c$, "freeze",
+function(reverseModels){
+if (this.atomSetCount == 1 && this.collectionName == null) this.collectionName = this.getAtomSetAuxiliaryInfoValue(0, "name");
+if (reverseModels) this.reverseAtomSets();
+if (this.trajectoryStepCount > 1) this.finalizeTrajectory();
+this.getList(true);
+this.getList(false);
+for (var i = 0; i < this.atomSetCount; i++) {
+this.setModelInfoForSet("initialAtomCount", Integer.$valueOf(this.atomSetAtomCounts[i]), i);
+this.setModelInfoForSet("initialBondCount", Integer.$valueOf(this.atomSetBondCounts[i]), i);
+}
+}, "~B");
+Clazz.defineMethod(c$, "reverseAtomSets",
+function(){
+this.reverseArray(this.atomSetAtomIndexes);
+this.reverseArray(this.atomSetNumbers);
+this.reverseArray(this.atomSetAtomCounts);
+this.reverseArray(this.atomSetBondCounts);
+J.adapter.smarter.AtomSetCollection.reverseList(this.trajectorySteps);
+J.adapter.smarter.AtomSetCollection.reverseList(this.trajectoryNames);
+J.adapter.smarter.AtomSetCollection.reverseList(this.vibrationSteps);
+this.reverseObject(this.atomSetAuxiliaryInfo);
+for (var i = 0; i < this.ac; i++) this.atoms[i].atomSetIndex = this.atomSetCount - 1 - this.atoms[i].atomSetIndex;
+
+for (var i = 0; i < this.structureCount; i++) {
+var m = this.structures[i].modelStartEnd[0];
+if (m >= 0) {
+this.structures[i].modelStartEnd[0] = this.atomSetCount - 1 - this.structures[i].modelStartEnd[1];
+this.structures[i].modelStartEnd[1] = this.atomSetCount - 1 - m;
+}}
+for (var i = 0; i < this.bondCount; i++) this.bonds[i].atomSetIndex = this.atomSetCount - 1 - this.atoms[this.bonds[i].atomIndex1].atomSetIndex;
+
+this.reverseSets(this.bonds, this.bondCount);
+var lists = JU.AU.createArrayOfArrayList(this.atomSetCount);
+for (var i = 0; i < this.atomSetCount; i++) lists[i] = new JU.Lst();
+
+for (var i = 0; i < this.ac; i++) lists[this.atoms[i].atomSetIndex].addLast(this.atoms[i]);
+
+var newIndex = Clazz.newIntArray (this.ac, 0);
+var n = this.ac;
+for (var i = this.atomSetCount; --i >= 0; ) for (var j = lists[i].size(); --j >= 0; ) {
+var a = this.atoms[--n] = lists[i].get(j);
+newIndex[a.index] = n;
+a.index = n;
+}
+
+for (var i = 0; i < this.bondCount; i++) {
+this.bonds[i].atomIndex1 = newIndex[this.bonds[i].atomIndex1];
+this.bonds[i].atomIndex2 = newIndex[this.bonds[i].atomIndex2];
+}
+for (var i = 0; i < this.atomSetCount; i++) {
+var conect = this.getAtomSetAuxiliaryInfoValue(i, "PDB_CONECT_firstAtom_count_max");
+if (conect == null) continue;
+conect[0] = newIndex[conect[0]];
+conect[1] = this.atomSetAtomCounts[i];
+}
+});
+Clazz.defineMethod(c$, "reverseSets",
+function(o, n){
+var lists = JU.AU.createArrayOfArrayList(this.atomSetCount);
+for (var i = 0; i < this.atomSetCount; i++) lists[i] = new JU.Lst();
+
+for (var i = 0; i < n; i++) {
+var index = o[i].atomSetIndex;
+if (index < 0) return;
+lists[o[i].atomSetIndex].addLast(o[i]);
+}
+for (var i = this.atomSetCount; --i >= 0; ) for (var j = lists[i].size(); --j >= 0; ) o[--n] = lists[i].get(j);
+
+
+}, "~A,~N");
+Clazz.defineMethod(c$, "reverseObject",
+function(o){
+var n = this.atomSetCount;
+for (var i = Clazz.doubleToInt(n / 2); --i >= 0; ) JU.AU.swap(o, i, n - 1 - i);
+
+}, "~A");
+c$.reverseList = Clazz.defineMethod(c$, "reverseList",
+function(list){
+if (list == null) return;
+java.util.Collections.reverse(list);
+}, "JU.Lst");
+Clazz.defineMethod(c$, "reverseArray",
+function(a){
+var n = this.atomSetCount;
+for (var i = Clazz.doubleToInt(n / 2); --i >= 0; ) JU.AU.swapInt(a, i, n - 1 - i);
+
+}, "~A");
+Clazz.defineMethod(c$, "getList",
+function(isAltLoc){
+var i;
+for (i = this.ac; --i >= 0; ) if (this.atoms[i] != null && (isAltLoc ? this.atoms[i].altLoc : this.atoms[i].insertionCode) != '\0') break;
+
+if (i < 0) return;
+var lists = new Array(this.atomSetCount);
+for (i = 0; i < this.atomSetCount; i++) lists[i] = "";
+
+var pt;
+for (i = 0; i < this.ac; i++) {
+if (this.atoms[i] == null) continue;
+var id = (isAltLoc ? this.atoms[i].altLoc : this.atoms[i].insertionCode);
+if (id != '\0' && lists[pt = this.atoms[i].atomSetIndex].indexOf(id) < 0) lists[pt] += id;
+}
+var type = (isAltLoc ? "altLocs" : "insertionCodes");
+for (i = 0; i < this.atomSetCount; i++) if (lists[i].length > 0) this.setModelInfoForSet(type, lists[i], i);
+
+}, "~B");
+Clazz.defineMethod(c$, "finish",
+function(){
+if (this.reader != null) this.reader.finalizeModelSet();
+ else if (this.readerList != null) for (var i = 0; i < this.readerList.size(); i++) this.readerList.get(i).finalizeModelSet();
+
+this.atoms = null;
+this.atomSetAtomCounts = Clazz.newIntArray (16, 0);
+this.atomSetAuxiliaryInfo = new Array(16);
+this.atomSetInfo = new java.util.Hashtable();
+this.atomSetCount = 0;
+this.atomSetNumbers = Clazz.newIntArray (16, 0);
+this.atomSymbolicMap = new java.util.Hashtable();
+this.bonds = null;
+this.iSet = -1;
+this.readerList = null;
+this.xtalSymmetry = null;
+this.structures = new Array(16);
+this.structureCount = 0;
+this.trajectorySteps = null;
+this.vibrationSteps = null;
+});
+Clazz.defineMethod(c$, "discardPreviousAtoms",
+function(){
+for (var i = this.ac; --i >= 0; ) this.atoms[i] = null;
+
+this.ac = 0;
+this.clearMap();
+this.atomSetCount = 0;
+this.iSet = -1;
+for (var i = this.atomSetAuxiliaryInfo.length; --i >= 0; ) {
+this.atomSetAtomCounts[i] = 0;
+this.atomSetBondCounts[i] = 0;
+this.atomSetAuxiliaryInfo[i] = null;
+}
+});
+Clazz.defineMethod(c$, "removeCurrentAtomSet",
+function(){
+if (this.iSet < 0) return;
+var ai = this.atomSetAtomIndexes[this.iSet];
+if (this.bsAtoms != null) this.bsAtoms.clearBits(ai, this.ac);
+this.ac = ai;
+this.atomSetAtomCounts[this.iSet] = 0;
+this.iSet--;
+this.atomSetCount--;
+this.reader.doCheckUnitCell = false;
+});
+Clazz.defineMethod(c$, "getHydrogenAtomCount",
+function(){
+var n = 0;
+for (var i = 0; i < this.ac; i++) if (this.atoms[i].elementNumber == 1 || this.atoms[i].elementSymbol.equals("H")) n++;
+
+return n;
+});
+Clazz.defineMethod(c$, "newCloneAtom",
+function(atom){
+var clone = atom.getClone();
+this.addAtom(clone);
+return clone;
+}, "J.adapter.smarter.Atom");
+Clazz.defineMethod(c$, "cloneFirstAtomSet",
+function(atomCount){
+if (!this.allowMultiple) return 0;
+this.newAtomSet();
+if (atomCount == 0) atomCount = this.atomSetAtomCounts[0];
+for (var i = 0; i < atomCount; ++i) this.newCloneAtom(this.atoms[i]);
+
+return this.ac;
+}, "~N");
+Clazz.defineMethod(c$, "cloneAtomSetWithBonds",
+function(isLast){
+var nBonds = this.atomSetBondCounts[isLast ? this.iSet : 0];
+var atomIncrement = (isLast ? this.cloneLastAtomSet() : this.cloneFirstAtomSet(0));
+if (atomIncrement > 0) for (var i = 0; i < nBonds; i++) {
+var bond = this.bonds[this.bondCount - nBonds];
+this.addNewBondWithOrder(bond.atomIndex1 + atomIncrement, bond.atomIndex2 + atomIncrement, bond.order);
+}
+}, "~B");
+Clazz.defineMethod(c$, "cloneLastAtomSet",
+function(){
+return this.cloneLastAtomSetFromPoints(0, null);
+});
+Clazz.defineMethod(c$, "cloneLastAtomSetFromPoints",
+function(ac, pts){
+if (!this.allowMultiple) return 0;
+var count = (ac > 0 ? ac : this.getLastAtomSetAtomCount());
+var atomIndex = this.getLastAtomSetAtomIndex();
+this.newAtomSet();
+for (var i = 0; i < count; ++i) {
+var atom = this.newCloneAtom(this.atoms[atomIndex++]);
+if (pts != null) atom.setT(pts[i]);
+}
+return count;
+}, "~N,~A");
+Clazz.defineMethod(c$, "getLastAtomSetAtomCount",
+function(){
+return this.atomSetAtomCounts[this.iSet];
+});
+Clazz.defineMethod(c$, "getLastAtomSetAtomIndex",
+function(){
+return this.ac - this.atomSetAtomCounts[this.iSet];
+});
+Clazz.defineMethod(c$, "addNewAtom",
+function(){
+return this.addAtom( new J.adapter.smarter.Atom());
+});
+Clazz.defineMethod(c$, "addAtom",
+function(atom){
+if (this.ac == this.atoms.length) {
+if (this.ac > 200000) this.atoms = JU.AU.ensureLength(this.atoms, this.ac + 50000);
+ else this.atoms = JU.AU.doubleLength(this.atoms);
+}if (this.atomSetCount == 0) this.newAtomSet();
+atom.index = this.ac;
+this.atoms[this.ac++] = atom;
+atom.atomSetIndex = this.iSet;
+atom.atomSite = (this.fixedSite > 0 ? this.fixedSite - 1 : this.atomSetAtomCounts[this.iSet]++);
+return atom;
+}, "J.adapter.smarter.Atom");
+Clazz.defineMethod(c$, "addAtomWithMappedName",
+function(atom){
+var atomName = this.addAtom(atom).atomName;
+if (atomName != null) this.atomSymbolicMap.put(atomName, atom);
+}, "J.adapter.smarter.Atom");
+Clazz.defineMethod(c$, "addAtomWithMappedSerialNumber",
+function(atom){
+var atomSerial = this.addAtom(atom).atomSerial;
+if (atomSerial != -2147483648) this.atomSymbolicMap.put("" + atomSerial, atom);
+}, "J.adapter.smarter.Atom");
+Clazz.defineMethod(c$, "getAtomFromName",
+function(atomName){
+return this.atomSymbolicMap.get(atomName);
+}, "~S");
+Clazz.defineMethod(c$, "setAtomMapAnyCase",
+function(){
+this.atomMapAnyCase = true;
+var newMap = new java.util.Hashtable();
+newMap.putAll(this.atomSymbolicMap);
+for (var e, $e = this.atomSymbolicMap.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var name = e.getKey();
+var uc = name.toUpperCase();
+if (!uc.equals(name)) newMap.put(uc, e.getValue());
+}
+this.atomSymbolicMap = newMap;
+});
+Clazz.defineMethod(c$, "getAtomIndex",
+function(name){
+var a = this.atomSymbolicMap.get(name);
+if (a == null && this.atomMapAnyCase) a = this.atomSymbolicMap.get(name.toUpperCase());
+return (a == null ? -1 : a.index);
+}, "~S");
+Clazz.defineMethod(c$, "addNewBondWithOrder",
+function(atomIndex1, atomIndex2, order){
+var b = null;
+if (atomIndex1 >= 0 && atomIndex1 < this.ac && atomIndex2 >= 0 && atomIndex2 < this.ac && atomIndex1 != atomIndex2) {
+b = new J.adapter.smarter.Bond(atomIndex1, atomIndex2, order);
+this.addBond(b);
+}return b;
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "addNewBondFromNames",
+function(atomName1, atomName2, order){
+return this.addNewBondWithOrderA(this.getAtomFromName(atomName1), this.getAtomFromName(atomName2), order);
+}, "~S,~S,~N");
+Clazz.defineMethod(c$, "addNewBondWithOrderA",
+function(atom1, atom2, order){
+return (atom1 != null && atom2 != null ? this.addNewBondWithOrder(atom1.index, atom2.index, order) : null);
+}, "J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");
+Clazz.defineMethod(c$, "addBond",
+function(bond){
+if (this.trajectoryStepCount > 0) return;
+if (bond.atomIndex1 < 0 || bond.atomIndex2 < 0 || bond.order < 0 || bond.atomIndex1 == bond.atomIndex2 || this.atoms[bond.atomIndex1].atomSetIndex != this.atoms[bond.atomIndex2].atomSetIndex) {
+if (JU.Logger.debugging) {
+JU.Logger.debug(">>>>>>BAD BOND:" + bond.atomIndex1 + "-" + bond.atomIndex2 + " order=" + bond.order);
+}return;
+}this.addBondNoCheck(bond);
+}, "J.adapter.smarter.Bond");
+Clazz.defineMethod(c$, "addBondNoCheck",
+function(bond){
+if (this.bondCount == this.bonds.length) this.bonds = JU.AU.arrayCopyObject(this.bonds, this.bondCount + 1024);
+this.bonds[this.bondCount++] = bond;
+this.atomSetBondCounts[this.iSet]++;
+}, "J.adapter.smarter.Bond");
+Clazz.defineMethod(c$, "finalizeStructures",
+function(){
+if (this.structureCount == 0) return;
+this.bsStructuredModels = new JU.BS();
+var map = new java.util.Hashtable();
+for (var i = 0; i < this.structureCount; i++) {
+var s = this.structures[i];
+if (s.modelStartEnd[0] == -1) {
+s.modelStartEnd[0] = 0;
+s.modelStartEnd[1] = this.atomSetCount - 1;
+}this.bsStructuredModels.setBits(s.modelStartEnd[0], s.modelStartEnd[1] + 1);
+if (s.strandCount == 0) continue;
+var key = s.structureID + " " + s.modelStartEnd[0];
+var v = map.get(key);
+var count = (v == null ? 0 : v.intValue()) + 1;
+map.put(key, Integer.$valueOf(count));
+}
+for (var i = 0; i < this.structureCount; i++) {
+var s = this.structures[i];
+if (s.strandCount == 1) s.strandCount = map.get(s.structureID + " " + s.modelStartEnd[0]).intValue();
+}
+});
+Clazz.defineMethod(c$, "addStructure",
+function(structure){
+if (this.structureCount == this.structures.length) this.structures = JU.AU.arrayCopyObject(this.structures, this.structureCount + 32);
+this.structures[this.structureCount++] = structure;
+}, "J.adapter.smarter.Structure");
+Clazz.defineMethod(c$, "addVibrationVectorWithSymmetry",
+function(iatom, vx, vy, vz, withSymmetry){
+if (!withSymmetry) {
+this.addVibrationVector(iatom, vx, vy, vz);
+return;
+}var atomSite = this.atoms[iatom].atomSite;
+var atomSetIndex = this.atoms[iatom].atomSetIndex;
+for (var i = iatom; i < this.ac && this.atoms[i].atomSetIndex == atomSetIndex; i++) {
+if (this.atoms[i].atomSite == atomSite) this.addVibrationVector(i, vx, vy, vz);
+}
+}, "~N,~N,~N,~N,~B");
+Clazz.defineMethod(c$, "addVibrationVector",
+function(iatom, x, y, z){
+if (!this.allowMultiple) iatom = iatom % this.ac;
+return (this.atoms[iatom].vib = JU.V3.new3(x, y, z));
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "setCoordinatesAreFractional",
+function(tf){
+this.coordinatesAreFractional = tf;
+this.setCurrentModelInfo("coordinatesAreFractional", Boolean.$valueOf(tf));
+if (tf) this.setGlobalBoolean(0);
+}, "~B");
+Clazz.defineMethod(c$, "setAnisoBorU",
+function(atom, data, type){
+this.haveAnisou = true;
+atom.anisoBorU = data;
+data[6] = type;
+}, "J.adapter.smarter.Atom,~A,~N");
+Clazz.defineMethod(c$, "setU",
+function(atom, i, val){
+var data = atom.anisoBorU;
+if (data == null) this.setAnisoBorU(atom, data = Clazz.newFloatArray (8, 0), 8);
+data[i] = val;
+}, "J.adapter.smarter.Atom,~N,~N");
+Clazz.defineMethod(c$, "getXSymmetry",
+function(){
+if (this.xtalSymmetry == null) this.xtalSymmetry = (J.api.Interface.getOption("adapter.smarter.XtalSymmetry", this.reader.vwr, "file")).set(this.reader);
+return this.xtalSymmetry;
+});
+Clazz.defineMethod(c$, "getSymmetry",
+function(){
+return this.getXSymmetry().getSymmetry();
+});
+Clazz.defineMethod(c$, "setSymmetry",
+function(symmetry){
+return (symmetry == null ? null : this.getXSymmetry().setSymmetry(symmetry));
+}, "J.adapter.smarter.XtalSymmetry.FileSymmetry");
+Clazz.defineMethod(c$, "newFileSymmetry",
+function(){
+return this.getXSymmetry().newFileSymmetry();
+});
+Clazz.defineMethod(c$, "setTensors",
+function(){
+if (this.haveAnisou) this.getXSymmetry().setTensors();
+});
+Clazz.defineMethod(c$, "setInfo",
+function(key, value){
+if (value == null) this.atomSetInfo.remove(key);
+ else this.atomSetInfo.put(key, value);
+}, "~S,~O");
+Clazz.defineMethod(c$, "setAtomSetCollectionPartialCharges",
+function(auxKey){
+if (!this.atomSetInfo.containsKey(auxKey)) return false;
+var atomData = this.atomSetInfo.get(auxKey);
+var n = atomData.size();
+for (var i = this.ac; --i >= 0; ) this.atoms[i].partialCharge = atomData.get(i % n).floatValue();
+
+JU.Logger.info("Setting partial charges type " + auxKey);
+return true;
+}, "~S");
+Clazz.defineMethod(c$, "mapPartialCharge",
+function(atomName, charge){
+this.getAtomFromName(atomName).partialCharge = charge;
+}, "~S,~N");
+c$.fixPeriodic = Clazz.defineMethod(c$, "fixPeriodic",
+function(pt, pt0){
+pt.x = J.adapter.smarter.AtomSetCollection.fixPoint(pt.x, pt0.x);
+pt.y = J.adapter.smarter.AtomSetCollection.fixPoint(pt.y, pt0.y);
+pt.z = J.adapter.smarter.AtomSetCollection.fixPoint(pt.z, pt0.z);
+return pt;
+}, "JU.P3,JU.P3");
+c$.fixPoint = Clazz.defineMethod(c$, "fixPoint",
+function(x, x0){
+while (x - x0 > 0.9) {
+x -= 1;
+}
+while (x - x0 < -0.9) {
+x += 1;
+}
+return x;
+}, "~N,~N");
+Clazz.defineMethod(c$, "finalizeTrajectoryAs",
+function(trajectorySteps, vibrationSteps){
+this.trajectorySteps = trajectorySteps;
+this.vibrationSteps = vibrationSteps;
+this.trajectoryStepCount = trajectorySteps.size();
+this.finalizeTrajectory();
+}, "JU.Lst,JU.Lst");
+Clazz.defineMethod(c$, "finalizeTrajectory",
+function(){
+if (this.trajectoryStepCount == 0) return;
+var trajectory = this.trajectorySteps.get(0);
+var vibrations = (this.vibrationSteps == null ? null : this.vibrationSteps.get(0));
+var n = (this.bsAtoms == null ? this.ac : this.bsAtoms.cardinality());
+if (this.vibrationSteps != null && vibrations != null && vibrations.length < n || trajectory.length < n) {
+this.errorMessage = "File cannot be loaded as a trajectory";
+return;
+}var v = new JU.V3();
+for (var i = 0, ii = 0; i < this.ac; i++) {
+if (this.bsAtoms != null && !this.bsAtoms.get(i)) continue;
+if (this.vibrationSteps != null) this.atoms[i].vib = (vibrations == null ? v : vibrations[ii]);
+if (trajectory[ii] != null) this.atoms[i].setT(trajectory[ii]);
+ii++;
+}
+this.setInfo("trajectorySteps", this.trajectorySteps);
+if (this.vibrationSteps != null) this.setInfo("vibrationSteps", this.vibrationSteps);
+if (this.ac == 0) this.ac = trajectory.length;
+});
+Clazz.defineMethod(c$, "newAtomSet",
+function(){
+this.newAtomSetClear(true);
+});
+Clazz.defineMethod(c$, "newAtomSetClear",
+function(doClearMap){
+if (!this.allowMultiple && this.iSet >= 0) this.reader.discardPreviousAtoms();
+this.bondIndex0 = this.bondCount;
+if (this.isTrajectory) this.reader.discardPreviousAtoms();
+this.iSet = this.atomSetCount++;
+if (this.atomSetCount > this.atomSetNumbers.length) {
+this.atomSetAtomIndexes = JU.AU.doubleLengthI(this.atomSetAtomIndexes);
+this.atomSetAtomCounts = JU.AU.doubleLengthI(this.atomSetAtomCounts);
+this.atomSetBondCounts = JU.AU.doubleLengthI(this.atomSetBondCounts);
+this.atomSetAuxiliaryInfo = JU.AU.doubleLength(this.atomSetAuxiliaryInfo);
+}this.atomSetAtomIndexes[this.iSet] = this.ac;
+if (this.atomSetCount + this.trajectoryStepCount > this.atomSetNumbers.length) {
+this.atomSetNumbers = JU.AU.doubleLengthI(this.atomSetNumbers);
+}if (this.isTrajectory) {
+this.atomSetNumbers[this.iSet + this.trajectoryStepCount] = this.atomSetCount + this.trajectoryStepCount;
+} else {
+this.atomSetNumbers[this.iSet] = this.atomSetCount;
+}if (doClearMap) {
+this.clearMap();
+}this.setCurrentModelInfo("title", this.collectionName);
+}, "~B");
+Clazz.defineMethod(c$, "clearMap",
+function(){
+this.atomSymbolicMap.clear();
+this.atomMapAnyCase = false;
+});
+Clazz.defineMethod(c$, "getAtomSetAtomIndex",
+function(i){
+return this.atomSetAtomIndexes[i];
+}, "~N");
+Clazz.defineMethod(c$, "getAtomSetAtomCount",
+function(i){
+return this.atomSetAtomCounts[i];
+}, "~N");
+Clazz.defineMethod(c$, "getAtomSetBondCount",
+function(i){
+return this.atomSetBondCounts[i];
+}, "~N");
+Clazz.defineMethod(c$, "setAtomSetName",
+function(atomSetName){
+if (atomSetName == null) return;
+if (this.isTrajectory) {
+this.setTrajectoryName(atomSetName);
+return;
+}var name0 = (this.iSet < 0 ? null : this.getAtomSetName(this.iSet));
+this.setModelInfoForSet("name", atomSetName, this.iSet);
+if (this.reader != null && atomSetName.length > 0 && !atomSetName.equals(name0)) this.reader.appendLoadNote(atomSetName);
+if (!this.allowMultiple) this.setCollectionName(atomSetName);
+}, "~S");
+Clazz.defineMethod(c$, "setTrajectoryName",
+function(name){
+if (this.trajectoryStepCount == 0) return;
+if (this.trajectoryNames == null) {
+this.trajectoryNames = new JU.Lst();
+}for (var i = this.trajectoryNames.size(); i < this.trajectoryStepCount; i++) this.trajectoryNames.addLast(null);
+
+this.trajectoryNames.set(this.trajectoryStepCount - 1, name);
+}, "~S");
+Clazz.defineMethod(c$, "setCurrentAtomSetNumber",
+function(atomSetNumber){
+this.setAtomSetNumber(this.iSet + (this.isTrajectory ? this.trajectoryStepCount : 0), atomSetNumber);
+}, "~N");
+Clazz.defineMethod(c$, "setAtomSetNumber",
+function(index, atomSetNumber){
+this.atomSetNumbers[index] = atomSetNumber;
+}, "~N,~N");
+Clazz.defineMethod(c$, "setAtomSetModelProperty",
+function(key, value){
+this.setAtomSetModelPropertyForSet(key, value, this.iSet);
+}, "~S,~S");
+Clazz.defineMethod(c$, "setAtomSetModelPropertyForSet",
+function(key, value, atomSetIndex){
+var p = this.getAtomSetAuxiliaryInfoValue(atomSetIndex, "modelProperties");
+if (p == null) this.setModelInfoForSet("modelProperties", p = new java.util.Properties(), atomSetIndex);
+p.put(key, value);
+if (key.startsWith(".")) p.put(key.substring(1), value);
+}, "~S,~S,~N");
+Clazz.defineMethod(c$, "setAtomProperties",
+function(key, data, atomSetIndex, isGroup){
+if ((typeof(data)=='string') && !(data).endsWith("\n")) data = data + "\n";
+if (atomSetIndex < 0) atomSetIndex = this.iSet;
+var p = this.getAtomSetAuxiliaryInfoValue(atomSetIndex, "atomProperties");
+if (p == null) this.setModelInfoForSet("atomProperties", p = new java.util.Hashtable(), atomSetIndex);
+p.put(key, data);
+}, "~S,~O,~N,~B");
+Clazz.defineMethod(c$, "setAtomSetPartialCharges",
+function(auxKey){
+if (!this.atomSetAuxiliaryInfo[this.iSet].containsKey(auxKey)) {
+return false;
+}var atomData = this.getAtomSetAuxiliaryInfoValue(this.iSet, auxKey);
+for (var i = atomData.size(); --i >= 0; ) {
+this.atoms[i].partialCharge = atomData.get(i).floatValue();
+}
+return true;
+}, "~S");
+Clazz.defineMethod(c$, "getAtomSetAuxiliaryInfoValue",
+function(index, key){
+return this.atomSetAuxiliaryInfo[index >= 0 ? index : this.iSet].get(key);
+}, "~N,~S");
+Clazz.defineMethod(c$, "setCurrentModelInfo",
+function(key, value){
+this.setModelInfoForSet(key, value, this.iSet);
+}, "~S,~O");
+Clazz.defineMethod(c$, "setModelInfoForSet",
+function(key, value, atomSetIndex){
+if (atomSetIndex < 0) return;
+if (this.atomSetAuxiliaryInfo[atomSetIndex] == null) this.atomSetAuxiliaryInfo[atomSetIndex] = new java.util.Hashtable();
+if (value == null) this.atomSetAuxiliaryInfo[atomSetIndex].remove(key);
+ else this.atomSetAuxiliaryInfo[atomSetIndex].put(key, value);
+}, "~S,~O,~N");
+Clazz.defineMethod(c$, "getAtomSetNumber",
+function(atomSetIndex){
+return this.atomSetNumbers[atomSetIndex >= this.atomSetCount ? 0 : atomSetIndex];
+}, "~N");
+Clazz.defineMethod(c$, "getAtomSetName",
+function(atomSetIndex){
+if (this.trajectoryNames != null && atomSetIndex < this.trajectoryNames.size()) return this.trajectoryNames.get(atomSetIndex);
+if (atomSetIndex >= this.atomSetCount) atomSetIndex = this.atomSetCount - 1;
+return this.getAtomSetAuxiliaryInfoValue(atomSetIndex, "name");
+}, "~N");
+Clazz.defineMethod(c$, "getAtomSetAuxiliaryInfo",
+function(atomSetIndex){
+var i = (atomSetIndex >= this.atomSetCount ? this.atomSetCount - 1 : atomSetIndex);
+return (i < 0 ? null : this.atomSetAuxiliaryInfo[i]);
+}, "~N");
+Clazz.defineMethod(c$, "setAtomSetEnergy",
+function(energyString, value){
+if (this.iSet < 0) return;
+JU.Logger.info("Energy for model " + (this.iSet + 1) + " = " + energyString);
+this.setCurrentModelInfo("EnergyString", energyString);
+this.setCurrentModelInfo("Energy", Float.$valueOf(value));
+this.setAtomSetModelProperty("Energy", "" + value);
+}, "~S,~N");
+Clazz.defineMethod(c$, "setAtomSetFrequency",
+function(mode, pathKey, label, freq, units){
+this.setAtomSetModelProperty("FreqValue", freq);
+freq += " " + (units == null ? "cm^-1" : units);
+var name = (label == null ? "" : label + " ") + freq;
+this.setAtomSetName(name);
+this.setAtomSetModelProperty("Frequency", freq);
+this.setAtomSetModelProperty("Mode", "" + mode);
+this.setModelInfoForSet("vibrationalMode", Integer.$valueOf(mode), this.iSet);
+if (label != null) this.setAtomSetModelProperty("FrequencyLabel", label);
+this.setAtomSetModelProperty(".PATH", (pathKey == null ? "" : pathKey + J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Frequencies") + "Frequencies");
+return name;
+}, "~N,~S,~S,~S,~S");
+Clazz.defineMethod(c$, "getBondList",
+function(){
+var info = new Array(this.bondCount);
+for (var i = 0; i < this.bondCount; i++) {
+info[i] = Clazz.newArray(-1, [this.atoms[this.bonds[i].atomIndex1].atomName, this.atoms[this.bonds[i].atomIndex2].atomName, "" + this.bonds[i].order]);
+}
+return info;
+});
+Clazz.defineMethod(c$, "centralize",
+function(){
+var pt = new JU.P3();
+for (var i = 0; i < this.atomSetCount; i++) {
+var n = this.atomSetAtomCounts[i];
+var atom0 = this.atomSetAtomIndexes[i];
+pt.set(0, 0, 0);
+for (var j = atom0 + n; --j >= atom0; ) pt.add(this.atoms[j]);
+
+pt.scale(1 / n);
+for (var j = atom0 + n; --j >= atom0; ) this.atoms[j].sub(pt);
+
+}
+});
+Clazz.defineMethod(c$, "mergeTrajectories",
+function(a){
+if (!this.isTrajectory || !a.isTrajectory || this.vibrationSteps != null) return;
+for (var i = 0; i < a.trajectoryStepCount; i++) this.trajectorySteps.add(this.trajectoryStepCount++, a.trajectorySteps.get(i));
+
+this.setInfo("trajectorySteps", this.trajectorySteps);
+this.setInfo("ignoreUnitCell", a.atomSetInfo.get("ignoreUnitCell"));
+}, "J.adapter.smarter.AtomSetCollection");
+Clazz.defineMethod(c$, "removeAtomSet",
+function(imodel){
+if (this.bsAtoms == null) this.bsAtoms = JU.BSUtil.newBitSet2(0, this.ac);
+var i0 = this.atomSetAtomIndexes[imodel];
+var nAtoms = this.atomSetAtomCounts[imodel];
+var i1 = i0 + nAtoms;
+this.bsAtoms.clearBits(i0, i1);
+for (var i = i1; i < this.ac; i++) this.atoms[i].atomSetIndex--;
+
+for (var i = imodel + 1; i < this.atomSetCount; i++) {
+this.atomSetAuxiliaryInfo[i - 1] = this.atomSetAuxiliaryInfo[i];
+this.atomSetAtomIndexes[i - 1] = this.atomSetAtomIndexes[i];
+this.atomSetBondCounts[i - 1] = this.atomSetBondCounts[i];
+this.atomSetAtomCounts[i - 1] = this.atomSetAtomCounts[i];
+this.atomSetNumbers[i - 1] = this.atomSetNumbers[i];
+}
+for (var i = 0; i < this.bondCount; i++) this.bonds[i].atomSetIndex = this.atoms[this.bonds[i].atomIndex1].atomSetIndex;
+
+this.atomSetAuxiliaryInfo[--this.atomSetCount] = null;
+var n = 0;
+for (var i = 0; i < this.structureCount; i++) {
+var s = this.structures[i];
+if (s.modelStartEnd[0] == imodel && s.modelStartEnd[1] == imodel) {
+this.structures[i] = null;
+n++;
+}}
+if (n > 0) {
+var ss = new Array(this.structureCount - n);
+for (var i = 0, pt = 0; i < this.structureCount; i++) if (this.structures[i] != null) ss[pt++] = this.structures[i];
+
+this.structures = ss;
+}}, "~N");
+Clazz.defineMethod(c$, "removeLastUnselectedAtoms",
+function(){
+var n = this.ac;
+var nremoved = 0;
+var i0 = this.getLastAtomSetAtomIndex();
+var nnow = 0;
+for (var i = i0; i < n; i++) {
+if (!this.bsAtoms.get(i)) {
+nremoved++;
+this.ac--;
+this.atoms[i] = null;
+continue;
+}if (nremoved > 0) {
+this.atoms[this.atoms[i].index = i - nremoved] = this.atoms[i];
+this.atoms[i] = null;
+}nnow++;
+}
+this.atomSetAtomCounts[this.iSet] = nnow;
+if (nnow == 0) {
+this.iSet--;
+this.atomSetCount--;
+} else {
+this.bsAtoms.setBits(i0, i0 + nnow);
+}});
+Clazz.defineMethod(c$, "checkNoEmptyModel",
+function(){
+while (this.atomSetCount > 0 && this.atomSetAtomCounts[this.atomSetCount - 1] == 0) this.atomSetCount--;
+
+});
+Clazz.defineMethod(c$, "getBSAtoms",
+function(n){
+if (this.bsAtoms == null) {
+this.bsAtoms = new JU.BS();
+if (n != 0) this.bsAtoms.setBits(0, (n < 0 ? this.ac : n));
+}return this.bsAtoms;
+}, "~N");
+Clazz.defineMethod(c$, "setBSAtomsForSet",
+function(iSet){
+if (this.bsAtoms != null) {
+if (iSet < 0) iSet = this.iSet;
+var pt = this.atomSetAtomIndexes[iSet];
+if (this.bsAtoms.nextSetBit(pt) < 0) {
+var n = this.atomSetAtomCounts[iSet];
+this.bsAtoms.setBits(pt, pt + n);
+}}}, "~N");
+Clazz.defineMethod(c$, "fix2Stereo",
+function(){
+this.getBSAtoms(-1);
+for (var i = this.bondCount; --i >= 0; ) {
+var b = this.bonds[i];
+if (this.atoms[b.atomIndex2].elementSymbol.equals("H") && b.order != 1025 && b.order != 1041 && this.atoms[b.atomIndex1].elementSymbol.equals("C")) {
+this.bsAtoms.clear(b.atomIndex2);
+} else if (this.atoms[b.atomIndex1].elementSymbol.equals("H") && this.atoms[b.atomIndex2].elementSymbol.equals("C")) {
+this.bsAtoms.clear(b.atomIndex1);
+}}
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollectionReader.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollectionReader.js
new file mode 100755
index 000000000000..19771a96f821
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetCollectionReader.js
@@ -0,0 +1,1325 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["javajs.api.GenericLineReader", "JU.SB", "JV.Viewer"], "J.adapter.smarter.AtomSetCollectionReader", ["JU.BS", "$.Lst", "$.M3", "$.P3", "$.PT", "$.Quat", "$.V3", "J.adapter.smarter.Atom", "$.AtomSetCollection", "J.api.Interface", "$.JmolAdapter", "JU.BSUtil", "$.Logger", "$.SimpleUnitCell", "JV.FileManager", "$.JC"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isBinary = false;
+this.debugging = false;
+this.requiresBSFilter = false;
+this.primitiveToCrystal = null;
+this.asc = null;
+this.reader = null;
+this.binaryDoc = null;
+this.readerName = null;
+this.htParams = null;
+this.trajectorySteps = null;
+this.domains = null;
+this.validation = null;
+this.dssr = null;
+this.isConcatenated = false;
+this.addedData = null;
+this.addedDataKey = null;
+this.thisBiomolecule = null;
+this.lstNCS = null;
+this.floatifyJavaDouble = true;
+this.line = null;
+this.prevline = null;
+this.next = null;
+this.ptLine = 0;
+this.checkNearAtoms = true;
+this.latticeType = null;
+this.latticeCells = null;
+this.fillRange = null;
+this.doProcessLines = false;
+this.iHaveUnitCell = false;
+this.iHaveSymmetryOperators = false;
+this.continuing = true;
+this.vwr = null;
+this.doApplySymmetry = false;
+this.ignoreFileSymmetryOperators = false;
+this.isTrajectory = false;
+this.applySymmetryToBonds = false;
+this.doCheckUnitCell = false;
+this.getHeader = false;
+this.isSequential = false;
+this.optimize2D = false;
+this.noHydrogens = false;
+this.noMinimize = false;
+this.is2D = false;
+this.isMolecular = false;
+this.templateAtomCount = 0;
+this.modelNumber = 0;
+this.vibrationNumber = 0;
+this.desiredVibrationNumber = -2147483648;
+this.bsModels = null;
+this.useFileModelNumbers = false;
+this.havePartialChargeFilter = false;
+this.calculationType = "?";
+this.sgName = null;
+this.ignoreFileUnitCell = false;
+this.ignoreFileSpaceGroupName = false;
+this.unitCellParams = null;
+this.desiredModelNumber = -2147483648;
+this.symmetry = null;
+this.out = null;
+this.iHaveFractionalCoordinates = false;
+this.doPackUnitCell = false;
+this.ptSupercell = null;
+this.mustFinalizeModelSet = false;
+this.forcePacked = false;
+this.packingRange = null;
+this.cellSlop = 1.0E-4;
+this.rotateHexCell = false;
+this.isPrimitive = false;
+this.modDim = 0;
+this.lowPrecision = false;
+this.highprecision0 = false;
+this.loadNote = null;
+this.doConvertToFractional = false;
+this.fileCoordinatesAreFractional = false;
+this.merging = false;
+this.symmetryRange = 0;
+this.firstLastStep = null;
+this.lastModelNumber = 2147483647;
+this.desiredSpaceGroupIndex = -1;
+this.latticeScaling = NaN;
+this.unitCellOffset = null;
+this.unitCellOffsetFractional = false;
+this.moreUnitCellInfo = null;
+this.paramsLattice = null;
+this.paramsCentroid = false;
+this.paramsPacked = false;
+this.fileScaling = null;
+this.fileOffset = null;
+this.fileOffsetFractional = null;
+this.filePath = null;
+this.fileName = null;
+this.baseAtomIndex = 0;
+this.baseBondIndex = 0;
+this.stateScriptVersionInt = 2147483647;
+this.isFinalized = false;
+this.noPack = false;
+this.isSUPERCELL = false;
+this.precision = 0;
+this.haveModel = false;
+this.previousSpaceGroup = null;
+this.previousUnitCell = null;
+this.nMatrixElements = 0;
+this.ucItems = null;
+this.matUnitCellOrientation = null;
+this.bsFilter = null;
+this.filter = null;
+this.filterCased = null;
+this.haveAtomFilter = false;
+this.filterAltLoc = false;
+this.filterGroup3 = false;
+this.filterChain = false;
+this.filterAtomName = false;
+this.filterAtomType = false;
+this.filterAtomTypeStr = null;
+this.filterAtomNameTerminator = ";";
+this.filterElement = false;
+this.filterHetero = false;
+this.filterAllHetero = false;
+this.filterEveryNth = false;
+this.filterSymop = null;
+this.filterN = 0;
+this.nFiltered = 0;
+this.doSetOrientation = false;
+this.doCentralize = false;
+this.addVibrations = false;
+this.useAltNames = false;
+this.ignoreStructure = false;
+this.isDSSP1 = false;
+this.allowPDBFilter = false;
+this.doReadMolecularOrbitals = false;
+this.reverseModels = false;
+this.nameRequired = null;
+this.doCentroidUnitCell = false;
+this.centroidPacked = false;
+this.strSupercell = null;
+this.allow_a_len_1 = false;
+this.slabXY = false;
+this.polymerX = false;
+this.fixUnitCell = false;
+this.filteredPrecision = false;
+this.filter1 = null;
+this.filter2 = null;
+this.filter1Cased = null;
+this.filter2Cased = null;
+this.matRot = null;
+this.ms = null;
+this.vibsFractional = false;
+this.previousScript = null;
+this.siteScript = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomSetCollectionReader", null, javajs.api.GenericLineReader);
+Clazz.prepareFields (c$, function(){
+this.next = Clazz.newIntArray (1, 0);
+this.highprecision0 = JV.Viewer.isHighPrecision;
+this.loadNote = new JU.SB();
+});
+Clazz.defineMethod(c$, "getPackingRangeValue",
+function(def){
+return (this.packingRange != null ? this.packingRange.floatValue() : def != 0 ? def : 0.02);
+}, "~N");
+Clazz.defineMethod(c$, "setup",
+function(fullPath, htParams, readerOrDocument){
+this.setupASCR(fullPath, htParams, readerOrDocument);
+}, "~S,java.util.Map,~O");
+Clazz.defineMethod(c$, "setupASCR",
+function(fullPath, htParams, readerOrDocument){
+if (fullPath == null) return;
+this.debugging = JU.Logger.debugging;
+this.htParams = htParams;
+this.filePath = JV.FileManager.stripTypePrefix("" + htParams.get("fullPathName"));
+var i = this.filePath.lastIndexOf('/');
+this.fileName = this.filePath.substring(i + 1);
+if (Clazz.instanceOf(readerOrDocument,"java.io.BufferedReader")) this.reader = readerOrDocument;
+ else if (Clazz.instanceOf(readerOrDocument,"javajs.api.GenericBinaryDocument")) this.binaryDoc = readerOrDocument;
+}, "~S,java.util.Map,~O");
+Clazz.defineMethod(c$, "readData",
+function(){
+this.initialize();
+this.asc = new J.adapter.smarter.AtomSetCollection(this.readerName, this, null, null);
+try {
+this.initializeReader();
+if (this.binaryDoc == null) {
+if (this.line == null && this.continuing) this.rd();
+while (this.line != null && this.continuing) if (this.checkLine()) this.rd();
+
+} else {
+this.binaryDoc.setOutputChannel(this.out);
+this.processBinaryDocument();
+}this.finalizeSubclassReader();
+if (!this.isFinalized) this.finalizeReaderASCR();
+} catch (e) {
+JU.Logger.info("Reader error: " + e);
+e.printStackTrace();
+this.setError(e);
+}
+if (this.reader != null) this.reader.close();
+if (this.binaryDoc != null) this.binaryDoc.close();
+return this.finish();
+});
+Clazz.defineMethod(c$, "fixBaseIndices",
+function(){
+try {
+var ii = this.htParams.get("baseModelIndex");
+if (ii == null) return;
+var baseModelIndex = ii.intValue();
+this.baseAtomIndex += this.asc.ac;
+this.baseBondIndex += this.asc.bondCount;
+baseModelIndex += this.asc.atomSetCount;
+this.htParams.put("baseAtomIndex", Integer.$valueOf(this.baseAtomIndex));
+this.htParams.put("baseBondIndex", Integer.$valueOf(this.baseBondIndex));
+this.htParams.put("baseModelIndex", Integer.$valueOf(baseModelIndex));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+});
+Clazz.defineMethod(c$, "readDataObject",
+function(node){
+this.initialize();
+this.asc = new J.adapter.smarter.AtomSetCollection(this.readerName, this, null, null);
+this.initializeReader();
+this.processDOM(node);
+return this.finish();
+}, "~O");
+Clazz.defineMethod(c$, "processDOM",
+function(DOMNode){
+}, "~O");
+Clazz.defineMethod(c$, "processBinaryDocument",
+function(){
+});
+Clazz.defineMethod(c$, "initializeReader",
+function(){
+});
+Clazz.defineMethod(c$, "checkLine",
+function(){
+return true;
+});
+Clazz.defineMethod(c$, "checkLastModel",
+function(){
+if (this.isLastModel(this.modelNumber) && this.doProcessLines) return (this.continuing = this.doProcessLines = false);
+this.doProcessLines = false;
+return true;
+});
+Clazz.defineMethod(c$, "isLastModel",
+function(modelNumber){
+return (this.desiredModelNumber > 0 || modelNumber >= this.lastModelNumber);
+}, "~N");
+Clazz.defineMethod(c$, "appendLoadNote",
+function(info){
+if (info == null) {
+this.loadNote = new JU.SB();
+return;
+}this.loadNote.append(info).append("\n");
+JU.Logger.info(info);
+}, "~S");
+Clazz.defineMethod(c$, "initializeTrajectoryFile",
+function(){
+this.asc.addAtom( new J.adapter.smarter.Atom());
+this.trajectorySteps = this.htParams.get("trajectorySteps");
+if (this.trajectorySteps == null) this.htParams.put("trajectorySteps", this.trajectorySteps = new JU.Lst());
+});
+Clazz.defineMethod(c$, "finalizeSubclassReader",
+function(){
+});
+Clazz.defineMethod(c$, "finalizeReaderASCR",
+function(){
+this.isFinalized = true;
+if (this.asc.atomSetCount > 0) {
+if (this.asc.atomSetCount == 1) {
+this.asc.setCurrentModelInfo("dbName", this.htParams.get("dbName"));
+this.asc.setCurrentModelInfo("auxFiles", this.htParams.get("auxFiles"));
+}this.applySymmetryAndSetTrajectory();
+this.asc.finalizeStructures();
+if (this.doCentralize) this.asc.centralize();
+if (this.fillRange != null) this.asc.setInfo("boundbox", this.fillRange);
+var info = this.asc.getAtomSetAuxiliaryInfo(0);
+if (info != null) {
+if (this.domains != null) {
+this.asc.setGlobalBoolean(5);
+var s = (this.domains).getMapKeys(2, true);
+var pt = s.indexOf("{ ", 2);
+if (pt >= 0) s = s.substring(pt + 2);
+pt = s.indexOf("_metadata");
+if (pt < 0) pt = s.indexOf("metadata");
+if (pt >= 0) s = s.substring(0, pt);
+s = JU.PT.rep(JU.PT.replaceAllCharacters(s, "{}", "").trim(), "\n", "\n ") + "\n\nUse SHOW DOMAINS for details.";
+this.appendLoadNote("\nDomains loaded:\n " + s);
+for (var i = this.asc.atomSetCount; --i >= 0; ) {
+info = this.asc.getAtomSetAuxiliaryInfo(i);
+info.put("domains", this.domains);
+}
+}if (this.validation != null) {
+for (var i = this.asc.atomSetCount; --i >= 0; ) {
+info = this.asc.getAtomSetAuxiliaryInfo(i);
+info.put("validation", this.validation);
+}
+}if (this.dssr != null) {
+info.put("dssrJSON", Boolean.TRUE);
+for (var i = this.asc.atomSetCount; --i >= 0; ) {
+info = this.asc.getAtomSetAuxiliaryInfo(i);
+info.put("dssr", this.dssr);
+}
+}}}if (!this.floatifyJavaDouble) this.asc.setInfo("highPrecision", Boolean.TRUE);
+this.setLoadNote();
+});
+Clazz.defineMethod(c$, "setLoadNote",
+function(){
+var s = this.loadNote.toString();
+if (this.loadNote.length() > 0) this.asc.setInfo("modelLoadNote", s);
+return s;
+});
+Clazz.defineMethod(c$, "setIsPDB",
+function(){
+this.asc.setGlobalBoolean(4);
+if (this.htParams.get("pdbNoHydrogens") != null) this.asc.setInfo("pdbNoHydrogens", this.htParams.get("pdbNoHydrogens"));
+if (this.checkFilterKey("ADDHYDROGENS")) this.asc.setInfo("pdbAddHydrogens", Boolean.TRUE);
+});
+Clazz.defineMethod(c$, "setModelPDB",
+function(isPDB){
+if (isPDB) this.asc.setGlobalBoolean(4);
+ else this.asc.clearGlobalBoolean(4);
+this.asc.setCurrentModelInfo(JV.JC.getBoolName(4), isPDB ? Boolean.TRUE : null);
+}, "~B");
+Clazz.defineMethod(c$, "finish",
+function(){
+if (false != this.highprecision0) this.vwr.setBooleanPropertyTok("doubleprecision", 603979831, this.highprecision0);
+var s = this.htParams.get("loadState");
+this.asc.setInfo("loadState", s == null ? "" : s);
+s = this.htParams.get("smilesString");
+if (s != null) this.asc.setInfo("smilesString", s);
+if (!this.htParams.containsKey("templateAtomCount")) this.htParams.put("templateAtomCount", Integer.$valueOf(this.asc.ac));
+if (this.bsFilter != null) {
+this.htParams.put("filteredAtomCount", Integer.$valueOf(JU.BSUtil.cardinalityOf(this.bsFilter)));
+this.htParams.put("bsFilter", this.bsFilter);
+}if (!this.calculationType.equals("?")) this.asc.setInfo("calculationType", this.calculationType);
+var name = this.asc.fileTypeName;
+var fileType = name;
+if (fileType.indexOf("(") >= 0) fileType = fileType.substring(0, fileType.indexOf("("));
+for (var i = this.asc.atomSetCount; --i >= 0; ) {
+this.asc.setModelInfoForSet("fileName", this.filePath, i);
+this.asc.setModelInfoForSet("fileType", fileType, i);
+}
+this.asc.freeze(this.reverseModels);
+if (this.asc.errorMessage != null) return this.asc.errorMessage + "\nfor file " + this.filePath + "\ntype " + name;
+if (!this.merging && (this.asc.bsAtoms == null ? this.asc.ac == 0 : this.asc.bsAtoms.nextSetBit(0) < 0) && fileType.indexOf("DataOnly") < 0 && this.asc.atomSetInfo.get("dataOnly") == null) return "No atoms found\nfor file " + this.filePath + "\ntype " + name;
+this.fixBaseIndices();
+return this.asc;
+});
+Clazz.defineMethod(c$, "setError",
+function(e){
+var s = e.getMessage();
+if (this.line == null) this.asc.errorMessage = "Error reading file at end of file \n" + s;
+ else this.asc.errorMessage = "Error reading file at line " + this.ptLine + ":\n" + this.line + "\n" + s;
+e.printStackTrace();
+}, "Throwable");
+Clazz.defineMethod(c$, "initialize",
+function(){
+if (this.htParams.containsKey("baseAtomIndex")) this.baseAtomIndex = (this.htParams.get("baseAtomIndex")).intValue();
+if (this.htParams.containsKey("baseBondIndex")) this.baseBondIndex = (this.htParams.get("baseBondIndex")).intValue();
+this.initializeSymmetry();
+this.vwr = this.htParams.remove("vwr");
+if (this.htParams.containsKey("stateScriptVersionInt")) this.stateScriptVersionInt = (this.htParams.get("stateScriptVersionInt")).intValue();
+this.packingRange = this.htParams.get("packingRange");
+var isHighPrecision = (this.htParams.get("highPrecision") != null);
+if (this.packingRange == null && isHighPrecision) {
+this.floatifyJavaDouble = false;
+this.packingRange = Float.$valueOf(1.0E-4);
+}this.merging = this.htParams.containsKey("merging");
+this.getHeader = this.htParams.containsKey("getHeader");
+this.isSequential = this.htParams.containsKey("isSequential");
+this.readerName = this.htParams.get("readerName");
+if (this.htParams.containsKey("outputChannel")) this.out = this.htParams.get("outputChannel");
+if (this.htParams.containsKey("vibrationNumber")) this.desiredVibrationNumber = (this.htParams.get("vibrationNumber")).intValue();
+ else if (this.htParams.containsKey("modelNumber")) this.desiredModelNumber = (this.htParams.get("modelNumber")).intValue();
+this.applySymmetryToBonds = this.htParams.containsKey("applySymmetryToBonds");
+this.bsFilter = (this.requiresBSFilter ? this.htParams.get("bsFilter") : null);
+this.setFilter(null);
+this.fillRange = this.htParams.get("fillRange");
+this.paramsLattice = this.htParams.get("lattice");
+var o = this.htParams.get("supercell");
+this.noPack = this.checkFilterKey("NOPACK");
+if (this.strSupercell != null && !this.noPack) {
+this.forcePacked = true;
+}if (Clazz.instanceOf(o,"JU.P3")) {
+var s = this.ptSupercell = o;
+if (s.length() != 1) {
+this.strSupercell = (Clazz.floatToInt(s.x)) + "a," + (Clazz.floatToInt(s.y)) + "b," + (Clazz.floatToInt(s.z)) + "c";
+this.isSUPERCELL = true;
+}} else if ((typeof(o)=='string')) {
+this.strSupercell = o;
+this.isSUPERCELL = true;
+}var ptFile = (this.htParams.containsKey("ptFile") ? (this.htParams.get("ptFile")).intValue() : -1);
+this.isTrajectory = this.htParams.containsKey("isTrajectory");
+if (ptFile > 0 && this.htParams.containsKey("firstLastSteps")) {
+var val = (this.htParams.get("firstLastSteps")).get(ptFile - 1);
+if (Clazz.instanceOf(val,"JU.BS")) {
+this.bsModels = val;
+} else {
+this.firstLastStep = val;
+}} else if (this.htParams.containsKey("firstLastStep")) {
+this.firstLastStep = this.htParams.get("firstLastStep");
+} else if (this.htParams.containsKey("bsModels")) {
+this.bsModels = this.htParams.get("bsModels");
+}this.useFileModelNumbers = this.htParams.containsKey("useFileModelNumbers") || this.checkFilterKey("USEFILEMODELNUMBERS");
+if (this.htParams.containsKey("templateAtomCount")) this.templateAtomCount = (this.htParams.get("templateAtomCount")).intValue();
+if (this.bsModels != null || this.firstLastStep != null) this.desiredModelNumber = -2147483648;
+if (this.bsModels == null && this.firstLastStep != null) {
+if (this.firstLastStep[0] < 0) this.firstLastStep[0] = 0;
+if (this.firstLastStep[2] == 0 || this.firstLastStep[1] < this.firstLastStep[0]) this.firstLastStep[1] = -1;
+if (this.firstLastStep[2] < 1) this.firstLastStep[2] = 1;
+this.bsModels = JU.BSUtil.newAndSetBit(this.firstLastStep[0]);
+if (this.firstLastStep[1] > this.firstLastStep[0]) {
+for (var i = this.firstLastStep[0]; i <= this.firstLastStep[1]; i += this.firstLastStep[2]) this.bsModels.set(i);
+
+}}if (this.bsModels != null && (this.firstLastStep == null || this.firstLastStep[1] != -1)) this.lastModelNumber = this.bsModels.length();
+this.symmetryRange = (this.htParams.containsKey("symmetryRange") ? (this.htParams.get("symmetryRange")).floatValue() : 0);
+this.paramsCentroid = this.htParams.containsKey("centroid");
+this.paramsPacked = this.htParams.containsKey("packed");
+this.initializeSymmetryOptions();
+if (this.htParams.containsKey("spaceGroupIndex")) {
+this.desiredSpaceGroupIndex = (this.htParams.get("spaceGroupIndex")).intValue();
+if (this.desiredSpaceGroupIndex == -2) this.sgName = this.htParams.get("spaceGroupName");
+this.ignoreFileSpaceGroupName = (this.desiredSpaceGroupIndex == -2 || this.desiredSpaceGroupIndex >= 0);
+this.ignoreFileSymmetryOperators = (this.desiredSpaceGroupIndex != -1);
+}if (this.htParams.containsKey("unitCellOffset")) {
+this.fileScaling = JU.P3.new3(1, 1, 1);
+this.fileOffset = this.htParams.get("unitCellOffset");
+this.fileOffsetFractional = JU.P3.newP(this.fileOffset);
+this.unitCellOffsetFractional = this.htParams.containsKey("unitCellOffsetFractional");
+}if (this.htParams.containsKey("unitcell")) {
+var fParams = this.htParams.get("unitcell");
+if (this.merging) this.setFractionalCoordinates(true);
+if (fParams.length == 9) {
+this.addExplicitLatticeVector(0, fParams, 0);
+this.addExplicitLatticeVector(1, fParams, 3);
+this.addExplicitLatticeVector(2, fParams, 6);
+} else {
+this.setUnitCell(fParams[0], fParams[1], fParams[2], fParams[3], fParams[4], fParams[5]);
+}this.ignoreFileUnitCell = this.iHaveUnitCell;
+if (this.merging && !this.iHaveUnitCell) this.setFractionalCoordinates(false);
+}this.domains = this.htParams.get("domains");
+this.validation = this.htParams.get("validation");
+this.dssr = this.htParams.get("dssr");
+this.isConcatenated = this.htParams.containsKey("concatenate");
+});
+Clazz.defineMethod(c$, "parsePrecision",
+function(s){
+if (!this.filteredPrecision) {
+var pt = s.indexOf('.') + 1;
+if (pt >= 0) {
+var n = s.indexOf('(');
+if (n < 0) {
+this.precision = Math.max(this.precision, s.length - pt);
+} else {
+if (this.precision == 0) this.precision = n;
+this.precision = Math.min(this.precision, n - 1 - pt);
+}}}return this.parseFloatStr(s);
+}, "~S");
+Clazz.defineMethod(c$, "setLowPrecision",
+function(){
+this.lowPrecision = true;
+this.cellSlop = 1.0E-4;
+if (this.packingRange == null) this.packingRange = Double.$valueOf(1.0E-4);
+});
+Clazz.defineMethod(c$, "setPrecision",
+function(){
+var isHigh;
+if (this.lowPrecision) {
+isHigh = false;
+this.precision = 4;
+} else {
+if (this.precision > 1000) {
+this.precision -= 1000;
+} else {
+this.precision = Math.min(12, Math.max(4, this.precision));
+}isHigh = (this.precision >= 7);
+if (isHigh) {
+this.vwr.setBooleanProperty("doubleprecision", true);
+if (JV.Viewer.isHighPrecision) {
+this.cellSlop = 1.0E-12;
+if (!this.paramsPacked) this.packingRange = Double.$valueOf(this.cellSlop);
+this.asc.setInfo("highPrecision", Boolean.TRUE);
+} else {
+isHigh = false;
+this.precision = 6;
+this.appendLoadNote("Structure read has high precision but this version of Jmol uses float precision.\nUse JmolD.jar or JavaScript for full precision.");
+}}}if (!isHigh) {
+if (this.precision < 10) {
+this.cellSlop = Math.pow(10, -this.precision);
+}}this.symmetry.setPrecision(this.cellSlop);
+this.unitCellParams[26] = this.cellSlop;
+if (this.fileCoordinatesAreFractional) {
+for (var i = this.asc.ac, n = this.asc.getLastAtomSetAtomIndex(); --i >= n; ) {
+this.symmetry.twelfthify(this.asc.atoms[i]);
+}
+}this.appendLoadNote("Precision set to " + this.precision + "; packing set to " + (this.packingRange == null ? 0.02 : this.packingRange.floatValue()));
+});
+Clazz.defineMethod(c$, "initializeSymmetryOptions",
+function(){
+this.latticeCells = Clazz.newIntArray (4, 0);
+this.doApplySymmetry = false;
+var pt = this.paramsLattice;
+if (pt == null || pt.length() == 0) {
+if (!this.forcePacked && this.strSupercell == null) return;
+pt = JU.P3.new3(1, 1, 1);
+}this.latticeCells[0] = Clazz.floatToInt(pt.x);
+this.latticeCells[1] = Clazz.floatToInt(pt.y);
+this.latticeCells[2] = Clazz.floatToInt(pt.z);
+if (Clazz.instanceOf(pt,"JU.T4")) this.latticeCells[3] = Clazz.floatToInt((pt).w);
+this.doCentroidUnitCell = this.paramsCentroid;
+if (this.doCentroidUnitCell && (this.latticeCells[2] == -1 || this.latticeCells[2] == 0)) this.latticeCells[2] = 1;
+var isPacked = this.forcePacked || this.paramsPacked;
+this.centroidPacked = this.doCentroidUnitCell && isPacked;
+this.doPackUnitCell = !this.doCentroidUnitCell && (isPacked || this.latticeCells[2] < 0);
+this.doApplySymmetry = (this.latticeCells[0] > 0 && this.latticeCells[1] > 0);
+if (!this.doApplySymmetry) this.latticeCells = Clazz.newIntArray (3, 0);
+});
+Clazz.defineMethod(c$, "doGetModel",
+function(modelNumber, title){
+if (title != null && this.nameRequired != null && this.nameRequired.length > 0 && title.toUpperCase().indexOf(this.nameRequired) < 0) return false;
+var isOK = (this.bsModels == null ? this.desiredModelNumber < 1 || modelNumber == this.desiredModelNumber : modelNumber > this.lastModelNumber ? false : modelNumber > 0 && this.bsModels.get(modelNumber - 1) || this.haveModel && this.firstLastStep != null && this.firstLastStep[1] < 0 && (this.firstLastStep[2] < 2 || (modelNumber - 1 - this.firstLastStep[0]) % this.firstLastStep[2] == 0));
+if (isOK && this.desiredModelNumber == 0) this.discardPreviousAtoms();
+this.haveModel = new Boolean (this.haveModel | isOK).valueOf();
+if (isOK) this.doProcessLines = true;
+return isOK;
+}, "~N,~S");
+Clazz.defineMethod(c$, "discardPreviousAtoms",
+function(){
+this.asc.discardPreviousAtoms();
+});
+Clazz.defineMethod(c$, "initializeSymmetry",
+function(){
+this.previousSpaceGroup = this.sgName;
+this.previousUnitCell = this.unitCellParams;
+this.iHaveUnitCell = this.ignoreFileUnitCell;
+if (!this.ignoreFileUnitCell) {
+this.unitCellParams = Clazz.newFloatArray (27, 0);
+for (var i = 27; --i >= 0; ) this.unitCellParams[i] = NaN;
+
+this.unitCellParams[25] = this.latticeScaling;
+this.unitCellParams[26] = this.cellSlop;
+this.symmetry = null;
+}if (!this.ignoreFileSpaceGroupName) this.sgName = "unspecified!";
+this.doCheckUnitCell = false;
+});
+Clazz.defineMethod(c$, "newAtomSet",
+function(name){
+if (this.asc.iSet >= 0) {
+this.asc.newAtomSet();
+this.asc.setCollectionName("");
+} else {
+this.asc.setCollectionName(name);
+}this.asc.setModelInfoForSet("name", name, Math.max(0, this.asc.iSet));
+this.asc.setAtomSetName(name);
+}, "~S");
+Clazz.defineMethod(c$, "cloneLastAtomSet",
+function(ac, pts){
+var lastAtomCount = this.asc.getLastAtomSetAtomCount();
+this.asc.cloneLastAtomSetFromPoints(ac, pts);
+if (this.asc.haveUnitCell) {
+this.iHaveUnitCell = true;
+this.doCheckUnitCell = true;
+this.sgName = this.previousSpaceGroup;
+this.unitCellParams = this.previousUnitCell;
+}return lastAtomCount;
+}, "~N,~A");
+Clazz.defineMethod(c$, "setSpaceGroupName",
+function(name){
+if (this.ignoreFileSpaceGroupName || name == null) return;
+var s = name.trim();
+if (s.length == 0 || s.equals("HM:") || s.equals(this.sgName)) return;
+if (!s.equals("P1")) JU.Logger.info("Setting space group name to " + s);
+this.sgName = s;
+}, "~S");
+Clazz.defineMethod(c$, "setSymmetryOperator",
+function(xyz){
+if (this.ignoreFileSymmetryOperators) return -1;
+var isym = this.asc.getXSymmetry().addSpaceGroupOperation(xyz, true);
+if (isym < 0) JU.Logger.warn("Skippings symmetry operation " + xyz);
+this.iHaveSymmetryOperators = true;
+return isym;
+}, "~S");
+Clazz.defineMethod(c$, "initializeCartesianToFractional",
+function(){
+for (var i = 0; i < 16; i++) if (!Float.isNaN(this.unitCellParams[6 + i])) return;
+
+for (var i = 0; i < 16; i++) this.unitCellParams[6 + i] = ((i % 5 == 0 ? 1 : 0));
+
+this.nMatrixElements = 0;
+});
+Clazz.defineMethod(c$, "clearUnitCell",
+function(){
+if (this.ignoreFileUnitCell) return;
+for (var i = 6; i < 22; i++) this.unitCellParams[i] = NaN;
+
+this.checkUnitCell(6);
+});
+Clazz.defineMethod(c$, "setUnitCellItem",
+function(i, x){
+if (this.ignoreFileUnitCell) return;
+if (i == 0 && x == 1 && !this.allow_a_len_1 || i == 3 && x == 0) {
+if (this.ucItems == null) this.ucItems = Clazz.newFloatArray (6, 0);
+this.ucItems[i] = x;
+return;
+}if (this.ucItems != null && i < 6) this.ucItems[i] = x;
+if (!Float.isNaN(x) && i >= 6 && Float.isNaN(this.unitCellParams[6])) this.initializeCartesianToFractional();
+this.unitCellParams[i] = x;
+if (this.debugging) {
+JU.Logger.debug("setunitcellitem " + i + " " + x);
+}if (i < 6 || Float.isNaN(x)) this.iHaveUnitCell = this.checkUnitCell(6);
+ else if (++this.nMatrixElements == 12) this.iHaveUnitCell = this.checkUnitCell(22);
+}, "~N,~N");
+Clazz.defineMethod(c$, "setUnitCell",
+function(a, b, c, alpha, beta, gamma){
+if (this.ignoreFileUnitCell) return;
+this.clearUnitCell();
+this.unitCellParams[0] = a;
+this.unitCellParams[1] = b;
+this.unitCellParams[2] = c;
+if (alpha != 0) this.unitCellParams[3] = alpha;
+if (beta != 0) this.unitCellParams[4] = beta;
+if (gamma != 0) this.unitCellParams[5] = gamma;
+this.iHaveUnitCell = this.checkUnitCell(6);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "addExplicitLatticeVector",
+function(i, xyz, i0){
+if (this.ignoreFileUnitCell) return;
+if (i == 0) for (var j = 0; j < 6; j++) this.unitCellParams[j] = 0;
+
+i = 6 + i * 3;
+this.unitCellParams[i++] = xyz[i0++];
+this.unitCellParams[i++] = xyz[i0++];
+this.unitCellParams[i] = xyz[i0];
+if (Float.isNaN(this.unitCellParams[0])) {
+for (i = 0; i < 6; i++) this.unitCellParams[i] = -1;
+
+}this.iHaveUnitCell = this.checkUnitCell(15);
+if (this.iHaveUnitCell) {
+if (this.slabXY || this.polymerX) this.unitCellParams[2] = -1;
+if (this.polymerX) this.unitCellParams[1] = -1;
+}}, "~N,~A,~N");
+Clazz.defineMethod(c$, "checkUnitCell",
+function(n){
+for (var i = 0; i < n; i++) if (Float.isNaN(this.unitCellParams[i])) return false;
+
+this.fixFloatA(this.unitCellParams);
+if (n == 22 && this.unitCellParams[0] == 1) {
+if (this.unitCellParams[1] == 1 && this.unitCellParams[2] == 1 && this.unitCellParams[6] == 1 && this.unitCellParams[11] == 1 && this.unitCellParams[16] == 1) {
+return false;
+}}if (n == 6 && Float.isNaN(this.unitCellParams[6])) {
+if (this.slabXY && this.unitCellParams[2] > 0) {
+JU.SimpleUnitCell.addVectors(this.unitCellParams);
+this.unitCellParams[2] = -1;
+} else if (this.polymerX && this.unitCellParams[1] > 0) {
+JU.SimpleUnitCell.addVectors(this.unitCellParams);
+this.unitCellParams[1] = this.unitCellParams[2] = -1;
+}}if (this.doApplySymmetry) {
+this.getSymmetry();
+this.doConvertToFractional = !this.fileCoordinatesAreFractional;
+}return true;
+}, "~N");
+Clazz.defineMethod(c$, "getSymmetry",
+function(){
+if (!this.iHaveUnitCell) return null;
+if (this.symmetry == null) {
+(this.symmetry = this.asc.newFileSymmetry()).setUnitCellFromParams(this.unitCellParams, false, this.cellSlop);
+this.checkUnitCellOffset();
+}if (this.symmetry == null) this.iHaveUnitCell = false;
+ else this.symmetry.setSpaceGroupName(this.sgName);
+return this.symmetry;
+});
+Clazz.defineMethod(c$, "checkUnitCellOffset",
+function(){
+if (this.fileOffsetFractional == null || this.symmetry == null) return;
+this.fileOffset.setT(this.fileOffsetFractional);
+if (this.unitCellOffsetFractional != this.fileCoordinatesAreFractional) {
+if (this.unitCellOffsetFractional) this.symmetry.toCartesian(this.fileOffset, false);
+ else this.symmetry.toFractional(this.fileOffset, false);
+}});
+Clazz.defineMethod(c$, "fractionalizeCoordinates",
+function(toFrac){
+if (this.getSymmetry() == null) return;
+var a = this.asc.atoms;
+if (toFrac) for (var i = this.asc.ac; --i >= 0; ) this.symmetry.toFractional(a[i], false);
+
+ else for (var i = this.asc.ac; --i >= 0; ) this.symmetry.toCartesian(a[i], false);
+
+this.setFractionalCoordinates(toFrac);
+}, "~B");
+Clazz.defineMethod(c$, "setFractionalCoordinates",
+function(TF){
+this.iHaveFractionalCoordinates = this.fileCoordinatesAreFractional = TF;
+this.checkUnitCellOffset();
+}, "~B");
+Clazz.defineMethod(c$, "setFilterAtomTypeStr",
+function(s){
+this.filterAtomTypeStr = s;
+this.filterAtomNameTerminator = "\0";
+}, "~S");
+Clazz.defineMethod(c$, "setFilter",
+function(filter0){
+if (filter0 == null) {
+filter0 = this.htParams.get("filter");
+} else {
+this.bsFilter = null;
+this.filterCased = null;
+}if (this.filterCased == null) this.filterCased = (filter0 == null ? null : filter0 + ";");
+if (filter0 != null) filter0 = filter0.toUpperCase();
+this.filter = filter0;
+this.doSetOrientation = !this.checkFilterKey("NOORIENT");
+this.doCentralize = (!this.checkFilterKey("NOCENTER") && this.checkFilterKey("CENTER"));
+this.addVibrations = !this.checkFilterKey("NOVIB");
+this.ignoreStructure = this.checkFilterKey("DSSP");
+this.isDSSP1 = this.checkFilterKey("DSSP1");
+this.doReadMolecularOrbitals = !this.checkFilterKey("NOMO");
+this.useAltNames = this.checkFilterKey("ALTNAME");
+this.reverseModels = this.checkFilterKey("REVERSEMODELS");
+this.allow_a_len_1 = this.checkFilterKey("TOPOS");
+this.slabXY = this.checkFilterKey("SLABXY");
+this.polymerX = !this.slabXY && this.checkFilterKey("POLYMERX");
+this.noHydrogens = this.checkFilterKey("NOH");
+this.noMinimize = this.checkFilterKey("NOMIN");
+this.optimize2D = this.checkFilterKey("2D") && !this.noHydrogens && !this.noMinimize;
+if (this.filter == null) return;
+this.fixUnitCell = this.checkFilterKey("FIXUNITCELL");
+if (this.checkFilterKey("LOWPRECISION")) {
+this.setLowPrecision();
+}if (this.checkFilterKey("HETATM")) {
+this.filterHetero = true;
+this.filter = JU.PT.rep(this.filter, "HETATM", "HETATM-Y");
+this.filterCased = JU.PT.rep(this.filterCased, "HETATM", "HETATM-Y");
+}if (this.checkFilterKey("ATOM")) {
+this.filterHetero = true;
+this.filter = JU.PT.rep(this.filter, "ATOM", "HETATM-N");
+this.filterCased = JU.PT.rep(this.filterCased, "ATOM", "HETATM-N");
+}if (this.checkFilterKey("CELL=")) this.strSupercell = this.filter.substring(this.filter.indexOf("CELL=") + 5).toLowerCase();
+this.nameRequired = JU.PT.getQuotedAttribute(this.filter, "NAME");
+if (this.nameRequired != null) {
+if (this.nameRequired.startsWith("'")) this.nameRequired = JU.PT.split(this.nameRequired, "'")[1];
+ else if (this.nameRequired.startsWith("\"")) this.nameRequired = JU.PT.split(this.nameRequired, "\"")[1];
+this.filter = JU.PT.rep(this.filter, this.nameRequired, "");
+filter0 = this.filter = JU.PT.rep(this.filter, "NAME=", "");
+}this.filterAtomName = this.checkFilterKey("*.") || this.checkFilterKey("!.");
+if (this.filter.startsWith("_") || this.filter.startsWith("!_") || this.filter.indexOf(";_") >= 0) this.filterElement = this.checkFilterKey("_");
+this.filterGroup3 = this.checkFilterKey("[");
+this.filterChain = this.checkFilterKey(":");
+this.filterAltLoc = this.checkFilterKey("%");
+this.filterEveryNth = this.checkFilterKey("/=");
+this.filterAllHetero = this.checkFilterKey("ALLHET");
+if (this.filterEveryNth) this.filterN = this.parseIntAt(this.filter, this.filter.indexOf("/=") + 2);
+ else if (this.filter.startsWith("=") || this.filter.indexOf(";=") >= 0) this.filterAtomType = this.checkFilterKey("=");
+if (this.filterN == -2147483648) this.filterEveryNth = false;
+this.haveAtomFilter = this.filterAtomName || this.filterAtomType || this.filterElement || this.filterGroup3 || this.filterChain || this.filterAltLoc || this.filterHetero || this.filterEveryNth || this.checkFilterKey("/=");
+if (this.bsFilter == null) {
+this.bsFilter = new JU.BS();
+this.htParams.put("bsFilter", this.bsFilter);
+this.filter = (";" + this.filter + ";").$replace(',', ';');
+var p = this.getFilter("PRECISION=");
+if (p != null) {
+var prec = JU.PT.parseInt(p);
+if (prec > 0 && prec <= 16) {
+this.precision = 1000 + prec;
+this.filteredPrecision = true;
+}}var s = this.getFilter("LATTICESCALING=");
+if (s != null && this.unitCellParams.length > 25) this.unitCellParams[25] = this.latticeScaling = this.parseFloatStr(s);
+s = this.getFilter("SYMOP=");
+if (s != null) this.filterSymop = " " + s + " ";
+JU.Logger.info("filtering with " + this.filter);
+if (this.haveAtomFilter) {
+var ipt;
+this.filter1Cased = this.filterCased;
+this.filter2Cased = "";
+if ((ipt = this.filter.indexOf("|")) >= 0) {
+this.filter1Cased = this.filter.substring(0, ipt).trim() + ";";
+this.filter2Cased = ";" + this.filter.substring(ipt).trim();
+}this.filter1 = this.filter1Cased.toUpperCase();
+this.filter2 = (this.filter2Cased.length == 0 ? null : this.filter2Cased.toUpperCase());
+}}}, "~S");
+Clazz.defineMethod(c$, "getFilterWithCase",
+function(key){
+var pt = (this.filterCased == null ? -1 : this.filterCased.toUpperCase().indexOf(key.toUpperCase()));
+return (pt < 0 ? null : this.filterCased.substring(pt + key.length, this.filterCased.indexOf(";", pt)));
+}, "~S");
+Clazz.defineMethod(c$, "getFilter",
+function(key){
+var pt = (this.filter == null ? -1 : this.filter.indexOf(key));
+return (pt < 0 ? null : this.filter.substring(pt + key.length, this.filter.indexOf(";", pt)));
+}, "~S");
+Clazz.defineMethod(c$, "checkFilterKey",
+function(key){
+return (this.filter != null && this.filter.indexOf(key) >= 0);
+}, "~S");
+Clazz.defineMethod(c$, "checkAndRemoveFilterKey",
+function(key){
+if (!this.checkFilterKey(key)) return false;
+this.filter = JU.PT.rep(this.filter, key, "");
+if (this.filter.length < 3) this.filter = null;
+return true;
+}, "~S");
+Clazz.defineMethod(c$, "filterAtom",
+function(atom, iAtom){
+if (!this.haveAtomFilter) return true;
+var isOK = this.checkFilter(atom, this.filter1, this.filter1Cased);
+if (this.filter2 != null) isOK = new Boolean (isOK | this.checkFilter(atom, this.filter2, this.filter2Cased)).valueOf();
+if (isOK && this.filterEveryNth && (!atom.isHetero || !this.filterAllHetero)) isOK = (((this.nFiltered++) % this.filterN) == 0);
+this.bsFilter.setBitTo(iAtom >= 0 ? iAtom : this.asc.ac, isOK);
+return isOK;
+}, "J.adapter.smarter.Atom,~N");
+Clazz.defineMethod(c$, "checkFilter",
+function(atom, f, fCased){
+if (atom.isHetero && this.filterAllHetero) return true;
+return (!this.filterGroup3 || atom.group3 == null || !this.filterReject(f, "[", atom.group3.toUpperCase() + "]")) && (!this.filterAtomName || this.allowAtomName(atom.atomName, f)) && (this.filterAtomTypeStr == null || atom.atomName == null || atom.atomName.toUpperCase().indexOf("\0" + this.filterAtomTypeStr) >= 0) && (!this.filterElement || atom.elementSymbol == null || !this.filterReject(f, "_", atom.elementSymbol.toUpperCase() + ";")) && (!this.filterChain || atom.chainID == 0 || !this.filterReject(fCased, ":", "" + this.vwr.getChainIDStr(atom.chainID))) && (!this.filterAltLoc || atom.altLoc == '\0' || !this.filterReject(f, "%", "" + atom.altLoc)) && (!this.filterHetero || !this.allowPDBFilter || !this.filterReject(f, "HETATM", atom.isHetero ? "-Y" : "-N"));
+}, "J.adapter.smarter.Atom,~S,~S");
+Clazz.defineMethod(c$, "rejectAtomName",
+function(name){
+return this.filterAtomName && !this.allowAtomName(name, this.filter);
+}, "~S");
+Clazz.defineMethod(c$, "allowAtomName",
+function(atomName, f){
+return (atomName == null || !this.filterReject(f, ".", atomName.toUpperCase() + this.filterAtomNameTerminator));
+}, "~S,~S");
+Clazz.defineMethod(c$, "filterReject",
+function(f, code, atomCode){
+return (f.indexOf(code) >= 0 && (f.indexOf("!" + code) >= 0) == (f.indexOf(code + atomCode) >= 0));
+}, "~S,~S,~S");
+Clazz.defineMethod(c$, "set2D",
+function(){
+this.asc.setInfo("is2D", Boolean.TRUE);
+this.asc.getBSAtoms(-1);
+if (this.noHydrogens) {
+this.asc.setInfo("noHydrogen", Boolean.TRUE);
+this.optimize2D = false;
+}if (this.optimize2D) {
+this.asc.fix2Stereo();
+this.asc.setInfo("doMinimize", Boolean.TRUE);
+this.appendLoadNote("This model is 2D. Its 3D structure was generated.");
+} else {
+this.appendLoadNote("This model is 2D. Its 3D structure has not been generated; use LOAD \"\" FILTER \"2D\" to optimize 3D.");
+this.addJmolScript("select thismodel;wireframe only");
+}});
+Clazz.defineMethod(c$, "doGetVibration",
+function(vibrationNumber){
+return this.addVibrations && (this.desiredVibrationNumber <= 0 || vibrationNumber == this.desiredVibrationNumber);
+}, "~N");
+Clazz.defineMethod(c$, "setTransform",
+function(x1, y1, z1, x2, y2, z2, x3, y3, z3){
+if (this.matRot != null || !this.doSetOrientation) return;
+this.matRot = new JU.M3();
+var v = JU.V3.new3(x1, y1, z1);
+v.normalize();
+this.matRot.setColumnV(0, v);
+v.set(x2, y2, z2);
+v.normalize();
+this.matRot.setColumnV(1, v);
+v.set(x3, y3, z3);
+v.normalize();
+this.matRot.setColumnV(2, v);
+this.asc.setInfo("defaultOrientationMatrix", JU.M3.newM3(this.matRot));
+var q = JU.Quat.newM(this.matRot);
+this.asc.setInfo("defaultOrientationQuaternion", q);
+JU.Logger.info("defaultOrientationMatrix = " + this.matRot);
+}, "~N,~N,~N,~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "setAtomCoordXYZ",
+function(atom, x, y, z){
+atom.set(x, y, z);
+this.setAtomCoord(atom);
+}, "J.adapter.smarter.Atom,~N,~N,~N");
+Clazz.defineMethod(c$, "setAtomCoordScaled",
+function(atom, tokens, i, f){
+if (atom == null) atom = this.asc.addNewAtom();
+this.setAtomCoordXYZ(atom, this.parsePrecision(tokens[i]) * f, this.parsePrecision(tokens[i + 1]) * f, this.parsePrecision(tokens[i + 2]) * f);
+return atom;
+}, "J.adapter.smarter.Atom,~A,~N,~N");
+Clazz.defineMethod(c$, "setAtomCoordTokens",
+function(atom, tokens, i){
+this.setAtomCoordXYZ(atom, this.parsePrecision(tokens[i]), this.parsePrecision(tokens[i + 1]), this.parsePrecision(tokens[i + 2]));
+}, "J.adapter.smarter.Atom,~A,~N");
+Clazz.defineMethod(c$, "addAtomXYZSymName",
+function(tokens, i, sym, name){
+var atom = this.asc.addNewAtom();
+if (sym != null) atom.elementSymbol = sym;
+if (name != null) atom.atomName = name;
+this.setAtomCoordTokens(atom, tokens, i);
+return atom;
+}, "~A,~N,~S,~S");
+Clazz.defineMethod(c$, "setAtomCoord",
+function(atom){
+var mustFractionalize = (this.doConvertToFractional && !this.fileCoordinatesAreFractional && this.getSymmetry() != null);
+if (this.fileScaling != null) {
+atom.x = atom.x * this.fileScaling.x + this.fileOffset.x;
+atom.y = atom.y * this.fileScaling.y + this.fileOffset.y;
+atom.z = atom.z * this.fileScaling.z + this.fileOffset.z;
+}if (mustFractionalize) {
+if (!this.symmetry.haveUnitCell()) this.symmetry.setUnitCellFromParams(this.unitCellParams, false, NaN);
+this.symmetry.toFractional(atom, false);
+this.iHaveFractionalCoordinates = true;
+}if (this.floatifyJavaDouble && this.fileCoordinatesAreFractional) this.fixFloatPt(atom, 100000.0);
+this.doCheckUnitCell = true;
+}, "J.adapter.smarter.Atom");
+Clazz.defineMethod(c$, "addSites",
+function(htSites){
+this.asc.setCurrentModelInfo("pdbSites", htSites);
+var sites = "";
+for (var entry, $entry = htSites.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
+var name = entry.getKey();
+var htSite = entry.getValue();
+var ch;
+for (var i = name.length; --i >= 0; ) if (!JU.PT.isLetterOrDigit(ch = name.charAt(i)) && ch != '\'') name = name.substring(0, i) + "_" + name.substring(i + 1);
+
+var groups = htSite.get("groups");
+if (groups.length == 0) continue;
+this.addSiteScript("@site_" + name + " " + groups);
+this.addSiteScript("site_" + name + " = [\"" + JU.PT.rep(groups, ",", "\",\"") + "\"]");
+sites += ",\"site_" + name + "\"";
+}
+if (sites.length > 0) this.addSiteScript("site_list = [" + sites.substring(1) + "]");
+}, "java.util.Map");
+Clazz.defineMethod(c$, "applySymmetryAndSetTrajectory",
+function(){
+this.applySymTrajASCR();
+});
+Clazz.defineMethod(c$, "applySymTrajASCR",
+function(){
+if (this.forcePacked) this.initializeSymmetryOptions();
+var doApply = (this.iHaveUnitCell && this.doCheckUnitCell);
+var sym = null;
+if (doApply) {
+sym = this.getSymmetry();
+this.setPrecision();
+sym = this.asc.getXSymmetry().applySymmetryFromReader(sym);
+} else {
+this.asc.setTensors();
+}if (this.isTrajectory) this.asc.setTrajectory();
+if (this.moreUnitCellInfo != null) {
+this.asc.setCurrentModelInfo("moreUnitCellInfo", this.moreUnitCellInfo);
+this.moreUnitCellInfo = null;
+}this.finalizeSubclassSymmetry(sym != null);
+if (this.merging && sym != null && this.iHaveFractionalCoordinates && this.iHaveUnitCell && this.iHaveSymmetryOperators) {
+this.fractionalizeCoordinates(false);
+this.addJmolScript("modelkit spacegroup P1");
+}this.initializeSymmetry();
+return sym;
+});
+Clazz.defineMethod(c$, "finalizeSubclassSymmetry",
+function(haveSymmetry){
+}, "~B");
+Clazz.defineMethod(c$, "doPreSymmetry",
+function(){
+});
+Clazz.defineMethod(c$, "finalizeMOData",
+function(moData){
+this.asc.setCurrentModelInfo("moData", moData);
+if (moData == null) return;
+var orbitals = moData.get("mos");
+if (orbitals != null) JU.Logger.info(orbitals.size() + " molecular orbitals read in model " + this.asc.atomSetCount);
+}, "java.util.Map");
+c$.getElementSymbol = Clazz.defineMethod(c$, "getElementSymbol",
+function(elementNumber){
+return J.api.JmolAdapter.getElementSymbol(elementNumber);
+}, "~N");
+Clazz.defineMethod(c$, "fillDataBlock",
+function(data, minLineLen){
+var nLines = data.length;
+for (var i = 0; i < nLines; i++) {
+data[i] = JU.PT.getTokens(this.discardLinesUntilNonBlank());
+if (data[i].length < minLineLen) --i;
+}
+}, "~A,~N");
+Clazz.defineMethod(c$, "fill3x3",
+function(tokens, pt){
+var a = Clazz.newDoubleArray (3, 3, 0);
+var needTokens = (tokens == null);
+var pt0 = pt;
+for (var i = 0; i < 3; i++) {
+if (needTokens || pt >= tokens.length) {
+while ((tokens = JU.PT.getTokens(this.rd())).length < 3) {
+}
+pt = (pt0 < 0 ? tokens.length + pt0 : pt0);
+}for (var j = 0; j < 3; j++) a[i][j] = Double.$valueOf(tokens[pt++]).doubleValue();
+
+}
+return a;
+}, "~A,~N");
+Clazz.defineMethod(c$, "fillFloatArray",
+function(s, width, data){
+var tokens = new Array(0);
+var pt = 0;
+for (var i = 0; i < data.length; i++) {
+while (tokens != null && pt >= tokens.length) {
+if (s == null) s = this.rd();
+if (width == 0) {
+tokens = JU.PT.getTokens(s);
+} else {
+tokens = new Array(Clazz.doubleToInt(s.length / width));
+for (var j = 0; j < tokens.length; j++) tokens[j] = s.substring(j * width, (j + 1) * width);
+
+}s = null;
+pt = 0;
+}
+if (tokens == null) break;
+data[i] = this.parseFloatStr(tokens[pt++]);
+}
+return data;
+}, "~S,~N,~A");
+Clazz.defineMethod(c$, "fillFrequencyData",
+function(iAtom0, ac, modelAtomCount, ignore, isWide, col0, colWidth, atomIndexes, minLineLen, data){
+var withSymmetry = (ac != 0 && modelAtomCount != ac && data == null);
+if (ac == 0 && atomIndexes != null) ac = atomIndexes.length;
+var nLines = (isWide ? ac : ac * 3);
+var nFreq = ignore.length;
+if (data == null) {
+data = new Array(nLines);
+this.fillDataBlockFixed(data, col0, colWidth, minLineLen);
+} else if (!isWide) {
+var ptNonblank = minLineLen;
+this.fillDataBlockFixed(data, col0, colWidth, -ptNonblank);
+if (data[0] == null) return;
+iAtom0 += this.parseIntAt(this.line, ptNonblank - 5) - 1;
+}for (var i = 0, atomPt = 0; i < nLines; i++, atomPt++) {
+var values = data[i];
+var valuesY = (isWide ? null : data[++i]);
+var valuesZ = (isWide ? null : data[++i]);
+var dataPt = values.length - (isWide ? nFreq * 3 : nFreq) - 1;
+for (var j = 0, jj = 0; jj < nFreq; jj++) {
+++dataPt;
+var x = values[dataPt];
+if (x.charAt(0) == ')') x = x.substring(1);
+var vx = this.parseFloatStr(x);
+var vy = this.parseFloatStr(isWide ? values[++dataPt] : valuesY[dataPt]);
+var vz = this.parseFloatStr(isWide ? values[++dataPt] : valuesZ[dataPt]);
+if (ignore[jj]) continue;
+var iAtom = (atomIndexes == null ? atomPt : atomIndexes[atomPt]);
+if (iAtom < 0) continue;
+iAtom += iAtom0 + modelAtomCount * j++;
+if (this.debugging) JU.Logger.debug("atom " + iAtom + " vib" + j + ": " + vx + " " + vy + " " + vz);
+this.asc.addVibrationVectorWithSymmetry(iAtom, vx, vy, vz, withSymmetry);
+}
+}
+}, "~N,~N,~N,~A,~B,~N,~N,~A,~N,~A");
+Clazz.defineMethod(c$, "fillDataBlockFixed",
+function(data, col0, colWidth, minLineLen){
+if (colWidth == 0) {
+this.fillDataBlock(data, minLineLen);
+return;
+}var nLines = data.length;
+for (var i = 0; i < nLines; i++) {
+this.discardLinesUntilNonBlank();
+if (minLineLen < 0 && this.line.charAt(-minLineLen) == ' ') {
+data[0] = null;
+return;
+}var nFields = Clazz.doubleToInt((this.line.length - col0 + 1) / colWidth);
+data[i] = new Array(nFields);
+for (var j = 0, start = col0; j < nFields; j++, start += colWidth) data[i][j] = this.line.substring(start, Math.min(this.line.length, start + colWidth));
+
+}
+}, "~A,~N,~N,~N");
+Clazz.defineMethod(c$, "readLines",
+function(nLines){
+for (var i = nLines; --i >= 0; ) this.rd();
+
+return this.line;
+}, "~N");
+Clazz.defineMethod(c$, "discardLinesUntilStartsWith",
+function(startsWith){
+while (this.rd() != null && !this.line.startsWith(startsWith)) {
+}
+return this.line;
+}, "~S");
+Clazz.defineMethod(c$, "discardLinesUntilContains",
+function(containsMatch){
+while (this.rd() != null && this.line.indexOf(containsMatch) < 0) {
+}
+return this.line;
+}, "~S");
+Clazz.defineMethod(c$, "discardLinesUntilContains2",
+function(s1, s2){
+while (this.rd() != null && this.line.indexOf(s1) < 0 && this.line.indexOf(s2) < 0) {
+}
+return this.line;
+}, "~S,~S");
+Clazz.defineMethod(c$, "discardLinesUntilBlank",
+function(){
+while (this.rd() != null && this.line.trim().length != 0) {
+}
+return this.line;
+});
+Clazz.defineMethod(c$, "discardLinesUntilNonBlank",
+function(){
+while (this.rd() != null && this.line.trim().length == 0) {
+}
+return this.line;
+});
+Clazz.defineMethod(c$, "checkLineForScript",
+function(line){
+this.line = line;
+this.checkCurrentLineForScript();
+}, "~S");
+Clazz.defineMethod(c$, "checkCurrentLineForScript",
+function(){
+if (this.line.endsWith("#noautobond")) {
+this.line = this.line.substring(0, this.line.lastIndexOf('#')).trim();
+this.asc.setNoAutoBond();
+}var pt = this.line.indexOf("jmolscript:");
+if (pt >= 0) {
+var script = this.line.substring(pt + 11, this.line.length);
+if (script.indexOf("#") >= 0) {
+script = script.substring(0, script.indexOf("#"));
+}this.addJmolScript(script);
+this.line = this.line.substring(0, pt).trim();
+}});
+Clazz.defineMethod(c$, "addJmolScript",
+function(script){
+JU.Logger.info("#jmolScript: " + script);
+if (this.previousScript == null) this.previousScript = "";
+ else if (!this.previousScript.endsWith(";")) this.previousScript += ";";
+this.previousScript += script;
+this.asc.setInfo("jmolscript", this.previousScript);
+}, "~S");
+Clazz.defineMethod(c$, "addSiteScript",
+function(script){
+if (this.siteScript == null) this.siteScript = "";
+ else if (!this.siteScript.endsWith(";")) this.siteScript += ";";
+this.siteScript += script;
+this.asc.setInfo("sitescript", this.siteScript);
+}, "~S");
+Clazz.defineMethod(c$, "rd",
+function(){
+return this.RL();
+});
+Clazz.defineMethod(c$, "RL",
+function(){
+this.prevline = this.line;
+this.line = this.reader.readLine();
+if (this.out != null && this.line != null) this.out.append(this.line).append("\n");
+this.ptLine++;
+if (this.debugging && this.line != null) JU.Logger.info(this.line);
+return this.line;
+});
+c$.getStrings = Clazz.defineMethod(c$, "getStrings",
+function(sinfo, nFields, width){
+var fields = new Array(nFields);
+for (var i = 0, pt = 0; i < nFields; i++, pt += width) fields[i] = sinfo.substring(pt, pt + width);
+
+return fields;
+}, "~S,~N,~N");
+Clazz.defineMethod(c$, "getTokens",
+function(){
+return JU.PT.getTokens(this.line);
+});
+c$.getTokensFloat = Clazz.defineMethod(c$, "getTokensFloat",
+function(s, f, n){
+if (f == null) f = Clazz.newFloatArray (n, 0);
+JU.PT.parseFloatArrayDataN(JU.PT.getTokens(s), f, n);
+return f;
+}, "~S,~A,~N");
+Clazz.defineMethod(c$, "parseFloat",
+function(){
+return JU.PT.parseFloatNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "parseFloatStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseFloatNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseFloatRange",
+function(s, iStart, iEnd){
+this.next[0] = iStart;
+return JU.PT.parseFloatRange(s, iEnd, this.next);
+}, "~S,~N,~N");
+Clazz.defineMethod(c$, "parseInt",
+function(){
+return JU.PT.parseIntNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "parseIntStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseIntNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseIntAt",
+function(s, iStart){
+this.next[0] = iStart;
+return JU.PT.parseIntNext(s, this.next);
+}, "~S,~N");
+Clazz.defineMethod(c$, "parseIntRange",
+function(s, iStart, iEnd){
+this.next[0] = iStart;
+return JU.PT.parseIntRange(s, iEnd, this.next);
+}, "~S,~N,~N");
+Clazz.defineMethod(c$, "parseToken",
+function(){
+return JU.PT.parseTokenNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "parseTokenStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseTokenNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseTokenNext",
+function(s){
+return JU.PT.parseTokenNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseTokenRange",
+function(s, iStart, iEnd){
+this.next[0] = iStart;
+return JU.PT.parseTokenRange(s, iEnd, this.next);
+}, "~S,~N,~N");
+c$.getFortranFormatLengths = Clazz.defineMethod(c$, "getFortranFormatLengths",
+function(s){
+var vdata = new JU.Lst();
+var n = 0;
+var c = 0;
+var factor = 1;
+var inN = false;
+var inCount = true;
+s += ",";
+for (var i = 0; i < s.length; i++) {
+var ch = s.charAt(i);
+switch ((ch).charCodeAt(0)) {
+case 46:
+inN = false;
+continue;
+case 44:
+for (var j = 0; j < c; j++) vdata.addLast(Integer.$valueOf(n * factor));
+
+inN = false;
+inCount = true;
+c = 0;
+continue;
+case 88:
+n = c;
+c = 1;
+factor = -1;
+continue;
+}
+var isDigit = JU.PT.isDigit(ch);
+if (isDigit) {
+if (inN) n = n * 10 + ch.charCodeAt(0) - 48;
+ else if (inCount) c = c * 10 + ch.charCodeAt(0) - 48;
+} else if (JU.PT.isLetter(ch)) {
+n = 0;
+inN = true;
+inCount = false;
+factor = 1;
+} else {
+inN = false;
+}}
+return vdata;
+}, "~S");
+Clazz.defineMethod(c$, "read3Vectors",
+function(isBohr){
+var vectors = new Array(3);
+var f = Clazz.newFloatArray (3, 0);
+for (var i = 0; i < 3; i++) {
+if (i > 0 || Float.isNaN(this.parseFloatStr(this.line))) {
+this.rd();
+if (i == 0 && this.line != null) {
+i = -1;
+continue;
+}}this.fillFloatArray(this.line, 0, f);
+vectors[i] = new JU.V3();
+vectors[i].setA(f);
+if (isBohr) vectors[i].scale(0.5291772);
+}
+return vectors;
+}, "~B");
+Clazz.defineMethod(c$, "setElementAndIsotope",
+function(atom, str){
+var isotope = this.parseIntStr(str);
+if (isotope == -2147483648) {
+atom.elementSymbol = str;
+} else {
+str = str.substring(("" + isotope).length);
+atom.elementNumber = (str.length == 0 ? isotope : ((isotope << 7) + J.api.JmolAdapter.getElementNumber(str)));
+}}, "J.adapter.smarter.Atom,~S");
+Clazz.defineMethod(c$, "finalizeModelSet",
+function(){
+});
+Clazz.defineMethod(c$, "setChainID",
+function(atom, label){
+atom.chainID = this.vwr.getChainID(label, true);
+}, "J.adapter.smarter.Atom,~S");
+Clazz.overrideMethod(c$, "readNextLine",
+function(){
+if (this.rd() != null && this.line.indexOf("#jmolscript:") >= 0) this.checkCurrentLineForScript();
+return this.line;
+});
+Clazz.defineMethod(c$, "appendUunitCellInfo",
+function(info){
+if (this.moreUnitCellInfo == null) this.moreUnitCellInfo = new JU.Lst();
+this.moreUnitCellInfo.addLast(info);
+this.appendLoadNote(info);
+}, "~S");
+Clazz.defineMethod(c$, "getInterface",
+function(className){
+var o = J.api.Interface.getInterface(className, this.vwr, "file");
+if (o == null) throw new NullPointerException("Interface");
+return o;
+}, "~S");
+Clazz.defineMethod(c$, "forceSymmetry",
+function(andPack){
+if (andPack) this.doPackUnitCell = andPack;
+if (!this.doApplySymmetry) {
+this.doApplySymmetry = true;
+this.latticeCells[0] = this.latticeCells[1] = this.latticeCells[2] = 1;
+}}, "~B");
+Clazz.defineMethod(c$, "fixFloatA",
+function(pts){
+if (this.floatifyJavaDouble) for (var i = pts.length; --i >= 0; ) if (!Float.isNaN(pts[i])) pts[i] = JU.PT.fixFloat(pts[i], 100000.0);
+
+}, "~A");
+Clazz.defineMethod(c$, "fixDoubleA",
+function(pts){
+if (this.floatifyJavaDouble) for (var i = pts.length; --i >= 0; ) if (!Double.isNaN(pts[i])) pts[i] = JU.PT.fixDouble(pts[i], 100000.0);
+
+}, "~A");
+Clazz.defineMethod(c$, "fixFloatPt",
+function(pt, prec){
+if (this.floatifyJavaDouble) JU.PT.fixPtFloats(pt, prec);
+}, "JU.P3,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetObject.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetObject.js
new file mode 100755
index 000000000000..9db13d486e6e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/AtomSetObject.js
@@ -0,0 +1,7 @@
+Clazz.declarePackage("J.adapter.smarter");
+(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.atomSetIndex = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomSetObject", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Bond.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Bond.js
new file mode 100755
index 000000000000..5a34304cb2b7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Bond.js
@@ -0,0 +1,24 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["J.adapter.smarter.AtomSetObject"], "J.adapter.smarter.Bond", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.atomIndex1 = 0;
+this.atomIndex2 = 0;
+this.order = 0;
+this.radius = -1;
+this.colix = -1;
+this.uniqueID = -1;
+this.distance = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "Bond", J.adapter.smarter.AtomSetObject);
+Clazz.makeConstructor(c$,
+function(atomIndex1, atomIndex2, order){
+Clazz.superConstructor (this, J.adapter.smarter.Bond, []);
+this.atomIndex1 = atomIndex1;
+this.atomIndex2 = atomIndex2;
+this.order = order;
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return "[Bond " + this.atomIndex1 + " " + this.atomIndex2 + " " + this.order + "]";
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/BondIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/BondIterator.js
new file mode 100755
index 000000000000..9bd28bd28e76
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/BondIterator.js
@@ -0,0 +1,46 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["J.api.JmolAdapterBondIterator"], "J.adapter.smarter.BondIterator", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.bsAtoms = null;
+this.bonds = null;
+this.ibond = 0;
+this.bond = null;
+this.bondCount = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "BondIterator", J.api.JmolAdapterBondIterator);
+Clazz.makeConstructor(c$,
+function(asc){
+Clazz.superConstructor (this, J.adapter.smarter.BondIterator, []);
+this.bsAtoms = asc.bsAtoms;
+this.bonds = asc.bonds;
+this.bondCount = asc.bondCount;
+this.ibond = 0;
+}, "J.adapter.smarter.AtomSetCollection");
+Clazz.overrideMethod(c$, "hasNext",
+function(){
+if (this.ibond == this.bondCount) return false;
+while ((this.bond = this.bonds[this.ibond++]) == null || (this.bsAtoms != null && (!this.bsAtoms.get(this.bond.atomIndex1) || !this.bsAtoms.get(this.bond.atomIndex2)))) if (this.ibond == this.bondCount) return false;
+
+return true;
+});
+Clazz.overrideMethod(c$, "getAtomUniqueID1",
+function(){
+return Integer.$valueOf(this.bond.atomIndex1);
+});
+Clazz.overrideMethod(c$, "getAtomUniqueID2",
+function(){
+return Integer.$valueOf(this.bond.atomIndex2);
+});
+Clazz.overrideMethod(c$, "getEncodedOrder",
+function(){
+return this.bond.order;
+});
+Clazz.overrideMethod(c$, "getRadius",
+function(){
+return this.bond.radius;
+});
+Clazz.overrideMethod(c$, "getColix",
+function(){
+return this.bond.colix;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/MSInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/MSInterface.js
new file mode 100755
index 000000000000..19af8c9701da
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/MSInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.declareInterface(J.adapter.smarter, "MSInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Resolver.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Resolver.js
new file mode 100755
index 000000000000..cc9d71328548
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Resolver.js
@@ -0,0 +1,487 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(null, "J.adapter.smarter.Resolver", ["java.io.BufferedInputStream", "java.util.StringTokenizer", "JU.LimitedLineReader", "$.PT", "$.Rdr", "J.adapter.smarter.AtomSetCollectionReader", "$.SmarterJmolAdapter", "J.api.Interface", "JU.Logger", "JV.JC"], function(){
+var c$ = Clazz.declareType(J.adapter.smarter, "Resolver", null);
+c$.getReaderClassBase = Clazz.defineMethod(c$, "getReaderClassBase",
+function(type){
+var name = type + "Reader";
+if (type.startsWith("Xml")) return "J.adapter.readers." + "xml." + name;
+var key = ";" + type + ";";
+for (var i = 1; i < J.adapter.smarter.Resolver.readerSets.length; i += 2) if (J.adapter.smarter.Resolver.readerSets[i].indexOf(key) >= 0) return "J.adapter.readers." + J.adapter.smarter.Resolver.readerSets[i - 1] + name;
+
+return "J.adapter.readers." + "???." + name;
+}, "~S");
+c$.getFileType = Clazz.defineMethod(c$, "getFileType",
+function(br){
+try {
+return J.adapter.smarter.Resolver.determineAtomSetCollectionReader(br, null);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return null;
+} else {
+throw e;
+}
+}
+}, "java.io.BufferedReader");
+c$.getAtomCollectionReader = Clazz.defineMethod(c$, "getAtomCollectionReader",
+function(fullName, type, readerOrDocument, htParams, ptFile){
+var readerName;
+fullName = J.adapter.smarter.Resolver.fixDOSName(fullName);
+var errMsg = null;
+if (type == null && htParams != null) {
+type = J.adapter.smarter.Resolver.getFileTypefromFilter(htParams.get("filter"));
+}if (type != null) {
+readerName = J.adapter.smarter.Resolver.getReaderFromType(type);
+if (readerName == null) readerName = J.adapter.smarter.Resolver.getReaderFromType("Xml" + type);
+if (readerName == null) errMsg = "unrecognized file format type " + type + " file=" + fullName;
+ else JU.Logger.info("The Resolver assumes " + readerName + " file=" + fullName);
+} else {
+readerName = J.adapter.smarter.Resolver.determineAtomSetCollectionReader(readerOrDocument, htParams);
+if (readerName.charAt(0) == '\n') {
+type = (htParams == null ? null : htParams.get("defaultType"));
+if (type != null) {
+type = J.adapter.smarter.Resolver.getReaderFromType(type);
+if (type != null) readerName = type;
+}}if (readerName.charAt(0) == '\n') errMsg = "unrecognized file format for file\n" + fullName + "\n" + J.adapter.smarter.Resolver.split(readerName, 50);
+ else if (readerName.equals("spt")) errMsg = "NOTE: file recognized as a script file: " + fullName + "\n";
+ else if (!fullName.equals("ligand")) JU.Logger.info("The Resolver thinks " + readerName);
+}if (errMsg != null) {
+J.adapter.smarter.SmarterJmolAdapter.close(readerOrDocument);
+return errMsg;
+}htParams.put("ptFile", Integer.$valueOf(ptFile));
+if (ptFile <= 0) htParams.put("readerName", readerName);
+return J.adapter.smarter.Resolver.getReader(readerName, htParams);
+}, "~S,~S,~O,java.util.Map,~N");
+c$.getReader = Clazz.defineMethod(c$, "getReader",
+function(readerName, htParams){
+var rdr = null;
+var className = null;
+var err = null;
+className = J.adapter.smarter.Resolver.getReaderClassBase(readerName);
+if ((rdr = J.api.Interface.getInterface(className, null, "reader")) == null) {
+err = JV.JC.READER_NOT_FOUND + className;
+JU.Logger.error(err);
+return err;
+}return rdr;
+}, "~S,java.util.Map");
+c$.getReaderFromType = Clazz.defineMethod(c$, "getReaderFromType",
+function(type){
+if (type.endsWith("(XML)")) {
+type = "Xml" + type.substring(0, type.length - 5);
+}type = ";" + type.toLowerCase() + ";";
+if (";zmatrix;cfi;c;vfi;v;mnd;jag;gms;g;gau;mp;nw;orc;pqs;qc;".indexOf(type) >= 0) return "Input";
+var set;
+var pt;
+for (var i = J.adapter.smarter.Resolver.readerSets.length; --i >= 0; ) {
+if ((pt = (set = J.adapter.smarter.Resolver.readerSets[i--]).toLowerCase().indexOf(type)) >= 0) return set.substring(pt + 1, set.indexOf(";", pt + 2));
+}
+return null;
+}, "~S");
+c$.split = Clazz.defineMethod(c$, "split",
+function(a, n){
+var s = "";
+var l = a.length;
+for (var i = 0, j = 0; i < l; i = j) s += a.substring(i, (j = Math.min(i + n, l))) + "\n";
+
+return s;
+}, "~S,~N");
+c$.DOMResolve = Clazz.defineMethod(c$, "DOMResolve",
+function(htParams){
+var rdrName = J.adapter.smarter.Resolver.getXmlType(htParams.get("nameSpaceInfo"));
+if (JU.Logger.debugging) {
+JU.Logger.debug("The Resolver thinks " + rdrName);
+}htParams.put("readerName", rdrName);
+return J.adapter.smarter.Resolver.getReader("XmlReader", htParams);
+}, "java.util.Map");
+c$.determineAtomSetCollectionReader = Clazz.defineMethod(c$, "determineAtomSetCollectionReader",
+function(readerOrDocument, htParams){
+var readerName;
+if (Clazz.instanceOf(readerOrDocument,"javajs.api.GenericBinaryDocument")) {
+var doc = readerOrDocument;
+readerName = J.adapter.smarter.Resolver.getBinaryType(doc.getInputStream());
+return (readerName == null ? "binary file type not recognized" : readerName);
+}if (Clazz.instanceOf(readerOrDocument,"java.io.InputStream")) {
+readerName = J.adapter.smarter.Resolver.getBinaryType(readerOrDocument);
+if (readerName != null) return readerName;
+readerOrDocument = JU.Rdr.getBufferedReader( new java.io.BufferedInputStream(readerOrDocument), null);
+}var rdr = readerOrDocument;
+var llr = new JU.LimitedLineReader(rdr, 16384);
+var leader = llr.getHeader(64).trim();
+if (leader.length == 0) throw new java.io.EOFException("File contains no data.");
+if (leader.indexOf("PNG") == 1 && leader.indexOf("PNGJ") >= 0) return "pngj";
+if (leader.indexOf("PNG") == 1 || leader.indexOf("JPG") == 1 || leader.indexOf("JFIF") == 6) return "spt";
+if (leader.indexOf("\"num_pairs\"") >= 0) return "dssr";
+if (leader.indexOf("output.31\n") >= 0) return "GenNBO|output.31";
+if ((readerName = J.adapter.smarter.Resolver.checkFileStart(leader)) != null) {
+return (readerName.equals("Xml") ? J.adapter.smarter.Resolver.getXmlType(llr.getHeader(0)) : readerName);
+}var msg;
+var isJSONMap = (leader.charAt(0) == '{');
+var lines = new Array(16);
+var nLines = 0;
+for (var i = 0; i < lines.length; ++i) {
+lines[i] = llr.readLineWithNewline();
+if (lines[i].length > 0) nLines++;
+}
+if ((readerName = J.adapter.smarter.Resolver.checkSpecial1(nLines, lines, leader)) != null) return readerName;
+if ((readerName = J.adapter.smarter.Resolver.checkLineStarts(lines)) != null) return readerName;
+if ((readerName = J.adapter.smarter.Resolver.checkHeaderContains(llr.getHeader(0))) != null) {
+return readerName;
+}if ((readerName = J.adapter.smarter.Resolver.checkSpecial2(lines)) != null) return readerName;
+if (isJSONMap) {
+var json = rdr.readLine();
+if ((readerName = J.adapter.smarter.Resolver.checkJSONContains(json)) != null) {
+if (htParams != null) htParams.put("fileData", json);
+return readerName;
+}msg = (htParams == null ? null : json.substring(0, Math.min(100, json.length)));
+} else {
+msg = (htParams == null ? null : "\n" + lines[0] + "\n" + lines[1] + "\n" + lines[2] + "\n");
+}return msg;
+}, "~O,java.util.Map");
+c$.getBinaryType = Clazz.defineMethod(c$, "getBinaryType",
+function(inputStream){
+var magic4 = null;
+return (JU.Rdr.isPickleS(inputStream) ? "PyMOL" : (JU.Rdr.getMagic(inputStream, 1)[0] & 0xFF) == 0xDE ? "MMTF" : (JU.Rdr.getMagic(inputStream, 10)[9] & 0xFF) == 0xB6 ? "BCIF" : J.adapter.smarter.Resolver.bytesMatch((magic4 = JU.Rdr.getMagic(inputStream, 4)), J.adapter.smarter.Resolver.cdxMagic) ? "CDX" : J.adapter.smarter.Resolver.bytesMatch(magic4, J.adapter.smarter.Resolver.cmdfMagic) ? "Cmdf" : null);
+}, "java.io.InputStream");
+c$.bytesMatch = Clazz.defineMethod(c$, "bytesMatch",
+function(a, b){
+if (b.length > a.length) return false;
+for (var i = b.length; --i >= 0; ) {
+if (a[i] != b[i]) return false;
+}
+return true;
+}, "~A,~A");
+c$.checkFileStart = Clazz.defineMethod(c$, "checkFileStart",
+function(leader){
+for (var i = 0; i < J.adapter.smarter.Resolver.fileStartsWithRecords.length; ++i) {
+var recordTags = J.adapter.smarter.Resolver.fileStartsWithRecords[i];
+for (var j = 1; j < recordTags.length; ++j) {
+var recordTag = recordTags[j];
+if (leader.startsWith(recordTag)) return recordTags[0];
+}
+}
+return null;
+}, "~S");
+c$.checkSpecial1 = Clazz.defineMethod(c$, "checkSpecial1",
+function(nLines, lines, leader){
+if (nLines == 1 && lines[0].length > 0 && JU.PT.isDigit(lines[0].charAt(0))) return "Jme";
+if (J.adapter.smarter.Resolver.checkMopacGraphf(lines)) return "MopacGraphf";
+if (J.adapter.smarter.Resolver.checkOdyssey(lines)) return "Odyssey";
+switch (J.adapter.smarter.Resolver.checkMol(lines)) {
+case 1:
+case 3:
+case 2000:
+case 3000:
+return "Mol";
+}
+switch (J.adapter.smarter.Resolver.checkXyz(lines)) {
+case 1:
+return "Xyz";
+case 2:
+return "Bilbao";
+case 3:
+return "PWmat";
+}
+if (J.adapter.smarter.Resolver.checkAlchemy(lines[0])) return "Alchemy";
+if (J.adapter.smarter.Resolver.checkFoldingXyz(lines)) return "FoldingXyz";
+if (J.adapter.smarter.Resolver.checkXSF(lines)) return "Xcrysden";
+if (J.adapter.smarter.Resolver.checkCube(lines)) return "Cube";
+if (J.adapter.smarter.Resolver.checkWien2k(lines)) return "Wien2k";
+if (J.adapter.smarter.Resolver.checkAims(lines)) return "Aims";
+if (J.adapter.smarter.Resolver.checkGenNBO(lines, leader)) return "GenNBO";
+return null;
+}, "~N,~A,~S");
+c$.checkXSF = Clazz.defineMethod(c$, "checkXSF",
+function(lines){
+var i = 0;
+while (lines[i].length == 0) {
+i++;
+}
+return (lines[i].startsWith("ANIMSTEPS ") || lines[i].equals("ATOMS\n") && JU.PT.parseInt(lines[i + 1]) > 0);
+}, "~A");
+c$.checkAims = Clazz.defineMethod(c$, "checkAims",
+function(lines){
+for (var i = 0; i < lines.length; i++) {
+if (lines[i].startsWith("mol 1")) return false;
+var tokens = JU.PT.getTokens(lines[i]);
+if (tokens.length == 0) continue;
+if (tokens[0].startsWith("atom") && tokens.length > 4 && Float.isNaN(JU.PT.parseFloat(tokens[4])) || tokens[0].startsWith("multipole") && tokens.length >= 6 || tokens[0].startsWith("lattice_vector") && tokens.length >= 4) return true;
+}
+return false;
+}, "~A");
+c$.checkAlchemy = Clazz.defineMethod(c$, "checkAlchemy",
+function(line){
+var pt;
+if ((pt = line.indexOf("ATOMS")) > 0 && line.indexOf("BONDS") > pt) {
+var n = JU.PT.parseInt(line.substring(0, pt).trim());
+return (n > 0);
+}return false;
+}, "~S");
+c$.isInt = Clazz.defineMethod(c$, "isInt",
+function(s){
+J.adapter.smarter.Resolver.n[0] = 0;
+s = s.trim();
+return s.length > 0 && JU.PT.parseIntNext(s, J.adapter.smarter.Resolver.n) != -2147483648 && J.adapter.smarter.Resolver.n[0] == s.length;
+}, "~S");
+c$.isFloat = Clazz.defineMethod(c$, "isFloat",
+function(s){
+return !Float.isNaN(JU.PT.parseFloat(s));
+}, "~S");
+c$.checkCube = Clazz.defineMethod(c$, "checkCube",
+function(lines){
+for (var j = 2; j <= 5; j++) {
+var tokens2 = new java.util.StringTokenizer(lines[j]);
+var n = tokens2.countTokens();
+if (!(n == 4 || j == 2 && n == 5) || !J.adapter.smarter.Resolver.isInt(tokens2.nextToken())) return false;
+for (var i = 3; --i >= 0; ) if (!J.adapter.smarter.Resolver.isFloat(tokens2.nextToken())) return false;
+
+if (n == 5 && !J.adapter.smarter.Resolver.isInt(tokens2.nextToken())) return false;
+}
+return true;
+}, "~A");
+c$.checkFoldingXyz = Clazz.defineMethod(c$, "checkFoldingXyz",
+function(lines){
+var tokens = new java.util.StringTokenizer(lines[0].trim(), " \t");
+if (tokens.countTokens() < 2 || !J.adapter.smarter.Resolver.isInt(tokens.nextToken().trim())) return false;
+var secondLine = lines[1].trim();
+if (secondLine.length == 0) secondLine = lines[2].trim();
+tokens = new java.util.StringTokenizer(secondLine, " \t");
+return (tokens.countTokens() > 0 && J.adapter.smarter.Resolver.isInt(tokens.nextToken().trim()));
+}, "~A");
+c$.checkGenNBO = Clazz.defineMethod(c$, "checkGenNBO",
+function(lines, leader){
+return (leader.indexOf("$GENNBO") >= 0 || lines[1].startsWith(" Basis set information needed for plotting orbitals") || lines[1].indexOf("s in the AO basis:") >= 0 || lines[1].indexOf("***** NBO ") >= 0 || lines[2].indexOf(" N A T U R A L A T O M I C O R B I T A L") >= 0);
+}, "~A,~S");
+c$.checkMol = Clazz.defineMethod(c$, "checkMol",
+function(lines){
+var line4trimmed = ("X" + lines[3]).trim().toUpperCase();
+if (line4trimmed.length < 7 || line4trimmed.indexOf(".") >= 0 || lines[0].startsWith("data_")) return 0;
+if (line4trimmed.endsWith("V2000")) return 2000;
+if (line4trimmed.endsWith("V3000")) return 3000;
+var n1 = JU.PT.parseInt(lines[3].substring(0, 3).trim());
+var n2 = JU.PT.parseInt(lines[3].substring(3, 6).trim());
+return (n1 > 0 && n2 >= 0 && lines[0].indexOf("@") != 0 && lines[1].indexOf("@") != 0 && lines[2].indexOf("@") != 0 ? 3 : 0);
+}, "~A");
+c$.checkMopacGraphf = Clazz.defineMethod(c$, "checkMopacGraphf",
+function(lines){
+return (lines[0].indexOf("MOPAC-Graphical data") > 2);
+}, "~A");
+c$.checkOdyssey = Clazz.defineMethod(c$, "checkOdyssey",
+function(lines){
+var i;
+for (i = 0; i < lines.length; i++) if (!lines[i].startsWith("C ") && lines[i].length != 0) break;
+
+if (i >= lines.length || lines[i].charAt(0) != ' ' || (i = i + 2) + 1 >= lines.length) return false;
+var l = lines[i];
+if (l.length < 3) return false;
+var spin = JU.PT.parseInt(l.substring(2).trim());
+var charge = JU.PT.parseInt(l.substring(0, 2).trim());
+if ((l = lines[i + 1]).length < 2) return false;
+var atom1 = JU.PT.parseInt(l.substring(0, 2).trim());
+if (spin < 0 || spin > 5 || atom1 <= 0 || charge == -2147483648 || charge > 5) return false;
+var atomline = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(l, null, 5);
+return !Float.isNaN(atomline[1]) && !Float.isNaN(atomline[2]) && !Float.isNaN(atomline[3]) && Float.isNaN(atomline[4]);
+}, "~A");
+c$.checkWien2k = Clazz.defineMethod(c$, "checkWien2k",
+function(lines){
+return (lines[2].startsWith("MODE OF CALC=") || lines[2].startsWith(" RELA") || lines[2].startsWith(" NREL"));
+}, "~A");
+c$.checkXyz = Clazz.defineMethod(c$, "checkXyz",
+function(lines){
+var checkPWM = false;
+var i = JU.PT.parseInt(lines[0]);
+if (i >= 0 && lines[0].trim().equals("" + i)) {
+if (J.adapter.smarter.Resolver.isInt(lines[2])) return 2;
+checkPWM = true;
+}if (lines[0].indexOf("Bilbao Crys") >= 0) return 2;
+var s;
+if ((checkPWM || lines.length > 5 && i > 0) && ((s = lines[1].trim().toUpperCase()).startsWith("LATTICE VECTOR") || s.equals("LATTICE"))) return 3;
+return (checkPWM ? 1 : 0);
+}, "~A");
+c$.checkLineStarts = Clazz.defineMethod(c$, "checkLineStarts",
+function(lines){
+for (var i = 0; i < J.adapter.smarter.Resolver.lineStartsWithRecords.length; ++i) {
+var recordTags = J.adapter.smarter.Resolver.lineStartsWithRecords[i];
+for (var j = 1; j < recordTags.length; ++j) {
+var recordTag = recordTags[j];
+for (var k = 0; k < lines.length; k++) {
+if (lines[k].startsWith(recordTag)) return recordTags[0];
+}
+}
+}
+return null;
+}, "~A");
+c$.checkHeaderContains = Clazz.defineMethod(c$, "checkHeaderContains",
+function(header){
+for (var i = 0; i < J.adapter.smarter.Resolver.headerContainsRecords.length; ++i) {
+var fileType = J.adapter.smarter.Resolver.checkHeaderRecords(header, J.adapter.smarter.Resolver.headerContainsRecords[i]);
+if (fileType != null) return fileType;
+}
+return null;
+}, "~S");
+c$.checkJSONContains = Clazz.defineMethod(c$, "checkJSONContains",
+function(header){
+for (var i = 0; i < J.adapter.smarter.Resolver.jsonContainsRecords.length; ++i) {
+var fileType = J.adapter.smarter.Resolver.checkHeaderRecords(header, J.adapter.smarter.Resolver.jsonContainsRecords[i]);
+if (fileType != null) return fileType;
+}
+return null;
+}, "~S");
+c$.checkHeaderRecords = Clazz.defineMethod(c$, "checkHeaderRecords",
+function(header, recordTags){
+for (var j = 1; j < recordTags.length; ++j) {
+var recordTag = recordTags[j];
+if (header.indexOf(recordTag) < 0) continue;
+var type = recordTags[0];
+if (!type.equals("Xml")) return type;
+if (header.indexOf("/AFLOWDATA/") >= 0 || header.indexOf("-- Structure PRE --") >= 0) return "AFLOW";
+return (header.indexOf("= 0) ? J.adapter.smarter.Resolver.getXmlType(header) : null);
+}
+return null;
+}, "~S,~A");
+c$.getXmlType = Clazz.defineMethod(c$, "getXmlType",
+function(header){
+if (header.indexOf("http://www.molpro.net/") >= 0) {
+return "XmlMolpro";
+}if (header.indexOf("odyssey") >= 0) {
+return "XmlOdyssey";
+}if (header.indexOf("C3XML") >= 0) {
+return "XmlChem3d";
+}if (header.indexOf("CDXML") >= 0) {
+return "XmlCdx";
+}if (header.indexOf("arguslab") >= 0) {
+return "XmlArgus";
+}if (header.indexOf("jvxl") >= 0 || header.indexOf("http://www.xml-cml.org/schema") >= 0 || header.indexOf("cml:") >= 0 || header.indexOf("") >= 0) {
+return "XmlCml";
+}if (header.indexOf("XSD") >= 0) {
+return "XmlXsd";
+}if (header.indexOf(">vasp") >= 0) {
+return "XmlVasp";
+}if (header.indexOf("") >= 0) {
+return "XmlQE";
+}return "XmlCml(unidentified)";
+}, "~S");
+c$.checkSpecial2 = Clazz.defineMethod(c$, "checkSpecial2",
+function(lines){
+if (J.adapter.smarter.Resolver.checkGromacs(lines)) return "Gromacs";
+if (J.adapter.smarter.Resolver.checkCrystal(lines)) return "Crystal";
+if (J.adapter.smarter.Resolver.checkFAH(lines)) return "FAH";
+var s = J.adapter.smarter.Resolver.checkCastepVaspSiesta(lines);
+if (s != null) return s;
+return null;
+}, "~A");
+c$.checkFAH = Clazz.defineMethod(c$, "checkFAH",
+function(lines){
+var s = lines[0].trim() + lines[2].trim();
+return s.equals("{\"atoms\": [");
+}, "~A");
+c$.checkCrystal = Clazz.defineMethod(c$, "checkCrystal",
+function(lines){
+var s = lines[1].trim();
+if (s.equals("SLAB") || s.equals("MOLECULE") || s.equals("CRYSTAL") || s.equals("POLYMER") || (s = lines[3]).equals("SLAB") || s.equals("MOLECULE") || s.equals("POLYMER")) return true;
+for (var i = 0; i < lines.length; i++) {
+if (lines[i].trim().equals("OPTGEOM") || lines[i].trim().equals("FREQCALC") || lines[i].contains("DOVESI") || lines[i].contains("TORINO") || lines[i].contains("http://www.crystal.unito.it") || lines[i].contains("Pcrystal") || lines[i].contains("MPPcrystal") || lines[i].contains("crystal executable")) return true;
+}
+return false;
+}, "~A");
+c$.checkGromacs = Clazz.defineMethod(c$, "checkGromacs",
+function(lines){
+if (JU.PT.parseInt(lines[1]) == -2147483648) return false;
+var len = -1;
+for (var i = 2; i < 16 && len != 0; i++) if ((len = lines[i].length) != 69 && len != 45 && len != 0) return false;
+
+return true;
+}, "~A");
+c$.checkCastepVaspSiesta = Clazz.defineMethod(c$, "checkCastepVaspSiesta",
+function(lines){
+for (var i = 0; i < lines.length; i++) {
+var line = lines[i].toUpperCase();
+if (line.indexOf("FREQUENCIES IN CM-1") == 1 || line.contains("CASTEP") || line.startsWith("%BLOCK LATTICE_ABC") || line.startsWith("%BLOCK LATTICE_CART") || line.startsWith("%BLOCK POSITIONS_FRAC") || line.startsWith("%BLOCK POSITIONS_ABS") || line.contains("<-- E")) return "Castep";
+if (line.contains("%BLOCK")) return "Siesta";
+if (i >= 6 && i < 10 && (line.startsWith("DIRECT") || line.startsWith("CARTESIAN"))) return "VaspPoscar";
+}
+return null;
+}, "~A");
+c$.getFileTypefromFilter = Clazz.defineMethod(c$, "getFileTypefromFilter",
+function(filter){
+var pt = (filter == null ? -1 : filter.toLowerCase().indexOf("filetype"));
+return (pt < 0 ? null : filter.substring(pt + 8, (filter + ";").indexOf(";", pt)).$replace('=', ' ').trim());
+}, "~S");
+c$.fixDOSName = Clazz.defineMethod(c$, "fixDOSName",
+function(fileName){
+return (fileName.indexOf(":\\") >= 0 ? fileName.$replace('\\', '/') : fileName);
+}, "~S");
+c$.readerSets = Clazz.newArray(-1, ["cif.", ";Cif;Cif2;MMCif;MMTF;MagCif;BCIF;", "molxyz.", ";Mol3D;Mol;Xyz;", "more.", ";AFLOW;BinaryDcd;CDX;Gromacs;Jcampdx;MdCrd;MdTop;Mol2;TlsDataOnly;", "quantum.", ";Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GaussianFchk;GaussianWfn;Jaguar;Molden;MopacGraphf;GenNBO;NWChem;Psi;Qchem;QCJSON;WebMO;Orca;MO;Ams;", "pdb.", ";Pdb;Pqr;P2n;JmolData;", "pymol.", ";PyMOL;", "simple.", ";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;Input;FAH;", "spartan.", ";Spartan;SpartanSmol;Odyssey;", "xtal.", ";Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;VaspPoscar;Wien2k;Xcrysden;PWmat;Optimade;Cmdf;", "xml.", ";XmlCdx;XmlArgus;XmlCml;XmlChem3d;XmlMolpro;XmlOdyssey;XmlXsd;XmlVasp;XmlQE;"]);
+c$.cdxMagic = Clazz.newByteArray(-1, ['V', 'j', 'C', 'D']);
+c$.cmdfMagic = Clazz.newByteArray(-1, ['C', 'M', 'D', 'F']);
+c$.sptRecords = Clazz.newArray(-1, ["spt", "# Jmol state", "# Jmol script", "JmolManifest"]);
+c$.m3dStartRecords = Clazz.newArray(-1, ["Alchemy", "STRUCTURE 1.00 1"]);
+c$.cubeFileStartRecords = Clazz.newArray(-1, ["Cube", "JVXL", "#JVXL"]);
+c$.mol2Records = Clazz.newArray(-1, ["Mol2", "mol2", "@"]);
+c$.webmoFileStartRecords = Clazz.newArray(-1, ["WebMO", "[HEADER]"]);
+c$.moldenFileStartRecords = Clazz.newArray(-1, ["Molden", "[Molden", "MOLDEN", "[MOLDEN"]);
+c$.dcdFileStartRecords = Clazz.newArray(-1, ["BinaryDcd", "T\0\0\0CORD", "\0\0\0TCORD"]);
+c$.tlsDataOnlyFileStartRecords = Clazz.newArray(-1, ["TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"]);
+c$.inputFileStartRecords = Clazz.newArray(-1, ["Input", "#ZMATRIX", "%mem=", "AM1", "$rungauss"]);
+c$.magresFileStartRecords = Clazz.newArray(-1, ["Magres", "#$magres", "# magres"]);
+c$.pymolStartRecords = Clazz.newArray(-1, ["PyMOL", "}q"]);
+c$.janaStartRecords = Clazz.newArray(-1, ["Jana", "Version Jana"]);
+c$.jsonStartRecords = Clazz.newArray(-1, ["JSON", "{\"mol\":"]);
+c$.jcampdxStartRecords = Clazz.newArray(-1, ["Jcampdx", "##TITLE"]);
+c$.jmoldataStartRecords = Clazz.newArray(-1, ["JmolData", "REMARK 6 Jmol"]);
+c$.pqrStartRecords = Clazz.newArray(-1, ["Pqr", "REMARK 1 PQR", "REMARK The B-factors"]);
+c$.p2nStartRecords = Clazz.newArray(-1, ["P2n", "REMARK 1 P2N"]);
+c$.cif2StartRecords = Clazz.newArray(-1, ["Cif2", "#\\#CIF_2", "\u00EF\u00BB\u00BF#\\#CIF_2"]);
+c$.xmlStartRecords = Clazz.newArray(-1, ["Xml", "Bilbao Crystallographic Server<"]);
+c$.xmlContainsRecords = Clazz.newArray(-1, ["Xml", "", " 0 && size <= 3 && f.startsWith("{")) {
+var type = (f.contains("version\":\"DSSR") ? "dssr" : f.contains("/outliers/") ? "validation" : "domains");
+var x = vwr.parseJSONMap(f);
+if (x != null) htParams.put(type, (type.equals("dssr") ? x : JS.SV.getVariableMap(x)));
+continue;
+}if (name.indexOf("|") >= 0) name = JU.PT.rep(name, "_", "/");
+if (i == 1) {
+if (name.indexOf("/rna3dhub/") >= 0) {
+s += "\n_rna3d \n;" + f + "\n;\n";
+continue;
+}if (name.indexOf("/dssr/") >= 0) {
+s += "\n_dssr \n;" + f + "\n;\n";
+continue;
+}}s += f;
+if (!s.endsWith("\n")) s += "\n";
+}
+size = 1;
+reader = JU.Rdr.getBR(s);
+}var readers = (getReadersOnly ? new Array(size) : null);
+var atomsets = (getReadersOnly ? null : new Array(size));
+var r = null;
+for (var i = 0; i < size; i++) {
+try {
+htParams.put("vwr", vwr);
+if (reader == null) reader = filesReader.getBufferedReaderOrBinaryDocument(i, false);
+if (!(Clazz.instanceOf(reader,"java.io.BufferedReader") || Clazz.instanceOf(reader,"javajs.api.GenericBinaryDocument"))) return reader;
+var fullPathName = names[i];
+htParams.put("fullPathName", fullPathName);
+var ret = J.adapter.smarter.Resolver.getAtomCollectionReader(names[i], (types == null ? null : types[i]), reader, htParams, i);
+if (!(Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollectionReader"))) return ret;
+r = ret;
+r.setup(null, null, null);
+if (r.isBinary) {
+r.setup(names[i], htParams, filesReader.getBufferedReaderOrBinaryDocument(i, true));
+} else {
+r.setup(names[i], htParams, reader);
+}reader = null;
+if (getReadersOnly) {
+readers[i] = r;
+} else {
+ret = r.readData();
+if (!(Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection"))) return ret;
+atomsets[i] = ret;
+if (atomsets[i].errorMessage != null) return atomsets[i].errorMessage;
+}} catch (e) {
+JU.Logger.error("" + e);
+e.printStackTrace();
+return "" + e;
+}
+}
+if (getReadersOnly) return readers;
+return this.getAtomSetCollectionFromSet(readers, atomsets, htParams);
+}, "J.api.JmolFilesReaderInterface,~A,~A,java.util.Map,~B");
+Clazz.overrideMethod(c$, "getAtomSetCollectionFromSet",
+function(readerSet, atomsets, htParams){
+var readers = readerSet;
+var asc = (atomsets == null ? new Array(readers.length) : atomsets);
+if (atomsets == null) {
+for (var i = 0; i < readers.length; i++) {
+if (readers[i] != null) try {
+var ret = readers[i].readData();
+if (!(Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection"))) return ret;
+asc[i] = ret;
+if (asc[i].errorMessage != null) return asc[i].errorMessage;
+} catch (e) {
+JU.Logger.error("" + e);
+return "" + e;
+}
+}
+}var result;
+if (htParams.containsKey("trajectorySteps")) {
+result = asc[0];
+try {
+if (asc.length > 1) asc[0].setInfo("ignoreUnitCell", asc[1].atomSetInfo.get("ignoreUnitCell"));
+result.finalizeTrajectoryAs(htParams.get("trajectorySteps"), htParams.get("vibrationSteps"));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (result.errorMessage == null) result.errorMessage = "" + e;
+} else {
+throw e;
+}
+}
+} else if (asc[0].isTrajectory) {
+result = asc[0];
+for (var i = 1; i < asc.length; i++) asc[0].mergeTrajectories(asc[i]);
+
+} else {
+result = (asc.length == 1 ? asc[0] : new J.adapter.smarter.AtomSetCollection("Array", null, asc, null));
+}return (result.errorMessage == null ? result : result.errorMessage);
+}, "~O,~O,java.util.Map");
+Clazz.overrideMethod(c$, "getAtomSetCollectionFromDOM",
+function(DOMNode, htParams){
+throw new UnsupportedOperationException();
+}, "~O,java.util.Map");
+Clazz.overrideMethod(c$, "finish",
+function(asc){
+(asc).finish();
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomSetCollectionName",
+function(asc){
+return (asc).collectionName;
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomSetCollectionAuxiliaryInfo",
+function(asc){
+return (asc).atomSetInfo;
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomSetCount",
+function(asc){
+return (asc).atomSetCount;
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomSetNumber",
+function(asc, atomSetIndex){
+return (asc).getAtomSetNumber(atomSetIndex);
+}, "~O,~N");
+Clazz.overrideMethod(c$, "getAtomSetName",
+function(asc, atomSetIndex){
+return (asc).getAtomSetName(atomSetIndex);
+}, "~O,~N");
+Clazz.overrideMethod(c$, "getAtomSetAuxiliaryInfo",
+function(asc, atomSetIndex){
+return (asc).getAtomSetAuxiliaryInfo(atomSetIndex);
+}, "~O,~N");
+Clazz.overrideMethod(c$, "getHydrogenAtomCount",
+function(asc){
+return (asc).getHydrogenAtomCount();
+}, "~O");
+Clazz.overrideMethod(c$, "getBondList",
+function(asc){
+return (asc).getBondList();
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomCount",
+function(asc, atomSetIndex){
+var a = asc;
+if (atomSetIndex < 0) return (a.bsAtoms == null ? a.ac : a.bsAtoms.cardinality());
+if (a.bsAtoms == null) return a.getAtomSetAtomCount(atomSetIndex);
+var b = JU.BSUtil.copy(a.bsAtoms);
+var i0 = a.getAtomSetAtomIndex(atomSetIndex);
+b.and(JU.BSUtil.newBitSet2(i0, i0 + a.getAtomSetAtomCount(atomSetIndex)));
+return b.cardinality();
+}, "~O,~N");
+Clazz.overrideMethod(c$, "coordinatesAreFractional",
+function(asc){
+return (asc).coordinatesAreFractional;
+}, "~O");
+Clazz.overrideMethod(c$, "getAtomIterator",
+function(asc){
+return new J.adapter.smarter.AtomIterator(asc);
+}, "~O");
+Clazz.overrideMethod(c$, "getBondIterator",
+function(asc){
+return ((asc).bondCount == 0 ? null : new J.adapter.smarter.BondIterator(asc));
+}, "~O");
+Clazz.overrideMethod(c$, "getStructureIterator",
+function(asc){
+return (asc).structureCount == 0 ? null : new J.adapter.smarter.StructureIterator(asc);
+}, "~O");
+c$.close = Clazz.defineMethod(c$, "close",
+function(bufferedReader){
+if (Clazz.instanceOf(bufferedReader,"java.io.BufferedReader")) (bufferedReader).close();
+ else (bufferedReader).close();
+}, "~O");
+c$.PATH_SEPARATOR = System.getProperty("path.separator", "/");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Structure.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Structure.js
new file mode 100755
index 000000000000..35228b9fc847
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/Structure.js
@@ -0,0 +1,74 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(null, "J.adapter.smarter.Structure", ["J.c.STR"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.structureType = null;
+this.substructureType = null;
+this.structureID = null;
+this.strandID = null;
+this.strandCount = 0;
+this.startSequenceNumber = 0;
+this.startChainID = 0;
+this.startInsertionCode = '\0';
+this.endSequenceNumber = 0;
+this.endChainID = 0;
+this.endInsertionCode = '\0';
+this.atomStartEnd = null;
+this.modelStartEnd = null;
+this.bsAll = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "Structure", null, Cloneable);
+Clazz.prepareFields (c$, function(){
+this.atomStartEnd = Clazz.newIntArray (2, 0);
+this.modelStartEnd = Clazz.newIntArray(-1, [-1, -1]);
+});
+Clazz.makeConstructor(c$,
+function(modelIndex, structureType, substructureType, structureID, strandID, strandCount, bsAll){
+if (bsAll != null) {
+this.modelStartEnd = Clazz.newIntArray(-1, [0, modelIndex]);
+this.bsAll = bsAll;
+return;
+}this.structureType = structureType;
+this.substructureType = substructureType;
+if (structureID == null) return;
+this.modelStartEnd[0] = this.modelStartEnd[1] = modelIndex;
+this.structureID = structureID;
+this.strandCount = strandCount;
+this.strandID = strandID;
+}, "~N,J.c.STR,J.c.STR,~S,~S,~N,~A");
+c$.getHelixType = Clazz.defineMethod(c$, "getHelixType",
+function(type){
+switch (type) {
+case 1:
+return J.c.STR.HELIXALPHA;
+case 3:
+return J.c.STR.HELIXPI;
+case 5:
+return J.c.STR.HELIX310;
+}
+return J.c.STR.HELIX;
+}, "~N");
+Clazz.defineMethod(c$, "set",
+function(startChainID, startSequenceNumber, startInsertionCode, endChainID, endSequenceNumber, endInsertionCode, istart, iend){
+this.startChainID = startChainID;
+this.startSequenceNumber = startSequenceNumber;
+this.startInsertionCode = startInsertionCode;
+this.endChainID = endChainID;
+this.endSequenceNumber = endSequenceNumber;
+this.endInsertionCode = endInsertionCode;
+this.atomStartEnd[0] = istart;
+this.atomStartEnd[1] = iend;
+}, "~N,~N,~S,~N,~N,~S,~N,~N");
+Clazz.defineMethod(c$, "clone",
+function(){
+var s = null;
+try {
+s = Clazz.superCall(this, J.adapter.smarter.Structure, "clone", []);
+} catch (e) {
+if (Clazz.exceptionOf(e,"CloneNotSupportedException")){
+} else {
+throw e;
+}
+}
+return s;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/StructureIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/StructureIterator.js
new file mode 100755
index 000000000000..f14bf0331cd7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/StructureIterator.js
@@ -0,0 +1,85 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["J.api.JmolAdapterStructureIterator"], "J.adapter.smarter.StructureIterator", ["J.api.JmolAdapter"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.structureCount = 0;
+this.structures = null;
+this.structure = null;
+this.istructure = 0;
+this.bsModelsDefined = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "StructureIterator", J.api.JmolAdapterStructureIterator);
+Clazz.makeConstructor(c$,
+function(asc){
+Clazz.superConstructor (this, J.adapter.smarter.StructureIterator, []);
+this.structureCount = asc.structureCount;
+this.structures = asc.structures;
+this.istructure = 0;
+this.bsModelsDefined = asc.bsStructuredModels;
+}, "J.adapter.smarter.AtomSetCollection");
+Clazz.overrideMethod(c$, "hasNext",
+function(){
+if (this.istructure == this.structureCount) return false;
+this.structure = this.structures[this.istructure++];
+return true;
+});
+Clazz.overrideMethod(c$, "getStructureType",
+function(){
+return this.structure.structureType;
+});
+Clazz.overrideMethod(c$, "getSubstructureType",
+function(){
+return this.structure.substructureType;
+});
+Clazz.overrideMethod(c$, "getStructureID",
+function(){
+return this.structure.structureID;
+});
+Clazz.overrideMethod(c$, "getStrandID",
+function(){
+return this.structure.strandID;
+});
+Clazz.overrideMethod(c$, "getStartChainID",
+function(){
+return this.structure.startChainID;
+});
+Clazz.overrideMethod(c$, "getStartSequenceNumber",
+function(){
+return this.structure.startSequenceNumber;
+});
+Clazz.overrideMethod(c$, "getStartInsertionCode",
+function(){
+return J.api.JmolAdapter.canonizeInsertionCode(this.structure.startInsertionCode);
+});
+Clazz.overrideMethod(c$, "getEndChainID",
+function(){
+return this.structure.endChainID;
+});
+Clazz.overrideMethod(c$, "getEndSequenceNumber",
+function(){
+return this.structure.endSequenceNumber;
+});
+Clazz.overrideMethod(c$, "getEndInsertionCode",
+function(){
+return this.structure.endInsertionCode;
+});
+Clazz.overrideMethod(c$, "getStrandCount",
+function(){
+return this.structure.strandCount;
+});
+Clazz.overrideMethod(c$, "getStructuredModels",
+function(){
+return this.bsModelsDefined;
+});
+Clazz.overrideMethod(c$, "getAtomIndices",
+function(){
+return this.structure.atomStartEnd;
+});
+Clazz.overrideMethod(c$, "getModelIndices",
+function(){
+return this.structure.modelStartEnd;
+});
+Clazz.overrideMethod(c$, "getBSAll",
+function(){
+return this.structure.bsAll;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/XtalSymmetry.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/XtalSymmetry.js
new file mode 100755
index 000000000000..ce3990a49d03
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/smarter/XtalSymmetry.js
@@ -0,0 +1,1162 @@
+Clazz.declarePackage("J.adapter.smarter");
+Clazz.load(["JS.Symmetry", "JU.P3", "$.SB"], "J.adapter.smarter.XtalSymmetry", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.M3", "$.M4", "$.P3i", "$.PT", "$.V3", "J.adapter.smarter.Atom", "JS.SpaceGroup", "$.SymmetryOperation", "$.UnitCell", "JU.BSUtil", "$.Logger", "$.SimpleUnitCell"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.acr = null;
+this.applySymmetryToBonds = false;
+this.asc = null;
+this.baseSymmetry = null;
+this.bondCount0 = 0;
+this.bondsFound = null;
+this.centroidPacked = false;
+this.checkAll = false;
+this.checkNearAtoms = false;
+this.crystalReaderLatticeOpsOnly = false;
+this.disorderMap = null;
+this.disorderMapMax = 0;
+this.doCentroidUnitCell = false;
+this.doNormalize = true;
+this.doPackUnitCell = false;
+this.filterSymop = null;
+this.firstAtom = 0;
+this.latticeCells = null;
+this.latticeOp = 0;
+this.mident = null;
+this.minXYZ = null;
+this.maxXYZ = null;
+this.minXYZ0 = null;
+this.maxXYZ0 = null;
+this.mTemp = null;
+this.ndims = 3;
+this.noSymmetryCount = 0;
+this.nVib = 0;
+this.packingRange = 0;
+this.ptOffset = null;
+this.ptTemp = null;
+this.rminx = 0;
+this.rminy = 0;
+this.rminz = 0;
+this.rmaxx = 0;
+this.rmaxy = 0;
+this.rmaxz = 0;
+this.symmetry = null;
+this.symmetryRange = 0;
+this.trajectoryUnitCells = null;
+this.unitCellParams = null;
+this.unitCellTranslations = null;
+Clazz.instantialize(this, arguments);}, J.adapter.smarter, "XtalSymmetry", null);
+Clazz.prepareFields (c$, function(){
+this.bondsFound = new JU.SB();
+this.ptOffset = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.defineMethod(c$, "addRotatedTensor",
+function(a, t, iSym, reset, symmetry){
+if (this.ptTemp == null) {
+this.ptTemp = new JU.P3();
+this.mTemp = new JU.M3();
+}return a.addTensor((this.acr.getInterface("JU.Tensor")).setFromEigenVectors(symmetry.rotateAxes(iSym, t.eigenVectors, this.ptTemp, this.mTemp), t.eigenValues, t.isIsotropic ? "iso" : t.type, t.id, t), null, reset);
+}, "J.adapter.smarter.Atom,JU.Tensor,~N,~B,J.adapter.smarter.XtalSymmetry.FileSymmetry");
+Clazz.defineMethod(c$, "applySymmetryBio",
+function(thisBiomolecule, applySymmetryToBonds, filter){
+var biomts = thisBiomolecule.get("biomts");
+var len = biomts.size();
+if (this.mident == null) {
+this.mident = new JU.M4();
+this.mident.setIdentity();
+}this.acr.lstNCS = null;
+this.setLatticeCells();
+var lc = (this.latticeCells != null && this.latticeCells[0] != 0 ? Clazz.newIntArray (3, 0) : null);
+if (lc != null) for (var i = 0; i < 3; i++) lc[i] = this.latticeCells[i];
+
+this.latticeCells = null;
+var bmChains = this.acr.getFilterWithCase("BMCHAINS");
+var fixBMChains = (bmChains == null ? -1 : bmChains.length < 2 ? 0 : JU.PT.parseInt(bmChains.substring(1)));
+if (fixBMChains == -2147483648) {
+fixBMChains = -(bmChains.charAt(1)).charCodeAt(0);
+}var particleMode = (filter.indexOf("BYCHAIN") >= 0 ? 1 : filter.indexOf("BYSYMOP") >= 0 ? 2 : 0);
+this.doNormalize = false;
+var biomtchains = thisBiomolecule.get("chains");
+(this.symmetry = new J.adapter.smarter.XtalSymmetry.FileSymmetry()).setSpaceGroup(this.doNormalize);
+this.addSpaceGroupOperation("x,y,z", false);
+var name = thisBiomolecule.get("name");
+this.setAtomSetSpaceGroupName(this.acr.sgName = name);
+this.applySymmetryToBonds = applySymmetryToBonds;
+this.bondCount0 = this.asc.bondCount;
+this.firstAtom = this.asc.getLastAtomSetAtomIndex();
+var atomMax = this.asc.ac;
+var ht = new java.util.Hashtable();
+var nChain = 0;
+var atoms = this.asc.atoms;
+var addBonds = (this.bondCount0 > this.asc.bondIndex0 && applySymmetryToBonds);
+switch (particleMode) {
+case 1:
+for (var i = atomMax; --i >= this.firstAtom; ) {
+var id = Integer.$valueOf(atoms[i].chainID);
+var bs = ht.get(id);
+if (bs == null) {
+nChain++;
+ht.put(id, bs = new JU.BS());
+}bs.set(i);
+}
+this.asc.bsAtoms = new JU.BS();
+for (var i = 0; i < nChain; i++) {
+this.asc.bsAtoms.set(atomMax + i);
+var a = new J.adapter.smarter.Atom();
+a.set(0, 0, 0);
+a.radius = 16;
+this.asc.addAtom(a);
+}
+var ichain = 0;
+for (var e, $e = ht.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var a = atoms[atomMax + ichain++];
+var bs = e.getValue();
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) a.add(atoms[i]);
+
+a.scale(1 / bs.cardinality());
+a.atomName = "Pt" + ichain;
+a.chainID = e.getKey().intValue();
+}
+this.firstAtom = atomMax;
+atomMax += nChain;
+addBonds = false;
+break;
+case 2:
+this.asc.bsAtoms = new JU.BS();
+this.asc.bsAtoms.set(atomMax);
+var a = atoms[atomMax] = new J.adapter.smarter.Atom();
+a.set(0, 0, 0);
+for (var i = atomMax; --i >= this.firstAtom; ) a.add(atoms[i]);
+
+a.scale(1 / (atomMax - this.firstAtom));
+a.atomName = "Pt";
+a.radius = 16;
+this.asc.addAtom(a);
+this.firstAtom = atomMax++;
+addBonds = false;
+break;
+}
+var assemblyIdAtoms = thisBiomolecule.get("asemblyIdAtoms");
+if (filter.indexOf("#<") >= 0) {
+len = Math.min(len, JU.PT.parseInt(filter.substring(filter.indexOf("#<") + 2)) - 1);
+filter = JU.PT.rep(filter, "#<", "_<");
+}var maxChain = 0;
+for (var iAtom = this.firstAtom; iAtom < atomMax; iAtom++) {
+atoms[iAtom].bsSymmetry = new JU.BS();
+var chainID = atoms[iAtom].chainID;
+if (chainID > maxChain) maxChain = chainID;
+}
+var bsAtoms = this.asc.bsAtoms;
+var atomMap = (addBonds ? Clazz.newIntArray (this.asc.ac, 0) : null);
+for (var imt = (biomtchains == null ? 1 : 0); imt < len; imt++) {
+if (filter.indexOf("!#") >= 0) {
+if (filter.indexOf("!#" + (imt + 1) + ";") >= 0) continue;
+} else if (filter.indexOf("#") >= 0 && filter.indexOf("#" + (imt + 1) + ";") < 0) {
+continue;
+}var mat = biomts.get(imt);
+var notIdentity = !mat.equals(this.mident);
+var chains = (biomtchains == null ? null : biomtchains.get(imt));
+if (chains != null && assemblyIdAtoms != null) {
+bsAtoms = new JU.BS();
+for (var e, $e = assemblyIdAtoms.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) if (chains.indexOf(":" + e.getKey() + ";") >= 0) bsAtoms.or(e.getValue());
+
+if (this.asc.bsAtoms != null) bsAtoms.and(this.asc.bsAtoms);
+chains = null;
+}var lastID = -1;
+var id;
+var skipping = false;
+for (var iAtom = this.firstAtom; iAtom < atomMax; iAtom++) {
+if (bsAtoms != null) {
+skipping = !bsAtoms.get(iAtom);
+} else if (chains != null && (id = atoms[iAtom].chainID) != lastID) {
+skipping = (chains.indexOf(":" + this.acr.vwr.getChainIDStr(lastID = id) + ";") < 0);
+}if (skipping) continue;
+try {
+var atomSite = atoms[iAtom].atomSite;
+var atom1;
+if (addBonds) atomMap[atomSite] = this.asc.ac;
+atom1 = this.asc.newCloneAtom(atoms[iAtom]);
+atom1.bondingRadius = imt;
+this.asc.atomSymbolicMap.put("" + atom1.atomSerial, atom1);
+if (this.asc.bsAtoms != null) this.asc.bsAtoms.set(atom1.index);
+atom1.atomSite = atomSite;
+if (notIdentity) mat.rotTrans(atom1);
+atom1.bsSymmetry = JU.BSUtil.newAndSetBit(imt);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+this.asc.errorMessage = "appendAtomCollection error: " + e;
+} else {
+throw e;
+}
+}
+}
+if (notIdentity) this.symmetry.addBioMoleculeOperation(mat, false);
+if (addBonds) {
+for (var bondNum = this.asc.bondIndex0; bondNum < this.bondCount0; bondNum++) {
+var bond = this.asc.bonds[bondNum];
+var iAtom1 = atomMap[atoms[bond.atomIndex1].atomSite];
+var iAtom2 = atomMap[atoms[bond.atomIndex2].atomSite];
+this.asc.addNewBondWithOrder(iAtom1, iAtom2, bond.order);
+}
+}}
+if (biomtchains != null) {
+if (this.asc.bsAtoms == null) this.asc.bsAtoms = JU.BSUtil.newBitSet2(0, this.asc.ac);
+this.asc.bsAtoms.clearBits(this.firstAtom, atomMax);
+if (particleMode == 0) {
+if (fixBMChains != -1) {
+var assignABC = (fixBMChains != 0);
+var bsChains = (assignABC ? new JU.BS() : null);
+atoms = this.asc.atoms;
+var firstNew = 0;
+if (assignABC) {
+firstNew = (fixBMChains < 0 ? Math.max(-fixBMChains, maxChain + 1) : Math.max(maxChain + fixBMChains, 65));
+bsChains.setBits(0, firstNew - 1);
+bsChains.setBits(91, 97);
+bsChains.setBits(123, 200);
+}var bsAll = (this.asc.structureCount == 1 ? this.asc.structures[0].bsAll : null);
+var chainMap = new java.util.Hashtable();
+var knownMap = new java.util.Hashtable();
+var knownAtomMap = (bsAll == null ? null : new java.util.Hashtable());
+var lastKnownAtom = null;
+for (var i = atomMax, n = this.asc.ac; i < n; i++) {
+var ic = atoms[i].chainID;
+var isym = atoms[i].bsSymmetry.nextSetBit(0);
+var ch0 = this.acr.vwr.getChainIDStr(ic);
+var ch = (isym == 0 ? ch0 : ch0 + isym);
+var known = chainMap.get(ch);
+if (known == null) {
+if (assignABC && isym != 0) {
+var pt = (firstNew < 200 ? bsChains.nextClearBit(firstNew) : 200);
+if (pt < 200) {
+bsChains.set(pt);
+known = Integer.$valueOf(this.acr.vwr.getChainID("" + String.fromCharCode(pt), true));
+firstNew = pt;
+} else {
+}}if (known == null) known = Integer.$valueOf(this.acr.vwr.getChainID(ch, true));
+if (ch !== ch0) {
+knownMap.put(known, Integer.$valueOf(ic));
+if (bsAll != null) {
+if (lastKnownAtom != null) lastKnownAtom[1] = i;
+knownAtomMap.put(known, lastKnownAtom = Clazz.newIntArray(-1, [i, n]));
+}}chainMap.put(ch, known);
+}atoms[i].chainID = known.intValue();
+}
+if (this.asc.structureCount > 0) {
+var strucs = this.asc.structures;
+var nStruc = this.asc.structureCount;
+for (var e, $e = knownMap.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var known = e.getKey();
+var ch1 = known.intValue();
+var ch0 = e.getValue().intValue();
+for (var i = 0; i < nStruc; i++) {
+var s = strucs[i];
+if (s.bsAll != null) {
+} else if (s.startChainID == s.endChainID) {
+if (s.startChainID == ch0) {
+var s1 = s.clone();
+s1.startChainID = s1.endChainID = ch1;
+this.asc.addStructure(s1);
+}} else {
+System.err.println("XtalSymmetry not processing biomt chain structure " + this.acr.vwr.getChainIDStr(ch0) + " to " + this.acr.vwr.getChainIDStr(ch1));
+}}
+}
+}}var vConnect = this.asc.getAtomSetAuxiliaryInfoValue(-1, "PDB_CONECT_bonds");
+if (!addBonds && vConnect != null) {
+for (var i = vConnect.size(); --i >= 0; ) {
+var bond = vConnect.get(i);
+var a = this.asc.getAtomFromName("" + bond[0]);
+var b = this.asc.getAtomFromName("" + bond[1]);
+if (a != null && b != null && a.bondingRadius != b.bondingRadius && (bsAtoms == null || bsAtoms.get(a.index) && bsAtoms.get(b.index)) && a.distanceSquared(b) > 25.0) {
+vConnect.removeItemAt(i);
+System.out.println("long interchain bond removed for @" + a.atomSerial + "-@" + b.atomSerial);
+}}
+}}for (var i = atomMax, n = this.asc.ac; i < n; i++) {
+this.asc.atoms[i].bondingRadius = NaN;
+}
+}this.noSymmetryCount = atomMax - this.firstAtom;
+this.finalizeSymmetry(this.symmetry);
+this.setCurrentModelInfo(len, null, null);
+this.reset();
+}, "java.util.Map,~B,~S");
+Clazz.defineMethod(c$, "getBaseSymmetry",
+function(){
+return (this.baseSymmetry == null ? this.symmetry : this.baseSymmetry);
+});
+Clazz.defineMethod(c$, "getOverallSpan",
+function(){
+return (this.maxXYZ0 == null ? JU.V3.new3(this.maxXYZ.x - this.minXYZ.x, this.maxXYZ.y - this.minXYZ.y, this.maxXYZ.z - this.minXYZ.z) : JU.V3.newVsub(this.maxXYZ0, this.minXYZ0));
+});
+Clazz.defineMethod(c$, "getSymmetry",
+function(){
+return (this.symmetry == null ? (this.symmetry = new J.adapter.smarter.XtalSymmetry.FileSymmetry()) : this.symmetry);
+});
+Clazz.defineMethod(c$, "isWithinCell",
+function(ndims, pt, minX, maxX, minY, maxY, minZ, maxZ, slop){
+return (pt.x > minX - slop && pt.x < maxX + slop && (ndims < 2 || pt.y > minY - slop && pt.y < maxY + slop) && (ndims < 3 || pt.z > minZ - slop && pt.z < maxZ + slop));
+}, "~N,JU.P3,~N,~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "scaleFractionalVibs",
+function(){
+var params = this.acr.unitCellParams;
+var ptScale = JU.P3.new3(1 / params[0], 1 / params[1], 1 / params[2]);
+var i0 = this.asc.getAtomSetAtomIndex(this.asc.iSet);
+for (var i = this.asc.ac; --i >= i0; ) {
+var v = this.asc.atoms[i].vib;
+if (v != null) {
+v.scaleT(ptScale);
+}}
+});
+Clazz.defineMethod(c$, "set",
+function(reader){
+this.acr = reader;
+this.asc = reader.asc;
+this.getSymmetry();
+return this;
+}, "J.adapter.smarter.AtomSetCollectionReader");
+Clazz.defineMethod(c$, "setLatticeParameter",
+function(latt){
+this.symmetry.setSpaceGroup(this.doNormalize);
+this.symmetry.setLattice(latt);
+}, "~N");
+Clazz.defineMethod(c$, "setSpinVectors",
+function(){
+if (this.nVib > 0 || this.asc.iSet < 0 || !this.acr.vibsFractional) return this.nVib;
+var i0 = this.asc.getAtomSetAtomIndex(this.asc.iSet);
+var sym = this.getBaseSymmetry();
+for (var i = this.asc.ac; --i >= i0; ) {
+var v = this.asc.atoms[i].vib;
+if (v != null) {
+if (v.modDim > 0) {
+(v).setMoment();
+} else {
+v = v.clone();
+sym.toCartesian(v, true);
+this.asc.atoms[i].vib = v;
+}this.nVib++;
+}}
+return this.nVib;
+});
+Clazz.defineMethod(c$, "addSpaceGroupOperation",
+function(xyz, andSetLattice){
+this.symmetry.setSpaceGroup(this.doNormalize);
+if (andSetLattice && this.symmetry.getSpaceGroupOperationCount() == 1) this.setLatticeCells();
+return this.symmetry.addSpaceGroupOperation(xyz, 0);
+}, "~S,~B");
+Clazz.defineMethod(c$, "applySymmetryFromReader",
+function(readerSymmetry){
+this.asc.setCoordinatesAreFractional(this.acr.iHaveFractionalCoordinates);
+this.setAtomSetSpaceGroupName(this.acr.sgName);
+this.symmetryRange = this.acr.symmetryRange;
+this.asc.setInfo("symmetryRange", Float.$valueOf(this.symmetryRange));
+if (this.acr.doConvertToFractional || this.acr.fileCoordinatesAreFractional) {
+this.setLatticeCells();
+var doApplySymmetry = true;
+if (this.acr.ignoreFileSpaceGroupName || !this.acr.iHaveSymmetryOperators) {
+if (this.acr.unitCellParams[0] == 0 && this.acr.unitCellParams[2] == 0) {
+JU.SimpleUnitCell.fillParams(null, null, null, this.acr.unitCellParams);
+}if (!this.acr.merging || readerSymmetry == null) readerSymmetry = new J.adapter.smarter.XtalSymmetry.FileSymmetry();
+doApplySymmetry = readerSymmetry.createSpaceGroup(this.acr.desiredSpaceGroupIndex, (this.acr.sgName.indexOf("!") >= 0 ? "P1" : this.acr.sgName), this.acr.unitCellParams, this.acr.modDim);
+} else {
+this.acr.doPreSymmetry();
+readerSymmetry = null;
+}this.packingRange = this.acr.getPackingRangeValue(0);
+if (doApplySymmetry) {
+if (readerSymmetry != null) this.getSymmetry().setSpaceGroupTo(readerSymmetry.getSpaceGroup());
+this.applySymmetryLattice();
+if (readerSymmetry != null && this.filterSymop == null) this.setAtomSetSpaceGroupName(readerSymmetry.getSpaceGroupName());
+} else {
+this.setUnitCellSafely();
+}}if (this.acr.iHaveFractionalCoordinates && this.acr.merging && readerSymmetry != null) {
+var atoms = this.asc.atoms;
+for (var i = this.asc.getLastAtomSetAtomIndex(), n = this.asc.ac; i < n; i++) readerSymmetry.toCartesian(atoms[i], true);
+
+this.asc.setCoordinatesAreFractional(false);
+this.acr.addVibrations = false;
+}return this.symmetry;
+}, "J.adapter.smarter.XtalSymmetry.FileSymmetry");
+Clazz.defineMethod(c$, "setSymmetry",
+function(symmetry){
+return (this.symmetry = symmetry);
+}, "J.adapter.smarter.XtalSymmetry.FileSymmetry");
+Clazz.defineMethod(c$, "setTensors",
+function(){
+var n = this.asc.ac;
+for (var i = this.asc.getLastAtomSetAtomIndex(); i < n; i++) {
+var a = this.asc.atoms[i];
+if (a.anisoBorU == null) continue;
+a.addTensor(this.symmetry.getTensor(this.acr.vwr, a.anisoBorU), null, false);
+if (Float.isNaN(a.bfactor)) a.bfactor = a.anisoBorU[7] * 100;
+a.anisoBorU = null;
+}
+});
+Clazz.defineMethod(c$, "adjustRangeMinMax",
+function(oabc){
+var pa = new JU.P3();
+var pb = new JU.P3();
+var pc = new JU.P3();
+if (this.acr.forcePacked) {
+pa.setT(oabc[1]);
+pb.setT(oabc[2]);
+pc.setT(oabc[3]);
+pa.scale(this.packingRange);
+pb.scale(this.packingRange);
+pc.scale(this.packingRange);
+}oabc[0].scaleAdd2(this.minXYZ.x, oabc[1], oabc[0]);
+oabc[0].scaleAdd2(this.minXYZ.y, oabc[2], oabc[0]);
+oabc[0].scaleAdd2(this.minXYZ.z, oabc[3], oabc[0]);
+oabc[0].sub(pa);
+oabc[0].sub(pb);
+oabc[0].sub(pc);
+var pt = JU.P3.newP(oabc[0]);
+this.symmetry.toFractional(pt, true);
+this.setSymmetryMinMax(pt);
+oabc[1].scale(this.maxXYZ.x - this.minXYZ.x);
+oabc[2].scale(this.maxXYZ.y - this.minXYZ.y);
+oabc[3].scale(this.maxXYZ.z - this.minXYZ.z);
+oabc[1].scaleAdd2(2, pa, oabc[1]);
+oabc[2].scaleAdd2(2, pb, oabc[2]);
+oabc[3].scaleAdd2(2, pc, oabc[3]);
+for (var i = 0; i < 3; i++) {
+for (var j = i + 1; j < 4; j++) {
+pt.add2(oabc[i], oabc[j]);
+if (i != 0) pt.add(oabc[0]);
+this.symmetry.toFractional(pt, false);
+this.setSymmetryMinMax(pt);
+}
+}
+this.symmetry.toCartesian(pt, false);
+pt.add(oabc[1]);
+this.symmetry.toFractional(pt, false);
+this.setSymmetryMinMax(pt);
+this.minXYZ = JU.P3i.new3(Clazz.doubleToInt(Math.min(0, Math.floor(this.rminx + 0.001))), Clazz.doubleToInt(Math.min(0, Math.floor(this.rminy + 0.001))), Clazz.doubleToInt(Math.min(0, Math.floor(this.rminz + 0.001))));
+this.maxXYZ = JU.P3i.new3(Clazz.doubleToInt(Math.max(1, Math.ceil(this.rmaxx - 0.001))), Clazz.doubleToInt(Math.max(1, Math.ceil(this.rmaxy - 0.001))), Clazz.doubleToInt(Math.max(1, Math.ceil(this.rmaxz - 0.001))));
+}, "~A");
+Clazz.defineMethod(c$, "applyAllSymmetry",
+function(ms, bsAtoms){
+if (this.asc.ac == 0 || bsAtoms != null && bsAtoms.isEmpty()) return;
+var n = this.noSymmetryCount = this.asc.baseSymmetryAtomCount > 0 ? this.asc.baseSymmetryAtomCount : bsAtoms == null ? this.asc.getLastAtomSetAtomCount() : this.asc.ac - bsAtoms.nextSetBit(this.asc.getLastAtomSetAtomIndex());
+this.asc.setTensors();
+this.applySymmetryToBonds = this.acr.applySymmetryToBonds;
+this.doPackUnitCell = this.acr.doPackUnitCell && !this.applySymmetryToBonds;
+this.bondCount0 = this.asc.bondCount;
+this.ndims = JU.SimpleUnitCell.getDimensionFromParams(this.acr.unitCellParams);
+this.finalizeSymmetry(this.symmetry);
+var operationCount = this.symmetry.getSpaceGroupOperationCount();
+var excludedOps = (this.acr.thisBiomolecule == null ? null : new JU.BS());
+this.checkNearAtoms = this.acr.checkNearAtoms || excludedOps != null;
+JU.SimpleUnitCell.setMinMaxLatticeParameters(this.ndims, this.minXYZ, this.maxXYZ, 0);
+this.latticeOp = this.symmetry.getLatticeOp();
+this.crystalReaderLatticeOpsOnly = (this.asc.crystalReaderLatticeOpsOnly && this.latticeOp >= 0);
+if (this.doCentroidUnitCell) this.asc.setInfo("centroidMinMax", Clazz.newIntArray(-1, [this.minXYZ.x, this.minXYZ.y, this.minXYZ.z, this.maxXYZ.x, this.maxXYZ.y, this.maxXYZ.z, (this.centroidPacked ? 1 : 0)]));
+if (this.doCentroidUnitCell || this.acr.doPackUnitCell || this.symmetryRange != 0 && this.maxXYZ.x - this.minXYZ.x == 1 && this.maxXYZ.y - this.minXYZ.y == 1 && this.maxXYZ.z - this.minXYZ.z == 1) {
+this.minXYZ0 = JU.P3.new3(this.minXYZ.x, this.minXYZ.y, this.minXYZ.z);
+this.maxXYZ0 = JU.P3.new3(this.maxXYZ.x, this.maxXYZ.y, this.maxXYZ.z);
+if (ms != null) {
+ms.setMinMax0(this.minXYZ0, this.maxXYZ0);
+this.minXYZ.set(Clazz.floatToInt(this.minXYZ0.x), Clazz.floatToInt(this.minXYZ0.y), Clazz.floatToInt(this.minXYZ0.z));
+this.maxXYZ.set(Clazz.floatToInt(this.maxXYZ0.x), Clazz.floatToInt(this.maxXYZ0.y), Clazz.floatToInt(this.maxXYZ0.z));
+}switch (this.ndims) {
+case 3:
+this.minXYZ.z--;
+this.maxXYZ.z++;
+case 2:
+this.minXYZ.y--;
+this.maxXYZ.y++;
+case 1:
+this.minXYZ.x--;
+this.maxXYZ.x++;
+}
+}var nCells = (this.maxXYZ.x - this.minXYZ.x) * (this.maxXYZ.y - this.minXYZ.y) * (this.maxXYZ.z - this.minXYZ.z);
+var nsym = n * (this.crystalReaderLatticeOpsOnly ? 4 : operationCount);
+var cartesianCount = (this.checkNearAtoms || this.acr.thisBiomolecule != null ? nsym * nCells : this.symmetryRange > 0 ? nsym : 1);
+var cartesians = new Array(cartesianCount);
+var atoms = this.asc.atoms;
+for (var i = 0; i < n; i++) atoms[this.firstAtom + i].bsSymmetry = JU.BS.newN(operationCount * (nCells + 1));
+
+var pt = 0;
+this.unitCellTranslations = new Array(nCells);
+var iCell = 0;
+var cell555Count = 0;
+var absRange = Math.abs(this.symmetryRange);
+var checkCartesianRange = (this.symmetryRange != 0);
+var checkRangeNoSymmetry = (this.symmetryRange < 0);
+var checkRange111 = (this.symmetryRange > 0);
+if (checkCartesianRange) {
+this.rminx = this.rminy = this.rminz = 3.4028235E38;
+this.rmaxx = this.rmaxy = this.rmaxz = -3.4028235E38;
+}var sym = this.symmetry;
+var lastSymmetry = sym;
+this.checkAll = (this.crystalReaderLatticeOpsOnly || this.asc.atomSetCount == 1 && this.checkNearAtoms && this.latticeOp >= 0);
+var lstNCS = this.acr.lstNCS;
+if (lstNCS != null && lstNCS.get(0).m33 == 0) {
+var nOp = sym.getSpaceGroupOperationCount();
+var nn = lstNCS.size();
+for (var i = nn; --i >= 0; ) {
+var m = lstNCS.get(i);
+m.m33 = 1;
+sym.toFractionalM(m);
+}
+for (var i = 1; i < nOp; i++) {
+var m1 = sym.getSpaceGroupOperation(i);
+for (var j = 0; j < nn; j++) {
+var m = JU.M4.newM4(lstNCS.get(j));
+m.mul2(m1, m);
+if (this.doNormalize && this.noSymmetryCount > 0) JS.SymmetryOperation.normalizeOperationToCentroid(3, m, atoms, this.firstAtom, this.noSymmetryCount);
+lstNCS.addLast(m);
+}
+}
+}var pttemp = null;
+var op = sym.getSpaceGroupOperation(0);
+if (this.doPackUnitCell) {
+pttemp = new JU.P3();
+this.ptOffset.set(0, 0, 0);
+}var atomMap = (this.bondCount0 > this.asc.bondIndex0 && this.applySymmetryToBonds ? Clazz.newIntArray (n, 0) : null);
+var unitCells = Clazz.newIntArray (nCells, 0);
+for (var tx = this.minXYZ.x; tx < this.maxXYZ.x; tx++) {
+for (var ty = this.minXYZ.y; ty < this.maxXYZ.y; ty++) {
+for (var tz = this.minXYZ.z; tz < this.maxXYZ.z; tz++) {
+this.unitCellTranslations[iCell] = JU.V3.new3(tx, ty, tz);
+unitCells[iCell++] = 555 + tx * 100 + ty * 10 + tz;
+if (tx != 0 || ty != 0 || tz != 0 || cartesians.length == 0) continue;
+for (pt = 0; pt < n; pt++) {
+var atom = atoms[this.firstAtom + pt];
+if (ms != null) {
+sym = ms.getAtomSymmetry(atom, this.symmetry);
+if (sym !== lastSymmetry) {
+if (sym.getSpaceGroupOperationCount() == 0) this.finalizeSymmetry(lastSymmetry = sym);
+op = sym.getSpaceGroupOperation(0);
+}}var c = JU.P3.newP(atom);
+op.rotTrans(c);
+sym.toCartesian(c, false);
+if (this.doPackUnitCell) {
+sym.toUnitCellRnd(c, this.ptOffset);
+pttemp.setT(c);
+sym.toFractional(pttemp, false);
+this.acr.fixFloatPt(pttemp, 100000.0);
+if (bsAtoms == null) atom.setT(pttemp);
+ else if (atom.distance(pttemp) < 1.0E-4) bsAtoms.set(atom.index);
+ else {
+bsAtoms.clear(atom.index);
+continue;
+}}if (bsAtoms != null) atom.bsSymmetry.clearAll();
+atom.bsSymmetry.set(iCell * operationCount);
+atom.bsSymmetry.set(0);
+if (checkCartesianRange) this.setSymmetryMinMax(c);
+if (pt < cartesianCount) cartesians[pt] = c;
+}
+if (checkRangeNoSymmetry) {
+this.rminx -= absRange;
+this.rminy -= absRange;
+this.rminz -= absRange;
+this.rmaxx += absRange;
+this.rmaxy += absRange;
+this.rmaxz += absRange;
+}cell555Count = pt = this.symmetryAddAtoms(0, 0, 0, 0, pt, iCell * operationCount, cartesians, ms, excludedOps, atomMap);
+}
+}
+}
+if (checkRange111) {
+this.rminx -= absRange;
+this.rminy -= absRange;
+this.rminz -= absRange;
+this.rmaxx += absRange;
+this.rmaxy += absRange;
+this.rmaxz += absRange;
+}iCell = 0;
+for (var tx = this.minXYZ.x; tx < this.maxXYZ.x; tx++) {
+for (var ty = this.minXYZ.y; ty < this.maxXYZ.y; ty++) {
+for (var tz = this.minXYZ.z; tz < this.maxXYZ.z; tz++) {
+iCell++;
+if (tx != 0 || ty != 0 || tz != 0) pt = this.symmetryAddAtoms(tx, ty, tz, cell555Count, pt, iCell * operationCount, cartesians, ms, excludedOps, atomMap);
+}
+}
+}
+if (iCell * n == this.asc.ac - this.firstAtom) this.duplicateAtomProperties(iCell);
+this.setCurrentModelInfo(n, sym, unitCells);
+this.unitCellParams = null;
+this.reset();
+}, "J.adapter.smarter.MSInterface,JU.BS");
+Clazz.defineMethod(c$, "applyRangeSymmetry",
+function(bsAtoms){
+var range = this.acr.fillRange;
+bsAtoms = this.updateBSAtoms();
+this.acr.forcePacked = true;
+this.doPackUnitCell = false;
+var minXYZ2 = JU.P3i.new3(this.minXYZ.x, this.minXYZ.y, this.minXYZ.z);
+var maxXYZ2 = JU.P3i.new3(this.maxXYZ.x, this.maxXYZ.y, this.maxXYZ.z);
+var oabc = new Array(4);
+for (var i = 0; i < 4; i++) oabc[i] = JU.P3.newP(range[i]);
+
+this.setUnitCellSafely();
+this.adjustRangeMinMax(oabc);
+var superSymmetry = new J.adapter.smarter.XtalSymmetry.FileSymmetry();
+superSymmetry.getUnitCell(this.acr.fillRange, false, null);
+this.applyAllSymmetry(this.acr.ms, bsAtoms);
+var pt0 = new JU.P3();
+var atoms = this.asc.atoms;
+for (var i = this.asc.ac; --i >= this.firstAtom; ) {
+pt0.setT(atoms[i]);
+this.symmetry.toCartesian(pt0, false);
+superSymmetry.toFractional(pt0, false);
+if (this.acr.noPack ? !this.removePacking(this.ndims, pt0, minXYZ2.x, maxXYZ2.x, minXYZ2.y, maxXYZ2.y, minXYZ2.z, maxXYZ2.z, this.packingRange) : !this.isWithinCell(this.ndims, pt0, minXYZ2.x, maxXYZ2.x, minXYZ2.y, maxXYZ2.y, minXYZ2.z, maxXYZ2.z, this.packingRange)) bsAtoms.clear(i);
+}
+}, "JU.BS");
+Clazz.defineMethod(c$, "applySuperSymmetry",
+function(supercell, bsAtoms, iAtomFirst, oabc, pt0, vabc, slop){
+this.asc.setGlobalBoolean(7);
+var doPack0 = this.doPackUnitCell;
+this.doPackUnitCell = doPack0;
+this.applyAllSymmetry(this.acr.ms, null);
+this.doPackUnitCell = doPack0;
+var atoms = this.asc.atoms;
+var atomCount = this.asc.ac;
+for (var i = iAtomFirst; i < atomCount; i++) {
+this.symmetry.toCartesian(atoms[i], true);
+bsAtoms.set(i);
+}
+this.asc.setCurrentModelInfo("unitcell_conventional", this.symmetry.getV0abc("a,b,c", null));
+var va = vabc[0];
+var vb = vabc[1];
+var vc = vabc[2];
+this.symmetry = new J.adapter.smarter.XtalSymmetry.FileSymmetry();
+this.setUnitCell( Clazz.newFloatArray(-1, [0, 0, 0, 0, 0, 0, va.x, va.y, va.z, vb.x, vb.y, vb.z, vc.x, vc.y, vc.z, 0, 0, 0, 0, 0, 0, NaN, NaN, NaN, NaN, NaN, slop]), null, null);
+var name = oabc == null || supercell == null ? "P1" : "cell=" + supercell;
+this.setAtomSetSpaceGroupName(name);
+this.symmetry.setSpaceGroupName(name);
+this.symmetry.setSpaceGroup(this.doNormalize);
+this.symmetry.addSpaceGroupOperation("x,y,z", 0);
+if (pt0 != null && pt0.length() == 0) pt0 = null;
+if (pt0 != null) this.symmetry.toFractional(pt0, true);
+for (var i = iAtomFirst; i < atomCount; i++) {
+this.symmetry.toFractional(atoms[i], true);
+if (pt0 != null) atoms[i].sub(pt0);
+}
+this.asc.haveAnisou = false;
+this.asc.setCurrentModelInfo("matUnitCellOrientation", null);
+}, "~S,JU.BS,~N,~A,JU.P3,~A,~N");
+Clazz.defineMethod(c$, "applySymmetryLattice",
+function(){
+if (!this.asc.coordinatesAreFractional || this.symmetry.getSpaceGroup() == null) return;
+var maxX = this.latticeCells[0];
+var maxY = this.latticeCells[1];
+var maxZ = Math.abs(this.latticeCells[2]);
+var kcode = this.latticeCells[3];
+this.firstAtom = this.asc.getLastAtomSetAtomIndex();
+var bsAtoms = this.asc.bsAtoms;
+if (bsAtoms != null) {
+this.updateBSAtoms();
+this.firstAtom = bsAtoms.nextSetBit(this.firstAtom);
+}this.rminx = this.rminy = this.rminz = 3.4028235E38;
+this.rmaxx = this.rmaxy = this.rmaxz = -3.4028235E38;
+if (this.acr.latticeType == null) this.acr.latticeType = "" + this.symmetry.getLatticeType();
+if (this.acr.isPrimitive) {
+this.asc.setCurrentModelInfo("isprimitive", Boolean.TRUE);
+if (!"P".equals(this.acr.latticeType) || this.acr.primitiveToCrystal != null) {
+this.asc.setCurrentModelInfo("unitcell_conventional", this.symmetry.getConventionalUnitCell(this.acr.latticeType, this.acr.primitiveToCrystal));
+}}this.setUnitCellSafely();
+this.asc.setCurrentModelInfo("f2c", this.symmetry.getUnitCellF2C());
+var s = this.symmetry.getSpaceGroupTitle();
+if (s.indexOf("--") < 0) this.asc.setCurrentModelInfo("f2cTitle", s);
+this.asc.setCurrentModelInfo("f2cParams", this.symmetry.getUnitCellParams());
+if (this.acr.latticeType != null) {
+this.asc.setCurrentModelInfo("latticeType", this.acr.latticeType);
+if ((typeof(this.acr.fillRange)=='string')) {
+var range = this.setLatticeRange(this.acr.latticeType, this.acr.fillRange);
+if (range == null) {
+this.acr.appendLoadNote(this.acr.fillRange + " symmetry could not be implemented");
+this.acr.fillRange = null;
+} else {
+this.acr.fillRange = range;
+}}}this.baseSymmetry = this.symmetry;
+if (this.acr.fillRange != null) {
+this.setMinMax(this.ndims, kcode, maxX, maxY, maxZ);
+this.applyRangeSymmetry(bsAtoms);
+return;
+}var oabc = null;
+var slop = 1e-6;
+this.nVib = 0;
+var supercell = this.acr.strSupercell;
+var isSuper = (supercell != null && supercell.indexOf(",") >= 0);
+var matSuper = null;
+var pt0 = null;
+var vabc = new Array(3);
+if (isSuper) {
+matSuper = new JU.M4();
+if (this.mident == null) this.mident = new JU.M4();
+this.setUnitCellSafely();
+oabc = this.symmetry.getV0abc(supercell, matSuper);
+matSuper.transpose33();
+if (oabc != null && !matSuper.equals(this.mident)) {
+this.setMinMax(this.ndims, kcode, maxX, maxY, maxZ);
+pt0 = JU.P3.newP(oabc[0]);
+vabc[0] = JU.V3.newV(oabc[1]);
+vabc[1] = JU.V3.newV(oabc[2]);
+vabc[2] = JU.V3.newV(oabc[3]);
+this.adjustRangeMinMax(oabc);
+}}var iAtomFirst = this.asc.getLastAtomSetAtomIndex();
+if (bsAtoms != null) iAtomFirst = bsAtoms.nextSetBit(iAtomFirst);
+if (this.rminx == 3.4028235E38) {
+supercell = null;
+oabc = null;
+} else {
+bsAtoms = this.updateBSAtoms();
+slop = this.symmetry.getPrecision();
+this.applySuperSymmetry(supercell, bsAtoms, iAtomFirst, oabc, pt0, vabc, slop);
+}this.setMinMax(this.ndims, kcode, maxX, maxY, maxZ);
+if (oabc == null) {
+this.applyAllSymmetry(this.acr.ms, bsAtoms);
+if (!this.acr.noPack && (!this.applySymmetryToBonds || !this.acr.doPackUnitCell)) {
+return;
+}this.setMinMax(this.ndims, kcode, maxX, maxY, maxZ);
+}if (this.acr.forcePacked || this.acr.doPackUnitCell || this.acr.noPack) {
+this.trimToUnitCell(iAtomFirst);
+}this.updateSupercellAtomSites(matSuper, bsAtoms, slop);
+});
+Clazz.defineMethod(c$, "duplicateAtomProperties",
+function(nTimes){
+var p = this.asc.getAtomSetAuxiliaryInfoValue(-1, "atomProperties");
+if (p != null) for (var entry, $entry = p.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
+var key = entry.getKey();
+var val = entry.getValue();
+if ((typeof(val)=='string')) {
+var data = val;
+var s = new JU.SB();
+for (var i = nTimes; --i >= 0; ) s.append(data);
+
+p.put(key, s.toString());
+} else {
+var f = val;
+var fnew = Clazz.newFloatArray (f.length * nTimes, 0);
+for (var i = nTimes; --i >= 0; ) System.arraycopy(f, 0, fnew, i * f.length, f.length);
+
+}}
+}, "~N");
+Clazz.defineMethod(c$, "finalizeSymmetry",
+function(symmetry){
+var name = this.asc.getAtomSetAuxiliaryInfoValue(-1, "spaceGroup");
+symmetry.setFinalOperations(this.ndims, name, this.asc.atoms, this.firstAtom, this.noSymmetryCount, this.doNormalize, this.filterSymop);
+if (this.filterSymop != null || name == null || name.equals("unspecified!")) {
+this.setAtomSetSpaceGroupName(symmetry.getSpaceGroupName());
+}if (this.unitCellParams != null || Float.isNaN(this.acr.unitCellParams[0])) return;
+if (symmetry.fixUnitCell(this.acr.unitCellParams)) {
+this.acr.appendLoadNote("Unit cell parameters were adjusted to match space group!");
+}this.setUnitCellSafely();
+}, "J.adapter.smarter.XtalSymmetry.FileSymmetry");
+Clazz.defineMethod(c$, "removePacking",
+function(ndims, pt, minX, maxX, minY, maxY, minZ, maxZ, slop){
+return (pt.x > minX - slop && pt.x < maxX - slop && (ndims < 2 || pt.y > minY - slop && pt.y < maxY - slop) && (ndims < 3 || pt.z > minZ - slop && pt.z < maxZ - slop));
+}, "~N,JU.P3,~N,~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "reset",
+function(){
+this.asc.coordinatesAreFractional = false;
+this.asc.setCurrentModelInfo("hasSymmetry", Boolean.TRUE);
+this.asc.setGlobalBoolean(1);
+});
+Clazz.defineMethod(c$, "setAtomSetSpaceGroupName",
+function(spaceGroupName){
+this.symmetry.setSpaceGroupName(spaceGroupName);
+this.asc.setCurrentModelInfo("spaceGroup", spaceGroupName + "");
+}, "~S");
+Clazz.defineMethod(c$, "setCurrentModelInfo",
+function(n, sym, unitCells){
+if (sym == null) {
+this.asc.setCurrentModelInfo("presymmetryAtomCount", Integer.$valueOf(this.noSymmetryCount));
+this.asc.setCurrentModelInfo("biosymmetryCount", Integer.$valueOf(n));
+this.asc.setCurrentModelInfo("biosymmetry", this.symmetry);
+} else {
+this.asc.setCurrentModelInfo("presymmetryAtomCount", Integer.$valueOf(n));
+this.asc.setCurrentModelInfo("latticeDesignation", sym.getLatticeDesignation());
+this.asc.setCurrentModelInfo("ML_unitCellRange", unitCells);
+if (this.acr.isSUPERCELL) this.asc.setCurrentModelInfo("supercell", this.acr.strSupercell);
+}this.asc.setCurrentModelInfo("presymmetryAtomIndex", Integer.$valueOf(this.firstAtom));
+var operationCount = this.symmetry.getSpaceGroupOperationCount();
+if (operationCount > 0) {
+var symmetryList = new Array(operationCount);
+for (var i = 0; i < operationCount; i++) symmetryList[i] = "" + this.symmetry.getSpaceGroupXyz(i, this.doNormalize);
+
+this.asc.setCurrentModelInfo("symmetryOperations", symmetryList);
+this.asc.setCurrentModelInfo("symmetryOps", this.symmetry.getSymmetryOperations());
+}this.asc.setCurrentModelInfo("symmetryCount", Integer.$valueOf(operationCount));
+this.asc.setCurrentModelInfo("latticeType", this.acr.latticeType == null ? "P" : this.acr.latticeType);
+this.asc.setCurrentModelInfo("intlTableNo", this.symmetry.getIntTableNumber());
+this.asc.setCurrentModelInfo("intlTableIndex", this.symmetry.getSpaceGroupInfoObj("itaIndex", null, false, false));
+this.asc.setCurrentModelInfo("intlTableTransform", this.symmetry.getSpaceGroupInfoObj("itaTransform", null, false, false));
+this.asc.setCurrentModelInfo("intlTableJmolID", this.symmetry.getIntTableNumberFull());
+this.asc.setCurrentModelInfo("spaceGroupIndex", Integer.$valueOf(this.symmetry.getSpaceGroupIndex()));
+this.asc.setCurrentModelInfo("spaceGroupTitle", this.symmetry.getSpaceGroupTitle());
+if (this.acr.sgName == null || this.acr.sgName.indexOf("?") >= 0 || this.acr.sgName.indexOf("!") >= 0) this.setAtomSetSpaceGroupName(this.acr.sgName = this.symmetry.getSpaceGroupName());
+}, "~N,J.adapter.smarter.XtalSymmetry.FileSymmetry,~A");
+Clazz.defineMethod(c$, "setCurrentModelUCInfo",
+function(unitCellParams, unitCellOffset, matUnitCellOrientation){
+if (unitCellParams != null) this.asc.setCurrentModelInfo("unitCellParams", unitCellParams);
+if (unitCellOffset != null) this.asc.setCurrentModelInfo("unitCellOffset", unitCellOffset);
+if (matUnitCellOrientation != null) this.asc.setCurrentModelInfo("matUnitCellOrientation", matUnitCellOrientation);
+}, "~A,JU.P3,JU.M3");
+Clazz.defineMethod(c$, "setLatticeCells",
+function(){
+this.latticeCells = this.acr.latticeCells;
+var isLatticeRange = (this.latticeCells[0] <= 555 && this.latticeCells[1] >= 555 && (this.latticeCells[2] == 0 || this.latticeCells[2] == 1 || this.latticeCells[2] == -1));
+this.doNormalize = this.latticeCells[0] != 0 && (!isLatticeRange || this.latticeCells[2] == 1);
+this.applySymmetryToBonds = this.acr.applySymmetryToBonds;
+this.doPackUnitCell = this.acr.doPackUnitCell && !this.applySymmetryToBonds;
+this.doCentroidUnitCell = this.acr.doCentroidUnitCell;
+this.centroidPacked = this.acr.centroidPacked;
+this.filterSymop = this.acr.filterSymop;
+});
+Clazz.defineMethod(c$, "setLatticeRange",
+function(latticetype, rangeType){
+var range = null;
+var isRhombohedral = "R".equals(latticetype);
+if (rangeType.equals("conventional")) {
+range = this.symmetry.getConventionalUnitCell(latticetype, this.acr.primitiveToCrystal);
+} else if (rangeType.equals("primitive")) {
+range = this.symmetry.getUnitCellVectors();
+this.symmetry.toFromPrimitive(true, latticetype.charAt(0), range, this.acr.primitiveToCrystal);
+} else if (isRhombohedral && rangeType.equals("rhombohedral")) {
+if (this.symmetry.getUnitCellInfoType(7) == 1) {
+rangeType = "2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c";
+} else {
+rangeType = null;
+}} else if (isRhombohedral && rangeType.equals("trigonal")) {
+if (this.symmetry.getUnitCellInfoType(8) == 1) {
+rangeType = "a-b,b-c,a+b+c";
+} else {
+rangeType = null;
+}} else if (rangeType.indexOf(",") < 0 || rangeType.indexOf("a") < 0 || rangeType.indexOf("b") < 0 || rangeType.indexOf("c") < 0) {
+rangeType = null;
+} else {
+rangeType = null;
+}if (rangeType != null && range == null && (range = this.symmetry.getV0abc(rangeType, null)) == null) {
+rangeType = null;
+}if (rangeType == null) return null;
+this.acr.addJmolScript("unitcell " + JU.PT.esc(rangeType));
+return range;
+}, "~S,~S");
+Clazz.defineMethod(c$, "setMinMax",
+function(dim, kcode, maxX, maxY, maxZ){
+this.minXYZ = new JU.P3i();
+this.maxXYZ = JU.P3i.new3(maxX, maxY, maxZ);
+JU.SimpleUnitCell.setMinMaxLatticeParameters(dim, this.minXYZ, this.maxXYZ, kcode);
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "setSymmetryMinMax",
+function(c){
+if (this.rminx > c.x) this.rminx = c.x;
+if (this.rminy > c.y) this.rminy = c.y;
+if (this.rminz > c.z) this.rminz = c.z;
+if (this.rmaxx < c.x) this.rmaxx = c.x;
+if (this.rmaxy < c.y) this.rmaxy = c.y;
+if (this.rmaxz < c.z) this.rmaxz = c.z;
+}, "JU.P3");
+Clazz.defineMethod(c$, "setUnitCell",
+function(info, matUnitCellOrientation, unitCellOffset){
+this.unitCellParams = Clazz.newFloatArray (info.length, 0);
+for (var i = 0; i < info.length; i++) this.unitCellParams[i] = info[i];
+
+this.asc.haveUnitCell = true;
+if (this.asc.isTrajectory) {
+if (this.trajectoryUnitCells == null) {
+this.trajectoryUnitCells = new JU.Lst();
+this.asc.setInfo("unitCells", this.trajectoryUnitCells);
+}this.trajectoryUnitCells.addLast(this.unitCellParams);
+}this.asc.setGlobalBoolean(2);
+this.getSymmetry().setUnitCellFromParams(this.unitCellParams, false, this.unitCellParams[26]);
+if (unitCellOffset != null) this.symmetry.setOffsetPt(unitCellOffset);
+if (matUnitCellOrientation != null) this.symmetry.initializeOrientation(matUnitCellOrientation);
+this.setCurrentModelUCInfo(this.unitCellParams, unitCellOffset, matUnitCellOrientation);
+}, "~A,JU.M3,JU.P3");
+Clazz.defineMethod(c$, "setUnitCellSafely",
+function(){
+if (this.unitCellParams == null) this.setUnitCell(this.acr.unitCellParams, this.acr.matUnitCellOrientation, this.acr.unitCellOffset);
+});
+Clazz.defineMethod(c$, "symmetryAddAtoms",
+function(transX, transY, transZ, baseCount, pt, iCellOpPt, cartesians, ms, excludedOps, atomMap){
+var isBaseCell = (baseCount == 0);
+var addBonds = (atomMap != null);
+if (this.doPackUnitCell) this.ptOffset.set(transX, transY, transZ);
+var range2 = this.symmetryRange * this.symmetryRange;
+var checkRangeNoSymmetry = (this.symmetryRange < 0);
+var checkRange111 = (this.symmetryRange > 0);
+var checkSymmetryMinMax = (isBaseCell && checkRange111);
+checkRange111 = new Boolean (checkRange111 & !isBaseCell).valueOf();
+var nOp = this.symmetry.getSpaceGroupOperationCount();
+var lstNCS = this.acr.lstNCS;
+var nNCS = (lstNCS == null ? 0 : lstNCS.size());
+var nOperations = nOp + nNCS;
+nNCS = Clazz.doubleToInt(nNCS / nOp);
+var checkNearAtoms = (this.checkNearAtoms && (nOperations > 1 || this.doPackUnitCell));
+var checkSymmetryRange = (checkRangeNoSymmetry || checkRange111);
+var checkDistances = (checkNearAtoms || checkSymmetryRange);
+var checkOps = (excludedOps != null);
+var addCartesian = (checkNearAtoms || checkSymmetryMinMax);
+var bsAtoms = (this.acr.isMolecular ? null : this.asc.bsAtoms);
+var sym = this.symmetry;
+if (checkRangeNoSymmetry) baseCount = this.noSymmetryCount;
+var atomMax = this.firstAtom + this.noSymmetryCount;
+var bondAtomMin = (this.asc.firstAtomToBond < 0 ? atomMax : this.asc.firstAtomToBond);
+var pttemp = new JU.P3();
+var code = null;
+var minCartDist2 = (checkOps ? 0.01 : 1.0E-4);
+var subSystemId = '\u0000';
+var j00 = (bsAtoms == null ? this.firstAtom : bsAtoms.nextSetBit(this.firstAtom));
+out : for (var iSym = 0; iSym < nOperations; iSym++) {
+if (isBaseCell && iSym == 0 || this.crystalReaderLatticeOpsOnly && iSym > 0 && (iSym % this.latticeOp) != 0 || excludedOps != null && excludedOps.get(iSym)) continue;
+var pt0 = this.firstAtom + (checkNearAtoms ? pt : checkRange111 ? baseCount : 0);
+var spinOp = (iSym >= nOp ? 0 : this.asc.vibScale == 0 ? sym.getSpinOp(iSym) : this.asc.vibScale);
+var i0 = Math.max(this.firstAtom, (bsAtoms == null ? 0 : bsAtoms.nextSetBit(0)));
+var checkDistance = checkDistances;
+var spt = (iSym >= nOp ? Clazz.doubleToInt((iSym - nOp) / nNCS) : iSym);
+var cpt = spt + iCellOpPt;
+for (var i = i0; i < atomMax; i++) {
+var a = this.asc.atoms[i];
+if (bsAtoms != null && !bsAtoms.get(i)) continue;
+if (ms == null) {
+sym.newSpaceGroupPoint(a, iSym, (iSym >= nOp ? lstNCS.get(iSym - nOp) : null), transX, transY, transZ, pttemp);
+} else {
+sym = ms.getAtomSymmetry(a, this.symmetry);
+sym.newSpaceGroupPoint(a, iSym, null, transX, transY, transZ, pttemp);
+code = sym.getSpaceGroupOperationCode(iSym);
+if (code != null) {
+subSystemId = code.charAt(0);
+sym = ms.getSymmetryFromCode(code);
+if (sym.getSpaceGroupOperationCount() == 0) this.finalizeSymmetry(sym);
+}}this.acr.fixFloatPt(pttemp, 100000.0);
+var c = JU.P3.newP(pttemp);
+sym.toCartesian(c, false);
+if (this.doPackUnitCell) {
+sym.toUnitCellRnd(c, this.ptOffset);
+pttemp.setT(c);
+sym.toFractional(pttemp, false);
+this.acr.fixFloatPt(pttemp, 100000.0);
+if (!this.isWithinCell(this.ndims, pttemp, this.minXYZ0.x, this.maxXYZ0.x, this.minXYZ0.y, this.maxXYZ0.y, this.minXYZ0.z, this.maxXYZ0.z, this.packingRange)) {
+continue;
+}}if (checkSymmetryMinMax) this.setSymmetryMinMax(c);
+var special = null;
+if (checkDistance) {
+if (checkSymmetryRange && (c.x < this.rminx || c.y < this.rminy || c.z < this.rminz || c.x > this.rmaxx || c.y > this.rmaxy || c.z > this.rmaxz)) continue;
+var minDist2 = 3.4028235E38;
+var j0 = (this.checkAll ? this.asc.ac : pt0);
+var name = a.atomName;
+var id = (code == null ? a.altLoc : subSystemId);
+for (var j = j00; j < j0; j++) {
+if (bsAtoms != null && !bsAtoms.get(j)) continue;
+var pc = cartesians[j - this.firstAtom];
+if (pc == null) continue;
+var d2 = c.distanceSquared(pc);
+if (checkNearAtoms && d2 < minCartDist2) {
+if (checkOps) {
+excludedOps.set(iSym);
+continue out;
+}special = this.asc.atoms[j];
+if ((special.atomName == null || special.atomName.equals(name)) && special.altLoc == id) break;
+special = null;
+}if (checkRange111 && j < baseCount && d2 < minDist2) minDist2 = d2;
+}
+if (checkRange111 && minDist2 > range2) continue;
+}if (checkOps) {
+checkDistance = false;
+}var atomSite = a.atomSite;
+if (special != null) {
+if (addBonds) atomMap[atomSite] = special.index;
+special.bsSymmetry.set(cpt);
+special.bsSymmetry.set(spt);
+} else {
+if (addBonds) atomMap[atomSite] = this.asc.ac;
+var atom1 = a.copyTo(pttemp, this.asc);
+if (this.asc.bsAtoms != null) this.asc.bsAtoms.set(atom1.index);
+if (spinOp != 0 && atom1.vib != null) {
+sym.getSpaceGroupOperation(iSym).rotate(atom1.vib);
+atom1.vib.scale(spinOp);
+}if (atom1.isNegDisorder) {
+if (this.disorderMap == null) this.disorderMap = new java.util.Hashtable();
+var key = Integer.$valueOf(iSym * 1000 + atom1.altLoc.charCodeAt(0));
+var ch = this.disorderMap.get(key);
+if (ch == null) {
+if (this.disorderMapMax == 0 || this.disorderMapMax == 90) this.disorderMapMax = ('@').charCodeAt(0);
+this.disorderMap.put(key, ch = new Character(String.fromCharCode(++this.disorderMapMax)));
+}atom1.altLoc = ch.charValue();
+}atom1.atomSite = atomSite;
+if (code != null) atom1.altLoc = subSystemId;
+atom1.bsSymmetry = JU.BSUtil.newAndSetBit(cpt);
+atom1.bsSymmetry.set(spt);
+if (addCartesian) cartesians[pt++] = c;
+var tensors = a.tensors;
+if (tensors != null) {
+atom1.tensors = null;
+for (var j = tensors.size(); --j >= 0; ) {
+var t = tensors.get(j);
+if (t == null) continue;
+if (nOp == 1) atom1.addTensor(t.copyTensor(), null, false);
+ else this.addRotatedTensor(atom1, t, iSym, false, sym);
+}
+}}}
+if (addBonds) {
+var bonds = this.asc.bonds;
+var atoms = this.asc.atoms;
+var key;
+for (var bondNum = this.asc.bondIndex0; bondNum < this.bondCount0; bondNum++) {
+var bond = bonds[bondNum];
+var atom1 = atoms[bond.atomIndex1];
+var atom2 = atoms[bond.atomIndex2];
+if (atom1 == null || atom2 == null || atom2.atomSetIndex < atom1.atomSetIndex) continue;
+var ia1 = atomMap[atom1.atomSite];
+var ia2 = atomMap[atom2.atomSite];
+if (ia1 > ia2) {
+var i = ia1;
+ia1 = ia2;
+ia2 = i;
+}if (ia1 != ia2 && (ia1 >= bondAtomMin || ia2 >= bondAtomMin) && this.bondsFound.indexOf(key = "-" + ia1 + "," + ia2) < 0) {
+this.bondsFound.append(key);
+this.asc.addNewBondWithOrder(ia1, ia2, bond.order);
+}}
+}}
+return pt;
+}, "~N,~N,~N,~N,~N,~N,~A,J.adapter.smarter.MSInterface,JU.BS,~A");
+Clazz.defineMethod(c$, "trimToUnitCell",
+function(iAtomFirst){
+var atoms = this.asc.atoms;
+var bs = this.updateBSAtoms();
+if (this.acr.noPack) {
+for (var i = bs.nextSetBit(iAtomFirst); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (!this.removePacking(this.ndims, atoms[i], this.minXYZ.x, this.maxXYZ.x, this.minXYZ.y, this.maxXYZ.y, this.minXYZ.z, this.maxXYZ.z, this.packingRange)) bs.clear(i);
+}
+} else {
+for (var i = bs.nextSetBit(iAtomFirst); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (!this.isWithinCell(this.ndims, atoms[i], this.minXYZ.x, this.maxXYZ.x, this.minXYZ.y, this.maxXYZ.y, this.minXYZ.z, this.maxXYZ.z, this.packingRange)) bs.clear(i);
+}
+}}, "~N");
+Clazz.defineMethod(c$, "updateBSAtoms",
+function(){
+var bs = this.asc.bsAtoms;
+if (bs == null) bs = this.asc.bsAtoms = JU.BSUtil.newBitSet2(0, this.asc.ac);
+if (bs.nextSetBit(this.firstAtom) < 0) bs.setBits(this.firstAtom, this.asc.ac);
+return bs;
+});
+Clazz.defineMethod(c$, "updateSupercellAtomSites",
+function(matSuper, bsAtoms, slop){
+var n = bsAtoms.cardinality();
+var baseAtoms = new Array(n);
+var nbase = 0;
+var slop2 = slop * slop;
+for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var a = this.asc.atoms[i];
+var p = new J.adapter.smarter.Atom();
+p.setT(a);
+if (matSuper != null) {
+matSuper.rotTrans(p);
+JU.SimpleUnitCell.unitizeDimRnd(3, p, slop);
+}p.atomSerial = a.atomSite;
+p.atomSite = a.atomSite;
+this.symmetry.unitize(p);
+var found = false;
+for (var ib = 0; ib < nbase; ib++) {
+var b = baseAtoms[ib];
+if (p.atomSerial == b.atomSerial && p.distanceSquared(b) < slop2) {
+found = true;
+a.atomSite = b.atomSite;
+break;
+}}
+if (!found) {
+a.atomSite = p.atomSite = nbase;
+baseAtoms[nbase++] = p;
+}}
+}, "JU.M4,JU.BS,~N");
+Clazz.defineMethod(c$, "newFileSymmetry",
+function(){
+return new J.adapter.smarter.XtalSymmetry.FileSymmetry();
+});
+/*if3*/;(function(){
+var c$ = Clazz.declareType(J.adapter.smarter.XtalSymmetry, "FileSymmetry", JS.Symmetry);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.smarter.XtalSymmetry.FileSymmetry, []);
+});
+Clazz.defineMethod(c$, "addLatticeVectors",
+function(lattvecs){
+return this.spaceGroup.addLatticeVectors(lattvecs);
+}, "JU.Lst");
+Clazz.defineMethod(c$, "addSubSystemOp",
+function(code, rs, vs, sigma){
+this.spaceGroup.isSSG = true;
+var s = JS.SymmetryOperation.getXYZFromRsVs(rs, vs, false);
+var i = this.spaceGroup.addSymmetry(s, -1, true);
+this.spaceGroup.operations[i].setSigma(code, sigma);
+return s;
+}, "~S,JU.Matrix,JU.Matrix,JU.Matrix");
+Clazz.defineMethod(c$, "checkDistance",
+function(f1, f2, distance, dx, iRange, jRange, kRange, ptOffset){
+return this.unitCell.checkDistance(f1, f2, distance, dx, iRange, jRange, kRange, ptOffset);
+}, "JU.P3,JU.P3,~N,~N,~N,~N,~N,JU.P3");
+Clazz.defineMethod(c$, "createSpaceGroup",
+function(desiredSpaceGroupIndex, name, data, modDim){
+this.spaceGroup = JS.SpaceGroup.createSpaceGroup(desiredSpaceGroupIndex, name, data, modDim);
+if (this.spaceGroup != null && JU.Logger.debugging) JU.Logger.debug("using generated space group " + this.spaceGroup.dumpInfo());
+return this.spaceGroup != null;
+}, "~N,~S,~O,~N");
+Clazz.defineMethod(c$, "fcoord",
+function(p){
+return JS.SymmetryOperation.fcoord(p, " ");
+}, "JU.T3");
+Clazz.defineMethod(c$, "getMatrixFromString",
+function(xyz, rotTransMatrix){
+JS.SymmetryOperation.getMatrixFromString(null, xyz, rotTransMatrix, false, true, false);
+}, "~S,~A");
+Clazz.defineMethod(c$, "getSpaceGroupOperationCode",
+function(iOp){
+return this.spaceGroup.operations[iOp].subsystemCode;
+}, "~N");
+Clazz.defineMethod(c$, "getTensor",
+function(vwr, parBorU){
+if (parBorU == null) return null;
+if (this.unitCell == null) this.unitCell = JS.UnitCell.fromParams( Clazz.newFloatArray(-1, [1, 1, 1, 90, 90, 90]), true, 1.0E-4);
+return this.unitCell.getTensor(vwr, parBorU);
+}, "JV.Viewer,~A");
+Clazz.defineMethod(c$, "getSpaceGroupTitle",
+function(){
+var s = this.getSpaceGroupName();
+return (s.startsWith("cell=") ? s : this.spaceGroup != null ? this.spaceGroup.asString() : this.unitCell != null && this.unitCell.name.length > 0 ? "cell=" + this.unitCell.name : "");
+});
+Clazz.defineMethod(c$, "setPrecision",
+function(prec){
+this.unitCell.setPrecision(prec);
+}, "~N");
+Clazz.defineMethod(c$, "toFractionalM",
+function(m){
+if (!this.$isBio) this.unitCell.toFractionalM(m);
+}, "JU.M4");
+Clazz.defineMethod(c$, "toUnitCellRnd",
+function(pt, offset){
+this.unitCell.toUnitCellRnd(pt, offset);
+}, "JU.T3,JU.T3");
+Clazz.defineMethod(c$, "twelfthify",
+function(pt){
+this.unitCell.twelfthify(pt);
+}, "JU.P3");
+Clazz.defineMethod(c$, "getConventionalUnitCell",
+function(latticeType, primitiveToCrystal){
+return (this.unitCell == null || latticeType == null ? null : this.unitCell.getConventionalUnitCell(latticeType, primitiveToCrystal));
+}, "~S,JU.M3");
+Clazz.defineMethod(c$, "getSpaceGroupIndex",
+function(){
+return this.spaceGroup.getIndex();
+});
+Clazz.defineMethod(c$, "getUnitCellF2C",
+function(){
+return this.unitCell.getF2C();
+});
+Clazz.defineMethod(c$, "addInversion",
+function(){
+var ops = this.spaceGroup.operations;
+var inv = new JU.M4();
+inv.m00 = inv.m11 = inv.m22 = -1;
+inv.m33 = 1;
+var n = this.getSpaceGroupOperationCount();
+var m = new JU.M4();
+for (var i = 0; i < n; i++) {
+m.mul2(inv, ops[i]);
+var s = JS.SymmetryOperation.getXYZFromMatrix(m, true, true, false);
+this.addSpaceGroupOperation(s, 0);
+}
+});
+/*eoif3*/})();
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CDXMLWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CDXMLWriter.js
new file mode 100755
index 000000000000..b5ae7197019d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CDXMLWriter.js
@@ -0,0 +1,504 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.adapter.writers.CMLWriter", "java.util.Stack", "JU.SB"], "J.adapter.writers.CDXMLWriter", ["java.util.Hashtable", "JU.PT", "$.Rdr", "J.adapter.smarter.SmarterJmolAdapter"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.doc = null;
+this.objects = null;
+this.sb = null;
+this.sbpt = 0;
+this.id = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "CDXMLWriter", J.adapter.writers.CMLWriter);
+Clazz.prepareFields (c$, function(){
+this.objects = new java.util.Stack();
+this.sb = new JU.SB();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.writers.CDXMLWriter, []);
+});
+Clazz.overrideMethod(c$, "set",
+function(viewer, out, data){
+throw new NullPointerException("CDXMLWriter is not implemented for writing");
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+throw new NullPointerException("CDXMLWriter is not implemented for writing");
+}, "JU.BS");
+c$.fromCDX = Clazz.defineMethod(c$, "fromCDX",
+function(binaryDoc){
+return new J.adapter.writers.CDXMLWriter().cdxToCdxml(binaryDoc);
+}, "javajs.api.GenericBinaryDocument");
+c$.fromASC = Clazz.defineMethod(c$, "fromASC",
+function(asc){
+return new J.adapter.writers.CDXMLWriter().ascToCdxml(asc);
+}, "J.adapter.smarter.AtomSetCollection");
+Clazz.defineMethod(c$, "ascToCdxml",
+function(asc){
+var a = new J.adapter.smarter.SmarterJmolAdapter();
+var atomIterator = a.getAtomIterator(asc);
+var bondIterator = a.getBondIterator(asc);
+J.adapter.writers.CMLWriter.openDocument(this.sb);
+J.adapter.writers.CDXMLWriter.appendHeader(this.sb);
+J.adapter.writers.CMLWriter.openTag(this.sb, "page");
+this.id = 0;
+this.openID(this.sb, "fragment");
+J.adapter.writers.CMLWriter.terminateTag(this.sb);
+var indexToID = new java.util.Hashtable();
+while (atomIterator.hasNext()) {
+this.openID(this.sb, "n");
+indexToID.put(atomIterator.getUniqueID(), Integer.$valueOf(this.id));
+var xyz = atomIterator.getXYZ();
+var ele = atomIterator.getElement();
+var iso = atomIterator.getIsotope();
+var charge = atomIterator.getFormalCharge();
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "p", J.adapter.writers.CDXMLWriter.cdxCoord(xyz.x, 200) + " " + J.adapter.writers.CDXMLWriter.cdxCoord(-xyz.y, 400));
+if (ele != 6) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Element", "" + ele);
+if (iso != 0) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Isotope", "" + iso);
+if (charge != 0) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Charge", "" + charge);
+J.adapter.writers.CMLWriter.terminateEmptyTag(this.sb);
+}
+while (bondIterator.hasNext()) {
+this.openID(this.sb, "b");
+var id1 = bondIterator.getAtomUniqueID1();
+var id2 = bondIterator.getAtomUniqueID2();
+var order = "1";
+var display = null;
+var display2 = null;
+var bo = bondIterator.getEncodedOrder();
+switch (bo) {
+case 515:
+order = "1.5";
+display2 = "Dash";
+break;
+case 514:
+order = "2";
+break;
+default:
+if ((bo & 0x07) != 0) order = "" + (bo & 0x07);
+break;
+}
+switch (bo) {
+case 1025:
+order = "1";
+display = "WedgeBegin";
+break;
+case 1041:
+order = "1";
+display = "WedgedHashBegin";
+break;
+case 1057:
+order = "1";
+display = "Wavy";
+break;
+}
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "B", indexToID.get(id1).toString());
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "E", indexToID.get(id2).toString());
+if (!order.equals("1")) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Order", order);
+if (display != null) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Display", display);
+if (display2 != null) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Display2", display2);
+J.adapter.writers.CMLWriter.terminateEmptyTag(this.sb);
+}
+J.adapter.writers.CMLWriter.closeTag(this.sb, "fragment");
+J.adapter.writers.CMLWriter.closeTag(this.sb, "page");
+J.adapter.writers.CMLWriter.closeTag(this.sb, "CDXML");
+return this.sb.toString();
+}, "J.adapter.smarter.AtomSetCollection");
+c$.cdxCoord = Clazz.defineMethod(c$, "cdxCoord",
+function(x, off){
+return "" + (off + Math.round(x / 1.45 * 14.4 * 100) / 100);
+}, "~N,~N");
+Clazz.defineMethod(c$, "openID",
+function(sb, name){
+J.adapter.writers.CMLWriter.startOpenTag(sb, name);
+J.adapter.writers.CMLWriter.addAttribute(sb, "id", "" + ++this.id);
+}, "JU.SB,~S");
+Clazz.defineMethod(c$, "cdxToCdxml",
+function(doc){
+this.doc = doc;
+try {
+J.adapter.writers.CMLWriter.openDocument(this.sb);
+J.adapter.writers.CDXMLWriter.appendHeader(this.sb);
+doc.setStreamData(null, false);
+doc.seek(22);
+this.processObject(doc.readShort());
+this.sb.append("\n");
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(this.sb + "\n" + this.objects);
+e.printStackTrace();
+return null;
+} else {
+throw e;
+}
+}
+return this.sb.toString();
+}, "javajs.api.GenericBinaryDocument");
+c$.appendHeader = Clazz.defineMethod(c$, "appendHeader",
+function(sb){
+sb.append("\n");
+J.adapter.writers.CMLWriter.startOpenTag(sb, "CDXML");
+J.adapter.writers.CMLWriter.addAttributes(sb, J.adapter.writers.CDXMLWriter.cdxAttributes);
+J.adapter.writers.CMLWriter.terminateTag(sb);
+}, "JU.SB");
+Clazz.defineMethod(c$, "processObject",
+function(type){
+var id = this.doc.readInt();
+type = type & 0xFFFF;
+var terminated = false;
+var name = null;
+switch (type) {
+case 32768:
+case 32770:
+default:
+id = -2147483648;
+terminated = true;
+break;
+case 32769:
+name = "page";
+id = -2147483648;
+break;
+case 32771:
+name = "fragment";
+break;
+case 32772:
+name = "n";
+break;
+case 32773:
+name = "b";
+break;
+case 32774:
+name = "t";
+id = -2147483648;
+break;
+}
+this.sbpt = this.sb.length();
+this.objects.push(name);
+if (name != null) {
+J.adapter.writers.CMLWriter.startOpenTag(this.sb, name);
+if (id != -2147483648) {
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "id", "" + id);
+}}var prop;
+while ((prop = this.doc.readShort()) != 0) {
+if ((prop & 0x8000) != 0) {
+if (!terminated) {
+J.adapter.writers.CMLWriter.terminateTag(this.sb);
+terminated = true;
+}this.processObject(prop);
+continue;
+}var len = this.readLength();
+switch (type) {
+case 32772:
+this.writeNodeProperties(prop, len);
+break;
+case 32774:
+if (!terminated) {
+J.adapter.writers.CMLWriter.terminateTag(this.sb);
+terminated = true;
+}this.writeTextProperty(prop, len);
+break;
+case 32773:
+this.writeBondProperties(prop, len);
+break;
+default:
+this.skip(len);
+break;
+}
+}
+if (name != null) {
+if (!terminated) {
+J.adapter.writers.CMLWriter.terminateEmptyTag(this.sb);
+} else {
+J.adapter.writers.CMLWriter.closeTag(this.sb, name);
+}}}, "~N");
+Clazz.defineMethod(c$, "writeNodeProperties",
+function(prop, len){
+switch (prop) {
+case 512:
+var y = J.adapter.writers.CDXMLWriter.toPoint(this.readInt(len >> 1));
+var x = J.adapter.writers.CDXMLWriter.toPoint(this.readInt(len >> 1));
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "p", x + " " + y);
+break;
+case 1024:
+var nodeType = J.adapter.writers.CDXMLWriter.getNodeType(this.readInt(len));
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "NodeType", nodeType);
+break;
+case 1026:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "Element", "" + this.readInt(len));
+break;
+case 1056:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "Isotope", "" + this.readInt(len));
+break;
+case 1057:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "Charge", "" + this.readInt(len));
+break;
+case 16:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "Warning", this.readString(len));
+break;
+case 1073:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "BondOrdering", this.readArray());
+break;
+case 1285:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "ConnectionOrder", this.readArray());
+break;
+case 1074:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "Attachments", this.readArray());
+break;
+case 1075:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "GenericNickname", this.readString(len));
+break;
+default:
+this.skip(len);
+}
+}, "~N,~N");
+Clazz.defineMethod(c$, "writeBondProperties",
+function(prop, len){
+switch (prop) {
+case 1536:
+var order = J.adapter.writers.CDXMLWriter.getBondOrder(this.readInt(len));
+if (order == null) {
+this.removeObject();
+return;
+}J.adapter.writers.CMLWriter.addAttribute(this.sb, "Order", order);
+break;
+case 1537:
+var d = J.adapter.writers.CDXMLWriter.getBondDisplay(this.readInt(len));
+if (d == null) {
+this.removeObject();
+return;
+}J.adapter.writers.CMLWriter.addAttribute(this.sb, "Display", d);
+break;
+case 1538:
+var d2 = J.adapter.writers.CDXMLWriter.getBondDisplay(this.readInt(len));
+if (d2 != null) J.adapter.writers.CMLWriter.addAttribute(this.sb, "Display2", d2);
+break;
+case 1540:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "B", "" + this.readInt(len));
+break;
+case 1541:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "E", "" + this.readInt(len));
+break;
+case 1544:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "BeginAttach", "" + this.readInt(len));
+break;
+case 1545:
+J.adapter.writers.CMLWriter.addAttribute(this.sb, "EndAttach", "" + this.readInt(len));
+break;
+default:
+this.skip(len);
+}
+}, "~N,~N");
+Clazz.defineMethod(c$, "writeTextProperty",
+function(prop, len){
+switch (prop) {
+case 1792:
+var text = this.readString(len);
+System.out.println("CDXMLW text=" + text);
+J.adapter.writers.CMLWriter.openTag(this.sb, "s");
+this.sb.setLength(this.sb.length() - 1);
+this.sb.append(J.adapter.writers.CDXMLWriter.wrapCData(text));
+J.adapter.writers.CMLWriter.closeTag(this.sb, "s");
+break;
+default:
+this.skip(len);
+}
+}, "~N,~N");
+c$.wrapCData = Clazz.defineMethod(c$, "wrapCData",
+function(s){
+return (s.indexOf("&") < 0 && s.indexOf("<") < 0 ? s : "", "]]]]>") + "]]>");
+}, "~S");
+c$.getNodeType = Clazz.defineMethod(c$, "getNodeType",
+function(n){
+var name = null;
+switch (n) {
+case 0:
+return "Unspecified";
+case 1:
+return "Element";
+case 4:
+return "Nickname";
+case 5:
+return "Fragment";
+case 7:
+return "GenericNickname";
+case 10:
+return "MultiAttachment";
+case 11:
+return "VariableAttachment";
+case 12:
+return "ExternalConnectionPoint";
+case 2:
+name = "ElementList";
+break;
+case 3:
+name = "ElementListNickname";
+break;
+case 6:
+name = "Formula";
+break;
+case 8:
+name = "AnonymousAlternativeGroup";
+break;
+case 9:
+name = "NamedAnonymousGroup";
+break;
+case 13:
+name = "LinkNode";
+break;
+}
+System.err.println("CDXMLWriter Node type " + name + " not identified");
+return "_";
+}, "~N");
+c$.getBondDisplay = Clazz.defineMethod(c$, "getBondDisplay",
+function(i){
+switch (i) {
+case 0:
+return "Solid";
+case 1:
+return "Dash";
+case 2:
+return "Hash";
+case 3:
+return "WedgedHashBegin";
+case 4:
+return "WedgedHashEnd";
+case 5:
+return "Bold";
+case 6:
+return "WedgeBegin";
+case 7:
+return "WedgeEnd";
+case 8:
+return "Wavy";
+case 9:
+return "HollowWedgeBegin";
+case 10:
+return "HollowWedgeEnd";
+case 11:
+return "WavyWedgeBegin";
+case 12:
+return "WavyWedgeEnd";
+case 13:
+return "Dot";
+case 14:
+return "DashDot";
+}
+return null;
+}, "~N");
+c$.getBondOrder = Clazz.defineMethod(c$, "getBondOrder",
+function(i){
+switch (i) {
+case 1:
+return "1";
+case 2:
+return "2";
+case 4:
+return "3";
+case 8:
+return "4";
+case 16:
+return "5";
+case 32:
+return "6";
+case 64:
+return "0.5";
+case 128:
+return "1.5";
+case 256:
+return "2.5";
+case 512:
+return "3.5";
+case 1024:
+return "4.5";
+case 2048:
+return "5.5";
+case 4096:
+return "dative";
+case 8192:
+return "ionic";
+case 16384:
+return "hydrogen";
+case 32768:
+return "threecenter";
+}
+return null;
+}, "~N");
+Clazz.defineMethod(c$, "removeObject",
+function(){
+this.sb.setLength(this.sbpt);
+});
+Clazz.defineMethod(c$, "skip",
+function(len){
+this.doc.seek(this.doc.getPosition() + len);
+}, "~N");
+Clazz.defineMethod(c$, "readInt",
+function(len){
+switch (len) {
+case 1:
+return (256 + this.doc.readByte()) % 256;
+case 2:
+return this.doc.readShort();
+case 4:
+return this.doc.readInt();
+case 8:
+return this.doc.readLong();
+}
+System.err.println("CDXMLWriter.readInt len " + len);
+return 0;
+}, "~N");
+Clazz.defineMethod(c$, "readString",
+function(len){
+var nStyles = this.doc.readShort();
+len -= 2;
+switch (nStyles) {
+case 0:
+break;
+default:
+this.skip(nStyles * 10);
+len -= nStyles * 10;
+break;
+}
+return this.doc.readString(len);
+}, "~N");
+Clazz.defineMethod(c$, "readArray",
+function(){
+var s = "";
+for (var i = this.doc.readShort(); --i >= 0; ) {
+s += " " + this.doc.readInt();
+}
+return s.trim();
+});
+Clazz.defineMethod(c$, "readLength",
+function(){
+var len = this.doc.readShort();
+if (len == -1) {
+len = this.doc.readInt();
+}return len;
+});
+c$.toPoint = Clazz.defineMethod(c$, "toPoint",
+function(i){
+return Math.round(i / 655.36) / 100.0;
+}, "~N");
+c$.main = Clazz.defineMethod(c$, "main",
+function(args){
+}, "~A");
+c$.fromString = Clazz.defineMethod(c$, "fromString",
+function(vwr, type, mol){
+var htParams = new java.util.Hashtable();
+htParams.put("filter", "filetype=" + type);
+var o;
+try {
+o = vwr.getModelAdapter().getAtomSetCollectionFromReader("", JU.Rdr.getBR(mol), htParams);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+return null;
+} else {
+throw e;
+}
+}
+if ((typeof(o)=='string')) {
+return null;
+}return J.adapter.writers.CDXMLWriter.fromASC(o);
+}, "JV.Viewer,~S,~S");
+c$.cdxAttributes = Clazz.newArray(-1, ["HashSpacing", "2.50", "MarginWidth", "1.60", "LineWidth", "0.60", "BoldWidth", "2", "BondLength", "14.40", "BondSpacing", "18"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CIFWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CIFWriter.js
new file mode 100755
index 000000000000..668de09b7d1f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CIFWriter.js
@@ -0,0 +1,219 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.adapter.writers.XtlWriter", "J.api.JmolWriter", "JU.P3"], "J.adapter.writers.CIFWriter", ["JU.BS", "$.PT", "$.SB", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.oc = null;
+this.isP1 = false;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "CIFWriter", J.adapter.writers.XtlWriter, J.api.JmolWriter);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.writers.CIFWriter, []);
+});
+Clazz.overrideMethod(c$, "set",
+function(viewer, oc, data){
+this.vwr = viewer;
+this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
+this.isP1 = (data != null && data.length > 0 && "P1".equals(data[0]));
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+if (bs == null) bs = this.vwr.bsA();
+try {
+var mi = this.vwr.ms.at[bs.nextSetBit(0)].mi;
+var uc = this.vwr.getCurrentUnitCell();
+this.haveUnitCell = (uc != null);
+if (!this.haveUnitCell) uc = this.vwr.getSymTemp().setUnitCellFromParams(null, false, 0.00001);
+this.slop = uc.getPrecision();
+this.isHighPrecision = (this.slop == 1.0E-12);
+this.precision = Clazz.doubleToInt(-Math.log10(this.slop));
+var offset = uc.getFractionalOffset();
+var fractionalOffset = offset != null && (offset.x != Clazz.floatToInt(offset.x) || offset.y != Clazz.floatToInt(offset.y) || offset.z != Clazz.floatToInt(offset.z));
+var fset;
+var haveCustom = (fractionalOffset || (fset = uc.getUnitCellMultiplier()) != null && (fset.z == 1 ? !fset.equals(J.adapter.writers.CIFWriter.fset0) : fset.z != 0));
+var ucm = uc.getUnitCellMultiplied();
+this.isP1 = (this.isP1 || ucm !== uc || fractionalOffset || uc.getSpaceGroupOperationCount() < 2);
+uc = ucm;
+var modelAU = (!this.haveUnitCell ? bs : this.isP1 ? uc.removeDuplicates(this.vwr.ms, bs, false) : this.vwr.ms.am[mi].bsAsymmetricUnit);
+var bsOut;
+if (modelAU == null) {
+bsOut = bs;
+} else {
+bsOut = new JU.BS();
+bsOut.or(modelAU);
+bsOut.and(bs);
+}this.vwr.setErrorMessage(null, " (" + bsOut.cardinality() + " atoms)");
+if (bsOut.isEmpty()) return "";
+var sb = new JU.SB();
+sb.append("## CIF file created by Jmol " + JV.Viewer.getJmolVersion());
+if (haveCustom) {
+sb.append(JU.PT.rep("\n" + uc.getUnitCellInfo(false), "\n", "\n##Jmol_orig "));
+}sb.append("\ndata_global");
+var params = uc.getUnitCellAsArray(false);
+this.appendKey(sb, "_cell_length_a").append(this.cleanT(params[0]));
+this.appendKey(sb, "_cell_length_b").append(this.cleanT(params[1]));
+this.appendKey(sb, "_cell_length_c").append(this.cleanT(params[2]));
+this.appendKey(sb, "_cell_angle_alpha").append(this.cleanT(params[3]));
+this.appendKey(sb, "_cell_angle_beta").append(this.cleanT(params[4]));
+this.appendKey(sb, "_cell_angle_gamma").append(this.cleanT(params[5]));
+sb.append("\n");
+var n;
+var hallName;
+var hmName;
+var ita;
+if (this.isP1) {
+ita = "1";
+hallName = "P 1";
+hmName = "P1";
+n = 0;
+} else {
+uc.getSpaceGroupInfo(this.vwr.ms, null, mi, true, null);
+ita = uc.getSpaceGroupNameType("ITA");
+hallName = uc.getSpaceGroupNameType("Hall");
+hmName = uc.getSpaceGroupNameType("HM");
+n = uc.getSpaceGroupOperationCount();
+}this.appendKey(sb, "_space_group_IT_number").append(ita == null ? "?" : ita.toString());
+this.appendKey(sb, "_space_group_name_Hall").append(hallName == null || hallName.equals("?") ? "?" : "'" + hallName + "'");
+this.appendKey(sb, "_space_group_name_H-M_alt").append(hmName == null ? "?" : "'" + hmName + "'");
+sb.append("\n\nloop_\n_space_group_symop_id\n_space_group_symop_operation_xyz");
+if (n == 0) {
+sb.append("\n1 x,y,z");
+} else {
+for (var i = 0; i < n; i++) {
+sb.append("\n").appendI(i + 1).append("\t").append(uc.getSpaceGroupXyz(i, false).replaceAll(" ", ""));
+}
+}var atoms = this.vwr.ms.at;
+var elements = "";
+var haveOccupancy = false;
+var occ = (this.haveUnitCell ? this.vwr.ms.occupancies : null);
+if (occ != null) {
+for (var i = bsOut.nextSetBit(0); i >= 0; i = bsOut.nextSetBit(i + 1)) {
+if (occ[i] != 1) {
+haveOccupancy = true;
+break;
+}}
+}var haveAltLoc = false;
+for (var i = bsOut.nextSetBit(0); i >= 0; i = bsOut.nextSetBit(i + 1)) {
+if (atoms[i].altloc != '\0') {
+haveAltLoc = true;
+break;
+}}
+var sbLength = sb.length();
+sb.append("\n\nloop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z");
+if (haveAltLoc) {
+sb.append("\n_atom_site_disorder_group");
+}if (haveOccupancy) {
+sb.append("\n_atom_site_occupancy");
+} else if (!this.haveUnitCell) {
+sb.append("\n_atom_site_Cartn_x\n_atom_site_Cartn_y\n_atom_site_Cartn_z");
+}sb.append("\n");
+var jmol_atom = new JU.SB();
+jmol_atom.append("\n\nloop_\n_jmol_atom_index\n_jmol_atom_name\n_jmol_atom_site_label\n");
+var nAtoms = 0;
+var p = new JU.P3();
+var elemNums = Clazz.newIntArray (130, 0);
+for (var i = bsOut.nextSetBit(0); i >= 0; i = bsOut.nextSetBit(i + 1)) {
+var a = atoms[i];
+p.setT(a);
+if (this.haveUnitCell) {
+uc.toFractional(p, !this.isP1);
+}nAtoms++;
+var name = a.getAtomName();
+var sym = a.getElementSymbol();
+var elemno = a.getElementNumber();
+var key = sym + "\n";
+if (elements.indexOf(key) < 0) elements += key;
+var label = sym + ++elemNums[elemno];
+sb.append(JU.PT.formatS(label, 5, 0, true, false)).append(" ").append(JU.PT.formatS(sym, 3, 0, true, false)).append(this.clean(p.x)).append(this.clean(p.y)).append(this.clean(p.z));
+if (haveAltLoc) {
+sb.append(" ").appendC(a.altloc == '\0' ? '.' : a.altloc);
+}if (haveOccupancy) sb.append(" ").append(this.clean(occ[i] / 100));
+ else if (!this.haveUnitCell) sb.append(this.clean(a.x)).append(this.clean(a.y)).append(this.clean(a.z));
+sb.append("\n");
+jmol_atom.append(JU.PT.formatS("" + a.getIndex(), 3, 0, false, false)).append(" ");
+this.writeChecked(jmol_atom, name);
+jmol_atom.append(" ").append(JU.PT.formatS(label, 5, 0, false, false)).append("\n");
+}
+if (nAtoms > 0) {
+sb.append("\nloop_\n_atom_type_symbol\n").append(elements).append("\n");
+sb.appendSB(jmol_atom);
+} else {
+sb.setLength(sbLength);
+}sb.append("\n_jmol_atom_count " + nAtoms);
+sb.append("\n_jmol_precision " + this.precision + "\n");
+this.oc.append(sb.toString());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (!JV.Viewer.isJS) e.printStackTrace();
+} else {
+throw e;
+}
+}
+return this.toString();
+}, "JU.BS");
+Clazz.defineMethod(c$, "writeChecked",
+function(output, val){
+if (val == null || val.length == 0) {
+output.append(". ");
+return false;
+}var escape = val.charAt(0) == '_';
+var escapeCharStart = "'";
+var escapeCharEnd = "' ";
+var hasWhitespace = false;
+var hasSingle = false;
+var hasDouble = false;
+for (var i = 0; i < val.length; i++) {
+var c = val.charAt(i);
+switch ((c).charCodeAt(0)) {
+case 9:
+case 32:
+hasWhitespace = true;
+break;
+case 10:
+this.writeMultiline(output, val);
+return true;
+case 34:
+if (hasSingle) {
+this.writeMultiline(output, val);
+return true;
+}hasDouble = true;
+escape = true;
+escapeCharStart = "'";
+escapeCharEnd = "' ";
+break;
+case 39:
+if (hasDouble) {
+this.writeMultiline(output, val);
+return true;
+}escape = true;
+hasSingle = true;
+escapeCharStart = "\"";
+escapeCharEnd = "\" ";
+break;
+}
+}
+var fst = val.charAt(0);
+if (!escape && (fst == '#' || fst == '$' || fst == ';' || fst == '[' || fst == ']' || hasWhitespace)) {
+escapeCharStart = "'";
+escapeCharEnd = "' ";
+escape = true;
+}if (escape) {
+output.append(escapeCharStart).append(val).append(escapeCharEnd);
+} else {
+output.append(val).append(" ");
+}return false;
+}, "JU.SB,~S");
+Clazz.defineMethod(c$, "writeMultiline",
+function(output, val){
+output.append("\n;").append(val).append("\n;\n");
+}, "JU.SB,~S");
+Clazz.defineMethod(c$, "appendKey",
+function(sb, key){
+return sb.append("\n").append(JU.PT.formatS(key, 27, 0, true, false));
+}, "JU.SB,~S");
+Clazz.defineMethod(c$, "toString",
+function(){
+return (this.oc == null ? "" : this.oc.toString());
+});
+c$.fset0 = JU.P3.new3(555, 555, 1);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CMLWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CMLWriter.js
new file mode 100755
index 000000000000..4f0b1a5c6fbf
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/CMLWriter.js
@@ -0,0 +1,101 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.api.JmolWriter"], "J.adapter.writers.CMLWriter", ["JU.BS", "$.PT", "$.SB", "JU.Edge"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.oc = null;
+this.atomsMax = 0;
+this.addBonds = false;
+this.doTransform = false;
+this.allTrajectories = false;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "CMLWriter", null, J.api.JmolWriter);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set",
+function(viewer, out, data){
+this.vwr = viewer;
+this.oc = (this.oc == null ? this.vwr.getOutputChannel(null, null) : this.oc);
+this.atomsMax = (data[0]).intValue();
+this.addBonds = (data[1]).booleanValue();
+this.doTransform = (data[2]).booleanValue();
+this.allTrajectories = (data[3]).booleanValue();
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+var sb = new JU.SB();
+var nAtoms = bs.cardinality();
+if (nAtoms == 0) return "";
+J.adapter.writers.CMLWriter.openTag(sb, "molecule");
+J.adapter.writers.CMLWriter.openTag(sb, "atomArray");
+var bsAtoms = new JU.BS();
+var atoms = this.vwr.ms.at;
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (--this.atomsMax < 0) break;
+var atom = atoms[i];
+var name = atom.getAtomName();
+JU.PT.rep(name, "\"", "''");
+bsAtoms.set(atom.i);
+J.adapter.writers.CMLWriter.appendEmptyTag(sb, "atom", Clazz.newArray(-1, ["id", "a" + (atom.i + 1), "title", atom.getAtomName(), "elementType", atom.getElementSymbol(), "x3", "" + atom.x, "y3", "" + atom.y, "z3", "" + atom.z]));
+}
+J.adapter.writers.CMLWriter.closeTag(sb, "atomArray");
+if (this.addBonds) {
+J.adapter.writers.CMLWriter.openTag(sb, "bondArray");
+var bondCount = this.vwr.ms.bondCount;
+var bonds = this.vwr.ms.bo;
+for (var i = 0; i < bondCount; i++) {
+var bond = bonds[i];
+var a1 = bond.atom1;
+var a2 = bond.atom2;
+if (!bsAtoms.get(a1.i) || !bsAtoms.get(a2.i)) continue;
+var order = JU.Edge.getCmlBondOrder(bond.order);
+if (order == null) continue;
+J.adapter.writers.CMLWriter.appendEmptyTag(sb, "bond", Clazz.newArray(-1, ["atomRefs2", "a" + (bond.atom1.i + 1) + " a" + (bond.atom2.i + 1), "order", order]));
+}
+J.adapter.writers.CMLWriter.closeTag(sb, "bondArray");
+}J.adapter.writers.CMLWriter.closeTag(sb, "molecule");
+this.oc.append(sb.toString());
+return this.toString();
+}, "JU.BS");
+c$.openDocument = Clazz.defineMethod(c$, "openDocument",
+function(sb){
+sb.append("\n");
+}, "JU.SB");
+c$.openTag = Clazz.defineMethod(c$, "openTag",
+function(sb, name){
+sb.append("<").append(name).append(">\n");
+}, "JU.SB,~S");
+c$.startOpenTag = Clazz.defineMethod(c$, "startOpenTag",
+function(sb, name){
+sb.append("<").append(name);
+}, "JU.SB,~S");
+c$.terminateTag = Clazz.defineMethod(c$, "terminateTag",
+function(sb){
+sb.append(">\n");
+}, "JU.SB");
+c$.terminateEmptyTag = Clazz.defineMethod(c$, "terminateEmptyTag",
+function(sb){
+sb.append("/>\n");
+}, "JU.SB");
+c$.appendEmptyTag = Clazz.defineMethod(c$, "appendEmptyTag",
+function(sb, name, attributes){
+J.adapter.writers.CMLWriter.startOpenTag(sb, name);
+J.adapter.writers.CMLWriter.addAttributes(sb, attributes);
+J.adapter.writers.CMLWriter.terminateEmptyTag(sb);
+}, "JU.SB,~S,~A");
+c$.addAttributes = Clazz.defineMethod(c$, "addAttributes",
+function(sb, attributes){
+for (var i = 0; i < attributes.length; i++) {
+J.adapter.writers.CMLWriter.addAttribute(sb, attributes[i], attributes[++i]);
+}
+}, "JU.SB,~A");
+c$.addAttribute = Clazz.defineMethod(c$, "addAttribute",
+function(sb, key, val){
+sb.append(" ").append(key).append("=").append(JU.PT.esc(val));
+}, "JU.SB,~S,~S");
+c$.closeTag = Clazz.defineMethod(c$, "closeTag",
+function(sb, name){
+sb.append("\n");
+}, "JU.SB,~S");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return (this.oc == null ? "" : this.oc.toString());
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/MOLWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/MOLWriter.js
new file mode 100755
index 000000000000..baabf99ec14c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/MOLWriter.js
@@ -0,0 +1,252 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(null, "J.adapter.writers.MOLWriter", ["java.util.Arrays", "$.Hashtable", "JU.Lst", "$.Measure", "$.P3", "$.PT", "$.SB", "$.V3", "JS.T", "JU.Elements", "$.Escape", "JV.PropertyManager", "$.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.ptTemp = null;
+this.vNorm = null;
+this.vTemp = null;
+this.connections = null;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "MOLWriter", null);
+/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "setViewer",
+function(vwr){
+this.vwr = vwr;
+return this;
+}, "JV.Viewer");
+Clazz.defineMethod(c$, "addMolFile",
+function(title, iModel, mol, bsAtoms, bsBonds, asV3000, asJSON, noAromatic, q, is2d){
+var nAtoms = bsAtoms.cardinality();
+var nBonds = bsBonds.cardinality();
+if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999)) return false;
+if (!asJSON) {
+if (title.length > 80) title = title.substring(0, 77) + "...";
+mol.append(title).append("\n");
+var version = JV.Viewer.getJmolVersion();
+mol.append(JV.PropertyManager.getSDFDateLine("__Jmol-" + version, is2d));
+mol.append("Jmol version ").append(version).append(" EXTRACT: ").append(JU.Escape.eBS(bsAtoms)).append("\n");
+}var asSDF = (iModel >= 0);
+var molData = (asSDF ? this.vwr.ms.getInfo(iModel, "molData") : null);
+var _keyList = (asSDF ? this.vwr.ms.getInfo(iModel, "molDataKeys") : null);
+var ms = this.vwr.ms;
+var atomMap = Clazz.newIntArray (ms.ac, 0);
+var pTemp = new JU.P3();
+if (asV3000) {
+mol.append(" 0 0 0 0 0 0 999 V3000");
+} else if (asJSON) {
+mol.append("{\"mol\":{\"createdBy\":\"Jmol " + JV.Viewer.getJmolVersion() + "\",\"a\":[");
+} else {
+JU.PT.rightJustify(mol, " ", "" + nAtoms);
+JU.PT.rightJustify(mol, " ", "" + nBonds);
+mol.append(" 0 0 0 0 999 V2000");
+}if (!asJSON) mol.append("\n");
+if (asV3000) {
+mol.append("M V30 BEGIN CTAB\nM V30 COUNTS ").appendI(nAtoms).append(" ").appendI(nBonds).append(" 0 0 0\n").append("M V30 BEGIN ATOM\n");
+}var o = (molData == null ? null : molData.get("atom_value_name"));
+if (Clazz.instanceOf(o,"JS.SV")) o = (o).asString();
+var valueType = (o == null ? 0 : JS.T.getTokFromName("" + o));
+var atomValues = (valueType == 0 && !asSDF ? null : new JU.SB());
+for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+this.getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp, asV3000, asJSON, atomValues, valueType, asSDF);
+}
+if (asV3000) {
+mol.append("M V30 END ATOM\nM V30 BEGIN BOND\n");
+} else if (asJSON) {
+mol.append("],\"b\":[");
+}for (var i = bsBonds.nextSetBit(0), n = 0; i >= 0; i = bsBonds.nextSetBit(i + 1)) {
+this.getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON, noAromatic, is2d);
+}
+if (asV3000) {
+mol.append("M V30 END BOND\nM V30 END CTAB\n");
+}if (asJSON) mol.append("]}}");
+ else {
+if (atomValues != null && atomValues.length() > 0) mol.append(atomValues.toString());
+mol.append("M END\n");
+}if (asSDF) {
+try {
+var pc = ms.getPartialCharges();
+if (molData == null) molData = new java.util.Hashtable();
+var sb = new JU.SB();
+if (pc != null) {
+sb.appendI(nAtoms).appendC('\n');
+for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) sb.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');
+
+molData.put("jmol_partial_charges", sb.toString());
+}sb.setLength(0);
+sb.appendI(nAtoms).appendC('\n');
+for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var name = ms.at[i].getAtomName().trim();
+if (name.length == 0) name = ".";
+sb.appendI(++n).append(" ").append(name.$replace(' ', '_')).appendC('\n');
+}
+molData.put("jmol_atom_names", sb.toString());
+if (_keyList == null) _keyList = new JU.Lst();
+for (var key, $key = molData.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) if (!_keyList.contains(key)) _keyList.addLast(key);
+
+for (var i = 0, n = _keyList.size(); i < n; i++) {
+var key = _keyList.get(i);
+if (key.startsWith(">")) continue;
+o = molData.get(key);
+if (Clazz.instanceOf(o,"JS.SV")) o = (o).asString();
+mol.append("> <" + key.toUpperCase() + ">\n");
+this.output80CharWrap(mol, o.toString(), 80);
+mol.append("\n\n");
+}
+} catch (e) {
+}
+mol.append("$$$$\n");
+}return true;
+}, "~S,~N,JU.SB,JU.BS,JU.BS,~B,~B,~B,JU.Quat,~B");
+Clazz.defineMethod(c$, "getAtomRecordMOL",
+function(iModel, ms, mol, n, a, q, pTemp, asV3000, asJSON, atomValues, tokValue, asSDF){
+ms.getPointTransf(iModel, a, q, pTemp);
+var elemNo = a.getElementNumber();
+var sym = (a.isDeleted() ? "Xx" : JU.Elements.elementSymbolFromNumber(elemNo));
+var isotope = a.getIsotopeNumber();
+var charge = a.getFormalCharge();
+var o = Clazz.newArray(-1, [pTemp]);
+if (asV3000) {
+mol.append("M V30 ").appendI(n).append(" ").append(sym).append(JU.PT.sprintf(" %12.5p %12.5p %12.5p 0", "p", o));
+if (charge != 0) mol.append(" CHG=").appendI(charge);
+if (isotope != 0) mol.append(" MASS=").appendI(isotope);
+mol.append("\n");
+} else if (asJSON) {
+if (n != 1) mol.append(",");
+mol.append("{");
+if (a.getElementNumber() != 6) mol.append("\"l\":\"").append(a.getElementSymbol()).append("\",");
+if (charge != 0) mol.append("\"c\":").appendI(charge).append(",");
+if (isotope != 0) mol.append("\"m\":").appendI(isotope).append(",");
+mol.append("\"x\":").appendF(a.x).append(",\"y\":").appendF(a.y).append(",\"z\":").appendF(a.z).append("}");
+} else {
+mol.append(JU.PT.sprintf("%10.4p%10.4p%10.4p", "p", o));
+mol.append(" ").append(sym);
+if (sym.length == 1) mol.append(" ");
+JU.PT.rightJustify(mol, " ", "" + (isotope > 0 ? isotope - JU.Elements.getNaturalIsotope(a.getElementNumber()) : 0));
+if (asSDF && isotope > 0) {
+atomValues.append("M ISO 1");
+JU.PT.rightJustify(atomValues, " ", "" + n);
+JU.PT.rightJustify(atomValues, " ", "" + isotope);
+atomValues.append("\n");
+}JU.PT.rightJustify(mol, " ", "" + (charge == 0 ? 0 : 4 - charge));
+mol.append(" ").append(this.getAtomParity(a));
+mol.append(" 0 0 0\n");
+var label = (tokValue == 0 || asV3000 ? null : this.getAtomPropertyAsString(a, tokValue));
+if (label != null && (label = label.trim()).length > 0) {
+var sn = " " + n + " ";
+atomValues.append("V ").append(sn.substring(sn.length - 4));
+this.output80CharWrap(atomValues, label, 73);
+}}}, "~N,JM.ModelSet,JU.SB,~N,JM.Atom,JU.Quat,JU.P3,~B,~B,JU.SB,~N,~B");
+Clazz.defineMethod(c$, "getAtomParity",
+function(a){
+if (a.getCovalentBondCount() == 4) {
+if (this.connections == null) {
+this.connections = Clazz.newIntArray (4, 0);
+this.vTemp = new JU.V3();
+this.vNorm = new JU.V3();
+}var bonds = a.bonds;
+var nH = 0;
+for (var pt = 0, i = bonds.length; --i >= 0; ) {
+if (bonds[i].isCovalent()) {
+var b = bonds[i].getOtherAtom(a);
+if (b.getAtomicAndIsotopeNumber() == 1) nH++;
+this.connections[pt++] = b.i;
+}}
+if (nH < 3) {
+java.util.Arrays.sort(this.connections);
+var atoms = this.vwr.ms.at;
+JU.Measure.getNormalThroughPoints(atoms[this.connections[0]], atoms[this.connections[1]], atoms[this.connections[2]], this.vNorm, this.vTemp);
+this.vTemp.sub2(atoms[this.connections[3]], atoms[this.connections[0]]);
+return (this.vTemp.dot(this.vNorm) > 0 ? "1" : "2");
+}}return "0";
+}, "JM.Atom");
+Clazz.defineMethod(c$, "getAtomPropertyAsString",
+function(a, tok){
+switch (tok & 1136656384) {
+case 1094713344:
+var i = a.atomPropertyInt(tok);
+return (tok == 1765808134 ? JU.PT.trim(JU.Escape.escapeColor(i), "[x]").toUpperCase() : "" + i);
+case 1086324736:
+return a.atomPropertyString(this.vwr, tok);
+case 1111490560:
+var f = a.atomPropertyFloat(this.vwr, tok, null);
+return (Float.isNaN(f) ? null : "" + f);
+default:
+if (this.ptTemp == null) this.ptTemp = new JU.P3();
+a.atomPropertyTuple(this.vwr, tok, this.ptTemp);
+return (this.ptTemp == null ? null : this.ptTemp.toString());
+}
+}, "JM.Atom,~N");
+Clazz.defineMethod(c$, "getBondRecordMOL",
+function(mol, n, b, atomMap, asV3000, asJSON, noAromatic, is2d){
+var a1 = atomMap[b.atom1.i];
+var a2 = atomMap[b.atom2.i];
+var order = b.getValence();
+var cfg = "";
+if (order > 3) order = 1;
+if (is2d) {
+if (asJSON) {
+} else {
+switch (b.order) {
+case 1057:
+cfg = (asV3000 ? " CFG=3" : " 4");
+break;
+case 1025:
+cfg = (asV3000 ? " CFG=1" : " 1");
+break;
+case 1041:
+cfg = (asV3000 ? " CFG=2" : " 3");
+break;
+default:
+cfg = " 0";
+break;
+}
+}}switch (b.order & 131071) {
+case 515:
+order = (asJSON ? -3 : 4);
+break;
+case 66:
+order = (asJSON ? -3 : 5);
+break;
+case 513:
+order = (asJSON || noAromatic ? 1 : 6);
+break;
+case 514:
+order = (asJSON || noAromatic ? 2 : 7);
+break;
+case 33:
+order = (asJSON ? -1 : 8);
+break;
+}
+if (asV3000) {
+mol.append("M V30 ").appendI(n).append(" ").appendI(order).append(" ").appendI(a1).append(" ").appendI(a2).append(cfg).appendC('\n');
+} else if (asJSON) {
+if (n != 1) mol.append(",");
+mol.append("{\"b\":").appendI(a1 - 1).append(",\"e\":").appendI(a2 - 1);
+if (order != 1) {
+mol.append(",\"o\":");
+if (order < 0) {
+mol.appendF(-order / 2);
+} else {
+mol.appendI(order);
+}}mol.append("}");
+} else {
+JU.PT.rightJustify(mol, " ", "" + a1);
+JU.PT.rightJustify(mol, " ", "" + a2);
+mol.append(" ").appendI(order).append(cfg).append("\n");
+}}, "JU.SB,~N,JM.Bond,~A,~B,~B,~B,~B");
+Clazz.defineMethod(c$, "output80CharWrap",
+function(mol, data, maxN){
+if (maxN < 80) data = JU.PT.rep(data, "\n", "|");
+var lines = JU.PT.split(JU.PT.trim(JU.PT.rep(data, "\n\n", "\n"), "\n"), "\n");
+for (var i = 0; i < lines.length; i++) this.outputLines(mol, lines[i], maxN);
+
+}, "JU.SB,~S,~N");
+Clazz.defineMethod(c$, "outputLines",
+function(mol, data, maxN){
+var done = false;
+for (var i = 0, n = data.length; i < n && !done; i += 80) {
+mol.append(data.substring(i, Math.min(i + maxN, n)));
+if (!(done = (maxN != 80)) && i + 80 < n) mol.append("+");
+mol.append("\n");
+}
+}, "JU.SB,~S,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PDBWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PDBWriter.js
new file mode 100755
index 000000000000..5f840dba05ce
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PDBWriter.js
@@ -0,0 +1,177 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.api.JmolWriter"], "J.adapter.writers.PDBWriter", ["java.util.Arrays", "$.Date", "$.Hashtable", "JU.Lst", "$.P3", "$.PT", "JM.LabelToken", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.oc = null;
+this.isPQR = false;
+this.doTransform = false;
+this.allTrajectories = false;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "PDBWriter", null, J.api.JmolWriter);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set",
+function(viewer, oc, data){
+this.vwr = viewer;
+this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
+this.isPQR = (data[0]).booleanValue();
+this.doTransform = (data[1]).booleanValue();
+this.allTrajectories = (data[2]).booleanValue();
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+var type = this.oc.getType();
+this.isPQR = new Boolean (this.isPQR | (type != null && type.indexOf("PQR") >= 0)).valueOf();
+this.doTransform = new Boolean (this.doTransform | (type != null && type.indexOf("-coord true") >= 0)).valueOf();
+var atoms = this.vwr.ms.at;
+var models = this.vwr.ms.am;
+var occTemp = "%6.2Q%6.2b ";
+if (this.isPQR) {
+occTemp = "%8.4P%7.4V ";
+var charge = 0;
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) charge += atoms[i].getPartialCharge();
+
+this.oc.append("REMARK 1 PQR file generated by Jmol " + JV.Viewer.getJmolVersion()).append("\nREMARK 1 " + "created " + ( new java.util.Date())).append("\nREMARK 1 Forcefield Used: unknown\nREMARK 1").append("\nREMARK 5").append("\nREMARK 6 Total charge on this protein: " + charge + " e\nREMARK 6\n");
+}var iModel = atoms[bs.nextSetBit(0)].mi;
+var iModelLast = -1;
+var lastAtomIndex = bs.length() - 1;
+var lastModelIndex = atoms[lastAtomIndex].mi;
+var isMultipleModels = (iModel != lastModelIndex);
+var bsModels = this.vwr.ms.getModelBS(bs, true);
+var nModels = bsModels.cardinality();
+var lines = new JU.Lst();
+var isMultipleBondPDB = models[iModel].isPdbWithMultipleBonds;
+var uniqueAtomNumbers = false;
+if (nModels > 1) {
+var conectArray = null;
+for (var nFiles = 0, i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) {
+var a = this.vwr.ms.getModelAuxiliaryInfo(i).get("PDB_CONECT_bonds");
+if (a !== conectArray || !this.vwr.ms.am[i].isBioModel) {
+conectArray = a;
+if (nFiles++ > 0) {
+uniqueAtomNumbers = true;
+break;
+}}}
+}var tokens;
+var ptTemp = new JU.P3();
+var o = Clazz.newArray(-1, [ptTemp]);
+var q = (this.doTransform ? this.vwr.tm.getRotationQ() : null);
+var map = new java.util.Hashtable();
+var isBiomodel = false;
+var firstAtomIndexNew = (uniqueAtomNumbers ? Clazz.newIntArray (nModels, 0) : null);
+var modelPt = 0;
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var a = atoms[i];
+isBiomodel = models[a.mi].isBioModel;
+if (isMultipleModels && a.mi != iModelLast) {
+if (iModelLast != -1) {
+modelPt = this.fixPDBFormat(lines, map, this.oc, firstAtomIndexNew, modelPt);
+this.oc.append("ENDMDL\n");
+}lines = new JU.Lst();
+iModel = iModelLast = a.mi;
+this.oc.append("MODEL " + (iModelLast + 1) + "\n");
+}var sa = a.getAtomName();
+var leftJustify = (a.getElementSymbol().length == 2 || sa.length >= 4 || JU.PT.isDigit(sa.charAt(0)));
+var isHetero = a.isHetero();
+if (!isBiomodel) tokens = (leftJustify ? JM.LabelToken.compile(this.vwr, "HETATM%5.-5i %-4.4a%1AUNK %1c 1%1E _XYZ_" + occTemp, '\0', null) : JM.LabelToken.compile(this.vwr, "HETATM%5.-5i %-3.3a%1AUNK %1c 1%1E _XYZ_" + occTemp, '\0', null));
+ else if (isHetero) tokens = (leftJustify ? JM.LabelToken.compile(this.vwr, "HETATM%5.-5i %-4.4a%1A%3.3n %1c%4.-4R%1E _XYZ_" + occTemp, '\0', null) : JM.LabelToken.compile(this.vwr, "HETATM%5.-5i %-3.3a%1A%3.3n %1c%4.-4R%1E _XYZ_" + occTemp, '\0', null));
+ else tokens = (leftJustify ? JM.LabelToken.compile(this.vwr, "ATOM %5.-5i %-4.4a%1A%3.3n %1c%4.-4R%1E _XYZ_" + occTemp, '\0', null) : JM.LabelToken.compile(this.vwr, "ATOM %5.-5i %-3.3a%1A%3.3n %1c%4.-4R%1E _XYZ_" + occTemp, '\0', null));
+var XX = a.getElementSymbolIso(false).toUpperCase();
+XX = this.pdbKey(a.group.getBioPolymerIndexInModel()) + this.pdbKey(a.group.groupIndex) + JM.LabelToken.formatLabelAtomArray(this.vwr, a, tokens, '\0', null, ptTemp) + (XX.length == 1 ? " " + XX : XX.substring(0, 2)) + " ";
+this.vwr.ms.getPointTransf(-1, a, q, ptTemp);
+var xyz = JU.PT.sprintf("%8.3p%8.3p%8.3p", "p", o);
+if (xyz.length > 24) xyz = JU.PT.sprintf("%8.2p%8.2p%8.2p", "p", o);
+XX = JU.PT.rep(XX, "_XYZ_", xyz);
+lines.addLast(XX);
+}
+this.fixPDBFormat(lines, map, this.oc, firstAtomIndexNew, modelPt);
+if (isMultipleModels) this.oc.append("ENDMDL\n");
+modelPt = -1;
+iModelLast = -1;
+var conectKey = "" + (isMultipleModels ? modelPt : 0);
+isBiomodel = false;
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var a = atoms[i];
+if (a.mi != iModelLast) {
+var m = models[a.mi];
+iModelLast = a.mi;
+isBiomodel = m.isBioModel;
+modelPt++;
+}var isHetero = (!isBiomodel || a.isHetero());
+var isCysS = !isHetero && (a.getElementNumber() == 16);
+if (isHetero || isMultipleBondPDB || isCysS) {
+var bonds = a.bonds;
+if (bonds == null) continue;
+for (var j = 0; j < bonds.length; j++) {
+var b = bonds[j];
+var iThis = a.getAtomNumber();
+var a2 = b.getOtherAtom(a);
+if (!bs.get(a2.i)) continue;
+var n = b.getCovalentOrder();
+if (n == 1 && (isMultipleBondPDB && !isHetero && !isCysS || isCysS && a2.getElementNumber() != 16)) continue;
+var iOther = a2.getAtomNumber();
+switch (n) {
+case 2:
+case 3:
+if (iOther < iThis) continue;
+case 1:
+var inew = map.get(conectKey + "." + Integer.$valueOf(iThis));
+var inew2 = map.get(conectKey + "." + Integer.$valueOf(iOther));
+if (inew == null || inew2 == null) break;
+this.oc.append("CONECT").append(JU.PT.formatStringS("%5s", "s", "" + inew));
+var s = JU.PT.formatStringS("%5s", "s", "" + inew2);
+for (var k = 0; k < n; k++) this.oc.append(s);
+
+this.oc.append("\n");
+break;
+}
+}
+}}
+return this.toString();
+}, "JU.BS");
+Clazz.defineMethod(c$, "pdbKey",
+function(np){
+var xp = (np < 0 ? "~999" : " " + np);
+return xp.substring(xp.length - 4);
+}, "~N");
+Clazz.defineMethod(c$, "fixPDBFormat",
+function(lines, map, out, firstAtomIndexNew, modelPt){
+lines.addLast("~999~999XXXXXX99999999999999999999~99~");
+var alines = new Array(lines.size());
+lines.toArray(alines);
+java.util.Arrays.sort(alines);
+lines.clear();
+for (var i = 0, n = alines.length; i < n; i++) {
+lines.addLast(alines[i]);
+}
+var lastPoly = null;
+var lastLine = null;
+var n = lines.size();
+var newAtomNumber = 0;
+var iBase = (firstAtomIndexNew == null ? 0 : firstAtomIndexNew[modelPt]);
+for (var i = 0; i < n; i++) {
+var s = lines.get(i);
+var poly = s.substring(0, 4);
+s = s.substring(8);
+var isTerm = false;
+var isLast = (s.indexOf("~99~") >= 0);
+if (!poly.equals(lastPoly) || isLast) {
+if (lastPoly != null && !lastPoly.equals("~999")) {
+isTerm = true;
+s = "TER " + lastLine.substring(6, 11) + " " + lastLine.substring(17, 27);
+lines.add(i, poly + "~~~~" + s);
+n++;
+}lastPoly = poly;
+}if (isLast && !isTerm) break;
+lastLine = s;
+newAtomNumber = i + 1 + iBase;
+if (map != null && !isTerm) map.put("" + modelPt + "." + Integer.$valueOf(JU.PT.parseInt(s.substring(6, 11))), Integer.$valueOf(newAtomNumber));
+var si = " " + newAtomNumber;
+out.append(s.substring(0, 6)).append(si.substring(si.length - 5)).append(s.substring(11)).append("\n");
+}
+if (firstAtomIndexNew != null && ++modelPt < firstAtomIndexNew.length) firstAtomIndexNew[modelPt] = newAtomNumber;
+return modelPt;
+}, "JU.Lst,java.util.Map,JU.OC,~A,~N");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return (this.oc == null ? "" : this.oc.toString());
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PWMATWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PWMATWriter.js
new file mode 100755
index 000000000000..7a83092e2fba
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/PWMATWriter.js
@@ -0,0 +1,186 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.adapter.writers.XtlWriter", "J.api.JmolWriter"], "J.adapter.writers.PWMATWriter", ["JU.P3", "$.PT", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.oc = null;
+this.uc = null;
+this.names = null;
+this.bs = null;
+this.isSlab = false;
+this.writeGlobals = false;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "PWMATWriter", J.adapter.writers.XtlWriter, J.api.JmolWriter);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.writers.PWMATWriter, []);
+this.isHighPrecision = true;
+});
+Clazz.overrideMethod(c$, "set",
+function(viewer, oc, data){
+this.vwr = viewer;
+this.isSlab = (data != null && data[0] != null && data[0].equals("slab"));
+this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+if (bs == null) bs = this.vwr.bsA();
+try {
+this.uc = this.vwr.ms.getUnitCellForAtom(bs.nextSetBit(0));
+this.bs = (this.isSlab ? bs : this.uc.removeDuplicates(this.vwr.ms, bs, false));
+this.names = this.vwr.getDataObj("property_pwm_*", null, -1);
+this.writeHeader();
+this.writeLattice();
+this.writePositions();
+this.writeDataBlocks();
+if (this.writeGlobals) this.writeGlobalBlocks();
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.err.println("Error writing PWmat file " + e);
+} else {
+throw e;
+}
+}
+return this.toString();
+}, "JU.BS");
+Clazz.defineMethod(c$, "writeHeader",
+function(){
+this.oc.append(JU.PT.formatStringI("%12i\n", "i", this.bs.cardinality()));
+});
+Clazz.defineMethod(c$, "writeLattice",
+function(){
+this.oc.append("Lattice vector\n");
+if (this.uc == null) {
+this.uc = this.vwr.getSymTemp();
+var bb = this.vwr.getBoundBoxCornerVector();
+var len = Math.round(bb.length() * 2);
+this.uc.setUnitCellFromParams( Clazz.newFloatArray(-1, [len, len, len, 90, 90, 90]), false, 1.0E-12);
+}var abc = this.uc.getUnitCellVectors();
+var f = "%18.10p%18.10p%18.10p\n";
+this.oc.append(JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[1]])));
+this.oc.append(JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[2]])));
+this.oc.append(JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[3]])));
+JU.Logger.info("PWMATWriter: LATTICE VECTORS");
+});
+Clazz.defineMethod(c$, "writePositions",
+function(){
+var cx = this.getData("CONSTRAINTS_X");
+var cy = (cx == null ? null : this.getData("CONSTRAINTS_Y"));
+var cz = (cy == null ? null : this.getData("CONSTRAINTS_Z"));
+this.oc.append("Position, move_x, move_y, move_z\n");
+var f = "%4i%40s" + (cz == null ? " 1 1 1" : "%4i%4i%4i") + "\n";
+var a = this.vwr.ms.at;
+var p = new JU.P3();
+for (var ic = 0, i = this.bs.nextSetBit(0); i >= 0; i = this.bs.nextSetBit(i + 1), ic++) {
+p.setT(a[i]);
+this.uc.toFractional(p, false);
+var coord = this.clean(p.x) + this.clean(p.y) + this.clean(p.z);
+if (cz == null) {
+this.oc.append(JU.PT.sprintf(f, "is", Clazz.newArray(-1, [Integer.$valueOf(a[i].getElementNumber()), coord])));
+} else {
+var ix = Clazz.floatToInt(cx[ic]);
+var iy = Clazz.floatToInt(cy[ic]);
+var iz = Clazz.floatToInt(cz[ic]);
+this.oc.append(JU.PT.sprintf(f, "isiii", Clazz.newArray(-1, [Integer.$valueOf(a[i].getElementNumber()), coord, Integer.$valueOf(ix), Integer.$valueOf(iy), Integer.$valueOf(iz)])));
+}}
+JU.Logger.info("PWMATWriter: POSITIONS");
+});
+Clazz.defineMethod(c$, "getData",
+function(name){
+name = "property_pwm_" + name.toLowerCase();
+for (var i = this.names.size(); --i >= 0; ) {
+var n = this.names.get(i);
+if (name.equalsIgnoreCase(n)) {
+this.names.removeItemAt(i);
+return this.vwr.getDataObj(n, this.bs, 1);
+}}
+return null;
+}, "~S");
+Clazz.defineMethod(c$, "getVectors",
+function(name){
+var vectors = Clazz.newArray(-1, [this.getData(name + "_x"), this.getData(name + "_y"), this.getData(name + "_z")]);
+return (vectors[0] == null || vectors[1] == null || vectors[2] == null ? null : vectors);
+}, "~S");
+Clazz.defineMethod(c$, "writeDataBlocks",
+function(){
+this.writeVectors("FORCE");
+this.writeVectors("VELOCITY");
+this.writeMagnetic();
+this.writeMoreData();
+});
+Clazz.defineMethod(c$, "writeVectors",
+function(name){
+var xyz = this.getVectors(name);
+if (xyz == null) return;
+var a = this.vwr.ms.at;
+var p = new JU.P3();
+this.oc.append(name.toUpperCase()).append("\n");
+var f = "%4i%18.12p%18.12p%18.12p\n";
+for (var ic = 0, i = this.bs.nextSetBit(0); i >= 0; i = this.bs.nextSetBit(i + 1), ic++) {
+p.set(xyz[0][ic], xyz[1][ic], xyz[2][ic]);
+this.oc.append(JU.PT.sprintf(f, "ip", Clazz.newArray(-1, [Integer.$valueOf(a[i].getElementNumber()), p])));
+}
+JU.Logger.info("PWMATWriter: " + name);
+}, "~S");
+Clazz.defineMethod(c$, "writeMagnetic",
+function(){
+var m = this.writeItems("MAGNETIC");
+if (m == null) return;
+this.writeItem2(m, "CONSTRAINT_MAG");
+});
+Clazz.defineMethod(c$, "writeItem2",
+function(m, name){
+var v = this.getData(name);
+if (v == null) return;
+var a = this.vwr.ms.at;
+this.oc.append(name.toUpperCase()).append("\n");
+var f = "%4i%18.12f%18.12f\n";
+for (var ic = 0, i = this.bs.nextSetBit(0); i >= 0; i = this.bs.nextSetBit(i + 1), ic++) {
+this.oc.append(JU.PT.sprintf(f, "iff", Clazz.newArray(-1, [Integer.$valueOf(a[i].getElementNumber()), Float.$valueOf(m[ic]), Float.$valueOf(v[ic])])));
+}
+}, "~A,~S");
+Clazz.defineMethod(c$, "writeItems",
+function(name){
+var m = this.getData(name);
+if (m == null) return null;
+var a = this.vwr.ms.at;
+name = name.toUpperCase();
+this.oc.append(name).append("\n");
+var f = "%4i%18.12f\n";
+for (var ic = 0, i = this.bs.nextSetBit(0); i >= 0; i = this.bs.nextSetBit(i + 1), ic++) {
+this.oc.append(JU.PT.sprintf(f, "if", Clazz.newArray(-1, [Integer.$valueOf(a[i].getElementNumber()), Float.$valueOf(m[ic])])));
+}
+JU.Logger.info("PWMATWriter: " + name);
+return m;
+}, "~S");
+Clazz.defineMethod(c$, "writeMoreData",
+function(){
+var n = this.names.size();
+var i0 = 0;
+while (this.names.size() > i0 && --n >= 0) {
+var name = this.names.get(i0).substring(13);
+System.out.println(name);
+if (name.endsWith("_y") || name.endsWith("_z")) {
+i0++;
+continue;
+}if (name.endsWith("_x")) {
+this.writeVectors(name.substring(0, name.length - 2));
+i0 = 0;
+} else {
+this.writeItems(name);
+}}
+});
+Clazz.defineMethod(c$, "writeGlobalBlocks",
+function(){
+var globals = this.vwr.getModelForAtomIndex(this.bs.nextSetBit(0)).auxiliaryInfo.get("globalPWmatData");
+if (globals != null) for (var e, $e = globals.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+this.oc.append(e.getKey()).append("\n");
+var lines = e.getValue();
+for (var i = 0; i < lines.length; i++) this.oc.append(lines[i]).append("\n");
+
+}
+});
+Clazz.overrideMethod(c$, "toString",
+function(){
+return (this.oc == null ? "" : this.oc.toString());
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/QCJSONWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/QCJSONWriter.js
new file mode 100755
index 000000000000..99472ce8fa5b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/QCJSONWriter.js
@@ -0,0 +1,468 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["JU.SB", "J.api.JmolWriter", "JU.JSONWriter", "java.util.Hashtable"], "J.adapter.writers.QCJSONWriter", ["java.util.Date", "JU.DF", "$.P3", "$.PT", "org.qcschema.QCSchemaUnits"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.moBases = null;
+this.htBasisMap = null;
+this.filterMOs = false;
+this.vwr = null;
+this.basisID = 0;
+this.shells = null;
+this.dfCoefMaps = null;
+if (!Clazz.isClassDefined("J.adapter.writers.QCJSONWriter.SparseArray")) {
+J.adapter.writers.QCJSONWriter.$QCJSONWriter$SparseArray$ ();
+}
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "QCJSONWriter", JU.JSONWriter, J.api.JmolWriter);
+Clazz.prepareFields (c$, function(){
+this.moBases = new java.util.Hashtable();
+this.htBasisMap = new java.util.Hashtable();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.adapter.writers.QCJSONWriter, []);
+});
+Clazz.overrideMethod(c$, "set",
+function(viewer, oc, data){
+this.vwr = viewer;
+this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
+this.setWriteNullAsString(false);
+this.setStream(oc);
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+this.writeJSON();
+return this.toString();
+}, "JU.BS");
+Clazz.defineMethod(c$, "toString",
+function(){
+return (this.oc == null ? "{}" : this.oc.toString());
+});
+Clazz.defineMethod(c$, "writeJSON",
+function(){
+this.openSchema();
+this.writeMagic();
+this.oc.append(",\n");
+this.writeSchemaMetadata();
+this.writeJobs();
+this.closeSchema();
+});
+Clazz.defineMethod(c$, "writeSchemaMetadata",
+function(){
+this.mapOpen();
+this.mapAddKeyValue("__jmol_created", new java.util.Date(), ",\n");
+this.mapAddKeyValue("__jmol_source", this.vwr.getP("_modelFile"), "");
+this.mapClose();
+});
+Clazz.defineMethod(c$, "openSchema",
+function(){
+this.arrayOpen(false);
+});
+Clazz.defineMethod(c$, "writeMagic",
+function(){
+this.writeString(org.qcschema.QCSchemaUnits.version);
+});
+Clazz.defineMethod(c$, "closeSchema",
+function(){
+this.oc.append("\n");
+this.arrayClose(false);
+this.closeStream();
+});
+Clazz.defineMethod(c$, "writeJobs",
+function(){
+this.writeJob(1);
+});
+Clazz.defineMethod(c$, "writeJob",
+function(iJob){
+this.append(",\n");
+this.mapOpen();
+{
+this.mapAddKeyValue("__jmol_block", "Job " + iJob, ",\n");
+this.writeJobMetadata();
+this.writeModels();
+this.writeMOBases();
+}this.mapClose();
+}, "~N");
+Clazz.defineMethod(c$, "writeJobMetadata",
+function(){
+this.mapAddKey("metadata");
+this.mapOpen();
+{
+this.mapAddMapAllExcept("__jmol_info", this.vwr.getModelSetAuxiliaryInfo(), ";group3Counts;properties;group3Lists;models;unitCellParams;");
+}this.mapClose();
+});
+Clazz.defineMethod(c$, "writeModels",
+function(){
+var nModels = this.vwr.ms.mc;
+this.oc.append(",\n");
+this.mapAddKey("steps");
+this.arrayOpen(true);
+{
+this.oc.append("\n");
+for (var i = 0; i < nModels; ) {
+if (i > 0) this.append(",\n");
+i = this.writeModel(i);
+}
+}this.arrayClose(true);
+});
+Clazz.defineMethod(c$, "writeModel",
+function(modelIndex){
+var nextModel = modelIndex + 1;
+this.append("");
+this.mapOpen();
+{
+this.mapAddKeyValue("__jmol_block", "Model " + (modelIndex + 1), ",\n");
+this.writeTopology(modelIndex);
+if (this.isVibration(modelIndex)) {
+this.oc.append(",\n");
+nextModel = this.writeVibrations(modelIndex);
+}if (this.haveMOData(modelIndex)) {
+this.oc.append(",\n");
+this.writeMOData(modelIndex);
+}this.oc.append(",\n");
+this.writeModelMetadata(modelIndex);
+}this.mapClose();
+this.oc.append("\n");
+return nextModel;
+}, "~N");
+Clazz.defineMethod(c$, "writeTopology",
+function(modelIndex){
+this.mapAddKey("topology");
+this.mapOpen();
+{
+this.writeAtoms(modelIndex);
+this.writeBonds(modelIndex);
+}this.mapClose();
+}, "~N");
+Clazz.defineMethod(c$, "getProperty",
+function(modelIndex, key){
+var props = (modelIndex >= this.vwr.ms.am.length ? null : this.vwr.ms.am[modelIndex].auxiliaryInfo.get("modelProperties"));
+return (props == null ? null : props.get(key));
+}, "~N,~S");
+Clazz.defineMethod(c$, "isVibration",
+function(modelIndex){
+return (this.vwr.ms.getLastVibrationVector(modelIndex, 0) >= 0);
+}, "~N");
+Clazz.defineMethod(c$, "writeModelMetadata",
+function(modelIndex){
+this.mapAddKey("metadata");
+this.mapOpen();
+{
+this.mapAddMapAllExcept("__jmol_info", this.vwr.ms.am[modelIndex].auxiliaryInfo, ";.PATH;PATH;fileName;moData;unitCellParams;");
+}this.mapClose();
+}, "~N");
+Clazz.defineMethod(c$, "writeAtoms",
+function(modelIndex){
+var symbols = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
+var numbers = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
+var charges = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
+var names = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
+var types = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
+this.mapAddKey("atoms");
+this.mapOpen();
+{
+var unitCell = this.vwr.ms.getUnitCell(modelIndex);
+var isFractional = (unitCell != null && !unitCell.isBio());
+if (isFractional) {
+var params = unitCell.getUnitCellAsArray(false);
+this.writePrefix_Units("unit_cell", "angstroms");
+this.mapAddKeyValue("unit_cell", params, ",\n");
+}this.writePrefix_Units("coords", isFractional ? "fractional" : "angstroms");
+this.mapAddKey("coords");
+this.arrayOpen(true);
+{
+this.oc.append("\n");
+var bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
+var last = bs.length() - 1;
+var pt = new JU.P3();
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var a = this.vwr.ms.at[i];
+this.append("");
+pt.setT(a);
+if (isFractional) unitCell.toFractional(pt, false);
+this.oc.append(this.formatNumber(pt.x)).append(",\t").append(this.formatNumber(pt.y)).append(",\t").append(this.formatNumber(pt.z)).append(i < last ? ",\n" : "\n");
+symbols.add(JU.PT.esc(a.getElementSymbol()));
+numbers.add("" + a.getElementNumber());
+charges.add("" + a.getPartialCharge());
+var name = a.getAtomName();
+names.add(name);
+var type = a.getAtomType();
+types.add(type.equals(name) ? null : type);
+}
+}this.arrayClose(true);
+this.oc.append(",\n");
+if (charges.isNumericAndNonZero()) {
+this.mapAddKeyValueRaw("charge", charges, ",\n");
+}if (types.hasValues()) {
+this.mapAddKeyValueRaw("types", types, ",\n");
+}this.mapAddKeyValueRaw("symbol", symbols, ",\n");
+this.mapAddKeyValueRaw("atom_number", numbers, "\n");
+}this.mapClose();
+}, "~N");
+Clazz.defineMethod(c$, "formatNumber",
+function(x){
+return (x < 0 ? "" : " ") + JU.DF.formatDecimal(x, -6);
+}, "~N");
+Clazz.defineMethod(c$, "writePrefix_Units",
+function(prefix, units){
+this.mapAddKeyValueRaw(prefix + "_units", org.qcschema.QCSchemaUnits.getUnitsJSON(units, false), ",\n");
+}, "~S,~S");
+Clazz.defineMethod(c$, "writeBonds",
+function(modelIndex){
+}, "~N");
+Clazz.defineMethod(c$, "writeVibrations",
+function(modelIndex){
+this.mapAddKey("vibrations");
+this.arrayOpen(true);
+{
+this.oc.append("\n");
+var sep = null;
+var ivib = 0;
+modelIndex--;
+while (this.isVibration(++modelIndex)) {
+if (sep != null) this.oc.append(sep);
+sep = ",\n";
+this.append("");
+this.mapOpen();
+{
+this.mapAddKeyValue("__jmol_block", "Vibration " + (++ivib), ",\n");
+var value = this.getProperty(modelIndex, "FreqValue");
+var freq = this.getProperty(modelIndex, "Frequency");
+var intensity = this.getProperty(modelIndex, "IRIntensity");
+var tokens;
+if (value == null) {
+System.out.println("model " + modelIndex + " has no _M.properties.FreqValue");
+}if (freq == null) {
+System.out.println("model " + modelIndex + " has no _M.properties.Frequency");
+} else {
+tokens = JU.PT.split(freq, " ");
+if (tokens.length == 1) {
+System.out.println("model " + modelIndex + " has no frequency units");
+}this.writeMapKeyValueUnits("frequency", value, tokens[1]);
+}if (intensity != null) {
+tokens = JU.PT.split(intensity, " ");
+this.writeMapKeyValueUnits("ir_intensity", tokens[0], tokens[1]);
+}var label = this.getProperty(modelIndex, "FrequencyLabel");
+if (label != null) this.mapAddKeyValue("label", label, ",\n");
+this.mapAddKey("vectors");
+this.arrayOpen(true);
+{
+this.oc.append("\n");
+var bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
+var last = bs.length() - 1;
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var a = this.vwr.ms.at[i];
+var v = a.getVibrationVector();
+this.append("");
+this.oc.append(this.formatNumber(v.x)).append(",\t").append(this.formatNumber(v.y)).append(",\t").append(this.formatNumber(v.z)).append(i < last ? ",\n" : "\n");
+}
+}this.arrayClose(true);
+}this.append("");
+this.mapClose();
+}
+}this.oc.append("\n");
+this.arrayClose(true);
+return modelIndex;
+}, "~N");
+Clazz.defineMethod(c$, "writeMapKeyValueUnits",
+function(key, value, units){
+this.mapAddKeyValueRaw(key, "{\"value\":" + value + ",\"units\":" + org.qcschema.QCSchemaUnits.getUnitsJSON(units, false) + "}", ",\n");
+}, "~S,~O,~S");
+Clazz.defineMethod(c$, "haveMOData",
+function(modelIndex){
+return (this.getAuxiliaryData(modelIndex, "moData") != null);
+}, "~N");
+Clazz.defineMethod(c$, "getAuxiliaryData",
+function(modelIndex, key){
+return this.vwr.ms.am[modelIndex].auxiliaryInfo.get(key);
+}, "~N,~S");
+Clazz.defineMethod(c$, "writeMOData",
+function(modelIndex){
+var moData = this.getAuxiliaryData(modelIndex, "moData");
+var moDataJSON = new java.util.Hashtable();
+moDataJSON.put("orbitals", moData.get("mos"));
+var units = moData.get("EnergyUnits");
+if (units == null) units = "?";
+moDataJSON.put("orbitals_energy_units", org.qcschema.QCSchemaUnits.getUnitsJSON(units, true));
+moDataJSON.put("__jmol_normalized", Boolean.$valueOf(moData.get("isNormalized") === Boolean.TRUE));
+var type = moData.get("calculationType");
+moDataJSON.put("__jmol_calculation_type", type == null ? "?" : type);
+this.setDFCoord(moData);
+moDataJSON.put("basis_id", this.addBasis(moData));
+this.filterMOs = true;
+this.setModifyKeys(J.adapter.writers.QCJSONWriter.fixIntegration());
+this.mapAddKeyValue("molecular_orbitals", moDataJSON, "\n");
+this.setModifyKeys(null);
+this.filterMOs = false;
+this.append("");
+}, "~N");
+c$.fixIntegration = Clazz.defineMethod(c$, "fixIntegration",
+function(){
+if (J.adapter.writers.QCJSONWriter.integrationKeyMap == null) {
+J.adapter.writers.QCJSONWriter.integrationKeyMap = new java.util.Hashtable();
+J.adapter.writers.QCJSONWriter.integrationKeyMap.put("integration", "__jmol_integration");
+}return J.adapter.writers.QCJSONWriter.integrationKeyMap;
+});
+Clazz.overrideMethod(c$, "getAndCheckValue",
+function(map, key){
+if (this.filterMOs) {
+if (key.equals("dfCoefMaps")) return null;
+if (key.equals("symmetry")) return (map.get(key)).$replace('_', ' ').trim();
+if (key.equals("coefficients") && this.dfCoefMaps != null) {
+return this.fixCoefficients(map.get(key));
+}}return map.get(key);
+}, "java.util.Map,~S");
+Clazz.defineMethod(c$, "fixCoefficients",
+function(coeffs){
+var c = Clazz.newDoubleArray (coeffs.length, 0);
+for (var i = 0, n = this.shells.size(); i < n; i++) {
+var shell = this.shells.get(i);
+var type = shell[1];
+var map = this.dfCoefMaps[type];
+for (var j = 0, coefPtr = 0; j < map.length; j++, coefPtr++) c[coefPtr + j] = coeffs[coefPtr + map[j]];
+
+}
+return c;
+}, "~A");
+Clazz.defineMethod(c$, "setDFCoord",
+function(moData){
+this.dfCoefMaps = moData.get("dfCoefMaps");
+if (this.dfCoefMaps != null) {
+var haveMap = false;
+for (var i = 0; !haveMap && i < this.dfCoefMaps.length; i++) {
+var m = this.dfCoefMaps[i];
+for (var j = 0; j < m.length; j++) if (m[j] != 0) {
+haveMap = true;
+break;
+}
+}
+if (!haveMap) this.dfCoefMaps = null;
+}}, "java.util.Map");
+Clazz.defineMethod(c$, "addBasis",
+function(moData){
+var hash = 1;
+var gaussians = moData.get("gaussians");
+if (gaussians != null) {
+hash ^= gaussians.hashCode();
+}this.shells = moData.get("shells");
+if (this.shells != null) {
+hash ^= this.shells.hashCode();
+}var slaters = moData.get("slaters");
+if (slaters != null) {
+hash ^= slaters.hashCode();
+}var strHash = "" + hash;
+var key = this.htBasisMap.get(strHash);
+if (key == null) {
+this.htBasisMap.put(strHash, key = "MOBASIS_" + ++this.basisID);
+var map = new java.util.Hashtable();
+if (gaussians != null) map.put("gaussians", gaussians);
+if (this.shells != null) {
+map.put("shells", this.shells);
+}if (slaters != null) map.put("slaters", slaters);
+this.moBases.put(key, map);
+}return key;
+}, "java.util.Map");
+Clazz.defineMethod(c$, "writeMOBases",
+function(){
+if (this.moBases.isEmpty()) return;
+this.oc.append(",\n");
+this.mapAddKey("mo_bases");
+this.mapOpen();
+{
+var sep = null;
+for (var key, $key = this.moBases.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) {
+if (key.startsWith("!")) continue;
+this.append(sep);
+this.mapAddKeyValue(key, this.moBases.get(key), "\n");
+sep = ",\n";
+}
+}this.mapClose();
+this.moBases.clear();
+});
+Clazz.defineMethod(c$, "writeObject",
+function(o){
+if (Clazz.instanceOf(o,"J.quantum.SlaterData")) {
+this.oc.append(o.toString());
+} else {
+Clazz.superCall(this, J.adapter.writers.QCJSONWriter, "writeObject", [o]);
+}}, "~O");
+c$.$QCJSONWriter$SparseArray$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.repeatCount = 0;
+this.elementCount = 0;
+this.$lastElement = null;
+this.sep = "";
+this.type = null;
+this.isRLE = false;
+Clazz.instantialize(this, arguments);}, J.adapter.writers.QCJSONWriter, "SparseArray", JU.SB);
+Clazz.makeConstructor(c$,
+function(type){
+Clazz.superConstructor (this, J.adapter.writers.QCJSONWriter.SparseArray, []);
+this.type = type;
+this.isRLE = (type.equals("_RLE_"));
+}, "~S");
+Clazz.defineMethod(c$, "add",
+function(element){
+if (element == null) element = "null";
+if (!this.isRLE) {
+this.append(this.sep);
+this.append(element);
+this.sep = ",";
+return;
+}if (this.repeatCount > 0 && !element.equals(this.$lastElement)) {
+this.append(this.sep);
+this.appendI(this.repeatCount);
+this.sep = ",";
+this.append(this.sep);
+this.append(this.$lastElement);
+this.repeatCount = 0;
+}this.$lastElement = element;
+this.repeatCount++;
+this.elementCount++;
+}, "~S");
+Clazz.defineMethod(c$, "lastElement",
+function(){
+return this.$lastElement;
+});
+Clazz.defineMethod(c$, "isEmpty",
+function(){
+return (this.elementCount == 0);
+});
+Clazz.defineMethod(c$, "allNaN",
+function(){
+return (this.allSame() && JU.PT.parseFloat(this.$lastElement) == NaN);
+});
+Clazz.defineMethod(c$, "allNull",
+function(){
+return (this.allSame() && this.$lastElement.equals("null"));
+});
+Clazz.defineMethod(c$, "allEmptyString",
+function(){
+return (this.allSame() && this.$lastElement.equals(""));
+});
+Clazz.defineMethod(c$, "allSame",
+function(){
+return (!this.isEmpty() && this.elementCount == this.repeatCount);
+});
+Clazz.defineMethod(c$, "allZero",
+function(){
+return (this.allSame() && JU.PT.parseFloat(this.$lastElement) != NaN);
+});
+Clazz.defineMethod(c$, "hasValues",
+function(){
+return (!this.allSame() || !this.allNull() && !this.allEmptyString());
+});
+Clazz.defineMethod(c$, "isNumericAndNonZero",
+function(){
+return (this.allSame() && !this.allNaN() && !this.allZero());
+});
+Clazz.defineMethod(c$, "toString",
+function(){
+var s = Clazz.superCall(this, J.adapter.writers.QCJSONWriter.SparseArray, "toString", []);
+return (s.length == 0 ? "[]" : "[\"" + this.type + "\"," + s + (this.repeatCount > 0 ? this.sep + this.repeatCount + "," + this.$lastElement : "") + "]");
+});
+/*eoif4*/})();
+};
+c$.integrationKeyMap = null;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XSFWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XSFWriter.js
new file mode 100755
index 000000000000..a2786dad656c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XSFWriter.js
@@ -0,0 +1,69 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(["J.api.JmolWriter"], "J.adapter.writers.XSFWriter", ["JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.oc = null;
+this.uc = null;
+this.len = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "XSFWriter", null, J.api.JmolWriter);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set",
+function(viewer, oc, data){
+this.vwr = viewer;
+this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
+}, "JV.Viewer,JU.OC,~A");
+Clazz.overrideMethod(c$, "write",
+function(bs){
+if (bs == null) bs = this.vwr.bsA();
+this.len = bs.length();
+if (this.len == 0) return "";
+try {
+var a = this.vwr.ms.at;
+var i0 = bs.nextSetBit(0);
+this.uc = this.vwr.ms.getUnitCellForAtom(i0);
+var model1 = a[i0].getModelIndex();
+var model2 = a[this.len - 1].getModelIndex();
+var isAnim = (model2 != model1);
+if (isAnim) {
+var nModels = this.vwr.ms.getModelBS(bs, false).cardinality();
+this.oc.append("ANIMSTEPS " + nModels + "\n");
+}if (this.uc != null) this.oc.append("CRYSTAL\n");
+var f = "%4i%18.12p%18.12p%18.12p\n";
+var prefix = (this.uc == null ? "ATOMS" : "PRIMCOORD");
+for (var lastmi = -1, imodel = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var atom = a[i];
+var mi = atom.getModelIndex();
+if (mi != lastmi) {
+var sn = (isAnim ? " " + (++imodel) : "");
+var header = prefix + sn + "\n";
+this.uc = this.vwr.ms.getUnitCellForAtom(i);
+if (this.uc == null) {
+this.oc.append(header);
+} else {
+this.writeLattice(sn);
+this.oc.append(header);
+var bsm = this.vwr.restrictToModel(bs, mi);
+this.oc.append(JU.PT.formatStringI("%6i 1\n", "i", bsm.cardinality()));
+}lastmi = mi;
+}this.oc.append(JU.PT.sprintf(f, "ip", Clazz.newArray(-1, [Integer.$valueOf(atom.getElementNumber()), atom])));
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+return this.toString();
+}, "JU.BS");
+Clazz.defineMethod(c$, "writeLattice",
+function(sn){
+var abc = this.uc.getUnitCellVectors();
+var f = "%18.10p%18.10p%18.10p\n";
+var s = JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[1]])) + JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[2]])) + JU.PT.sprintf(f, "p", Clazz.newArray(-1, [abc[3]]));
+this.oc.append("PRIMVEC" + sn + "\n").append(s).append("CONVVEC" + sn + "\n").append(s);
+}, "~S");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return (this.oc == null ? "" : this.oc.toString());
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XtlWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XtlWriter.js
new file mode 100755
index 000000000000..e226b45e2082
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/adapter/writers/XtlWriter.js
@@ -0,0 +1,53 @@
+Clazz.declarePackage("J.adapter.writers");
+Clazz.load(null, "J.adapter.writers.XtlWriter", ["JU.PT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.haveUnitCell = true;
+this.isHighPrecision = true;
+this.slop = 0;
+this.precision = 0;
+Clazz.instantialize(this, arguments);}, J.adapter.writers, "XtlWriter", null);
+Clazz.defineMethod(c$, "clean",
+function(d){
+if (!this.isHighPrecision) return this.cleanF(d);
+var t;
+return (!this.haveUnitCell || (t = J.adapter.writers.XtlWriter.twelfthsOf(d)) < 0 ? JU.PT.formatF(d, 18, 12, false, false) : (d < 0 ? " -" : " ") + J.adapter.writers.XtlWriter.twelfths[t]);
+}, "~N");
+c$.twelfthsOf = Clazz.defineMethod(c$, "twelfthsOf",
+function(f){
+if (f == 0) return 0;
+f = Math.abs(f * 12);
+var i = Math.round(f);
+return (i <= 12 && Math.abs(f - i) < J.adapter.writers.XtlWriter.SLOPD * 12 ? i : -1);
+}, "~N");
+Clazz.defineMethod(c$, "cleanF",
+function(f){
+var t;
+if (this.slop != 0) return this.cleanSlop(f);
+return (!this.haveUnitCell || (t = J.adapter.writers.XtlWriter.twelfthsOfF(f)) < 0 ? JU.PT.formatF(f, 12, 7, false, false) : (f < 0 ? " -" : " ") + J.adapter.writers.XtlWriter.twelfthsF[t]);
+}, "~N");
+Clazz.defineMethod(c$, "cleanSlop",
+function(f){
+return JU.PT.formatF(f, this.precision + 6, this.precision, false, false);
+}, "~N");
+c$.twelfthsOfF = Clazz.defineMethod(c$, "twelfthsOfF",
+function(f){
+if (f == 0) return 0;
+f = Math.abs(f * 12);
+var i = Math.round(f);
+return (i <= 12 && Math.abs(f - i) < J.adapter.writers.XtlWriter.SLOPF * 12 ? i : -1);
+}, "~N");
+Clazz.defineMethod(c$, "cleanT",
+function(d){
+var s = this.clean(d);
+if (this.isHighPrecision) return s;
+var i = s.length;
+while (--i >= 2 && s.charAt(i) == '0' && s.charAt(i - 1) != '.') {
+}
+return s.substring(0, i + 1);
+}, "~N");
+c$.SLOPD = 0.000000000010;
+c$.SLOPF = 0.0000010;
+c$.twelfths = Clazz.newArray(-1, ["0.000000000000", "0.083333333333", "0.166666666667", "0.250000000000", "0.333333333333", "0.416666666667", "0.500000000000", "0.583333333333", "0.666666666667", "0.750000000000", "0.833333333333", "0.916666666667", "1.000000000000"]);
+c$.twelfthsF = Clazz.newArray(-1, ["0.0000000", "0.0833333", "0.1666667", "0.2500000", "0.3333333", "0.4166667", "0.5000000", "0.5833333", "0.6666667", "0.7500000", "0.8333333", "0.9166667", "1.0000000"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/AtomIndexIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/AtomIndexIterator.js
new file mode 100755
index 000000000000..ef9ba3f961e3
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/AtomIndexIterator.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "AtomIndexIterator");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/EventManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/EventManager.js
new file mode 100755
index 000000000000..af6fe18aa780
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/EventManager.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "EventManager");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/FontManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/FontManager.js
new file mode 100755
index 000000000000..4dfb6dca0524
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/FontManager.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "FontManager");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericFileInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericFileInterface.js
new file mode 100755
index 000000000000..cd49d0b119cb
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericFileInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "GenericFileInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericGraphics.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericGraphics.js
new file mode 100755
index 000000000000..95f2e81446f6
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericGraphics.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "GenericGraphics");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericImageDialog.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericImageDialog.js
new file mode 100755
index 000000000000..88fe29beafe2
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericImageDialog.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "GenericImageDialog");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMenuInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMenuInterface.js
new file mode 100755
index 000000000000..75e3e50e7869
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMenuInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "GenericMenuInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMouseInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMouseInterface.js
new file mode 100755
index 000000000000..de3dd80f6730
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericMouseInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "GenericMouseInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/GenericPlatform.js b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericPlatform.js
new file mode 100755
index 000000000000..a6a14d17cae5
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/GenericPlatform.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+Clazz.load(["J.api.FontManager"], "J.api.GenericPlatform", null, function(){
+var c$ = Clazz.declareInterface(J.api, "GenericPlatform", J.api.FontManager);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/Interface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/Interface.js
new file mode 100755
index 000000000000..817ca2cf62af
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/Interface.js
@@ -0,0 +1,31 @@
+Clazz.declarePackage("J.api");
+Clazz.load(null, "J.api.Interface", ["JU.Logger"], function(){
+var c$ = Clazz.declareType(J.api, "Interface", null);
+c$.getInterface = Clazz.defineMethod(c$, "getInterface",
+function(name, vwr, state){
+try {
+var x = Clazz._4Name(name);
+return (x == null ? null : x.newInstance());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Interface.java Error creating instance for " + name + ": \n" + e);
+return null;
+} else {
+throw e;
+}
+}
+}, "~S,JV.Viewer,~S");
+c$.getOption = Clazz.defineMethod(c$, "getOption",
+function(className, vwr, state){
+return J.api.Interface.getInterface("J." + className, vwr, state);
+}, "~S,JV.Viewer,~S");
+c$.getUtil = Clazz.defineMethod(c$, "getUtil",
+function(name, vwr, state){
+return J.api.Interface.getInterface("JU." + name, vwr, state);
+}, "~S,JV.Viewer,~S");
+c$.getSymmetry = Clazz.defineMethod(c$, "getSymmetry",
+function(vwr, state){
+return J.api.Interface.getInterface("JS.Symmetry", vwr, state);
+}, "JV.Viewer,~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JSVInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JSVInterface.js
new file mode 100755
index 000000000000..e8286be15ee9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JSVInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JSVInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAbstractButton.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAbstractButton.js
new file mode 100755
index 000000000000..230c6172f485
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAbstractButton.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAbstractButton");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapter.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapter.js
new file mode 100755
index 000000000000..5a970dfed349
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapter.js
@@ -0,0 +1,52 @@
+Clazz.declarePackage("J.api");
+Clazz.load(null, "J.api.JmolAdapter", ["JU.PT", "J.api.JmolViewer", "JU.Elements"], function(){
+var c$ = Clazz.declareType(J.api, "JmolAdapter", null);
+c$.getElementSymbol = Clazz.defineMethod(c$, "getElementSymbol",
+function(elementNumber){
+return JU.Elements.elementSymbolFromNumber(elementNumber);
+}, "~N");
+c$.getElementNumber = Clazz.defineMethod(c$, "getElementNumber",
+function(elementSymbol){
+return JU.Elements.elementNumberFromSymbol(elementSymbol, false);
+}, "~S");
+c$.getNaturalIsotope = Clazz.defineMethod(c$, "getNaturalIsotope",
+function(elementNumber){
+return JU.Elements.getNaturalIsotope(elementNumber);
+}, "~N");
+c$.getBondingRadius = Clazz.defineMethod(c$, "getBondingRadius",
+function(atomicNumberWithIsotope, charge){
+return JU.Elements.getBondingRadius(atomicNumberWithIsotope, charge);
+}, "~N,~N");
+Clazz.defineMethod(c$, "getAtomSetCollectionFromReaderType",
+function(name, type, bufferedReader, htParams){
+var a = this.getAtomSetCollectionReader(name, type, bufferedReader, (J.api.JmolViewer.allocateViewer(null, this)).setLoadParameters(htParams, false));
+if ((typeof(a)=='string')) return a;
+return this.getAtomSetCollection(a);
+}, "~S,~S,~O,java.util.Map");
+Clazz.defineMethod(c$, "openBufferedReader",
+function(name, bufferedReader){
+return this.getAtomSetCollectionFromReaderType(name, null, bufferedReader, null);
+}, "~S,java.io.BufferedReader");
+Clazz.defineMethod(c$, "openBufferedReader",
+function(name, bufferedReader, htParams){
+return this.getAtomSetCollectionFromReaderType(name, null, bufferedReader, htParams);
+}, "~S,java.io.BufferedReader,java.util.Map");
+Clazz.defineMethod(c$, "openBufferedReader",
+function(name, type, bufferedReader){
+return this.getAtomSetCollectionFromReaderType(name, type, bufferedReader, null);
+}, "~S,~S,java.io.BufferedReader");
+c$.canonizeAlphaDigit = Clazz.defineMethod(c$, "canonizeAlphaDigit",
+function(ch){
+return (JU.PT.isLetterOrDigit(ch) ? ch : '\0');
+}, "~S");
+c$.canonizeInsertionCode = Clazz.defineMethod(c$, "canonizeInsertionCode",
+function(insertionCode){
+return J.api.JmolAdapter.canonizeAlphaDigit(insertionCode);
+}, "~S");
+c$.canonizeAlternateLocationID = Clazz.defineMethod(c$, "canonizeAlternateLocationID",
+function(altLoc){
+return J.api.JmolAdapter.canonizeAlphaDigit(altLoc);
+}, "~S");
+c$.cellParamNames = Clazz.newArray(-1, ["_cell_length_a", "_cell_length_b", "_cell_length_c", "_cell_angle_alpha", "_cell_angle_beta", "_cell_angle_gamma"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterAtomIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterAtomIterator.js
new file mode 100755
index 000000000000..ca7497ebb788
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterAtomIterator.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAdapterAtomIterator");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterBondIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterBondIterator.js
new file mode 100755
index 000000000000..f163aa233164
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterBondIterator.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+(function(){
+var c$ = Clazz.declareType(J.api, "JmolAdapterBondIterator", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterStructureIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterStructureIterator.js
new file mode 100755
index 000000000000..e2a51ddf1d2b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAdapterStructureIterator.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+(function(){
+var c$ = Clazz.declareType(J.api, "JmolAdapterStructureIterator", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAnnotationParser.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAnnotationParser.js
new file mode 100755
index 000000000000..859ec05f9f33
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAnnotationParser.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAnnotationParser");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppAPI.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppAPI.js
new file mode 100755
index 000000000000..531ed31a4ba2
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppAPI.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAppAPI");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppConsoleInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppConsoleInterface.js
new file mode 100755
index 000000000000..a140be61ad14
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppConsoleInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAppConsoleInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppletInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppletInterface.js
new file mode 100755
index 000000000000..310e80e9d81c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAppletInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAppletInterface", J.api.JmolSyncInterface);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAudioPlayer.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAudioPlayer.js
new file mode 100755
index 000000000000..aa8890609073
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolAudioPlayer.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolAudioPlayer");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolCallbackListener.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolCallbackListener.js
new file mode 100755
index 000000000000..09aa371b28a0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolCallbackListener.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolCallbackListener");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDataManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDataManager.js
new file mode 100755
index 000000000000..93676efd0f10
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDataManager.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+(function(){
+var c$ = Clazz.declareInterface(J.api, "JmolDataManager");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDialogInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDialogInterface.js
new file mode 100755
index 000000000000..8b594896fff6
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDialogInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolDialogInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDropEditor.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDropEditor.js
new file mode 100755
index 000000000000..db026c0b1ccb
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolDropEditor.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolDropEditor");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolEnvCalc.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolEnvCalc.js
new file mode 100755
index 000000000000..c9a29b476841
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolEnvCalc.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolEnvCalc");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolFilesReaderInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolFilesReaderInterface.js
new file mode 100755
index 000000000000..b77bcf1274e1
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolFilesReaderInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolFilesReaderInterface", Runnable);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGestureServerInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGestureServerInterface.js
new file mode 100755
index 000000000000..3e371645b3e9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGestureServerInterface.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+(function(){
+var c$ = Clazz.declareInterface(J.api, "JmolGestureServerInterface");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGraphicsInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGraphicsInterface.js
new file mode 100755
index 000000000000..3817ed490dd0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolGraphicsInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolGraphicsInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolInChI.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolInChI.js
new file mode 100755
index 000000000000..fc5cb21b044c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolInChI.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolInChI");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLParser.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLParser.js
new file mode 100755
index 000000000000..0ba5cd63a79c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLParser.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolJDXMOLParser");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLReader.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLReader.js
new file mode 100755
index 000000000000..eb4c74d501ad
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJDXMOLReader.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolJDXMOLReader");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJSpecView.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJSpecView.js
new file mode 100755
index 000000000000..e47dd118d426
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolJSpecView.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolJSpecView");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMeasurementClient.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMeasurementClient.js
new file mode 100755
index 000000000000..d11b522d2ad0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMeasurementClient.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolMeasurementClient");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolModulationSet.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolModulationSet.js
new file mode 100755
index 000000000000..0de82eedbeb8
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolModulationSet.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolModulationSet");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMovieCreatorInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMovieCreatorInterface.js
new file mode 100755
index 000000000000..53b9a701cd50
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolMovieCreatorInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolMovieCreatorInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNMRInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNMRInterface.js
new file mode 100755
index 000000000000..104a57d771cd
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNMRInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolNMRInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNavigatorInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNavigatorInterface.js
new file mode 100755
index 000000000000..602976d69778
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolNavigatorInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolNavigatorInterface", Runnable);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolParallelProcessor.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolParallelProcessor.js
new file mode 100755
index 000000000000..d1db103b4484
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolParallelProcessor.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolParallelProcessor");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPdfCreatorInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPdfCreatorInterface.js
new file mode 100755
index 000000000000..9ec369aab9a7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPdfCreatorInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolPdfCreatorInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPropertyManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPropertyManager.js
new file mode 100755
index 000000000000..8b1d42cb1474
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolPropertyManager.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolPropertyManager");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRendererInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRendererInterface.js
new file mode 100755
index 000000000000..b1ffac29bb53
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRendererInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolRendererInterface", J.api.JmolGraphicsInterface);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRepaintManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRepaintManager.js
new file mode 100755
index 000000000000..a26d4e09d2c0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolRepaintManager.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolRepaintManager");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSceneGenerator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSceneGenerator.js
new file mode 100755
index 000000000000..6f283fb39dc6
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSceneGenerator.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolSceneGenerator");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEditorInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEditorInterface.js
new file mode 100755
index 000000000000..5d407c5ec45b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEditorInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolScriptEditorInterface", J.api.JmolDropEditor);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEvaluator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEvaluator.js
new file mode 100755
index 000000000000..84deaf578701
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptEvaluator.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolScriptEvaluator");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptFunction.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptFunction.js
new file mode 100755
index 000000000000..e9723ee3ee32
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptFunction.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolScriptFunction");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptManager.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptManager.js
new file mode 100755
index 000000000000..a4e92f6d3021
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolScriptManager.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.api");
+(function(){
+var c$ = Clazz.declareInterface(J.api, "JmolScriptManager");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSelectionListener.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSelectionListener.js
new file mode 100755
index 000000000000..195a4d790eb0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSelectionListener.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolSelectionListener");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolStatusListener.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolStatusListener.js
new file mode 100755
index 000000000000..f5ee7da8122f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolStatusListener.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolStatusListener", J.api.JmolCallbackListener);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSyncInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSyncInterface.js
new file mode 100755
index 000000000000..73cc277436e4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolSyncInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolSyncInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolTouchSimulatorInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolTouchSimulatorInterface.js
new file mode 100755
index 000000000000..42042893360f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolTouchSimulatorInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolTouchSimulatorInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolViewer.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolViewer.js
new file mode 100755
index 000000000000..145f858dcf70
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolViewer.js
@@ -0,0 +1,63 @@
+Clazz.declarePackage("J.api");
+Clazz.load(null, "J.api.JmolViewer", ["java.util.Hashtable", "JV.JC"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.menuStructure = null;
+this.apiPlatform = null;
+Clazz.instantialize(this, arguments);}, J.api, "JmolViewer", null);
+c$.allocateViewer = Clazz.defineMethod(c$, "allocateViewer",
+function(display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, implementedPlatform){
+var info = new java.util.Hashtable();
+if (display != null) info.put("display", display);
+if (modelAdapter != null) info.put("adapter", modelAdapter);
+if (statusListener != null) info.put("statuslistener", statusListener);
+if (implementedPlatform != null) info.put("platform", implementedPlatform);
+if (commandOptions != null) info.put("options", commandOptions);
+if (fullName != null) info.put("fullname", fullName);
+if (documentBase != null) info.put("documentbase", documentBase);
+if (codeBase != null) info.put("codebase", codeBase);
+info.put("isApp", Boolean.TRUE);
+return new JV.Viewer(info);
+}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,J.api.GenericPlatform");
+c$.allocateViewer = Clazz.defineMethod(c$, "allocateViewer",
+function(container, jmolAdapter){
+return J.api.JmolViewer.allocateViewer(container, jmolAdapter, null, null, null, null, null, null);
+}, "~O,J.api.JmolAdapter");
+c$.allocateViewer = Clazz.defineMethod(c$, "allocateViewer",
+function(display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener){
+return J.api.JmolViewer.allocateViewer(display, modelAdapter, fullName, documentBase, codeBase, commandOptions, statusListener, null);
+}, "~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener");
+Clazz.defineMethod(c$, "setConsole",
+function(console){
+this.getProperty("DATA_API", "getAppConsole", console);
+}, "J.api.JmolAppConsoleInterface");
+c$.getJmolVersion = Clazz.defineMethod(c$, "getJmolVersion",
+function(){
+return JV.Viewer.getJmolVersion();
+});
+c$.getJmolVersionNoDate = Clazz.defineMethod(c$, "getJmolVersionNoDate",
+function(){
+return JV.JC.version;
+});
+Clazz.defineMethod(c$, "openReader",
+function(fullPathName, reader){
+return this.openReader(fullPathName == null ? "String" : fullPathName, null, reader);
+}, "~S,~O");
+Clazz.defineMethod(c$, "openFileAsync",
+function(fileName){
+this.openFileAsyncSpecial(fileName, 0);
+}, "~S");
+Clazz.defineMethod(c$, "renderScreenImage",
+function(g, currentSize, rectClip){
+this.apiPlatform.renderScreenImage(g, currentSize);
+}, "~O,~O,~O");
+Clazz.defineMethod(c$, "runScriptCautiously",
+function(script){
+return null;
+}, "~S");
+Clazz.defineMethod(c$, "dispose",
+function(){
+});
+{
+}{
+}});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolWriter.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolWriter.js
new file mode 100755
index 000000000000..a19de06a9217
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolWriter.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolWriter");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/JmolZipUtilities.js b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolZipUtilities.js
new file mode 100755
index 000000000000..6b704b75152a
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/JmolZipUtilities.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "JmolZipUtilities");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/PlatformViewer.js b/config/plugins/visualizations/jmol/static/j2s/J/api/PlatformViewer.js
new file mode 100755
index 000000000000..a663e7b92bff
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/PlatformViewer.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "PlatformViewer");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/PymolAtomReader.js b/config/plugins/visualizations/jmol/static/j2s/J/api/PymolAtomReader.js
new file mode 100755
index 000000000000..cdb3e92a8f11
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/PymolAtomReader.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "PymolAtomReader");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/SC.js b/config/plugins/visualizations/jmol/static/j2s/J/api/SC.js
new file mode 100755
index 000000000000..363219457876
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/SC.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "SC");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/SmilesMatcherInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/SmilesMatcherInterface.js
new file mode 100755
index 000000000000..a75863465eaa
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/SmilesMatcherInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "SmilesMatcherInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/SymmetryInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/SymmetryInterface.js
new file mode 100755
index 000000000000..03b418a0bf07
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/SymmetryInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "SymmetryInterface");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/Translator.js b/config/plugins/visualizations/jmol/static/j2s/J/api/Translator.js
new file mode 100755
index 000000000000..abcb60cb0919
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/Translator.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api");
+Clazz.declareInterface(J.api, "Translator");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/js/GenericConsoleTextArea.js b/config/plugins/visualizations/jmol/static/j2s/J/api/js/GenericConsoleTextArea.js
new file mode 100755
index 000000000000..937133757c09
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/js/GenericConsoleTextArea.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api.js");
+Clazz.declareInterface(J.api.js, "GenericConsoleTextArea");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSConsole.js b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSConsole.js
new file mode 100755
index 000000000000..72297327044c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSConsole.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api.js");
+Clazz.declareInterface(J.api.js, "JSConsole");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSmolAppletObject.js b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSmolAppletObject.js
new file mode 100755
index 000000000000..e523fac88813
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JSmolAppletObject.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api.js");
+Clazz.declareInterface(J.api.js, "JSmolAppletObject", javajs.api.js.JSAppletObject);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/api/js/JmolToJSmolInterface.js b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JmolToJSmolInterface.js
new file mode 100755
index 000000000000..4845cab94f20
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/api/js/JmolToJSmolInterface.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.api.js");
+Clazz.declareInterface(J.api.js, "JmolToJSmolInterface", javajs.api.js.J2SObjectInterface);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/appletjs/Jmol.js b/config/plugins/visualizations/jmol/static/j2s/J/appletjs/Jmol.js
new file mode 100755
index 000000000000..564a8673c816
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/appletjs/Jmol.js
@@ -0,0 +1,18 @@
+Clazz.declarePackage("J.appletjs");
+Clazz.load(["JU.GenericApplet"], "J.appletjs.Jmol", ["java.util.Hashtable"], function(){
+var c$ = Clazz.declareType(J.appletjs, "Jmol", JU.GenericApplet);
+Clazz.makeConstructor(c$,
+function(vwrOptions){
+Clazz.superConstructor (this, J.appletjs.Jmol, []);
+this.htParams = new java.util.Hashtable();
+if (vwrOptions == null) vwrOptions = new java.util.Hashtable();
+this.vwrOptions = vwrOptions;
+for (var entry, $entry = vwrOptions.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) this.htParams.put(entry.getKey().toLowerCase(), entry.getValue());
+
+this.documentBase = "" + vwrOptions.get("documentBase");
+this.codeBase = "" + vwrOptions.get("codePath");
+JU.GenericApplet.isJS = true;
+this.init(this);
+}, "java.util.Map");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomData.js b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomData.js
new file mode 100755
index 000000000000..dcb03a9aa89c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomData.js
@@ -0,0 +1,39 @@
+Clazz.declarePackage("J.atomdata");
+Clazz.load(null, "J.atomdata.AtomData", ["JU.P3", "JU.BSUtil"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.programInfo = null;
+this.fileName = null;
+this.modelName = null;
+this.modelIndex = 0;
+this.bsSelected = null;
+this.bsIgnored = null;
+this.bsMolecules = null;
+this.radiusData = null;
+this.firstAtomIndex = 0;
+this.firstModelIndex = 0;
+this.lastModelIndex = 0;
+this.hAtomRadius = 0;
+this.atomIndex = null;
+this.atoms = null;
+this.xyz = null;
+this.atomRadius = null;
+this.atomicNumber = null;
+this.atomMolecule = null;
+this.hAtoms = null;
+this.ac = 0;
+this.hydrogenAtomCount = 0;
+this.adpMode = 0;
+Clazz.instantialize(this, arguments);}, J.atomdata, "AtomData", null);
+/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "transformXYZ",
+function(mat, bs){
+var p = new Array(this.xyz.length);
+if (bs == null) bs = JU.BSUtil.newBitSet2(0, this.xyz.length);
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (this.xyz[i] == null) continue;
+p[i] = JU.P3.newP(this.xyz[i]);
+mat.rotTrans(p[i]);
+}
+this.xyz = p;
+}, "JU.M4,JU.BS");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomDataServer.js b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomDataServer.js
new file mode 100755
index 000000000000..de7c53b088bd
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/AtomDataServer.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.atomdata");
+Clazz.declareInterface(J.atomdata, "AtomDataServer");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/atomdata/RadiusData.js b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/RadiusData.js
new file mode 100755
index 000000000000..d3bc8e1936ed
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/atomdata/RadiusData.js
@@ -0,0 +1,54 @@
+Clazz.declarePackage("J.atomdata");
+Clazz.load(["java.lang.Enum", "J.c.VDW"], "J.atomdata.RadiusData", ["JU.SB"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.info = null;
+this.factorType = null;
+this.vdwType = null;
+this.value = NaN;
+this.valueExtended = 0;
+this.values = null;
+Clazz.instantialize(this, arguments);}, J.atomdata, "RadiusData", null);
+Clazz.prepareFields (c$, function(){
+this.factorType = J.atomdata.RadiusData.EnumType.ABSOLUTE;
+this.vdwType = J.c.VDW.AUTO;
+});
+Clazz.makeConstructor(c$,
+function(values, value, factorType, vdwType){
+if (values != null) {
+this.values = values;
+this.value = 2147483647;
+return;
+}if (factorType == null) return;
+this.factorType = factorType;
+this.value = value;
+if (vdwType != null) this.vdwType = vdwType;
+}, "~A,~N,J.atomdata.RadiusData.EnumType,J.c.VDW");
+Clazz.overrideMethod(c$, "toString",
+function(){
+if (Float.isNaN(this.value)) return "";
+var sb = new JU.SB();
+switch (this.factorType) {
+case J.atomdata.RadiusData.EnumType.ABSOLUTE:
+sb.appendF(this.value);
+break;
+case J.atomdata.RadiusData.EnumType.OFFSET:
+sb.append(this.value > 0 ? "+" : "").appendF(this.value);
+break;
+case J.atomdata.RadiusData.EnumType.FACTOR:
+sb.appendI(Clazz.floatToInt(this.value * 100)).append("%");
+if (this.vdwType !== J.c.VDW.AUTO) sb.append(this.vdwType.getVdwLabel());
+break;
+case J.atomdata.RadiusData.EnumType.SCREEN:
+sb.appendI(Clazz.floatToInt(this.value));
+}
+return sb.toString();
+});
+/*if2*/;(function(){
+var c$ = Clazz.declareType(J.atomdata.RadiusData, "EnumType", Enum);
+Clazz.defineEnumConstant(c$, "ABSOLUTE", 0, []);
+Clazz.defineEnumConstant(c$, "OFFSET", 1, []);
+Clazz.defineEnumConstant(c$, "FACTOR", 2, []);
+Clazz.defineEnumConstant(c$, "SCREEN", 3, []);
+/*eoif2*/})();
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Event.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Event.js
new file mode 100755
index 000000000000..f8278e33d01e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Event.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.awtjs");
+(function(){
+var c$ = Clazz.declareType(J.awtjs, "Event", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Platform.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Platform.js
new file mode 100755
index 000000000000..3a25595fa49d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/Platform.js
@@ -0,0 +1,28 @@
+Clazz.declarePackage("J.awtjs");
+Clazz.load(["J.awtjs2d.Platform"], "J.awtjs.Platform", null, function(){
+var c$ = Clazz.declareType(J.awtjs, "Platform", J.awtjs2d.Platform);
+Clazz.overrideMethod(c$, "drawImage",
+function(g, img, x, y, width, height, isDTI){
+}, "~O,~O,~N,~N,~N,~N,~B");
+Clazz.overrideMethod(c$, "getTextPixels",
+function(text, font3d, gObj, image, width, height, ascent){
+return null;
+}, "~S,JU.Font,~O,~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "getGraphics",
+function(image){
+return null;
+}, "~O");
+Clazz.overrideMethod(c$, "getStaticGraphics",
+function(image, backgroundTransparent){
+return null;
+}, "~O,~B");
+Clazz.overrideMethod(c$, "newBufferedImage",
+function(image, w, h){
+return null;
+}, "~O,~N,~N");
+Clazz.overrideMethod(c$, "newOffScreenImage",
+function(w, h){
+return null;
+}, "~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs/README.txt b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/README.txt
new file mode 100755
index 000000000000..7104fe73ab52
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs/README.txt
@@ -0,0 +1,9 @@
+awtjs and awtjs.swing are minimal AWT/Swing-like
+implementations used by Jmol and JSpecView to
+provide consoles without any reference to AWT
+or Swing. It is a relatively simple implementation
+without many features. It does do the job for Jmol
+and JSpecView, and it is very tight, but I don't
+recommend it.
+
+Bob Hanson
\ No newline at end of file
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Display.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Display.js
new file mode 100755
index 000000000000..d7e35794716f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Display.js
@@ -0,0 +1,67 @@
+Clazz.declarePackage("J.awtjs2d");
+(function(){
+var c$ = Clazz.declareType(J.awtjs2d, "Display", null);
+c$.getFullScreenDimensions = Clazz.defineMethod(c$, "getFullScreenDimensions",
+function(canvas, widthHeight){
+{
+widthHeight[0] = canvas.width;
+widthHeight[1] = canvas.height;
+}}, "~O,~A");
+c$.hasFocus = Clazz.defineMethod(c$, "hasFocus",
+function(canvas){
+{
+}return true;
+}, "~O");
+c$.requestFocusInWindow = Clazz.defineMethod(c$, "requestFocusInWindow",
+function(canvas){
+{
+}}, "~O");
+c$.renderScreenImage = Clazz.defineMethod(c$, "renderScreenImage",
+function(vwr, g, size){
+{
+}}, "J.api.PlatformViewer,~O,~O");
+c$.prompt = Clazz.defineMethod(c$, "prompt",
+function(label, data, list, asButtons){
+{
+var s = (data == null ? alert(label) : prompt(label, data));
+if (s != null)return s;
+}return "null";
+}, "~S,~S,~A,~B");
+c$.convertPointFromScreen = Clazz.defineMethod(c$, "convertPointFromScreen",
+function(canvas, ptTemp){
+{
+}}, "~O,JU.P3");
+c$.drawImage = Clazz.defineMethod(c$, "drawImage",
+function(context, canvas, x, y, width, height, isDTI){
+{
+var buf8 = canvas.buf8;
+var buf32 = canvas.buf32;
+var n = canvas.width * canvas.height;
+var di = 1;
+if (isDTI) {
+var diw = width % 2;
+width = Math.floor(width/2);
+di = Math.floor(canvas.width/width);
+}
+var dw = (canvas.width - width || x) * 4;
+for (var i = 0, p = 0, j = x * 4; i < n;) {
+buf8[j++] = (buf32[i] >> 16) & 0xFF;
+buf8[j++] = (buf32[i] >> 8) & 0xFF;
+buf8[j++] = buf32[i] & 0xFF;
+buf8[j++] = 0xFF;
+i += di;
+if (++p%width==0) {
+if (diw) {
+i += 1;
+buf8[j] = 0;
+buf8[j+1] = 0;
+buf8[j+2] = 0;
+buf8[j+3] = 0;
+}
+j += dw;
+}
+}
+context.putImageData(canvas.imgdata,0,0);
+}}, "~O,~O,~N,~N,~N,~N,~B");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Image.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Image.js
new file mode 100755
index 000000000000..3578a86fbf4f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Image.js
@@ -0,0 +1,53 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(null, "J.awtjs2d.Image", ["J.awtjs2d.Platform"], function(){
+var c$ = Clazz.declareType(J.awtjs2d, "Image", null);
+c$.getWidth = Clazz.defineMethod(c$, "getWidth",
+function(canvas){
+{
+return (canvas.imageWidth ? canvas.imageWidth : canvas.width);
+}}, "~O");
+c$.getHeight = Clazz.defineMethod(c$, "getHeight",
+function(canvas){
+{
+return (canvas.imageHeight ? canvas.imageHeight : canvas.height);
+}}, "~O");
+c$.grabPixels = Clazz.defineMethod(c$, "grabPixels",
+function(context, width, height){
+var data = null;
+{
+data = context.getImageData(0, 0, width, height).data;
+}return J.awtjs2d.Image.toIntARGB(data);
+}, "~O,~N,~N");
+c$.toIntARGB = Clazz.defineMethod(c$, "toIntARGB",
+function(imgData){
+var n = Clazz.doubleToInt(imgData.length / 4);
+var iData = Clazz.newIntArray (n, 0);
+for (var i = 0, j = 0; i < n; ) {
+iData[i++] = (imgData[j++] << 16) | (imgData[j++] << 8) | imgData[j++] | (imgData[j++] << 24);
+}
+return iData;
+}, "~A");
+c$.getTextPixels = Clazz.defineMethod(c$, "getTextPixels",
+function(text, font3d, context, width, height, ascent){
+{
+context.fillStyle = "#000000";
+context.fillRect(0, 0, width, height);
+context.fillStyle = "#FFFFFF";
+context.font = font3d.font;
+context.fillText(text, 0, ascent);
+}return J.awtjs2d.Image.grabPixels(context, width, height);
+}, "~S,JU.Font,~O,~N,~N,~N");
+c$.allocateRgbImage = Clazz.defineMethod(c$, "allocateRgbImage",
+function(windowWidth, windowHeight, pBuffer, windowSize, backgroundTransparent, canvas){
+{
+if (canvas == null)
+canvas = {width:windowWidth,height:windowHeight};
+canvas.buf32 = pBuffer;
+}return canvas;
+}, "~N,~N,~A,~N,~B,~O");
+c$.getImageDialog = Clazz.defineMethod(c$, "getImageDialog",
+function(vwr, title, imageMap){
+return J.awtjs2d.Platform.Jmol().consoleGetImageDialog(vwr, title, imageMap);
+}, "JV.Viewer,~S,java.util.Map");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFile.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFile.js
new file mode 100755
index 000000000000..cd2db85abafb
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFile.js
@@ -0,0 +1,60 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.api.GenericFileInterface"], "J.awtjs2d.JSFile", ["JU.OC", "$.PT", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.name = null;
+this.fullName = null;
+Clazz.instantialize(this, arguments);}, J.awtjs2d, "JSFile", null, J.api.GenericFileInterface);
+Clazz.makeConstructor(c$,
+function(name){
+this.name = name.$replace('\\', '/');
+this.fullName = name;
+if (!this.fullName.startsWith("/") && JU.OC.urlTypeIndex(name) < 0) this.fullName = JV.Viewer.jsDocumentBase + "/" + this.fullName;
+this.fullName = JU.PT.rep(this.fullName, "/./", "/");
+name = name.substring(name.lastIndexOf("/") + 1);
+}, "~S");
+c$.newFile = Clazz.defineMethod(c$, "newFile",
+function(name){
+return new J.awtjs2d.JSFile(name);
+}, "~S");
+Clazz.overrideMethod(c$, "getParentAsFile",
+function(){
+var pt = this.fullName.lastIndexOf("/");
+return (pt < 0 ? null : new J.awtjs2d.JSFile(this.fullName.substring(0, pt)));
+});
+Clazz.overrideMethod(c$, "getFullPath",
+function(){
+return this.fullName;
+});
+Clazz.overrideMethod(c$, "getName",
+function(){
+return this.name;
+});
+Clazz.overrideMethod(c$, "isDirectory",
+function(){
+return this.fullName.endsWith("/");
+});
+Clazz.overrideMethod(c$, "length",
+function(){
+return 0;
+});
+c$.getURLContents = Clazz.defineMethod(c$, "getURLContents",
+function(url, outputBytes, post){
+try {
+var conn = url.openConnection();
+if (outputBytes != null) conn.outputBytes(outputBytes);
+ else if (post != null) conn.outputString(post);
+return conn.getContents();
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return e.toString();
+} else {
+throw e;
+}
+}
+}, "java.net.URL,~A,~S");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return this.fullName;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFont.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFont.js
new file mode 100755
index 000000000000..f87a739eb4a4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSFont.js
@@ -0,0 +1,39 @@
+Clazz.declarePackage("J.awtjs2d");
+(function(){
+var c$ = Clazz.declareType(J.awtjs2d, "JSFont", null);
+c$.newFont = Clazz.defineMethod(c$, "newFont",
+function(fontFace, isBold, isItalic, fontSize, type){
+fontFace = (fontFace.equals("Monospaced") ? "Courier" : fontFace.startsWith("Sans") ? "Helvetica Neue, Sans-serif" : "Serif");
+return (isBold ? "bold " : "") + (isItalic ? "italic " : "") + fontSize + type + " " + fontFace;
+}, "~S,~B,~B,~N,~S");
+c$.getFontMetrics = Clazz.defineMethod(c$, "getFontMetrics",
+function(font, context){
+{
+if (context.font != font.font) {
+context.font = font.font;
+font.font = context.font;
+context._fontAscent = Math.ceil(font.fontSize); //pt, not px
+// the descent is actually (px - pt)
+// but I know of no way of getting access to the drawn height
+context._fontDescent = Math.ceil(font.fontSize * 0.25);//approx
+}
+}return context;
+}, "JU.Font,~O");
+c$.getAscent = Clazz.defineMethod(c$, "getAscent",
+function(context){
+{
+return Math.ceil(context._fontAscent);
+}}, "~O");
+c$.getDescent = Clazz.defineMethod(c$, "getDescent",
+function(context){
+{
+return Math.ceil(context._fontDescent);
+}}, "~O");
+c$.stringWidth = Clazz.defineMethod(c$, "stringWidth",
+function(font, context, text){
+{
+context.font = font.font;
+return Math.ceil(context.measureText(text).width);
+}}, "JU.Font,~O,~S");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSJmolPopup.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSJmolPopup.js
new file mode 100755
index 000000000000..59fcde4e76ce
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSJmolPopup.js
@@ -0,0 +1,33 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.popup.JmolPopup"], "J.awtjs2d.JSJmolPopup", ["J.awtjs2d.JSPopupHelper"], function(){
+var c$ = Clazz.declareType(J.awtjs2d, "JSJmolPopup", J.popup.JmolPopup);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.awtjs2d.JSJmolPopup, []);
+this.helper = new J.awtjs2d.JSPopupHelper(this);
+});
+Clazz.overrideMethod(c$, "menuShowPopup",
+function(popup, x, y){
+try {
+(popup).show(this.isTainted ? this.vwr.html5Applet : null, x, y);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+this.isTainted = false;
+}, "J.api.SC,~N,~N");
+Clazz.overrideMethod(c$, "getUnknownCheckBoxScriptToRun",
+function(item, name, what, TF){
+return null;
+}, "J.api.SC,~S,~S,~B");
+Clazz.overrideMethod(c$, "getImageIcon",
+function(fileName){
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "menuFocusCallback",
+function(name, actionCommand, b){
+}, "~S,~S,~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSModelKitPopup.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSModelKitPopup.js
new file mode 100755
index 000000000000..727b439b1421
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSModelKitPopup.js
@@ -0,0 +1,41 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.modelkit.ModelKitPopup"], "J.awtjs2d.JSModelKitPopup", ["J.awtjs2d.JSPopupHelper"], function(){
+var c$ = Clazz.declareType(J.awtjs2d, "JSModelKitPopup", J.modelkit.ModelKitPopup);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.awtjs2d.JSModelKitPopup, []);
+this.helper = new J.awtjs2d.JSPopupHelper(this);
+});
+Clazz.overrideMethod(c$, "menuShowPopup",
+function(popup, x, y){
+try {
+(popup).show(this.isTainted ? this.vwr.html5Applet : null, x, y);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+this.isTainted = false;
+}, "J.api.SC,~N,~N");
+Clazz.overrideMethod(c$, "menuHidePopup",
+function(popup){
+try {
+(popup).setVisible(false);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+}, "J.api.SC");
+Clazz.overrideMethod(c$, "getImageIcon",
+function(fileName){
+return "J/modelkit/images/" + fileName;
+}, "~S");
+Clazz.overrideMethod(c$, "menuCheckBoxCallback",
+function(source){
+this.doMenuCheckBoxCallback(source);
+}, "J.api.SC");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSPopupHelper.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSPopupHelper.js
new file mode 100755
index 000000000000..a1c57f7d96f9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JSPopupHelper.js
@@ -0,0 +1,93 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.popup.PopupHelper"], "J.awtjs2d.JSPopupHelper", ["JS.ButtonGroup", "$.JCheckBoxMenuItem", "$.JMenu", "$.JMenuItem", "$.JPopupMenu", "$.JRadioButtonMenuItem"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.popup = null;
+this.buttonGroup = null;
+Clazz.instantialize(this, arguments);}, J.awtjs2d, "JSPopupHelper", null, J.popup.PopupHelper);
+Clazz.makeConstructor(c$,
+function(popup){
+this.popup = popup;
+}, "J.popup.GenericPopup");
+Clazz.overrideMethod(c$, "menuCreatePopup",
+function(name, applet){
+var j = new JS.JPopupMenu(name);
+j.setInvoker(applet);
+return j;
+}, "~S,~O");
+Clazz.overrideMethod(c$, "getMenu",
+function(name){
+var jm = new JS.JMenu();
+jm.setName(name);
+return jm;
+}, "~S");
+Clazz.overrideMethod(c$, "getMenuItem",
+function(text){
+return new JS.JMenuItem(text);
+}, "~S");
+Clazz.overrideMethod(c$, "getRadio",
+function(name){
+return new JS.JRadioButtonMenuItem();
+}, "~S");
+Clazz.overrideMethod(c$, "getCheckBox",
+function(name){
+return new JS.JCheckBoxMenuItem();
+}, "~S");
+Clazz.overrideMethod(c$, "menuAddButtonGroup",
+function(item){
+if (item == null) {
+if (this.buttonGroup != null && this.buttonGroup.getButtonCount() > 0) this.buttonGroup = null;
+return;
+}if (this.buttonGroup == null) this.buttonGroup = new JS.ButtonGroup();
+this.buttonGroup.add(item);
+}, "J.api.SC");
+Clazz.overrideMethod(c$, "getItemType",
+function(m){
+return (m).btnType;
+}, "J.api.SC");
+Clazz.overrideMethod(c$, "menuInsertSubMenu",
+function(menu, subMenu, index){
+(subMenu).setParent(menu);
+}, "J.api.SC,J.api.SC,~N");
+Clazz.overrideMethod(c$, "getSwingComponent",
+function(component){
+return component;
+}, "~O");
+Clazz.overrideMethod(c$, "menuClearListeners",
+function(menu){
+if (menu != null) (menu).disposeMenu();
+}, "J.api.SC");
+Clazz.defineMethod(c$, "itemStateChanged",
+function(e){
+if (this.popup != null) this.popup.menuCheckBoxCallback(e.getSource());
+}, "java.awt.event.ItemEvent");
+Clazz.defineMethod(c$, "actionPerformed",
+function(e){
+if (this.popup != null) this.popup.menuClickCallback(e.getSource(), e.getActionCommand());
+}, "java.awt.event.ActionEvent");
+Clazz.overrideMethod(c$, "getButtonGroup",
+function(){
+return this.buttonGroup;
+});
+Clazz.defineMethod(c$, "handleEvent",
+function(e){
+var type = "" + e.getID();
+if (type === "mouseenter") this.mouseEntered(e);
+ else if (type === "mouseleave") this.mouseExited(e);
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseEntered",
+function(e){
+var jmi = e.getSource();
+this.popup.menuFocusCallback(jmi.getName(), jmi.getActionCommand(), true);
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseExited",
+function(e){
+var jmi = e.getSource();
+this.popup.menuFocusCallback(jmi.getName(), jmi.getActionCommand(), false);
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod(c$, "dispose",
+function(popupMenu){
+this.menuClearListeners(popupMenu);
+this.popup = null;
+}, "J.api.SC");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JsG2D.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JsG2D.js
new file mode 100755
index 000000000000..386a35c4012d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/JsG2D.js
@@ -0,0 +1,180 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.api.GenericGraphics"], "J.awtjs2d.JsG2D", ["JU.CU", "JS.Color", "J.awtjs2d.Platform"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.windowWidth = 0;
+this.windowHeight = 0;
+this.isShifted = false;
+this.inPath = false;
+Clazz.instantialize(this, arguments);}, J.awtjs2d, "JsG2D", null, J.api.GenericGraphics);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "getColor4",
+function(r, g, b, a){
+return JS.Color.get4(r, g, b, a);
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "getColor3",
+function(r, g, b){
+return JS.Color.get3(r, g, b);
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "getColor1",
+function(rgb){
+return JS.Color.get1(rgb);
+}, "~N");
+Clazz.overrideMethod(c$, "newGrayScaleImage",
+function(context, image, width, height, grayBuffer){
+return J.awtjs2d.Platform.Jmol().newGrayScaleImage(context, image, width, height, grayBuffer);
+}, "~O,~O,~N,~N,~A");
+Clazz.overrideMethod(c$, "drawGrayScaleImage",
+function(g, image, destX0, destY0, destX1, destY1, srcX0, srcY0, srcX1, srcY1){
+var iw;
+var ih;
+{
+iw = image.w;
+ih = image.h;
+}var dw = (destX1 - destX0 + 1);
+var dh = (destY1 - destY0 + 1);
+var sw = (srcX1 - srcX0 + 1);
+var sh = (srcY1 - srcY0 + 1);
+var x = -srcX0 * dw / sw;
+var w = iw * dw / sw;
+var y = -srcY0 * dh / sh;
+var h = ih * dh / sh;
+{
+image.width = w;
+image.height = h;
+var div = image.div;
+var layer = image.layer;
+layer.style.left = destX0 + "px";
+layer.style.top = destY0 + "px";
+layer.style.width = dw + "px";
+layer.style.height = dh+ "px";
+div.style.left= x + "px";
+div.style.top = y + "px";
+div.style.width = w + "px";
+div.style.height = h + "px";
+}}, "~O,~O,~N,~N,~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawLine",
+function(g, x0, y0, x1, y1){
+var inPath = this.inPath;
+{
+if (!inPath) g.beginPath();
+g.moveTo(x0, y0);
+g.lineTo(x1, y1);
+if (!inPath) g.stroke();
+}}, "~O,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawCircle",
+function(g, x, y, diameter){
+{
+var r = diameter/2;
+g.beginPath();
+g.arc(x + r, y + r, r, 0, 2 * Math.PI, false);
+g.stroke();
+}}, "~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawPolygon",
+function(g, ayPoints, axPoints, nPoints){
+this.doPoly(g, ayPoints, axPoints, nPoints, false);
+}, "~O,~A,~A,~N");
+Clazz.defineMethod(c$, "doPoly",
+function(g, axPoints, ayPoints, nPoints, doFill){
+{
+g.beginPath();
+g.moveTo(axPoints[0], ayPoints[0]);
+for (var i = 1; i < nPoints; i++)
+g.lineTo(axPoints[i], ayPoints[i]);
+if (doFill)
+g.fill();
+else
+g.stroke();
+}}, "~O,~A,~A,~N,~B");
+Clazz.overrideMethod(c$, "drawRect",
+function(g, x, y, width, height){
+{
+g.beginPath();
+g.rect(x ,y, width, height);
+g.stroke();
+}}, "~O,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawString",
+function(g, s, x, y){
+{
+g.fillText(s,x,y);
+}}, "~O,~S,~N,~N");
+Clazz.overrideMethod(c$, "drawStringRotated",
+function(g, s, x, y, angle){
+}, "~O,~S,~N,~N,~N");
+Clazz.overrideMethod(c$, "fillBackground",
+function(g, bgcolor){
+if (bgcolor == null) {
+{
+if (!this.isShifted) {
+g.translate(-0.5, -0.5);
+this.isShifted = true;
+}
+g.clearRect(0,0, this.windowWidth, this.windowHeight);
+return;
+}}this.setGraphicsColor(g, bgcolor);
+this.fillRect(g, 0, 0, this.windowWidth, this.windowHeight);
+}, "~O,javajs.api.GenericColor");
+Clazz.overrideMethod(c$, "fillCircle",
+function(g, x, y, diameter){
+{
+var r = diameter/2;
+g.beginPath();
+g.arc(x + r, y + r, r, 0, 2 * Math.PI, false);
+g.fill();
+}}, "~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "fillPolygon",
+function(g, ayPoints, axPoints, nPoints){
+this.doPoly(g, ayPoints, axPoints, nPoints, true);
+}, "~O,~A,~A,~N");
+Clazz.overrideMethod(c$, "fillRect",
+function(g, x, y, width, height){
+{
+g.fillRect(x, y, width, height);
+}}, "~O,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "setGraphicsColor",
+function(g, c){
+var s = JU.CU.toCSSString(c);
+{
+g.fillStyle = g.strokeStyle = s;
+}}, "~O,javajs.api.GenericColor");
+Clazz.overrideMethod(c$, "setFont",
+function(g, font){
+var s = font.getInfo();
+var pt = s.indexOf(" ");
+s = s.substring(0, pt) + "px" + s.substring(pt);
+{
+g.font = s;
+}return font;
+}, "~O,JU.Font");
+Clazz.overrideMethod(c$, "setStrokeBold",
+function(g, tf){
+{
+g.lineWidth = (tf ? 2 : 1);
+}}, "~O,~B");
+Clazz.overrideMethod(c$, "setWindowParameters",
+function(width, height){
+this.windowWidth = width;
+this.windowHeight = height;
+}, "~N,~N");
+Clazz.overrideMethod(c$, "translateScale",
+function(g, x, y, scale){
+}, "~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "canDoLineTo",
+function(){
+return true;
+});
+Clazz.overrideMethod(c$, "doStroke",
+function(g, isBegin){
+this.inPath = isBegin;
+{
+if (isBegin) {
+g.beginPath();
+} else {
+g.stroke();
+}
+}}, "~O,~B");
+Clazz.overrideMethod(c$, "lineTo",
+function(g, x2, y2){
+{
+g.lineTo(x2, y2);
+}}, "~O,~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Mouse.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Mouse.js
new file mode 100755
index 000000000000..83cb4b26c36b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Mouse.js
@@ -0,0 +1,290 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.api.GenericMouseInterface"], "J.awtjs2d.Mouse", ["JU.PT", "$.V3", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.manager = null;
+this.keyBuffer = "";
+this.isMouseDown = false;
+this.wheeling = false;
+this.modifiersDown = 0;
+this.xWhenPressed = 0;
+this.yWhenPressed = 0;
+this.modifiersWhenPressed10 = 0;
+Clazz.instantialize(this, arguments);}, J.awtjs2d, "Mouse", null, J.api.GenericMouseInterface);
+Clazz.makeConstructor(c$,
+function(privateKey, vwr, display){
+this.vwr = vwr;
+this.manager = this.vwr.acm;
+}, "~N,JV.Viewer,~O");
+Clazz.overrideMethod(c$, "clear",
+function(){
+});
+Clazz.overrideMethod(c$, "dispose",
+function(){
+});
+Clazz.overrideMethod(c$, "processEvent",
+function(id, x, y, modifiers, time){
+if (id != 507) modifiers = J.awtjs2d.Mouse.applyLeftMouse(modifiers);
+switch (id) {
+case 507:
+this.wheeled(time, x, modifiers);
+break;
+case 501:
+this.xWhenPressed = x;
+this.yWhenPressed = y;
+this.modifiersWhenPressed10 = modifiers;
+this.pressed(time, x, y, modifiers, false);
+break;
+case 506:
+this.dragged(time, x, y);
+break;
+case 504:
+this.entry(time, x, y, false);
+break;
+case 505:
+this.entry(time, x, y, true);
+break;
+case 503:
+this.moved(time, x, y, modifiers);
+break;
+case 502:
+this.released(time, x, y, modifiers);
+if (x == this.xWhenPressed && y == this.yWhenPressed && modifiers == this.modifiersWhenPressed10) {
+this.clicked(time, x, y, modifiers, 1);
+}break;
+default:
+return false;
+}
+return true;
+}, "~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "processTwoPointGesture",
+function(touches){
+if (touches[0].length < 2) return;
+var t1 = touches[0];
+var t2 = touches[1];
+var t1first = t1[0];
+var t1last = t1[t2.length - 1];
+var x1first = t1first[0];
+var x1last = t1last[0];
+var dx1 = x1last - x1first;
+var y1first = t1first[1];
+var y1last = t1last[1];
+var dy1 = y1last - y1first;
+var v1 = JU.V3.new3(dx1, dy1, 0);
+var d1 = v1.length();
+var t2first = t2[0];
+var t2last = t2[t2.length - 1];
+var x2first = t2first[0];
+var x2last = t2last[0];
+var dx2 = x2last - x2first;
+var y2first = t2first[1];
+var y2last = t2last[1];
+var dy2 = y2last - y2first;
+var v2 = JU.V3.new3(dx2, dy2, 0);
+var d2 = v2.length();
+if (d1 < 1 || d2 < 1) return;
+v1.normalize();
+v2.normalize();
+var cos12 = (v1.dot(v2));
+if (cos12 > 0.8) {
+var deltaX = Clazz.floatToInt(x1last - t1[t1.length - 2][0]);
+var deltaY = Clazz.floatToInt(y1last - t1[t1.length - 2][1]);
+this.vwr.translateXYBy(deltaX, deltaY);
+} else if (cos12 < -0.8) {
+v1 = JU.V3.new3(x2first - x1first, y2first - y1first, 0);
+v2 = JU.V3.new3(x2last - x1last, y2last - y1last, 0);
+var dx = v2.length() - v1.length();
+this.wheeled(System.currentTimeMillis(), dx < 0 ? -1 : 1, 32);
+}}, "~A");
+Clazz.defineMethod(c$, "mouseClicked",
+function(e){
+this.clicked(e.getWhen(), e.getX(), e.getY(), e.getModifiers(), e.getClickCount());
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseEntered",
+function(e){
+this.entry(e.getWhen(), e.getX(), e.getY(), false);
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseExited",
+function(e){
+this.entry(e.getWhen(), e.getX(), e.getY(), true);
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mousePressed",
+function(e){
+this.pressed(e.getWhen(), e.getX(), e.getY(), e.getModifiers(), e.isPopupTrigger());
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseReleased",
+function(e){
+this.released(e.getWhen(), e.getX(), e.getY(), e.getModifiers());
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseDragged",
+function(e){
+var modifiers = e.getModifiers();
+if ((modifiers & 28) == 0) modifiers |= 16;
+this.dragged(e.getWhen(), e.getX(), e.getY());
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseMoved",
+function(e){
+this.moved(e.getWhen(), e.getX(), e.getY(), e.getModifiers());
+}, "java.awt.event.MouseEvent");
+Clazz.defineMethod(c$, "mouseWheelMoved",
+function(e){
+e.consume();
+this.wheeled(e.getWhen(), e.getWheelRotation(), e.getModifiers());
+}, "java.awt.event.MouseWheelEvent");
+Clazz.defineMethod(c$, "keyTyped",
+function(ke){
+ke.consume();
+if (!this.vwr.menuEnabled()) return;
+var ch = ke.getKeyChar();
+var modifiers = ke.getModifiers();
+if (JU.Logger.debuggingHigh) JU.Logger.debug("MouseManager keyTyped: " + ch + " " + (0 + ch.charCodeAt(0)) + " " + modifiers);
+if (modifiers != 0 && modifiers != 1) {
+switch ((ch).charCodeAt(0)) {
+case String.fromCharCode(11):
+case 107:
+var isON = !this.vwr.getBooleanProperty("allowKeyStrokes");
+switch (modifiers) {
+case 2:
+this.vwr.setBooleanProperty("allowKeyStrokes", isON);
+this.vwr.setBooleanProperty("showKeyStrokes", true);
+break;
+case 10:
+case 1:
+this.vwr.setBooleanProperty("allowKeyStrokes", isON);
+this.vwr.setBooleanProperty("showKeyStrokes", false);
+break;
+}
+this.clearKeyBuffer();
+this.vwr.refresh(3, "showkey");
+break;
+case 22:
+case 118:
+switch (modifiers) {
+case 2:
+break;
+}
+break;
+case 26:
+case 122:
+switch (modifiers) {
+case 2:
+this.vwr.undoMoveAction(4165, 1);
+break;
+case 3:
+this.vwr.undoMoveAction(4140, 1);
+break;
+}
+break;
+case 25:
+case 121:
+switch (modifiers) {
+case 2:
+this.vwr.undoMoveAction(4140, 1);
+break;
+}
+break;
+}
+return;
+}if (!this.vwr.getBooleanProperty("allowKeyStrokes")) return;
+this.addKeyBuffer(ke.getModifiers() == 1 ? Character.toUpperCase(ch) : ch);
+}, "java.awt.event.KeyEvent");
+Clazz.defineMethod(c$, "keyPressed",
+function(ke){
+if (this.vwr.isApplet) ke.consume();
+this.manager.keyPressed(ke.getKeyCode(), ke.getModifiers());
+}, "java.awt.event.KeyEvent");
+Clazz.defineMethod(c$, "keyReleased",
+function(ke){
+ke.consume();
+this.manager.keyReleased(ke.getKeyCode());
+}, "java.awt.event.KeyEvent");
+Clazz.defineMethod(c$, "clearKeyBuffer",
+function(){
+if (this.keyBuffer.length == 0) return;
+this.keyBuffer = "";
+if (this.vwr.getBooleanProperty("showKeyStrokes")) this.vwr.evalStringQuietSync("!set echo _KEYSTROKES; set echo bottom left;echo \"\"", true, true);
+});
+Clazz.defineMethod(c$, "addKeyBuffer",
+function(ch){
+if (ch.charCodeAt(0) == 10) {
+this.sendKeyBuffer();
+return;
+}if (ch.charCodeAt(0) == 8) {
+if (this.keyBuffer.length > 0) this.keyBuffer = this.keyBuffer.substring(0, this.keyBuffer.length - 1);
+} else {
+this.keyBuffer += ch;
+}if (this.vwr.getBooleanProperty("showKeyStrokes")) this.vwr.evalStringQuietSync("!set echo _KEYSTROKES; set echo bottom left;echo " + JU.PT.esc("\1" + this.keyBuffer), true, true);
+}, "~S");
+Clazz.defineMethod(c$, "sendKeyBuffer",
+function(){
+var kb = this.keyBuffer;
+if (this.vwr.getBooleanProperty("showKeyStrokes")) this.vwr.evalStringQuietSync("!set echo _KEYSTROKES; set echo bottom left;echo " + JU.PT.esc(this.keyBuffer), true, true);
+this.clearKeyBuffer();
+this.vwr.evalStringQuietSync(kb, false, true);
+});
+Clazz.defineMethod(c$, "entry",
+function(time, x, y, isExit){
+this.wheeling = false;
+this.isMouseDown = false;
+this.modifiersDown = 0;
+this.manager.mouseEnterExit(time, x, y, isExit);
+}, "~N,~N,~N,~B");
+Clazz.defineMethod(c$, "clicked",
+function(time, x, y, modifiers, clickCount){
+this.clearKeyBuffer();
+this.manager.mouseAction(2, time, x, y, 1, modifiers);
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "moved",
+function(time, x, y, modifiers){
+this.clearKeyBuffer();
+if (this.isMouseDown) this.manager.mouseAction(1, time, x, y, 0, this.modifiersDown);
+ else this.manager.mouseAction(0, time, x, y, 0, modifiers);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "wheeled",
+function(time, rotation, modifiers){
+this.clearKeyBuffer();
+this.wheeling = true;
+this.manager.mouseAction(3, time, 0, rotation, 0, modifiers & -29 | 32);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "pressed",
+function(time, x, y, modifiers, isPopupTrigger){
+this.clearKeyBuffer();
+this.isMouseDown = true;
+this.modifiersDown = modifiers;
+this.wheeling = false;
+this.manager.mouseAction(4, time, x, y, 0, modifiers);
+}, "~N,~N,~N,~N,~B");
+Clazz.defineMethod(c$, "released",
+function(time, x, y, modifiers){
+this.isMouseDown = false;
+this.modifiersDown = 0;
+this.wheeling = false;
+this.manager.mouseAction(5, time, x, y, 0, modifiers);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "dragged",
+function(time, x, y){
+if (this.wheeling) return;
+if ((this.modifiersDown & 20) == 20) this.modifiersDown = this.modifiersDown & -5 | 2;
+this.manager.mouseAction(1, time, x, y, 0, this.modifiersDown);
+}, "~N,~N,~N");
+c$.applyLeftMouse = Clazz.defineMethod(c$, "applyLeftMouse",
+function(modifiers){
+return ((modifiers & 28) == 0) ? (modifiers | 16) : modifiers;
+}, "~N");
+Clazz.overrideMethod(c$, "processKeyEvent",
+function(event){
+var e = event;
+switch (e.getID()) {
+case 401:
+this.keyPressed(e);
+break;
+case 402:
+this.keyReleased(e);
+break;
+case 400:
+this.keyTyped(e);
+break;
+}
+}, "~O");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Platform.js b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Platform.js
new file mode 100755
index 000000000000..9a4991dab4d3
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/awtjs2d/Platform.js
@@ -0,0 +1,288 @@
+Clazz.declarePackage("J.awtjs2d");
+Clazz.load(["J.api.GenericPlatform"], "J.awtjs2d.Platform", ["java.net.URL", "JU.AjaxURLStreamHandlerFactory", "$.Rdr", "J.api.Interface", "J.awtjs2d.Display", "$.Image", "$.JSFile", "$.JSFont", "$.Mouse"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.canvas = null;
+this.vwr = null;
+this.context = null;
+Clazz.instantialize(this, arguments);}, J.awtjs2d, "Platform", null, J.api.GenericPlatform);
+Clazz.overrideMethod(c$, "setViewer",
+function(vwr, canvas){
+{
+this.vwr = vwr;
+if (canvas == null) {
+canvas = document.createElement('canvas');
+this.context = canvas.getContext("2d");
+} else {
+this.context = canvas.getContext("2d");
+canvas.imgdata = this.context.getImageData(0, 0, canvas.width, canvas.height);
+canvas.buf8 = canvas.imgdata.data;
+}
+}this.canvas = canvas;
+try {
+java.net.URL.setURLStreamHandlerFactory( new JU.AjaxURLStreamHandlerFactory());
+} catch (e) {
+}
+}, "J.api.PlatformViewer,~O");
+Clazz.overrideMethod(c$, "isSingleThreaded",
+function(){
+return true;
+});
+Clazz.overrideMethod(c$, "getJsObjectInfo",
+function(jsObject, method, args){
+{
+return (method == null ? null : method == "localName" ? jsObject[0]["nodeName"] : args == null ? jsObject[0][method] : jsObject[0][method](args[0]));
+}}, "~A,~S,~A");
+Clazz.overrideMethod(c$, "isHeadless",
+function(){
+return false;
+});
+Clazz.overrideMethod(c$, "getMouseManager",
+function(privateKey, display){
+return new J.awtjs2d.Mouse(privateKey, this.vwr, display);
+}, "~N,~O");
+Clazz.overrideMethod(c$, "convertPointFromScreen",
+function(canvas, ptTemp){
+J.awtjs2d.Display.convertPointFromScreen(canvas, ptTemp);
+}, "~O,JU.P3");
+Clazz.overrideMethod(c$, "getFullScreenDimensions",
+function(canvas, widthHeight){
+J.awtjs2d.Display.getFullScreenDimensions(canvas, widthHeight);
+}, "~O,~A");
+Clazz.overrideMethod(c$, "getMenuPopup",
+function(menuStructure, type){
+var c = (type == 'j' ? "awtjs2d.JSJmolPopup" : "awtjs2d.JSModelKitPopup");
+var jmolpopup = J.api.Interface.getOption(c, this.vwr, "popup");
+try {
+if (jmolpopup != null) jmolpopup.jpiInitialize(this.vwr, menuStructure);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+c = "Exception creating " + c + ":" + e;
+System.out.println(c);
+return null;
+} else {
+throw e;
+}
+}
+return jmolpopup;
+}, "~S,~S");
+Clazz.overrideMethod(c$, "hasFocus",
+function(canvas){
+return J.awtjs2d.Display.hasFocus(canvas);
+}, "~O");
+Clazz.overrideMethod(c$, "prompt",
+function(label, data, list, asButtons){
+return J.awtjs2d.Display.prompt(label, data, list, asButtons);
+}, "~S,~S,~A,~B");
+Clazz.overrideMethod(c$, "renderScreenImage",
+function(context, size){
+J.awtjs2d.Display.renderScreenImage(this.vwr, context, size);
+}, "~O,~O");
+Clazz.overrideMethod(c$, "drawImage",
+function(context, canvas, x, y, width, height, isDTI){
+J.awtjs2d.Display.drawImage(context, canvas, x, y, width, height, isDTI);
+}, "~O,~O,~N,~N,~N,~N,~B");
+Clazz.overrideMethod(c$, "requestFocusInWindow",
+function(canvas){
+J.awtjs2d.Display.requestFocusInWindow(canvas);
+}, "~O");
+Clazz.overrideMethod(c$, "repaint",
+function(canvas){
+var jmol = null;
+{
+jmol = (self.Jmol && Jmol.repaint ? Jmol : null);
+}if (jmol != null) jmol.repaint((this.vwr).html5Applet, true);
+}, "~O");
+Clazz.overrideMethod(c$, "setTransparentCursor",
+function(canvas){
+}, "~O");
+Clazz.overrideMethod(c$, "setCursor",
+function(c, canvas){
+J.awtjs2d.Platform.Jmol().setCursor((this.vwr).html5Applet, c);
+}, "~N,~O");
+Clazz.overrideMethod(c$, "allocateRgbImage",
+function(windowWidth, windowHeight, pBuffer, windowSize, backgroundTransparent, isImageWrite){
+if (pBuffer == null) {
+pBuffer = this.grabPixels(null, 0, 0, null);
+{
+windowWidth = this.canvas.width;
+windowHeight = this.canvas.height;
+}}return J.awtjs2d.Image.allocateRgbImage(windowWidth, windowHeight, pBuffer, windowSize, backgroundTransparent, (isImageWrite ? null : this.canvas));
+}, "~N,~N,~A,~N,~B,~B");
+Clazz.overrideMethod(c$, "notifyEndOfRendering",
+function(){
+});
+Clazz.overrideMethod(c$, "disposeGraphics",
+function(gOffscreen){
+}, "~O");
+Clazz.overrideMethod(c$, "grabPixels",
+function(canvas, width, height, pixels){
+var context2d = null;
+var isWebGL = (canvas == null);
+{
+if(isWebGL) { this.canvas = canvas =
+Jmol.loadImage(this,"webgl",""
++System.currentTimeMillis(),this
+.vwr.html5Applet._canvas.toDataURL(),null,null); width =
+canvas.imageWidth; height = canvas.imageHeight;
+canvas.imageWidth = 0; }
+if (canvas.image && (width != canvas.width || height !=
+canvas.height)) Jmol.setCanvasImage(canvas, width, height);
+if (canvas.buf32) return canvas.buf32; context2d =
+canvas.getContext('2d');
+}var buf = J.awtjs2d.Image.grabPixels(context2d, width, height);
+{
+canvas.buf32 = buf;
+}if (isWebGL) for (var i = buf.length; --i >= 0; ) if (buf[i] == 0) buf[i] = -1;
+
+return buf;
+}, "~O,~N,~N,~A");
+Clazz.overrideMethod(c$, "drawImageToBuffer",
+function(gOffscreen, imageOffscreen, canvas, width, height, bgcolor){
+return this.grabPixels(canvas, width, height, null);
+}, "~O,~O,~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "getTextPixels",
+function(text, font3d, context, image, width, height, ascent){
+return J.awtjs2d.Image.getTextPixels(text, font3d, context, width, height, ascent);
+}, "~S,JU.Font,~O,~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "flushImage",
+function(imagePixelBuffer){
+}, "~O");
+Clazz.overrideMethod(c$, "getGraphics",
+function(canvas){
+{
+return (canvas == null ? this.context : canvas.getContext("2d"));
+}}, "~O");
+Clazz.overrideMethod(c$, "getImageHeight",
+function(canvas){
+return (canvas == null ? -1 : J.awtjs2d.Image.getHeight(canvas));
+}, "~O");
+Clazz.overrideMethod(c$, "getImageWidth",
+function(canvas){
+return (canvas == null ? -1 : J.awtjs2d.Image.getWidth(canvas));
+}, "~O");
+Clazz.overrideMethod(c$, "getStaticGraphics",
+function(image, backgroundTransparent){
+return this.getGraphics(image);
+}, "~O,~B");
+Clazz.overrideMethod(c$, "newBufferedImage",
+function(image, w, h){
+return J.awtjs2d.Platform.Jmol().getHiddenCanvas((this.vwr).html5Applet, "stereoImage", w, h);
+}, "~O,~N,~N");
+Clazz.overrideMethod(c$, "newOffScreenImage",
+function(w, h){
+return J.awtjs2d.Platform.Jmol().getHiddenCanvas((this.vwr).html5Applet, "textImage", w, h);
+}, "~N,~N");
+Clazz.overrideMethod(c$, "waitForDisplay",
+function(echoNameAndPath, zipBytes){
+return false;
+}, "~O,~O");
+Clazz.overrideMethod(c$, "createImage",
+function(name_path_bytes){
+var echoName = (name_path_bytes)[0];
+var path = (name_path_bytes)[1];
+var bytes = (name_path_bytes)[2];
+var vwr = this.vwr;
+var sc = (bytes == null ? vwr.getEvalContextAndHoldQueue(vwr.eval) : null);
+var f = null;
+{
+f = function(canvas, pathOrError) { vwr.loadImageData(canvas, pathOrError, echoName, sc) };
+}return J.awtjs2d.Platform.Jmol().loadImage(this, echoName, path, bytes, f);
+}, "~O");
+Clazz.overrideMethod(c$, "fontStringWidth",
+function(font, text){
+return J.awtjs2d.JSFont.stringWidth(font, this.context, text);
+}, "JU.Font,~S");
+Clazz.overrideMethod(c$, "getFontAscent",
+function(context){
+return J.awtjs2d.JSFont.getAscent(context);
+}, "~O");
+Clazz.overrideMethod(c$, "getFontDescent",
+function(context){
+return J.awtjs2d.JSFont.getDescent(context);
+}, "~O");
+Clazz.overrideMethod(c$, "getFontMetrics",
+function(font, context){
+return J.awtjs2d.JSFont.getFontMetrics(font, context == null ? this.context : context);
+}, "JU.Font,~O");
+Clazz.overrideMethod(c$, "newFont",
+function(fontFace, isBold, isItalic, fontSize){
+return J.awtjs2d.JSFont.newFont(fontFace, isBold, isItalic, fontSize, "px");
+}, "~S,~B,~B,~N");
+Clazz.overrideMethod(c$, "getDateFormat",
+function(isoType){
+{
+if (isoType == null) {
+} else if (isoType.indexOf("8824") >= 0) {
+var d = new Date();
+var x = d.toString().split(" ");
+var MM = "0" + (1 + d.getMonth()); MM = MM.substring(MM.length - 2);
+var dd = "0" + d.getDate(); dd = dd.substring(dd.length - 2);
+return x[3] + MM + dd + x[4].replace(/\:/g,"") + x[5].substring(3,6) + "'" + x[5].substring(6,8) + "'"
+} else if (isoType.indexOf("8601") >= 0){
+var d = new Date();
+var x = d.toString().split(" ");
+// Firefox now doing this?
+if (x.length == 1)
+return x;
+var MM = "0" + (1 + d.getMonth()); MM = MM.substring(MM.length - 2);
+var dd = "0" + d.getDate(); dd = dd.substring(dd.length - 2);
+return x[3] + '-' + MM + '-' + dd + 'T' + x[4]
+}
+return ("" + (new Date())).split(" (")[0];
+}}, "~S");
+Clazz.overrideMethod(c$, "newFile",
+function(name){
+return new J.awtjs2d.JSFile(name);
+}, "~S");
+Clazz.overrideMethod(c$, "getBufferedFileInputStream",
+function(name){
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "getURLContents",
+function(url, outputBytes, post, asString){
+return J.awtjs2d.Platform.getURLContentsStatic(url, outputBytes, post, asString);
+}, "java.net.URL,~A,~S,~B");
+c$.getURLContentsStatic = Clazz.defineMethod(c$, "getURLContentsStatic",
+function(url, outputBytes, post, asString){
+var ret = J.awtjs2d.JSFile.getURLContents(url, outputBytes, post);
+try {
+return (!asString ? ret : (typeof(ret)=='string') ? ret : Clazz.instanceOf(ret,"JU.SB") ? (ret).toString() : Clazz.instanceOf(ret,Array) ? String.instantialize(ret) : String.instantialize(JU.Rdr.getStreamAsBytes(ret, null)));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return "" + e;
+} else {
+throw e;
+}
+}
+}, "java.net.URL,~A,~S,~B");
+Clazz.overrideMethod(c$, "getLocalUrl",
+function(fileName){
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "getImageDialog",
+function(title, imageMap){
+return J.awtjs2d.Image.getImageDialog(this.vwr, title, imageMap);
+}, "~S,java.util.Map");
+c$.Jmol = Clazz.defineMethod(c$, "Jmol",
+function(){
+{
+return Jmol;
+}});
+Clazz.overrideMethod(c$, "forceAsyncLoad",
+function(filename){
+return J.awtjs2d.Platform.Jmol().isBinaryUrl(filename);
+}, "~S");
+Clazz.overrideMethod(c$, "getInChI",
+function(){
+return (J.awtjs2d.Platform.inchi == null ? (J.awtjs2d.Platform.inchi = J.api.Interface.getInterface("J.inchi.InChIJS", this.vwr, "platform")) : J.awtjs2d.Platform.inchi);
+});
+Clazz.overrideMethod(c$, "confirm",
+function(msg, msgNo){
+var ok = false;
+if (ok) return 0;
+if (msgNo != null) ok = false;
+return (ok ? 1 : 2);
+}, "~S,~S");
+c$.inchi = null;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspf.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspf.js
new file mode 100755
index 000000000000..fe4ec1518e7e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspf.js
@@ -0,0 +1,60 @@
+Clazz.declarePackage("J.bspt");
+Clazz.load(null, "J.bspt.Bspf", ["JU.AU", "J.bspt.Bspt"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.dimMax = 0;
+this.bspts = null;
+this.isValid = false;
+this.bsptsValid = null;
+this.cubeIterators = null;
+Clazz.instantialize(this, arguments);}, J.bspt, "Bspf", null);
+Clazz.makeConstructor(c$,
+function(dimMax){
+this.dimMax = dimMax;
+this.bspts = new Array(1);
+this.bsptsValid = Clazz.newBooleanArray(1, false);
+this.cubeIterators = new Array(0);
+}, "~N");
+Clazz.defineMethod(c$, "validateModel",
+function(i, isValid){
+this.bsptsValid[i] = isValid;
+}, "~N,~B");
+Clazz.defineMethod(c$, "isInitializedIndex",
+function(bsptIndex){
+return this.bspts.length > bsptIndex && this.bspts[bsptIndex] != null && this.bsptsValid[bsptIndex];
+}, "~N");
+Clazz.defineMethod(c$, "addTuple",
+function(bsptIndex, tuple){
+if (bsptIndex >= this.bspts.length) {
+this.bspts = JU.AU.arrayCopyObject(this.bspts, bsptIndex + 1);
+this.bsptsValid = JU.AU.arrayCopyBool(this.bsptsValid, bsptIndex + 1);
+}var bspt = this.bspts[bsptIndex];
+if (bspt == null) {
+bspt = this.bspts[bsptIndex] = new J.bspt.Bspt(this.dimMax, bsptIndex);
+}bspt.addTuple(tuple);
+}, "~N,JU.P3");
+Clazz.defineMethod(c$, "stats",
+function(){
+for (var i = 0; i < this.bspts.length; ++i) if (this.bspts[i] != null) this.bspts[i].stats();
+
+});
+Clazz.defineMethod(c$, "getCubeIterator",
+function(bsptIndex){
+if (bsptIndex < 0) return this.getNewCubeIterator(-1 - bsptIndex);
+if (bsptIndex >= this.cubeIterators.length) this.cubeIterators = JU.AU.arrayCopyObject(this.cubeIterators, bsptIndex + 1);
+if (this.cubeIterators[bsptIndex] == null && this.bspts[bsptIndex] != null) this.cubeIterators[bsptIndex] = this.getNewCubeIterator(bsptIndex);
+this.cubeIterators[bsptIndex].set(this.bspts[bsptIndex]);
+return this.cubeIterators[bsptIndex];
+}, "~N");
+Clazz.defineMethod(c$, "getNewCubeIterator",
+function(bsptIndex){
+return this.bspts[bsptIndex].allocateCubeIterator();
+}, "~N");
+Clazz.defineMethod(c$, "initialize",
+function(modelIndex, atoms, modelAtomBitSet){
+if (this.bspts[modelIndex] != null) this.bspts[modelIndex].reset();
+for (var i = modelAtomBitSet.nextSetBit(0); i >= 0; i = modelAtomBitSet.nextSetBit(i + 1)) this.addTuple(modelIndex, atoms[i]);
+
+this.bsptsValid[modelIndex] = true;
+}, "~N,~A,JU.BS");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspt.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspt.js
new file mode 100755
index 000000000000..f5f7d30e074e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Bspt.js
@@ -0,0 +1,32 @@
+Clazz.declarePackage("J.bspt");
+Clazz.load(null, "J.bspt.Bspt", ["J.bspt.CubeIterator", "$.Leaf"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.treeDepth = 0;
+this.dimMax = 0;
+this.index = 0;
+this.eleRoot = null;
+Clazz.instantialize(this, arguments);}, J.bspt, "Bspt", null);
+Clazz.makeConstructor(c$,
+function(dimMax, index){
+this.dimMax = dimMax;
+this.index = index;
+this.reset();
+}, "~N,~N");
+Clazz.defineMethod(c$, "reset",
+function(){
+this.eleRoot = new J.bspt.Leaf(this, null, 0);
+this.treeDepth = 1;
+});
+Clazz.defineMethod(c$, "addTuple",
+function(tuple){
+this.eleRoot = this.eleRoot.addTuple(0, tuple);
+}, "JU.T3");
+Clazz.defineMethod(c$, "stats",
+function(){
+});
+Clazz.defineMethod(c$, "allocateCubeIterator",
+function(){
+return new J.bspt.CubeIterator(this);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/CubeIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/CubeIterator.js
new file mode 100755
index 000000000000..182122379d98
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/CubeIterator.js
@@ -0,0 +1,103 @@
+Clazz.declarePackage("J.bspt");
+(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.bspt = null;
+this.stack = null;
+this.sp = 0;
+this.leafIndex = 0;
+this.leaf = null;
+this.radius = 0;
+this.cx = 0;
+this.cy = 0;
+this.cz = 0;
+this.dx = 0;
+this.dy = 0;
+this.dz = 0;
+this.tHemisphere = false;
+Clazz.instantialize(this, arguments);}, J.bspt, "CubeIterator", null);
+Clazz.makeConstructor(c$,
+function(bspt){
+this.set(bspt);
+}, "J.bspt.Bspt");
+Clazz.defineMethod(c$, "set",
+function(bspt){
+this.bspt = bspt;
+this.stack = new Array(bspt.treeDepth);
+}, "J.bspt.Bspt");
+Clazz.defineMethod(c$, "initialize",
+function(center, radius, hemisphereOnly){
+this.radius = radius;
+this.tHemisphere = false;
+this.cx = center.x;
+this.cy = center.y;
+this.cz = center.z;
+this.leaf = null;
+if (this.stack.length < this.bspt.treeDepth) this.set(this.bspt);
+this.stack[0] = this.bspt.eleRoot;
+this.sp = 1;
+this.findLeftLeaf();
+this.tHemisphere = hemisphereOnly;
+}, "JU.T3,~N,~B");
+Clazz.defineMethod(c$, "release",
+function(){
+this.set(this.bspt);
+});
+Clazz.defineMethod(c$, "hasMoreElements",
+function(){
+while (this.leaf != null) {
+for (; this.leafIndex < this.leaf.count; ++this.leafIndex) if (this.isWithinRadius(this.leaf.tuples[this.leafIndex])) return true;
+
+this.findLeftLeaf();
+}
+return false;
+});
+Clazz.defineMethod(c$, "nextElement",
+function(){
+return this.leaf.tuples[this.leafIndex++];
+});
+Clazz.defineMethod(c$, "foundDistance2",
+function(){
+return this.dx * this.dx + this.dy * this.dy + this.dz * this.dz;
+});
+Clazz.defineMethod(c$, "findLeftLeaf",
+function(){
+this.leaf = null;
+if (this.sp == 0) return;
+var ele = this.stack[--this.sp];
+while (Clazz.instanceOf(ele,"J.bspt.Node")) {
+var node = ele;
+var minValue;
+switch (node.dim) {
+case 0:
+minValue = this.cx;
+break;
+case 1:
+minValue = this.cy;
+break;
+case 2:
+default:
+minValue = this.cz;
+break;
+}
+var maxValue = minValue + this.radius;
+if (!this.tHemisphere || node.dim != 0) minValue -= this.radius;
+if (minValue <= node.maxLeft && maxValue >= node.minLeft) {
+if (maxValue >= node.minRight && minValue <= node.maxRight) {
+this.stack[this.sp++] = node.eleRight;
+}ele = node.eleLeft;
+} else if (maxValue >= node.minRight && minValue <= node.maxRight) {
+ele = node.eleRight;
+} else {
+if (this.sp == 0) return;
+ele = this.stack[--this.sp];
+}}
+this.leaf = ele;
+this.leafIndex = 0;
+});
+Clazz.defineMethod(c$, "isWithinRadius",
+function(t){
+this.dx = t.x - this.cx;
+return ((!this.tHemisphere || this.dx >= 0) && (this.dx = Math.abs(this.dx)) <= this.radius && (this.dy = Math.abs(t.y - this.cy)) <= this.radius && (this.dz = Math.abs(t.z - this.cz)) <= this.radius);
+}, "JU.T3");
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/Element.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Element.js
new file mode 100755
index 000000000000..a8df7f79b59d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Element.js
@@ -0,0 +1,8 @@
+Clazz.declarePackage("J.bspt");
+(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.bspt = null;
+this.count = 0;
+Clazz.instantialize(this, arguments);}, J.bspt, "Element", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/Leaf.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Leaf.js
new file mode 100755
index 000000000000..7fe1ed436301
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Leaf.js
@@ -0,0 +1,43 @@
+Clazz.declarePackage("J.bspt");
+Clazz.load(["J.bspt.Element"], "J.bspt.Leaf", ["J.bspt.Node"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.tuples = null;
+Clazz.instantialize(this, arguments);}, J.bspt, "Leaf", J.bspt.Element);
+Clazz.makeConstructor(c$,
+function(bspt, leaf, countToKeep){
+this.bspt = bspt;
+this.count = 0;
+this.tuples = new Array(2);
+if (leaf == null) return;
+for (var i = countToKeep; i < 2; ++i) {
+this.tuples[this.count++] = leaf.tuples[i];
+leaf.tuples[i] = null;
+}
+leaf.count = countToKeep;
+}, "J.bspt.Bspt,J.bspt.Leaf,~N");
+Clazz.defineMethod(c$, "sort",
+function(dim){
+for (var i = this.count; --i > 0; ) {
+var champion = this.tuples[i];
+var championValue = J.bspt.Node.getDimensionValue(champion, dim);
+for (var j = i; --j >= 0; ) {
+var challenger = this.tuples[j];
+var challengerValue = J.bspt.Node.getDimensionValue(challenger, dim);
+if (challengerValue > championValue) {
+this.tuples[i] = challenger;
+this.tuples[j] = champion;
+champion = challenger;
+championValue = challengerValue;
+}}
+}
+}, "~N");
+Clazz.overrideMethod(c$, "addTuple",
+function(level, tuple){
+if (this.count < 2) {
+this.tuples[this.count++] = tuple;
+return this;
+}var node = new J.bspt.Node(this.bspt, level, this);
+return node.addTuple(level, tuple);
+}, "~N,JU.T3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/Node.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Node.js
new file mode 100755
index 000000000000..5ffb3da63efe
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/Node.js
@@ -0,0 +1,72 @@
+Clazz.declarePackage("J.bspt");
+Clazz.load(["J.bspt.Element"], "J.bspt.Node", ["J.bspt.Leaf"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.dim = 0;
+this.minLeft = 0;
+this.maxLeft = 0;
+this.eleLeft = null;
+this.minRight = 0;
+this.maxRight = 0;
+this.eleRight = null;
+Clazz.instantialize(this, arguments);}, J.bspt, "Node", J.bspt.Element);
+Clazz.makeConstructor(c$,
+function(bspt, level, leafLeft){
+this.bspt = bspt;
+if (level == bspt.treeDepth) {
+bspt.treeDepth = level + 1;
+}if (leafLeft.count != 2) throw new NullPointerException();
+this.dim = level % bspt.dimMax;
+leafLeft.sort(this.dim);
+var leafRight = new J.bspt.Leaf(bspt, leafLeft, 1);
+this.minLeft = J.bspt.Node.getDimensionValue(leafLeft.tuples[0], this.dim);
+this.maxLeft = J.bspt.Node.getDimensionValue(leafLeft.tuples[leafLeft.count - 1], this.dim);
+this.minRight = J.bspt.Node.getDimensionValue(leafRight.tuples[0], this.dim);
+this.maxRight = J.bspt.Node.getDimensionValue(leafRight.tuples[leafRight.count - 1], this.dim);
+this.eleLeft = leafLeft;
+this.eleRight = leafRight;
+this.count = 2;
+}, "J.bspt.Bspt,~N,J.bspt.Leaf");
+Clazz.defineMethod(c$, "addTuple",
+function(level, tuple){
+var dimValue = J.bspt.Node.getDimensionValue(tuple, this.dim);
+++this.count;
+var addLeft;
+if (dimValue < this.maxLeft) {
+addLeft = true;
+} else if (dimValue > this.minRight) {
+addLeft = false;
+} else if (dimValue == this.maxLeft) {
+if (dimValue == this.minRight) {
+if (this.eleLeft.count < this.eleRight.count) addLeft = true;
+ else addLeft = false;
+} else {
+addLeft = true;
+}} else if (dimValue == this.minRight) {
+addLeft = false;
+} else {
+if (this.eleLeft.count < this.eleRight.count) addLeft = true;
+ else addLeft = false;
+}if (addLeft) {
+if (dimValue < this.minLeft) this.minLeft = dimValue;
+ else if (dimValue > this.maxLeft) this.maxLeft = dimValue;
+this.eleLeft = this.eleLeft.addTuple(level + 1, tuple);
+} else {
+if (dimValue < this.minRight) this.minRight = dimValue;
+ else if (dimValue > this.maxRight) this.maxRight = dimValue;
+this.eleRight = this.eleRight.addTuple(level + 1, tuple);
+}return this;
+}, "~N,JU.T3");
+c$.getDimensionValue = Clazz.defineMethod(c$, "getDimensionValue",
+function(pt, dim){
+if (pt == null) System.out.println("bspt.Node ???");
+switch (dim) {
+case 0:
+return pt.x;
+case 1:
+return pt.y;
+default:
+return pt.z;
+}
+}, "JU.T3,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/PointIterator.js b/config/plugins/visualizations/jmol/static/j2s/J/bspt/PointIterator.js
new file mode 100755
index 000000000000..89df94da09fe
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/PointIterator.js
@@ -0,0 +1,96 @@
+Clazz.declarePackage("J.bspt");
+Clazz.load(null, "J.bspt.PointIterator", ["JU.BS", "$.Lst", "$.P3", "J.bspt.Bspt", "JU.BSUtil", "$.Point3fi"], function(){
+var c$ = Clazz.declareType(J.bspt, "PointIterator", null);
+c$.withinDistPoints = Clazz.defineMethod(c$, "withinDistPoints",
+function(distance, pt, ap3, ap31, bsSelected, ret){
+var pts = new JU.Lst();
+var bspt = new J.bspt.Bspt(3, 0);
+var iter;
+if (pt != null && Float.isNaN(pt.x)) {
+var pt3 = new Array(ap3.length);
+var p;
+for (var i = pt3.length; --i >= 0; ) {
+var p3 = ap3[i];
+if (p3 == null) return 0;
+if (bsSelected == null) {
+p = new JU.Point3fi();
+p.setT(p3);
+p.i = i;
+pt3[i] = p;
+bspt.addTuple(p);
+} else {
+bspt.addTuple(p3);
+}}
+iter = bspt.allocateCubeIterator();
+var bsp;
+if (bsSelected != null) {
+bsp = JU.BS.newN(ap31.length);
+for (var i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1)) {
+iter.initialize(ap31[i], distance, false);
+var d2 = distance * distance;
+while (iter.hasMoreElements()) {
+if (iter.nextElement().distanceSquared(ap31[i]) <= d2) {
+bsp.set(i);
+break;
+}}
+}
+ret[0] = bsp;
+return 10;
+}bsp = JU.BSUtil.newBitSet2(0, ap3.length);
+for (var i = pt3.length; --i >= 0; ) {
+iter.initialize(p = pt3[i], distance, false);
+var d2 = distance * distance;
+var n = 0;
+while (iter.hasMoreElements()) {
+var pt2 = iter.nextElement();
+if (bsp.get(pt2.i) && pt2.distanceSquared(p) <= d2 && (++n > 1)) bsp.clear(pt2.i);
+}
+}
+for (var i = bsp.nextSetBit(0); i >= 0; i = bsp.nextSetBit(i + 1)) pts.addLast(JU.P3.newP(pt3[i]));
+
+ret[0] = pts;
+return 1073742001;
+}if (distance == 0) {
+if (ap31 == null) {
+var d2 = 3.4028235E38;
+var pt3 = null;
+for (var i = ap3.length; --i >= 0; ) {
+var pta = ap3[i];
+distance = pta.distanceSquared(pt);
+if (distance < d2) {
+pt3 = pta;
+d2 = distance;
+}}
+ret[0] = (pt3 == null ? "" : pt3);
+return (pt3 == null ? 4 : 134217751);
+}var ptsOut = Clazz.newIntArray (ap31.length, 0);
+for (var i = ptsOut.length; --i >= 0; ) {
+var d2 = 3.4028235E38;
+var imin = -1;
+pt = ap31[i];
+for (var j = ap3.length; --j >= 0; ) {
+var pta = ap3[j];
+distance = pta.distanceSquared(pt);
+if (distance < d2) {
+imin = j;
+d2 = distance;
+}}
+ptsOut[i] = imin;
+}
+ret[0] = ptsOut;
+return 1275068418;
+}for (var i = ap3.length; --i >= 0; ) bspt.addTuple(ap3[i]);
+
+iter = bspt.allocateCubeIterator();
+iter.initialize(pt, distance, false);
+var d2 = distance * distance;
+while (iter.hasMoreElements()) {
+var pt2 = iter.nextElement();
+if (pt2.distanceSquared(pt) <= d2) pts.addLast(pt2);
+}
+iter.release();
+ret[0] = pts;
+return 1073742001;
+}, "~N,JU.P3,~A,~A,JU.BS,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/bspt/package.html b/config/plugins/visualizations/jmol/static/j2s/J/bspt/package.html
new file mode 100755
index 000000000000..84a3f4c08c13
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/bspt/package.html
@@ -0,0 +1,45 @@
+
+
+
+
+
+
+
+
+ Provides Binary Space Partitioning Functionality to spacially
+ separate data structures in n-dimensions
+
+
+
+ For some useful background info, search the web for "bsp tree faq".
+
+
+
+
+
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/CBK.js b/config/plugins/visualizations/jmol/static/j2s/J/c/CBK.js
new file mode 100755
index 000000000000..154e8188c3c5
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/CBK.js
@@ -0,0 +1,47 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.CBK", ["JU.SB"], function(){
+var c$ = Clazz.declareType(J.c, "CBK", Enum);
+c$.getCallback = Clazz.defineMethod(c$, "getCallback",
+function(name){
+name = name.toUpperCase();
+var pt = name.indexOf("CALLBACK");
+if (pt > 0) name = name.substring(0, pt);
+for (var item, $item = 0, $$item = J.c.CBK.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.name().equalsIgnoreCase(name)) return item;
+
+return null;
+}, "~S");
+c$.getNameList = Clazz.defineMethod(c$, "getNameList",
+function(){
+if (J.c.CBK.nameList == null) {
+var names = new JU.SB();
+for (var item, $item = 0, $$item = J.c.CBK.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) names.append(item.name().toLowerCase()).append("Callback;");
+
+J.c.CBK.nameList = names.toString();
+}return J.c.CBK.nameList;
+});
+c$.nameList = null;
+Clazz.defineEnumConstant(c$, "ANIMFRAME", 0, []);
+Clazz.defineEnumConstant(c$, "APPLETREADY", 1, []);
+Clazz.defineEnumConstant(c$, "ATOMMOVED", 2, []);
+Clazz.defineEnumConstant(c$, "AUDIO", 3, []);
+Clazz.defineEnumConstant(c$, "CLICK", 4, []);
+Clazz.defineEnumConstant(c$, "DRAGDROP", 5, []);
+Clazz.defineEnumConstant(c$, "ECHO", 6, []);
+Clazz.defineEnumConstant(c$, "ERROR", 7, []);
+Clazz.defineEnumConstant(c$, "EVAL", 8, []);
+Clazz.defineEnumConstant(c$, "HOVER", 9, []);
+Clazz.defineEnumConstant(c$, "IMAGE", 10, []);
+Clazz.defineEnumConstant(c$, "LOADSTRUCT", 11, []);
+Clazz.defineEnumConstant(c$, "MEASURE", 12, []);
+Clazz.defineEnumConstant(c$, "MESSAGE", 13, []);
+Clazz.defineEnumConstant(c$, "MINIMIZATION", 14, []);
+Clazz.defineEnumConstant(c$, "MODELKIT", 15, []);
+Clazz.defineEnumConstant(c$, "PICK", 16, []);
+Clazz.defineEnumConstant(c$, "RESIZE", 17, []);
+Clazz.defineEnumConstant(c$, "SCRIPT", 18, []);
+Clazz.defineEnumConstant(c$, "SELECT", 19, []);
+Clazz.defineEnumConstant(c$, "SERVICE", 20, []);
+Clazz.defineEnumConstant(c$, "STRUCTUREMODIFIED", 21, []);
+Clazz.defineEnumConstant(c$, "SYNC", 22, []);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/FIL.js b/config/plugins/visualizations/jmol/static/j2s/J/c/FIL.js
new file mode 100755
index 000000000000..b51f61a55601
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/FIL.js
@@ -0,0 +1,20 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.FIL", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.code = 0;
+Clazz.instantialize(this, arguments);}, J.c, "FIL", Enum);
+Clazz.defineMethod(c$, "getCode",
+function(){
+return this.code;
+});
+Clazz.makeConstructor(c$,
+function(code){
+this.code = code;
+}, "~N");
+Clazz.defineEnumConstant(c$, "DELETED", 0, [5]);
+Clazz.defineEnumConstant(c$, "CREATED", 1, [3]);
+Clazz.defineEnumConstant(c$, "CREATING_MODELSET", 2, [2]);
+Clazz.defineEnumConstant(c$, "ZAPPED", 3, [0]);
+Clazz.defineEnumConstant(c$, "NOT_LOADED", 4, [-1]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/HB.js b/config/plugins/visualizations/jmol/static/j2s/J/c/HB.js
new file mode 100755
index 000000000000..2270b02eb009
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/HB.js
@@ -0,0 +1,57 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.HB", null, function(){
+var c$ = Clazz.declareType(J.c, "HB", Enum);
+c$.getType = Clazz.defineMethod(c$, "getType",
+function(atom){
+var group = atom.group;
+var considerHydrogens = !atom.isHetero();
+switch (atom.getElementNumber()) {
+default:
+return J.c.HB.NOT;
+case 1:
+if (atom.getCovalentBondCount() == 0) return J.c.HB.DONOR;
+var bonds = atom.bonds;
+if (bonds == null) return J.c.HB.NOT;
+switch (bonds[0].getOtherAtom(atom).getElementNumber()) {
+case 7:
+case 8:
+case 16:
+return J.c.HB.DONOR;
+}
+return J.c.HB.NOT;
+case 7:
+if (atom === group.getNitrogenAtom()) return J.c.HB.DONOR;
+if (group.groupID == 9) return J.c.HB.UNKNOWN;
+if (atom.getCovalentHydrogenCount() > 0) return J.c.HB.DONOR;
+if (considerHydrogens) return J.c.HB.ACCEPTOR;
+switch (group.groupID) {
+case 2:
+case 3:
+case 12:
+case 6:
+case 19:
+return J.c.HB.DONOR;
+}
+return J.c.HB.UNKNOWN;
+case 8:
+if (atom === group.getCarbonylOxygenAtom() || atom.getFormalCharge() == -1) return J.c.HB.ACCEPTOR;
+if (atom.getCovalentBondCount() == 0 || atom.getCovalentHydrogenCount() > 0) return J.c.HB.UNKNOWN;
+if (considerHydrogens) return J.c.HB.ACCEPTOR;
+switch (group.groupID) {
+case 4:
+case 7:
+return J.c.HB.ACCEPTOR;
+}
+return J.c.HB.UNKNOWN;
+}
+}, "JM.Atom");
+c$.isPossibleHBond = Clazz.defineMethod(c$, "isPossibleHBond",
+function(typeA, typeB){
+return (typeA === J.c.HB.NOT || typeB === J.c.HB.NOT ? false : typeA === J.c.HB.UNKNOWN || typeA !== typeB);
+}, "J.c.HB,J.c.HB");
+Clazz.defineEnumConstant(c$, "NOT", 0, []);
+Clazz.defineEnumConstant(c$, "ACCEPTOR", 1, []);
+Clazz.defineEnumConstant(c$, "DONOR", 2, []);
+Clazz.defineEnumConstant(c$, "UNKNOWN", 3, []);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/PAL.js b/config/plugins/visualizations/jmol/static/j2s/J/c/PAL.js
new file mode 100755
index 000000000000..f6148fc58af5
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/PAL.js
@@ -0,0 +1,93 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.PAL", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.$$name = null;
+this.id = 0;
+Clazz.instantialize(this, arguments);}, J.c, "PAL", Enum);
+Clazz.makeConstructor(c$,
+function(name, id){
+this.$$name = name;
+this.id = id;
+}, "~S,~N");
+c$.pidOf = Clazz.defineMethod(c$, "pidOf",
+function(value){
+return (Clazz.instanceOf(value,"J.c.PAL") ? (value).id : Clazz.instanceOf(value, Byte) ? (value).byteValue() : J.c.PAL.UNKNOWN.id);
+}, "~O");
+c$.isPaletteVariable = Clazz.defineMethod(c$, "isPaletteVariable",
+function(pid){
+return ((pid & 64) != 0);
+}, "~N");
+c$.getPalette = Clazz.defineMethod(c$, "getPalette",
+function(paletteName){
+if (paletteName.indexOf('_') < 0) for (var item, $item = 0, $$item = J.c.PAL.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (paletteName.equalsIgnoreCase(item.$$name)) return item;
+
+return (paletteName.indexOf("property_") == 0 ? J.c.PAL.PROPERTY : J.c.PAL.UNKNOWN);
+}, "~S");
+c$.getPaletteID = Clazz.defineMethod(c$, "getPaletteID",
+function(paletteName){
+if (paletteName.indexOf('_') < 0) for (var item, $item = 0, $$item = J.c.PAL.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (paletteName.equalsIgnoreCase(item.$$name)) return item.id;
+
+return (paletteName.indexOf("property_") == 0 ? J.c.PAL.PROPERTY.id : J.c.PAL.UNKNOWN.id);
+}, "~S");
+c$.getPaletteName = Clazz.defineMethod(c$, "getPaletteName",
+function(pid){
+for (var item, $item = 0, $$item = J.c.PAL.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.id == pid) return item.$$name;
+
+return null;
+}, "~N");
+c$.PALETTE_VOLATILE = 0x40;
+c$.PALETTE_NONE = 0;
+c$.PALETTE_CPK = 1;
+c$.PALETTE_PARTIAL_CHARGE = 2;
+c$.PALETTE_FORMAL_CHARGE = 3;
+c$.PALETTE_TEMP = 68;
+c$.PALETTE_FIXEDTEMP = 5;
+c$.PALETTE_SURFACE = 70;
+c$.PALETTE_STRUCTURE = 7;
+c$.PALETTE_AMINO = 8;
+c$.PALETTE_SHAPELY = 9;
+c$.PALETTE_CHAIN = 10;
+c$.PALETTE_GROUP = 75;
+c$.PALETTE_MONOMER = 76;
+c$.PALETTE_MOLECULE = 77;
+c$.PALETTE_ALTLOC = 14;
+c$.PALETTE_INSERTION = 15;
+c$.PALETTE_JMOL = 16;
+c$.PALETTE_RASMOL = 17;
+c$.PALETTE_TYPE = 18;
+c$.PALETTE_ENERGY = 19;
+c$.PALETTE_PROPERTY = 84;
+c$.PALETTE_VARIABLE = 85;
+c$.PALETTE_STRAIGHTNESS = 86;
+c$.PALETTE_POLYMER = 87;
+c$.PALETTE_NUCLEIC = 24;
+c$.argbsCpkRasmol = Clazz.newIntArray(-1, [16716947, 33554431, 50315467, 62005794, 83951360, 113821896, 126849023, 149946368, 165324064, 184549631, 203590434, 226525328, 249210144, 268412160, 285198386, 285277952, 343965840, 377520272, 411074704, 427851920, 452961536, 480586282, 497363498, 514140714, 598026794, 796950672, 899686640, 956278016, 1339729184]);
+c$.argbsCpk = Clazz.newIntArray(-1, [0xFFFF1493, 0xFFFFFFFF, 0xFFD9FFFF, 0xFFCC80FF, 0xFFC2FF00, 0xFFFFB5B5, 0xFF909090, 0xFF3050F8, 0xFFFF0D0D, 0xFF90E050, 0xFFB3E3F5, 0xFFAB5CF2, 0xFF8AFF00, 0xFFBFA6A6, 0xFFF0C8A0, 0xFFFF8000, 0xFFFFFF30, 0xFF1FF01F, 0xFF80D1E3, 0xFF8F40D4, 0xFF3DFF00, 0xFFE6E6E6, 0xFFBFC2C7, 0xFFA6A6AB, 0xFF8A99C7, 0xFF9C7AC7, 0xFFE06633, 0xFFF090A0, 0xFF50D050, 0xFFC88033, 0xFF7D80B0, 0xFFC28F8F, 0xFF668F8F, 0xFFBD80E3, 0xFFFFA100, 0xFFA62929, 0xFF5CB8D1, 0xFF702EB0, 0xFF00FF00, 0xFF94FFFF, 0xFF94E0E0, 0xFF73C2C9, 0xFF54B5B5, 0xFF3B9E9E, 0xFF248F8F, 0xFF0A7D8C, 0xFF006985, 0xFFC0C0C0, 0xFFFFD98F, 0xFFA67573, 0xFF668080, 0xFF9E63B5, 0xFFD47A00, 0xFF940094, 0xFF429EB0, 0xFF57178F, 0xFF00C900, 0xFF70D4FF, 0xFFFFFFC7, 0xFFD9FFC7, 0xFFC7FFC7, 0xFFA3FFC7, 0xFF8FFFC7, 0xFF61FFC7, 0xFF45FFC7, 0xFF30FFC7, 0xFF1FFFC7, 0xFF00FF9C, 0xFF00E675, 0xFF00D452, 0xFF00BF38, 0xFF00AB24, 0xFF4DC2FF, 0xFF4DA6FF, 0xFF2194D6, 0xFF267DAB, 0xFF266696, 0xFF175487, 0xFFD0D0E0, 0xFFFFD123, 0xFFB8B8D0, 0xFFA6544D, 0xFF575961, 0xFF9E4FB5, 0xFFAB5C00, 0xFF754F45, 0xFF428296, 0xFF420066, 0xFF007D00, 0xFF70ABFA, 0xFF00BAFF, 0xFF00A1FF, 0xFF008FFF, 0xFF0080FF, 0xFF006BFF, 0xFF545CF2, 0xFF785CE3, 0xFF8A4FE3, 0xFFA136D4, 0xFFB31FD4, 0xFFB31FBA, 0xFFB30DA6, 0xFFBD0D87, 0xFFC70066, 0xFFCC0059, 0xFFD1004F, 0xFFD90045, 0xFFE00038, 0xFFE6002E, 0xFFEB0026]);
+Clazz.defineEnumConstant(c$, "UNKNOWN", 0, [null, 0xFF]);
+Clazz.defineEnumConstant(c$, "NONE", 1, ["none", 0]);
+Clazz.defineEnumConstant(c$, "CPK", 2, ["cpk", 1]);
+Clazz.defineEnumConstant(c$, "PARTIAL_CHARGE", 3, ["partialcharge", 2]);
+Clazz.defineEnumConstant(c$, "FORMAL_CHARGE", 4, ["formalcharge", 3]);
+Clazz.defineEnumConstant(c$, "TEMP", 5, ["temperature", 68]);
+Clazz.defineEnumConstant(c$, "FIXEDTEMP", 6, ["fixedtemperature", 5]);
+Clazz.defineEnumConstant(c$, "SURFACE", 7, ["surfacedistance", 70]);
+Clazz.defineEnumConstant(c$, "STRUCTURE", 8, ["structure", 7]);
+Clazz.defineEnumConstant(c$, "AMINO", 9, ["amino", 8]);
+Clazz.defineEnumConstant(c$, "SHAPELY", 10, ["shapely", 9]);
+Clazz.defineEnumConstant(c$, "CHAIN", 11, ["chain", 10]);
+Clazz.defineEnumConstant(c$, "GROUP", 12, ["group", 75]);
+Clazz.defineEnumConstant(c$, "MONOMER", 13, ["monomer", 76]);
+Clazz.defineEnumConstant(c$, "MOLECULE", 14, ["molecule", 77]);
+Clazz.defineEnumConstant(c$, "ALTLOC", 15, ["altloc", 14]);
+Clazz.defineEnumConstant(c$, "INSERTION", 16, ["insertion", 15]);
+Clazz.defineEnumConstant(c$, "JMOL", 17, ["jmol", 16]);
+Clazz.defineEnumConstant(c$, "RASMOL", 18, ["rasmol", 17]);
+Clazz.defineEnumConstant(c$, "TYPE", 19, ["type", 18]);
+Clazz.defineEnumConstant(c$, "ENERGY", 20, ["energy", 19]);
+Clazz.defineEnumConstant(c$, "PROPERTY", 21, ["property", 84]);
+Clazz.defineEnumConstant(c$, "VARIABLE", 22, ["variable", 85]);
+Clazz.defineEnumConstant(c$, "STRAIGHTNESS", 23, ["straightness", 86]);
+Clazz.defineEnumConstant(c$, "POLYMER", 24, ["polymer", 87]);
+Clazz.defineEnumConstant(c$, "NUCLEIC", 25, ["nucleic", 24]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/STER.js b/config/plugins/visualizations/jmol/static/j2s/J/c/STER.js
new file mode 100755
index 000000000000..724b5207cfac
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/STER.js
@@ -0,0 +1,34 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.STER", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.$$name = null;
+this.$isBiColor = false;
+Clazz.instantialize(this, arguments);}, J.c, "STER", Enum);
+Clazz.makeConstructor(c$,
+function(name, isBiColor){
+this.$$name = name;
+this.$isBiColor = isBiColor;
+}, "~S,~B");
+Clazz.defineMethod(c$, "getName",
+function(){
+return this.$$name;
+});
+Clazz.defineMethod(c$, "isBiColor",
+function(){
+return this.$isBiColor;
+});
+c$.getStereoMode = Clazz.defineMethod(c$, "getStereoMode",
+function(id){
+for (var item, $item = 0, $$item = J.c.STER.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (item.$$name.equalsIgnoreCase(id)) return item;
+
+return null;
+}, "~S");
+Clazz.defineEnumConstant(c$, "NONE", 0, ["OFF", false]);
+Clazz.defineEnumConstant(c$, "DOUBLE", 1, ["", false]);
+Clazz.defineEnumConstant(c$, "REDCYAN", 2, ["REDCYAN", true]);
+Clazz.defineEnumConstant(c$, "REDBLUE", 3, ["REDBLUE", true]);
+Clazz.defineEnumConstant(c$, "REDGREEN", 4, ["REDGREEN", true]);
+Clazz.defineEnumConstant(c$, "DTI", 5, ["DTI", false]);
+Clazz.defineEnumConstant(c$, "CUSTOM", 6, ["", true]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/STR.js b/config/plugins/visualizations/jmol/static/j2s/J/c/STR.js
new file mode 100755
index 000000000000..29a7a4c29f8e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/STR.js
@@ -0,0 +1,47 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.STR", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.id = 0;
+this.color = 0;
+Clazz.instantialize(this, arguments);}, J.c, "STR", Enum);
+Clazz.makeConstructor(c$,
+function(id, color){
+this.id = id;
+this.color = color;
+}, "~N,~N");
+Clazz.defineMethod(c$, "getId",
+function(){
+return this.id;
+});
+Clazz.defineMethod(c$, "getColor",
+function(){
+return this.color;
+});
+c$.getProteinStructureType = Clazz.defineMethod(c$, "getProteinStructureType",
+function(name){
+for (var item, $item = 0, $$item = J.c.STR.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (name.equalsIgnoreCase(item.name())) return (item.isProtein() ? item : J.c.STR.NOT);
+
+return J.c.STR.NOT;
+}, "~S");
+Clazz.defineMethod(c$, "getBioStructureTypeName",
+function(isGeneric){
+return (this.id < 0 ? "" : isGeneric && this.isProtein() ? "protein" : this.name());
+}, "~B");
+Clazz.defineMethod(c$, "isProtein",
+function(){
+return this.id >= 0 && this.id <= 3 || this.id >= 7;
+});
+Clazz.defineEnumConstant(c$, "NOT", 0, [-1, 0xFF808080]);
+Clazz.defineEnumConstant(c$, "NONE", 1, [0, 0xFFFFFFFF]);
+Clazz.defineEnumConstant(c$, "TURN", 2, [1, 0xFF6080FF]);
+Clazz.defineEnumConstant(c$, "SHEET", 3, [2, 0xFFFFC800]);
+Clazz.defineEnumConstant(c$, "HELIX", 4, [3, 0xFFFF0080]);
+Clazz.defineEnumConstant(c$, "DNA", 5, [4, 0xFFAE00FE]);
+Clazz.defineEnumConstant(c$, "RNA", 6, [5, 0xFFFD0162]);
+Clazz.defineEnumConstant(c$, "CARBOHYDRATE", 7, [6, 0xFFA6A6FA]);
+Clazz.defineEnumConstant(c$, "HELIX310", 8, [7, 0xFFA00080]);
+Clazz.defineEnumConstant(c$, "HELIXALPHA", 9, [8, 0xFFFF0080]);
+Clazz.defineEnumConstant(c$, "HELIXPI", 10, [9, 0xFF600080]);
+Clazz.defineEnumConstant(c$, "ANNOTATION", 11, [-2, 0]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/c/VDW.js b/config/plugins/visualizations/jmol/static/j2s/J/c/VDW.js
new file mode 100755
index 000000000000..d76b1c88defc
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/c/VDW.js
@@ -0,0 +1,47 @@
+Clazz.declarePackage("J.c");
+Clazz.load(["java.lang.Enum"], "J.c.VDW", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.pt = 0;
+this.type = null;
+this.type2 = null;
+Clazz.instantialize(this, arguments);}, J.c, "VDW", Enum);
+Clazz.makeConstructor(c$,
+function(pt, type, type2){
+this.pt = pt;
+this.type = type;
+this.type2 = type2;
+}, "~N,~S,~S");
+Clazz.defineMethod(c$, "getVdwLabel",
+function(){
+return (this.type == null ? this.type2 : this.type);
+});
+c$.getVdwType = Clazz.defineMethod(c$, "getVdwType",
+function(label){
+if (label != null) for (var item, $item = 0, $$item = J.c.VDW.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (label.equalsIgnoreCase(item.type)) return item;
+
+return null;
+}, "~S");
+c$.getVdwType2 = Clazz.defineMethod(c$, "getVdwType2",
+function(label){
+if (label != null) for (var item, $item = 0, $$item = J.c.VDW.values(); $item < $$item.length && ((item = $$item[$item]) || true); $item++) if (label.equalsIgnoreCase(item.type2)) return item;
+
+return null;
+}, "~S");
+Clazz.defineEnumConstant(c$, "JMOL", 0, [0, "Jmol", null]);
+Clazz.defineEnumConstant(c$, "BABEL", 1, [1, "Babel", null]);
+Clazz.defineEnumConstant(c$, "RASMOL", 2, [2, "RasMol", null]);
+Clazz.defineEnumConstant(c$, "BABEL21", 3, [3, "Babel21", null]);
+Clazz.defineEnumConstant(c$, "AUTO_JMOL", 4, [0, null, "Jmol"]);
+Clazz.defineEnumConstant(c$, "AUTO_BABEL", 5, [1, null, "Babel"]);
+Clazz.defineEnumConstant(c$, "AUTO_RASMOL", 6, [2, null, "RasMol"]);
+Clazz.defineEnumConstant(c$, "AUTO", 7, [0, "Auto", null]);
+Clazz.defineEnumConstant(c$, "USER", 8, [-1, "User", null]);
+Clazz.defineEnumConstant(c$, "ADPMAX", 9, [-1, null, "adpmax"]);
+Clazz.defineEnumConstant(c$, "ADPMIN", 10, [-1, null, "adpmin"]);
+Clazz.defineEnumConstant(c$, "HYDRO", 11, [-1, null, "hydrophobic"]);
+Clazz.defineEnumConstant(c$, "BONDING", 12, [-1, null, "bondingradius"]);
+Clazz.defineEnumConstant(c$, "TEMP", 13, [-1, null, "temperature"]);
+Clazz.defineEnumConstant(c$, "NOJMOL", 14, [-1, null, null]);
+Clazz.defineEnumConstant(c$, "NADA", 15, [-1, null, null]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/console/GenericConsole.js b/config/plugins/visualizations/jmol/static/j2s/J/console/GenericConsole.js
new file mode 100755
index 000000000000..59e674b1d686
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/console/GenericConsole.js
@@ -0,0 +1,404 @@
+Clazz.declarePackage("J.console");
+Clazz.load(["J.api.JmolAppConsoleInterface", "$.JmolCallbackListener", "java.util.Hashtable"], "J.console.GenericConsole", ["JU.PT", "J.c.CBK", "J.i18n.GT", "JS.T", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.input = null;
+this.output = null;
+this.vwr = null;
+this.menuMap = null;
+this.editButton = null;
+this.runButton = null;
+this.historyButton = null;
+this.stateButton = null;
+this.clearOutButton = null;
+this.clearInButton = null;
+this.loadButton = null;
+this.defaultMessage = null;
+this.label1 = null;
+this.nTab = 0;
+this.incompleteCmd = null;
+Clazz.instantialize(this, arguments);}, J.console, "GenericConsole", null, [J.api.JmolAppConsoleInterface, J.api.JmolCallbackListener]);
+Clazz.prepareFields (c$, function(){
+this.menuMap = new java.util.Hashtable();
+});
+Clazz.defineMethod(c$, "setViewer",
+function(vwr){
+this.vwr = vwr;
+if (J.console.GenericConsole.labels == null) {
+var l = new java.util.Hashtable();
+l.put("title", J.i18n.GT.$("Jmol Script Console") + " " + JV.Viewer.getJmolVersion());
+this.setupLabels(l);
+J.console.GenericConsole.labels = l;
+}}, "JV.Viewer");
+Clazz.defineMethod(c$, "addButton",
+function(b, label){
+b.addConsoleListener(this);
+this.menuMap.put(label, b);
+return b;
+}, "J.api.JmolAbstractButton,~S");
+Clazz.defineMethod(c$, "getLabel1",
+function(){
+return null;
+});
+Clazz.defineMethod(c$, "setupLabels",
+function(labels){
+labels.put("saveas", J.i18n.GT.$("&Save As..."));
+labels.put("file", J.i18n.GT.$("&File"));
+labels.put("close", J.i18n.GT.$("&Close"));
+this.setupLabels0(labels);
+}, "java.util.Map");
+Clazz.defineMethod(c$, "setupLabels0",
+function(labels){
+labels.put("help", J.i18n.GT.$("&Help"));
+labels.put("search", J.i18n.GT.$("&Search..."));
+labels.put("commands", J.i18n.GT.$("&Commands"));
+labels.put("functions", J.i18n.GT.$("Math &Functions"));
+labels.put("parameters", J.i18n.GT.$("Set &Parameters"));
+labels.put("more", J.i18n.GT.$("&More"));
+labels.put("Editor", J.i18n.GT.$("Editor"));
+labels.put("State", J.i18n.GT.$("State"));
+labels.put("Run", J.i18n.GT.$("Run"));
+labels.put("Clear Output", J.i18n.GT.$("Clear Output"));
+labels.put("Clear Input", J.i18n.GT.$("Clear Input"));
+labels.put("History", J.i18n.GT.$("History"));
+labels.put("Load", J.i18n.GT.$("Load"));
+labels.put("label1", J.i18n.GT.$("press CTRL-ENTER for new line or paste model data and press Load"));
+labels.put("default", J.i18n.GT.$("Messages will appear here. Enter commands in the box below. Click the console Help menu item for on-line help, which will appear in a new browser window."));
+}, "java.util.Map");
+Clazz.defineMethod(c$, "setLabels",
+function(){
+var doTranslate = J.i18n.GT.setDoTranslate(true);
+this.editButton = this.setButton("Editor");
+this.stateButton = this.setButton("State");
+this.runButton = this.setButton("Run");
+this.clearOutButton = this.setButton("Clear Output");
+this.clearInButton = this.setButton("Clear Input");
+this.historyButton = this.setButton("History");
+this.loadButton = this.setButton("Load");
+this.defaultMessage = J.console.GenericConsole.getLabel("default");
+this.setTitle();
+J.i18n.GT.setDoTranslate(doTranslate);
+});
+c$.getLabel = Clazz.defineMethod(c$, "getLabel",
+function(key){
+return J.console.GenericConsole.labels.get(key);
+}, "~S");
+Clazz.defineMethod(c$, "displayConsole",
+function(){
+this.layoutWindow(null);
+this.outputMsg(this.defaultMessage);
+});
+Clazz.defineMethod(c$, "updateLabels",
+function(){
+return;
+});
+Clazz.defineMethod(c$, "completeCommand",
+function(thisCmd){
+if (thisCmd.length == 0) return null;
+var strCommand = (this.nTab <= 0 || this.incompleteCmd == null ? thisCmd : this.incompleteCmd);
+this.incompleteCmd = strCommand;
+var splitCmd = J.console.GenericConsole.splitCommandLine(thisCmd);
+if (splitCmd == null) return null;
+var asCommand = splitCmd[2] == null;
+var inBrace = (splitCmd[3] != null);
+var notThis = splitCmd[asCommand ? 1 : 2];
+var s = splitCmd[1];
+if (notThis.length == 0) return null;
+var token = JS.T.getTokenFromName(s.trim().toLowerCase());
+var cmdtok = (token == null ? 0 : token.tok);
+var isSelect = JS.T.tokAttr(cmdtok, 12288);
+splitCmd = J.console.GenericConsole.splitCommandLine(strCommand);
+var cmd = null;
+if (!asCommand && (notThis.charAt(0) == '"' || notThis.charAt(0) == '\'')) {
+var q = notThis.charAt(0);
+notThis = JU.PT.trim(notThis, "\"\'");
+var stub = JU.PT.trim(splitCmd[2], "\"\'");
+cmd = this.nextFileName(stub, this.nTab);
+if (cmd != null) cmd = splitCmd[0] + splitCmd[1] + q + cmd + q;
+} else {
+var map = null;
+if (!asCommand) {
+notThis = s;
+if (inBrace || splitCmd[2].startsWith("$") || isSelect) {
+map = new java.util.Hashtable();
+this.vwr.getObjectMap(map, inBrace || isSelect ? '{' : splitCmd[2].startsWith("$") ? '$' : '0');
+}}cmd = JS.T.completeCommand(map, s.equalsIgnoreCase("set "), asCommand, asCommand ? splitCmd[1] : splitCmd[2], this.nTab);
+cmd = splitCmd[0] + (cmd == null ? notThis : asCommand ? cmd : splitCmd[1] + cmd);
+}return (cmd == null || cmd.equals(strCommand) ? null : cmd);
+}, "~S");
+Clazz.defineMethod(c$, "doAction",
+function(source){
+if (source === this.runButton) {
+this.execute(null);
+} else if (source === this.editButton) {
+this.vwr.getProperty("DATA_API", "scriptEditor", null);
+} else if (source === this.historyButton) {
+this.clearContent(this.vwr.getSetHistory(2147483647));
+} else if (source === this.stateButton) {
+this.clearContent(this.vwr.getStateInfo());
+} else if (source === this.clearInButton) {
+this.input.setText("");
+return;
+}if (source === this.clearOutButton) {
+this.output.setText("");
+return;
+}if (source === this.loadButton) {
+this.vwr.loadInlineAppend(this.input.getText(), false);
+return;
+}if (this.isMenuItem(source)) {
+this.execute((source).getName());
+return;
+}}, "~O");
+Clazz.defineMethod(c$, "execute",
+function(strCommand){
+var cmd = (strCommand == null ? this.input.getText() : strCommand);
+if (strCommand == null) this.input.setText(null);
+var strErrorMessage = this.vwr.script(cmd + "; ## GUI ##\u0001## EDITOR_IGNORE ##; ## GUI ##");
+if (strErrorMessage != null && !strErrorMessage.equals("pending")) this.outputMsg(strErrorMessage);
+}, "~S");
+Clazz.defineMethod(c$, "destroyConsole",
+function(){
+if (this.vwr.isApplet) this.vwr.getProperty("DATA_API", "getAppConsole", Boolean.FALSE);
+});
+c$.setAbstractButtonLabels = Clazz.defineMethod(c$, "setAbstractButtonLabels",
+function(menuMap, labels){
+for (var key, $key = menuMap.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) {
+var m = menuMap.get(key);
+var label = labels.get(key);
+if (key.indexOf("Tip") == key.length - 3) {
+m.setToolTipText(labels.get(key));
+} else {
+var mnemonic = J.console.GenericConsole.getMnemonic(label);
+if (mnemonic != ' ') m.setMnemonic(mnemonic);
+label = J.console.GenericConsole.getLabelWithoutMnemonic(label);
+m.setText(label);
+}}
+}, "java.util.Map,java.util.Map");
+c$.getLabelWithoutMnemonic = Clazz.defineMethod(c$, "getLabelWithoutMnemonic",
+function(label){
+if (label == null) {
+return null;
+}var index = label.indexOf('&');
+if (index == -1) {
+return label;
+}return label.substring(0, index) + ((index < label.length - 1) ? label.substring(index + 1) : "");
+}, "~S");
+c$.getMnemonic = Clazz.defineMethod(c$, "getMnemonic",
+function(label){
+if (label == null) {
+return ' ';
+}var index = label.indexOf('&');
+if ((index == -1) || (index == label.length - 1)) {
+return ' ';
+}return label.charAt(index + 1);
+}, "~S");
+c$.map = Clazz.defineMethod(c$, "map",
+function(button, key, label, menuMap){
+var mnemonic = J.console.GenericConsole.getMnemonic(label);
+if (mnemonic != ' ') (button).setMnemonic(mnemonic);
+if (menuMap != null) menuMap.put(key, button);
+}, "~O,~S,~S,java.util.Map");
+Clazz.overrideMethod(c$, "notifyEnabled",
+function(type){
+switch (type) {
+case J.c.CBK.ECHO:
+case J.c.CBK.MEASURE:
+case J.c.CBK.MESSAGE:
+case J.c.CBK.PICK:
+return true;
+case J.c.CBK.ANIMFRAME:
+case J.c.CBK.APPLETREADY:
+case J.c.CBK.ATOMMOVED:
+case J.c.CBK.AUDIO:
+case J.c.CBK.CLICK:
+case J.c.CBK.DRAGDROP:
+case J.c.CBK.ERROR:
+case J.c.CBK.EVAL:
+case J.c.CBK.HOVER:
+case J.c.CBK.IMAGE:
+case J.c.CBK.LOADSTRUCT:
+case J.c.CBK.MINIMIZATION:
+case J.c.CBK.MODELKIT:
+case J.c.CBK.SERVICE:
+case J.c.CBK.RESIZE:
+case J.c.CBK.SCRIPT:
+case J.c.CBK.SELECT:
+case J.c.CBK.STRUCTUREMODIFIED:
+case J.c.CBK.SYNC:
+break;
+}
+return false;
+}, "J.c.CBK");
+Clazz.overrideMethod(c$, "notifyCallback",
+function(type, data){
+var strInfo = (data == null || data[1] == null ? null : data[1].toString());
+switch (type) {
+case J.c.CBK.ECHO:
+this.sendConsoleEcho(strInfo);
+break;
+case J.c.CBK.MEASURE:
+var mystatus = data[3];
+if (mystatus.indexOf("Picked") >= 0 || mystatus.indexOf("Sequence") >= 0) this.sendConsoleMessage(strInfo);
+ else if (mystatus.indexOf("Completed") >= 0) this.sendConsoleEcho(strInfo);
+break;
+case J.c.CBK.MESSAGE:
+this.sendConsoleMessage(data == null ? null : strInfo);
+break;
+case J.c.CBK.PICK:
+this.sendConsoleMessage(strInfo);
+break;
+}
+}, "J.c.CBK,~A");
+Clazz.overrideMethod(c$, "getText",
+function(){
+return this.output.getText();
+});
+Clazz.overrideMethod(c$, "sendConsoleEcho",
+function(strEcho){
+if (strEcho == null) {
+this.updateLabels();
+this.outputMsg(null);
+strEcho = this.defaultMessage;
+} else if (strEcho.equals("\0")) {
+{
+Clazz.Console.clear();
+}strEcho = null;
+}this.outputMsg(strEcho);
+}, "~S");
+Clazz.defineMethod(c$, "outputMsg",
+function(message){
+var n = (message == null ? -1 : message.length);
+switch (n) {
+case -1:
+this.output.setText("");
+return;
+default:
+if (message.charAt(n - 1) == '\n') break;
+case 0:
+message += "\n";
+}
+this.output.append(message);
+}, "~S");
+Clazz.defineMethod(c$, "clearContent",
+function(text){
+this.output.setText(text);
+}, "~S");
+Clazz.overrideMethod(c$, "sendConsoleMessage",
+function(strInfo){
+if (strInfo != null && this.output.getText().startsWith(this.defaultMessage)) this.outputMsg(null);
+this.outputMsg(strInfo);
+}, "~S");
+Clazz.overrideMethod(c$, "setCallbackFunction",
+function(callbackType, callbackFunction){
+}, "~S,~S");
+Clazz.overrideMethod(c$, "zap",
+function(){
+});
+Clazz.defineMethod(c$, "recallCommand",
+function(up, pageUp){
+var cmd = this.vwr.getSetHistory(up ? -1 : 1);
+if (cmd != null) {
+cmd = this.trimGUI(cmd);
+this.input.setText(JU.PT.escUnicode(cmd));
+}}, "~B,~B");
+Clazz.defineMethod(c$, "trimGUI",
+function(cmd){
+var pt = cmd.indexOf("\u0001##");
+if (pt >= 0) cmd = cmd.substring(0, pt);
+pt = cmd.indexOf("; ## GUI ##");
+if (pt >= 0) cmd = cmd.substring(0, pt);
+return JU.PT.trim(cmd, "; ");
+}, "~S");
+Clazz.defineMethod(c$, "processKey",
+function(kcode, kid, isControlDown){
+var mode = 0;
+switch (kid) {
+case 401:
+switch (kcode) {
+case 9:
+var s = this.input.getText();
+if (s.endsWith("\n") || s.endsWith("\t")) return 0;
+mode = 1;
+if (this.input.getCaretPosition() == s.length) {
+var cmd = this.completeCommand(s);
+if (cmd != null) this.input.setText(JU.PT.escUnicode(cmd).$replace('\t', ' '));
+this.nTab++;
+return mode;
+}break;
+case 27:
+mode = 1;
+this.input.setText("");
+break;
+}
+this.nTab = 0;
+if (kcode == 10 && !isControlDown) {
+this.execute(null);
+return mode;
+}if (kcode == 38 || kcode == 40) {
+this.recallCommand(kcode == 38, false);
+return mode;
+}break;
+case 402:
+if (kcode == 10 && !isControlDown) return mode;
+break;
+}
+return mode | 2;
+}, "~N,~N,~B");
+c$.splitCommandLine = Clazz.defineMethod(c$, "splitCommandLine",
+function(cmd){
+var sout = new Array(4);
+var isEscaped1 = false;
+var isEscaped2 = false;
+var isEscaped = false;
+if (cmd.length == 0) return null;
+var ptQ = -1;
+var ptCmd = 0;
+var ptToken = 0;
+var nBrace = 0;
+var ch;
+for (var i = 0; i < cmd.length; i++) {
+switch ((ch = cmd.charAt(i)).charCodeAt(0)) {
+case 34:
+if (!isEscaped && !isEscaped1) {
+isEscaped2 = !isEscaped2;
+if (isEscaped2) ptQ = ptToken = i;
+}break;
+case 39:
+if (!isEscaped && !isEscaped2) {
+isEscaped1 = !isEscaped1;
+if (isEscaped1) ptQ = ptToken = i;
+}break;
+case 92:
+isEscaped = !isEscaped;
+continue;
+case 32:
+if (!isEscaped && !isEscaped1 && !isEscaped2) {
+ptToken = i + 1;
+ptQ = -1;
+}break;
+case 59:
+if (!isEscaped1 && !isEscaped2) {
+ptCmd = ptToken = i + 1;
+ptQ = -1;
+nBrace = 0;
+}break;
+case 123:
+case 125:
+if (!isEscaped1 && !isEscaped2) {
+nBrace += (ch == '{' ? 1 : -1);
+ptToken = i + 1;
+ptQ = -1;
+}break;
+default:
+if (!isEscaped1 && !isEscaped2) ptQ = -1;
+}
+isEscaped = false;
+}
+sout[0] = cmd.substring(0, ptCmd);
+sout[1] = (ptToken == ptCmd ? cmd.substring(ptCmd) : cmd.substring(ptCmd, (ptToken > ptQ ? ptToken : ptQ)));
+sout[2] = (ptToken == ptCmd ? null : cmd.substring(ptToken));
+sout[3] = (nBrace > 0 ? "{" : null);
+return sout;
+}, "~S");
+c$.labels = null;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/console/GenericTextArea.js b/config/plugins/visualizations/jmol/static/j2s/J/console/GenericTextArea.js
new file mode 100755
index 000000000000..13398b6ee370
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/console/GenericTextArea.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.console");
+Clazz.declareInterface(J.console, "GenericTextArea");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/console/ImageDialog.js b/config/plugins/visualizations/jmol/static/j2s/J/console/ImageDialog.js
new file mode 100755
index 000000000000..abb13fd38716
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/console/ImageDialog.js
@@ -0,0 +1,158 @@
+Clazz.declarePackage("J.console");
+Clazz.load(["javax.swing.JDialog", "$.JPanel", "J.api.GenericImageDialog"], "J.console.ImageDialog", ["java.util.Hashtable", "JU.PT", "javax.swing.JMenuBar", ], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.menubar = null;
+this.image = null;
+this.vwr = null;
+this.canvas = null;
+this.$title = null;
+this.imageMap = null;
+this.console = null;
+if (!Clazz.isClassDefined("J.console.ImageDialog.ImageCanvas")) {
+J.console.ImageDialog.$ImageDialog$ImageCanvas$ ();
+}
+Clazz.instantialize(this, arguments);}, J.console, "ImageDialog", javax.swing.JDialog, [J.api.GenericImageDialog, java.awt.event.WindowListener, java.awt.event.ActionListener]);
+Clazz.makeConstructor(c$,
+function(vwr, title, imageMap){
+Clazz.superConstructor(this, J.console.ImageDialog, [Clazz.instanceOf(J.awt.Platform.getWindow(vwr.display),"javax.swing.JFrame") ? J.awt.Platform.getWindow(vwr.display) : null, title, false]);
+this.vwr = vwr;
+this.setResizable(false);
+this.console = vwr.getConsole();
+this.addWindowListener(this);
+this.$title = title;
+this.imageMap = imageMap;
+imageMap.put(title, this);
+var wrapper = new javax.swing.JPanel( new java.awt.BorderLayout());
+wrapper.setBackground( new java.awt.Color(255, 0, 0));
+this.canvas = Clazz.innerTypeInstance(J.console.ImageDialog.ImageCanvas, this, null);
+wrapper.add(this.canvas, "Center");
+var container = new javax.swing.JPanel();
+container.setLayout( new java.awt.BorderLayout());
+this.menubar = new javax.swing.JMenuBar();
+this.menubar.add(this.createMenu());
+this.setJMenuBar(this.menubar);
+container.add(wrapper, "Center");
+this.getContentPane().add(container);
+this.pack();
+this.setLocation(100, 100);
+this.setVisible(true);
+}, "JV.Viewer,~S,java.util.Map");
+Clazz.defineMethod(c$, "createMenu",
+function(){
+var itemKeys = JU.PT.getTokens("saveas close");
+this.vwr.getConsole();
+var menu = this.console.newJMenu("file");
+for (var i = 0; i < itemKeys.length; i++) {
+var item = itemKeys[i];
+var mi = this.createMenuItem(item);
+menu.add(mi);
+}
+menu.setVisible(true);
+return menu;
+});
+Clazz.defineMethod(c$, "createMenuItem",
+function(cmd){
+var mi = this.console.newJMenuItem(cmd);
+mi.setActionCommand(cmd);
+mi.addActionListener(this);
+mi.setVisible(true);
+return mi;
+}, "~S");
+Clazz.overrideMethod(c$, "actionPerformed",
+function(e){
+var cmd = e.getActionCommand();
+if (cmd.equals("close")) {
+this.closeMe();
+} else if (cmd.equals("saveas")) {
+this.saveAs();
+}}, "java.awt.event.ActionEvent");
+Clazz.defineMethod(c$, "saveAs",
+function(){
+(((Clazz.isClassDefined("J.console.ImageDialog$2") ? 0 : J.console.ImageDialog.$ImageDialog$2$ ()), Clazz.innerTypeInstance(J.console.ImageDialog$2, this, null, ((Clazz.isClassDefined("J.console.ImageDialog$1") ? 0 : J.console.ImageDialog.$ImageDialog$1$ ()), Clazz.innerTypeInstance(J.console.ImageDialog$1, this, null))))).start();
+});
+Clazz.overrideMethod(c$, "closeMe",
+function(){
+this.imageMap.remove(this.$title);
+this.dispose();
+});
+Clazz.overrideMethod(c$, "setImage",
+function(oimage){
+if (oimage == null) {
+this.closeMe();
+return;
+}var w = (oimage).getWidth(null);
+var h = (oimage).getHeight(null);
+this.image = new java.awt.image.BufferedImage(w, h, 1);
+var g = this.image.getGraphics();
+g.setColor(java.awt.Color.white);
+g.fillRect(0, 0, w, h);
+g.drawImage(oimage, 0, 0, null);
+g.dispose();
+this.setTitle(this.$title + " [" + w + " x " + h + "]");
+var d = new java.awt.Dimension(w, h);
+this.canvas.setPreferredSize(d);
+this.setBackground(java.awt.Color.WHITE);
+this.getContentPane().setBackground(java.awt.Color.WHITE);
+this.pack();
+}, "~O");
+Clazz.overrideMethod(c$, "windowClosed",
+function(e){
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowOpened",
+function(e){
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowClosing",
+function(e){
+this.closeMe();
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowIconified",
+function(e){
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowDeiconified",
+function(e){
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowActivated",
+function(e){
+}, "java.awt.event.WindowEvent");
+Clazz.overrideMethod(c$, "windowDeactivated",
+function(e){
+}, "java.awt.event.WindowEvent");
+c$.$ImageDialog$ImageCanvas$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+Clazz.instantialize(this, arguments);}, J.console.ImageDialog, "ImageCanvas", javax.swing.JPanel);
+Clazz.overrideMethod(c$, "paintComponent",
+function(g){
+System.out.println(this.b$["J.console.ImageDialog"].image.getClass().getName());
+g.setColor(java.awt.Color.white);
+g.fillRect(0, 0, this.b$["J.console.ImageDialog"].image.getWidth(null), this.b$["J.console.ImageDialog"].image.getHeight(null));
+g.drawImage(this.b$["J.console.ImageDialog"].image, 0, 0, null);
+}, "java.awt.Graphics");
+/*eoif4*/})();
+};
+c$.$ImageDialog$2$=function(){
+/*if5*/;(function(){
+var c$ = Clazz.declareAnonymous(J.console, "ImageDialog$2", Thread);
+/*eoif5*/})();
+};
+c$.$ImageDialog$1$=function(){
+/*if5*/;(function(){
+var c$ = Clazz.declareAnonymous(J.console, "ImageDialog$1", null, Runnable);
+Clazz.overrideMethod(c$, "run",
+function(){
+var params = new java.util.Hashtable();
+var fname = this.b$["J.console.ImageDialog"].vwr.dialogAsk("Save Image", "jmol.png", params);
+if (fname == null) return;
+var type = "PNG";
+var pt = fname.lastIndexOf(".");
+if (pt > 0) type = fname.substring(pt + 1).toUpperCase();
+params.put("fileName", fname);
+params.put("type", type);
+params.put("image", this.b$["J.console.ImageDialog"].image);
+this.b$["J.console.ImageDialog"].vwr.showString(this.b$["J.console.ImageDialog"].vwr.processWriteOrCapture(params), false);
+});
+/*eoif5*/})();
+};
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/consolejs/AppletConsole.js b/config/plugins/visualizations/jmol/static/j2s/J/consolejs/AppletConsole.js
new file mode 100755
index 000000000000..df4ac5a04e16
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/consolejs/AppletConsole.js
@@ -0,0 +1,365 @@
+Clazz.declarePackage("J.consolejs");
+Clazz.load(["J.console.GenericConsole"], "J.consolejs.AppletConsole", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.jsConsole = null;
+Clazz.instantialize(this, arguments);}, J.consolejs, "AppletConsole", J.console.GenericConsole);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.consolejs.AppletConsole, []);
+});
+Clazz.overrideMethod(c$, "start",
+function(vwr){
+this.setViewer(vwr);
+this.setLabels();
+this.displayConsole();
+}, "JV.Viewer");
+Clazz.overrideMethod(c$, "layoutWindow",
+function(enabledButtons){
+{
+this.jsConsole = new Jmol.Console.JSConsole(this);
+}this.setTitle();
+}, "~S");
+Clazz.overrideMethod(c$, "setTitle",
+function(){
+if (this.jsConsole != null) this.jsConsole.setTitle(J.console.GenericConsole.getLabel("title"));
+});
+Clazz.overrideMethod(c$, "setVisible",
+function(visible){
+this.jsConsole.setVisible(visible);
+}, "~B");
+Clazz.overrideMethod(c$, "setButton",
+function(text){
+{
+return new Jmol.Console.Button(text);
+}}, "~S");
+Clazz.overrideMethod(c$, "dispose",
+function(){
+this.setVisible(false);
+});
+Clazz.overrideMethod(c$, "isMenuItem",
+function(source){
+return false;
+}, "~O");
+Clazz.overrideMethod(c$, "getScriptEditor",
+function(){
+return null;
+});
+Clazz.overrideMethod(c$, "nextFileName",
+function(stub, nTab){
+return null;
+}, "~S,~N");
+Clazz.overrideMethod(c$, "newJMenu",
+function(key){
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "newJMenuItem",
+function(key){
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "regainFocus",
+function(){
+});
+{
+{
+;Jmol.Console = {
+buttons:{},
+buttonWidth:100,
+click:function(id) {
+Jmol.Console.buttons[id].console.appletConsole.doAction(Jmol.Console.buttons[id]);
+}
+}
+Jmol.consoleGetImageDialog = function(vwr, title, imageMap) {
+// JmolObjectInterface
+return new Jmol.Console.Image(vwr, title, imageMap);
+}
+Jmol.Console.Image = function(vwr, title, imageMap) {
+// page designer may indicate one of three divs for images on the page:
+// _Image_app_holder for IMAGE command by itself (current app image)
+// _Image__holder for IMAGE ID "xxx" ... or IMAGE "xxx"
+// where cleaning is with .replace(/\W/g,"_")
+// _Image_holder for all images not identified as above
+// if a page div is not identified, then the image will be placed in a new floating div
+this.vwr = vwr;
+this.title = title;
+this.imageMap = imageMap;
+this.applet = vwr.html5Applet;
+var id = this.applet._id + "_Image";
+this.id = id + "_" + (title == "" ? "app" : title).replace(/\W/g,"_");
+var jqobj = Jmol._$(this.id + "_holder");
+if (!jqobj[0] && (jqobj = Jmol._$(id + "_holder"))[0])
+this.id = id;
+if (jqobj[0])
+this.div = jqobj;
+else
+Jmol.Console.createDOM(this, '');
+System.out.println("image " + this.id + " created");
+var obj = imageMap.get(this.id);
+if (obj)
+obj.closeMe();
+imageMap.put(this.id, this);
+imageMap.put(title, this);
+}
+Jmol.Console.Image.setCanvas = function(obj, canvas) {
+// this method can be customized as desired
+// it puts the canvas into a holder div
+Jmol.$append(Jmol._$(obj.id + "_holder"), canvas);
+Jmol.$html(obj.id + "_title", " close " + obj.title + " [" + canvas.width + " x " + canvas.height + "]
");
+}
+Jmol.Console.Image.closeImage = function(obj) {
+// this method can be customized as desired
+obj.imageMap.remove(obj.title);
+obj.imageMap.remove(obj.id);
+if (obj.div) {
+Jmol.$remove(obj.cid);
+} else {
+obj.dragBind(false);
+Jmol.$remove(obj.id);
+}
+}
+Jmol.Console.Image.prototype.setImage = function(canvas) {
+// called by Jmol asynchronously after image is loaded
+if (this.cid)
+Jmol.$remove(this.cid);
+var c = document.createElement("canvas");
+c.width = canvas.width;
+c.height = canvas.height;
+var cdx = c.getContext("2d");
+if (canvas.buf32) {
+// image buffer from current view
+// (note that buf32.length will be the same as buf8.length when images are antialiased)
+var imgData = cdx.getImageData(0, 0, c.width, c.height);
+var buf8 = imgData.data;
+var buf32 = canvas.buf32;
+var n = buf8.length >> 2;
+for (var i = 0, j = 0; i < n; i++) {
+buf8[j++] = (buf32[i] >> 16) & 0xFF;
+buf8[j++] = (buf32[i] >> 8) & 0xFF;
+buf8[j++] = buf32[i] & 0xFF;
+buf8[j++] = 0xFF;
+}
+cdx.putImageData(imgData, 0, 0);
+} else {
+// asynchronous load of image from file
+cdx.drawImage(canvas,0,0);
+}
+this.cid = c.id = this.id + "_image";
+Jmol.Console.Image.setCanvas(this, c);
+}
+Jmol.Console.Image.prototype.closeMe = function() {
+// called by Jmol
+Jmol.Console.Image.closeImage(this);
+}
+Jmol.Swing.setDraggable(Jmol.Console.Image);
+Jmol.Console.createDOM = function(obj, s, userConsole) {
+var id = obj.id;
+Jmol.Console.buttons[id] = obj;
+s = s.replace(/\$ID/g,id);
+if (userConsole && userConsole[0]) {
+Jmol.$html(userConsole,s);
+} else {
+Jmol.$after("body", s);
+obj.setContainer(Jmol._$(id));
+obj.setPosition();
+obj.dragBind(true);
+}
+}
+Jmol.Console.JSConsole = function(appletConsole) {
+this.applet = appletConsole.vwr.html5Applet;
+var id = this.id = this.applet._id+"_console";
+var console = this;
+console.appletConsole = appletConsole;
+console.input = appletConsole.input = new Jmol.Console.Input(console);
+console.output = appletConsole.output = new Jmol.Console.Output(console);
+// check to see if the user already has a div on the page with id such as "jmolApplet0_console"
+var userConsole = Jmol.$("#" + id);
+// set up this.appletConsole.input, this.appletconsole.output
+// set up buttons, which are already made by this time:
+// I would prefer NOT to use jQueryUI for this - just simple buttons with simple actions
+// create and insert HTML code
+var s = ''
+var w = 600, h = 362;
+if (userConsole[0]) {
+var dims = Jmol.$getSize(userConsole);
+if (dims[0] == 0)
+Jmol.$setSize(userConsole, w, h);
+w = dims[0] || w;
+h = dims[1] || h;
+} else {
+s = '' + s + '';
+}
+Jmol.Console.createDOM(this, s, userConsole);
+var setBtn = function(console, btn) {
+btn.console = console;
+btn.id = id + "_" + btn.label.replace(/\s/g,"_");
+Jmol.Console.buttons[btn.id] = btn;
+return btn.html();
+}
+s = setBtn(console, appletConsole.runButton)
++ setBtn(console, appletConsole.loadButton)
++ setBtn(console, appletConsole.clearInButton)
++ setBtn(console, appletConsole.clearOutButton)
++ setBtn(console, appletConsole.historyButton)
++ setBtn(console, appletConsole.stateButton);
+Jmol.$html(id + "_buttondiv", s);
+s = "";
+if (!userConsole[0])
+s += " close";
+s += " help";
+Jmol.$html(id + "_label1", s);
+if (userConsole[0]) {
+// leaves a little slop for margins
+w = w - 10;
+h = (h - Jmol.$getSize(id + "_label1")[1] - Jmol.$getSize(id + "_buttondiv")[1] - 20)/3;
+} else {
+w = w - 10;
+h = (h - 62)/3;
+}
+Jmol.$html(id + "_inputdiv", '');
+Jmol.$html(id + "_outputdiv", '');
+Jmol.Cache.setDragDrop(this.applet, "console_output");
+Jmol.Cache.setDragDrop(this.applet, "console_input");
+Jmol.$bind("#" + id + "_input", "keydown keypress keyup", function(event) { console.input.keyEvent(event) });
+Jmol.$bind("#" + id + "_input", "mousedown touchstart", function(event) { console.ignoreMouse=true });
+Jmol.$bind("#" + id + "_output", "mousedown touchstart", function(event) { console.ignoreMouse=true });
+console.setButton = function(text) {
+return new Jmol.Console.Button(this, text);
+}
+console.setVisible = function(b) {
+if (b)
+this.container.show();
+else
+this.container.hide();
+this.dragBind(b);
+}
+console.setTitle = function(title) {
+//Jmol.$html(this.id + "_title", title);
+}
+console.setVisible(false);
+}
+Jmol.Swing.setDraggable(Jmol.Console.JSConsole);
+Jmol.Console.Input = function(console) {
+this.console = console;
+this.id = console.id + "_input";
+// something like this....
+this.getText = function() {
+return Jmol.$val(this.id);
+}
+this.setText = function(text) {
+if (text == null)
+text = "";
+Jmol.$val(this.id, text);
+}
+this.keyEvent = function(ev) {
+// chrome/safari
+// for left paren:
+// keyCode which key originalEvent.keyIdentifier
+// keydown 57 57 - U+0039
+// keypress 40 40 - Down // why Down??
+//
+// for down arrow
+// keydown 40 40 - Down
+// ff, msie
+// for left paren:
+// keyCode which key originalEvent.keyIdentifier
+// keydown 57 57 ( -
+// keypress 0 40 ( -
+//
+// for down arrow
+// keydown 40 40 Down -
+// in all cases: normal keys (as well as backspace[8] and delete[46]) are keydown keypress keyup
+// special keys just keydown keyup
+// keyup is only once when repeated; same as keydown
+// ff/msie delivers key, chrome/safari does not
+// chrome/safari has "feature" that keyIdentifier for "(" is reported as "Down" and similar issues for many other keys
+//System.out.println(ev.type + " key:" + (!ev.key) + " keyCode:" + ev.keyCode + " which:" + ev.which + " " + ev.key + "--" + ev.originalEvent.keyIdentifier);
+var mode;
+var type = ev.type;
+var isCtrl = ev.ctrlKey;
+var kcode = ev.keyCode;
+if (kcode == 13)
+kcode=10;
+// keycode is deprecated, but is essential still
+if (type == "keyup") {
+mode = (kcode == 38 || kcode == 40 ? 1 : this.console.appletConsole.processKey(kcode, 402, isCtrl));
+if ((mode & 1) == 1)
+ev.preventDefault();
+return;
+}
+// includes keypress and keydown
+// only assign "key" for keydown, as keypress gives erroneous identifier in chrome/safari
+var isKeydown = (type == "keydown");
+var key = (isKeydown ? (ev.key || ev.originalEvent.keyIdentifier) : "");
+switch (kcode) {
+case 38: // up-arrow, possibly
+case 40: // down-arrow, possibly
+// must be keydown, not keypress to be arrow key
+if (!isKeydown)
+kcode = 0;
+break;
+case 8: // bs
+case 9: // tab
+case 10: // CR
+case 27: // esc
+// only these are of interest to Jmol
+break;
+default:
+kcode = 0; // nothing to report
+}
+mode = this.console.appletConsole.processKey(kcode, 401, isCtrl);
+if (isCtrl && kcode == 10)
+this.setText(this.getText() + "\n")
+if (mode == 0 && ev.keyCode == 9) {
+var me = this;
+setTimeout(function(){me.setText(me.getText() + "\t"); Jmol.$focus(me.id)},10);
+}
+// ignore if...
+if ((mode & 1) == 1 // Jmol has handled the key press
+|| key == "Up" || key == "Down" // up and down arrows
+|| isKeydown && ev.keyCode != 8 && ev.keyCode < 32 // a special character other than backspace, when keyDown
+) {
+ev.preventDefault();
+}
+}
+this.getCaretPosition = function() {
+var el = Jmol._$(this.id)[0];
+if('selectionStart' in el)
+return el.selectionStart;
+if(!('selection' in document))
+return 0;
+el.focus();
+var sel = document.selection.createRange();
+var len = document.selection.createRange().text.length;
+sel.moveStart('character', -el.value.length);
+return sel.text.length - len;
+}
+}
+Jmol.Console.Output = function(console) {
+this.id = console.id + "_output";
+this.getText = function() {
+return Jmol.$val(this.id);
+}
+this.setText = function(text) {
+if (text == null)
+text = "";
+Jmol.$val(this.id, text);
+}
+this.append = function(message, att) {
+this.setText(this.getText() + message);
+Jmol.$scrollTo(this.id, -1);
+}
+}
+Jmol.Console.Button = function(text) {
+this.label = text;
+}
+Jmol.Console.Button.prototype.addConsoleListener = function(appletConsole) {
+this.appletConsole = appletConsole;
+Jmol.Console.buttons[this.id] = this;
+}
+Jmol.Console.Button.prototype.html = function() {
+var s = ''
+return s;
+}
+;
+}}});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/consolejs/JSConsole.js b/config/plugins/visualizations/jmol/static/j2s/J/consolejs/JSConsole.js
new file mode 100755
index 000000000000..8ae96bafc80f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/consolejs/JSConsole.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.consolejs");
+Clazz.declareInterface(J.consolejs, "JSConsole");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dialog/Dialog.js b/config/plugins/visualizations/jmol/static/j2s/J/dialog/Dialog.js
new file mode 100755
index 000000000000..b3e40aabdbb1
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dialog/Dialog.js
@@ -0,0 +1,415 @@
+Clazz.declarePackage("J.dialog");
+Clazz.load(["javax.swing.JPanel", "javax.swing.event.ChangeListener", "javax.swing.filechooser.FileFilter", "J.api.JmolDialogInterface"], "J.dialog.Dialog", ["java.io.File", "javax.swing.JComboBox", "$.JFileChooser", "$.JOptionPane", "$.JSlider", "$.SwingUtilities", "$.UIManager", "javax.swing.border.TitledBorder", "J.dialog.FileChooser", "$.FilePreview", "J.i18n.GT", "JU.Logger", "JV.FileManager"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.extensions = null;
+this.choice = null;
+this.extension = null;
+this.qSliderJPEG = null;
+this.qSliderPNG = null;
+this.cb = null;
+this.qPanelJPEG = null;
+this.qPanelPNG = null;
+this.openPreview = null;
+this.initialFile = null;
+if (!Clazz.isClassDefined("J.dialog.Dialog.QualityListener")) {
+J.dialog.Dialog.$Dialog$QualityListener$ ();
+}
+if (!Clazz.isClassDefined("J.dialog.Dialog.ExportChoiceListener")) {
+J.dialog.Dialog.$Dialog$ExportChoiceListener$ ();
+}
+this.imageChoices = null;
+this.imageExtensions = null;
+this.outputFileName = null;
+this.dialogType = null;
+this.inputFileName = null;
+this.vwr = null;
+this.qualityJ = -1;
+this.qualityP = -1;
+this.imageType = null;
+Clazz.instantialize(this, arguments);}, J.dialog, "Dialog", javax.swing.JPanel, J.api.JmolDialogInterface);
+Clazz.prepareFields (c$, function(){
+this.extensions = new Array(10);
+this.imageChoices = Clazz.newArray(-1, ["JPEG", "PNG", "GIF", "PPM"]);
+this.imageExtensions = Clazz.newArray(-1, ["jpg", "png", "gif", "ppm"]);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.dialog.Dialog, []);
+});
+Clazz.overrideMethod(c$, "getOpenFileNameFromDialog",
+function(vwrOptions, vwr, fileName, jmolApp, windowName, allowAppend){
+if (J.dialog.Dialog.openChooser == null) {
+J.dialog.Dialog.openChooser = new J.dialog.FileChooser();
+var temp = javax.swing.UIManager.get("FileChooser.fileNameLabelText");
+javax.swing.UIManager.put("FileChooser.fileNameLabelText", J.i18n.GT.$("File or URL:"));
+J.dialog.Dialog.getXPlatformLook(J.dialog.Dialog.openChooser);
+javax.swing.UIManager.put("FileChooser.fileNameLabelText", temp);
+}if (this.openPreview == null && (vwr.isApplet || Boolean.$valueOf(System.getProperty("openFilePreview", "true")).booleanValue())) {
+this.openPreview = new J.dialog.FilePreview(vwr, J.dialog.Dialog.openChooser, allowAppend, vwrOptions);
+}if (jmolApp != null) {
+var dim = jmolApp.getHistoryWindowSize(windowName);
+if (dim != null) J.dialog.Dialog.openChooser.setDialogSize(dim);
+var loc = jmolApp.getHistoryWindowPosition(windowName);
+if (loc != null) J.dialog.Dialog.openChooser.setDialogLocation(loc);
+}J.dialog.Dialog.openChooser.resetChoosableFileFilters();
+if (this.openPreview != null) this.openPreview.setPreviewOptions(allowAppend);
+if (fileName != null) {
+var pt = fileName.lastIndexOf(".");
+var sType = fileName.substring(pt + 1);
+if (pt >= 0 && sType.length > 0) J.dialog.Dialog.openChooser.addChoosableFileFilter( new J.dialog.Dialog.TypeFilter(sType));
+if (fileName.indexOf(".") == 0) fileName = "Jmol" + fileName;
+if (fileName.length > 0) J.dialog.Dialog.openChooser.setSelectedFile( new java.io.File(fileName));
+}if (fileName == null || fileName.indexOf(":") < 0 && fileName.indexOf("/") != 0) {
+var dir = JV.FileManager.getLocalDirectory(vwr, true);
+J.dialog.Dialog.openChooser.setCurrentDirectory(dir);
+}var file = null;
+if (J.dialog.Dialog.openChooser.showOpenDialog(this) == 0) file = J.dialog.Dialog.openChooser.getSelectedFile();
+if (file == null) return this.closePreview();
+if (jmolApp != null) jmolApp.addHistoryWindowInfo(windowName, J.dialog.Dialog.openChooser.getDialog(), null);
+var url = vwr.getLocalUrl(file.getAbsolutePath());
+if (url != null) {
+fileName = url;
+} else {
+JV.FileManager.setLocalPath(vwr, file.getParent(), true);
+fileName = file.getAbsolutePath();
+}if (fileName.startsWith("/")) fileName = "file://" + fileName;
+var doCartoons = (jmolApp == null || allowAppend && this.openPreview != null && this.openPreview.isCartoonsSelected());
+var doAppend = (allowAppend && !JV.FileManager.isScriptType(fileName) && this.openPreview != null && this.openPreview.isAppendSelected());
+this.closePreview();
+return (doCartoons ? "" : "#NOCARTOONS#;") + (doAppend ? "#APPEND#;" : "") + fileName;
+}, "java.util.Map,JV.Viewer,~S,J.api.JmolAppAPI,~S,~B");
+Clazz.defineMethod(c$, "closePreview",
+function(){
+if (this.openPreview != null) this.openPreview.doUpdatePreview(null);
+return null;
+});
+Clazz.overrideMethod(c$, "getSaveFileNameFromDialog",
+function(vwr, fileName, type){
+if (J.dialog.Dialog.saveChooser == null) {
+J.dialog.Dialog.saveChooser = new javax.swing.JFileChooser();
+J.dialog.Dialog.getXPlatformLook(J.dialog.Dialog.saveChooser);
+}J.dialog.Dialog.saveChooser.setCurrentDirectory(JV.FileManager.getLocalDirectory(vwr, true));
+var file = null;
+J.dialog.Dialog.saveChooser.resetChoosableFileFilters();
+if (fileName != null) {
+var pt = fileName.lastIndexOf(".");
+var sType = fileName.substring(pt + 1);
+if (pt >= 0 && sType.length > 0) J.dialog.Dialog.saveChooser.addChoosableFileFilter( new J.dialog.Dialog.TypeFilter(sType));
+if (fileName.equals("*")) fileName = vwr.getModelSetFileName();
+if (fileName.indexOf(".") == 0) fileName = "Jmol" + fileName;
+file = new java.io.File(fileName);
+}if (type != null) J.dialog.Dialog.saveChooser.addChoosableFileFilter( new J.dialog.Dialog.TypeFilter(type));
+J.dialog.Dialog.saveChooser.setSelectedFile(file);
+if ((file = this.showSaveDialog(this, J.dialog.Dialog.saveChooser, file)) == null) return null;
+JV.FileManager.setLocalPath(vwr, file.getParent(), true);
+return file.getAbsolutePath();
+}, "JV.Viewer,~S,~S");
+Clazz.overrideMethod(c$, "getImageFileNameFromDialog",
+function(vwr, fileName, type, imageChoices, imageExtensions, qualityJPG0, qualityPNG0){
+if (qualityJPG0 < 0 || qualityJPG0 > 100) qualityJPG0 = J.dialog.Dialog.qualityJPG;
+if (qualityPNG0 < 0) qualityPNG0 = J.dialog.Dialog.qualityPNG;
+if (qualityPNG0 > 9) qualityPNG0 = 2;
+J.dialog.Dialog.qualityJPG = qualityJPG0;
+J.dialog.Dialog.qualityPNG = qualityPNG0;
+if (this.extension == null) this.extension = "jpg";
+if (J.dialog.Dialog.imageChooser == null) {
+J.dialog.Dialog.imageChooser = new javax.swing.JFileChooser();
+J.dialog.Dialog.getXPlatformLook(J.dialog.Dialog.imageChooser);
+}J.dialog.Dialog.imageChooser.setCurrentDirectory(JV.FileManager.getLocalDirectory(vwr, true));
+J.dialog.Dialog.imageChooser.resetChoosableFileFilters();
+var file = null;
+if (fileName == null) {
+fileName = vwr.getModelSetFileName();
+if (fileName.indexOf("?") >= 0) fileName = fileName.substring(0, fileName.indexOf("?"));
+var pathName = J.dialog.Dialog.imageChooser.getCurrentDirectory().getPath();
+if (fileName != null && pathName != null) {
+var extensionStart = fileName.lastIndexOf('.');
+if (extensionStart != -1) {
+fileName = fileName.substring(0, extensionStart) + "." + this.extension;
+}file = new java.io.File(pathName, fileName);
+}} else {
+if (fileName.indexOf(".") == 0) fileName = "Jmol" + fileName;
+file = new java.io.File(fileName);
+type = fileName.substring(fileName.lastIndexOf(".") + 1);
+for (var i = 0; i < imageExtensions.length; i++) if (type.equals(imageChoices[i]) || type.toLowerCase().equals(imageExtensions[i])) {
+type = imageChoices[i];
+break;
+}
+}this.createExportPanel(imageChoices, imageExtensions, type);
+J.dialog.Dialog.imageChooser.setSelectedFile(this.initialFile = file);
+if ((file = this.showSaveDialog(this, J.dialog.Dialog.imageChooser, file)) == null) return null;
+J.dialog.Dialog.qualityJPG = this.qSliderJPEG.getValue();
+J.dialog.Dialog.qualityPNG = this.qSliderPNG.getValue();
+if (this.cb.getSelectedIndex() >= 0) J.dialog.Dialog.defaultChoice = this.cb.getSelectedIndex();
+JV.FileManager.setLocalPath(vwr, file.getParent(), true);
+return file.getAbsolutePath();
+}, "JV.Viewer,~S,~S,~A,~A,~N,~N");
+Clazz.defineMethod(c$, "createExportPanel",
+function(choices, extensions, type){
+J.dialog.Dialog.imageChooser.setAccessory(this);
+this.setLayout( new java.awt.BorderLayout());
+if (type == null || type.equals("JPG")) type = "JPEG";
+for (J.dialog.Dialog.defaultChoice = choices.length; --J.dialog.Dialog.defaultChoice >= 1; ) if (choices[J.dialog.Dialog.defaultChoice].equals(type)) break;
+
+this.extension = extensions[J.dialog.Dialog.defaultChoice];
+this.choice = choices[J.dialog.Dialog.defaultChoice];
+this.extensions = extensions;
+J.dialog.Dialog.imageChooser.resetChoosableFileFilters();
+J.dialog.Dialog.imageChooser.addChoosableFileFilter( new J.dialog.Dialog.TypeFilter(this.extension));
+var cbPanel = new javax.swing.JPanel();
+cbPanel.setLayout( new java.awt.FlowLayout());
+cbPanel.setBorder( new javax.swing.border.TitledBorder(J.i18n.GT.$("Image Type")));
+this.cb = new javax.swing.JComboBox();
+for (var i = 0; i < choices.length; i++) {
+this.cb.addItem(choices[i]);
+}
+cbPanel.add(this.cb);
+this.cb.setSelectedIndex(J.dialog.Dialog.defaultChoice);
+this.cb.addItemListener(Clazz.innerTypeInstance(J.dialog.Dialog.ExportChoiceListener, this, null));
+this.add(cbPanel, "North");
+var qPanel2 = new javax.swing.JPanel();
+qPanel2.setLayout( new java.awt.BorderLayout());
+this.qPanelJPEG = new javax.swing.JPanel();
+this.qPanelJPEG.setLayout( new java.awt.BorderLayout());
+this.qPanelJPEG.setBorder( new javax.swing.border.TitledBorder(J.i18n.GT.i(J.i18n.GT.$("JPEG Quality ({0})"), J.dialog.Dialog.qualityJPG)));
+this.qSliderJPEG = new javax.swing.JSlider(0, 50, 100, J.dialog.Dialog.qualityJPG);
+this.qSliderJPEG.putClientProperty("JSlider.isFilled", Boolean.TRUE);
+this.qSliderJPEG.setPaintTicks(true);
+this.qSliderJPEG.setMajorTickSpacing(10);
+this.qSliderJPEG.setPaintLabels(true);
+this.qSliderJPEG.addChangeListener(Clazz.innerTypeInstance(J.dialog.Dialog.QualityListener, this, null, true, this.qSliderJPEG));
+this.qPanelJPEG.add(this.qSliderJPEG, "South");
+qPanel2.add(this.qPanelJPEG, "North");
+this.qPanelPNG = new javax.swing.JPanel();
+this.qPanelPNG.setLayout( new java.awt.BorderLayout());
+this.qPanelPNG.setBorder( new javax.swing.border.TitledBorder(J.i18n.GT.i(J.i18n.GT.$("PNG Compression ({0})"), J.dialog.Dialog.qualityPNG)));
+this.qSliderPNG = new javax.swing.JSlider(0, 0, 9, J.dialog.Dialog.qualityPNG);
+this.qSliderPNG.putClientProperty("JSlider.isFilled", Boolean.TRUE);
+this.qSliderPNG.setPaintTicks(true);
+this.qSliderPNG.setMajorTickSpacing(2);
+this.qSliderPNG.setPaintLabels(true);
+this.qSliderPNG.addChangeListener(Clazz.innerTypeInstance(J.dialog.Dialog.QualityListener, this, null, false, this.qSliderPNG));
+this.qPanelPNG.add(this.qSliderPNG, "South");
+qPanel2.add(this.qPanelPNG, "South");
+this.add(qPanel2, "South");
+}, "~A,~A,~S");
+Clazz.overrideMethod(c$, "getType",
+function(){
+return this.choice;
+});
+Clazz.overrideMethod(c$, "getQuality",
+function(sType){
+return (sType.equals("JPEG") || sType.equals("JPG") ? J.dialog.Dialog.qualityJPG : sType.equals("PNG") ? J.dialog.Dialog.qualityPNG : -1);
+}, "~S");
+c$.doOverWrite = Clazz.defineMethod(c$, "doOverWrite",
+function(chooser, file){
+var options = Clazz.newArray(-1, [J.i18n.GT.$("Yes"), J.i18n.GT.$("No")]);
+var opt = javax.swing.JOptionPane.showOptionDialog(chooser, J.i18n.GT.o(J.i18n.GT.$("Do you want to overwrite file {0}?"), file.getAbsolutePath()), J.i18n.GT.$("Warning"), -1, 2, null, options, options[0]);
+return (opt == 0);
+}, "javax.swing.JFileChooser,java.io.File");
+Clazz.defineMethod(c$, "showSaveDialog",
+function(c, chooser, file){
+while (true) {
+if (chooser.showSaveDialog(c) != 0) return null;
+if (this.cb != null && this.cb.getSelectedIndex() >= 0) J.dialog.Dialog.defaultChoice = this.cb.getSelectedIndex();
+if ((file = chooser.getSelectedFile()) == null || !file.exists() || J.dialog.Dialog.doOverWrite(chooser, file)) return file;
+}
+}, "java.awt.Component,javax.swing.JFileChooser,java.io.File");
+Clazz.overrideMethod(c$, "setupUI",
+function(forceNewTranslation){
+if (forceNewTranslation || !J.dialog.Dialog.haveTranslations) J.dialog.Dialog.setupUIManager();
+J.dialog.Dialog.haveTranslations = true;
+}, "~B");
+c$.setupUIManager = Clazz.defineMethod(c$, "setupUIManager",
+function(){
+javax.swing.UIManager.put("FileChooser.acceptAllFileFilterText", J.i18n.GT.$("All Files"));
+javax.swing.UIManager.put("FileChooser.cancelButtonText", J.i18n.GT.$("Cancel"));
+javax.swing.UIManager.put("FileChooser.cancelButtonToolTipText", J.i18n.GT.$("Abort file chooser dialog"));
+javax.swing.UIManager.put("FileChooser.detailsViewButtonAccessibleName", J.i18n.GT.$("Details"));
+javax.swing.UIManager.put("FileChooser.detailsViewButtonToolTipText", J.i18n.GT.$("Details"));
+javax.swing.UIManager.put("FileChooser.directoryDescriptionText", J.i18n.GT.$("Directory"));
+javax.swing.UIManager.put("FileChooser.directoryOpenButtonText", J.i18n.GT.$("Open"));
+javax.swing.UIManager.put("FileChooser.directoryOpenButtonToolTipText", J.i18n.GT.$("Open selected directory"));
+javax.swing.UIManager.put("FileChooser.fileAttrHeaderText", J.i18n.GT.$("Attributes"));
+javax.swing.UIManager.put("FileChooser.fileDateHeaderText", J.i18n.GT.$("Modified"));
+javax.swing.UIManager.put("FileChooser.fileDescriptionText", J.i18n.GT.$("Generic File"));
+javax.swing.UIManager.put("FileChooser.fileNameHeaderText", J.i18n.GT.$("Name"));
+javax.swing.UIManager.put("FileChooser.fileNameLabelText", J.i18n.GT.$("File Name:"));
+javax.swing.UIManager.put("FileChooser.fileSizeHeaderText", J.i18n.GT.$("Size"));
+javax.swing.UIManager.put("FileChooser.filesOfTypeLabelText", J.i18n.GT.$("Files of Type:"));
+javax.swing.UIManager.put("FileChooser.fileTypeHeaderText", J.i18n.GT.$("Type"));
+javax.swing.UIManager.put("FileChooser.helpButtonText", J.i18n.GT.$("Help"));
+javax.swing.UIManager.put("FileChooser.helpButtonToolTipText", J.i18n.GT.$("FileChooser help"));
+javax.swing.UIManager.put("FileChooser.homeFolderAccessibleName", J.i18n.GT.$("Home"));
+javax.swing.UIManager.put("FileChooser.homeFolderToolTipText", J.i18n.GT.$("Home"));
+javax.swing.UIManager.put("FileChooser.listViewButtonAccessibleName", J.i18n.GT.$("List"));
+javax.swing.UIManager.put("FileChooser.listViewButtonToolTipText", J.i18n.GT.$("List"));
+javax.swing.UIManager.put("FileChooser.lookInLabelText", J.i18n.GT.$("Look In:"));
+javax.swing.UIManager.put("FileChooser.newFolderErrorText", J.i18n.GT.$("Error creating new folder"));
+javax.swing.UIManager.put("FileChooser.newFolderAccessibleName", J.i18n.GT.$("New Folder"));
+javax.swing.UIManager.put("FileChooser.newFolderToolTipText", J.i18n.GT.$("Create New Folder"));
+javax.swing.UIManager.put("FileChooser.openButtonText", J.i18n.GT.$("Open"));
+javax.swing.UIManager.put("FileChooser.openButtonToolTipText", J.i18n.GT.$("Open selected file"));
+javax.swing.UIManager.put("FileChooser.openDialogTitleText", J.i18n.GT.$("Open"));
+javax.swing.UIManager.put("FileChooser.saveButtonText", J.i18n.GT.$("Save"));
+javax.swing.UIManager.put("FileChooser.saveButtonToolTipText", J.i18n.GT.$("Save selected file"));
+javax.swing.UIManager.put("FileChooser.saveDialogTitleText", J.i18n.GT.$("Save"));
+javax.swing.UIManager.put("FileChooser.saveInLabelText", J.i18n.GT.$("Save In:"));
+javax.swing.UIManager.put("FileChooser.updateButtonText", J.i18n.GT.$("Update"));
+javax.swing.UIManager.put("FileChooser.updateButtonToolTipText", J.i18n.GT.$("Update directory listing"));
+javax.swing.UIManager.put("FileChooser.upFolderAccessibleName", J.i18n.GT.$("Up"));
+javax.swing.UIManager.put("FileChooser.upFolderToolTipText", J.i18n.GT.$("Up One Level"));
+javax.swing.UIManager.put("OptionPane.cancelButtonText", J.i18n.GT.$("Cancel"));
+javax.swing.UIManager.put("OptionPane.noButtonText", J.i18n.GT.$("No"));
+javax.swing.UIManager.put("OptionPane.okButtonText", J.i18n.GT.$("OK"));
+javax.swing.UIManager.put("OptionPane.yesButtonText", J.i18n.GT.$("Yes"));
+});
+c$.getXPlatformLook = Clazz.defineMethod(c$, "getXPlatformLook",
+function(fc){
+if (J.dialog.Dialog.isMac) {
+var lnf = javax.swing.UIManager.getLookAndFeel();
+if (lnf.isNativeLookAndFeel()) {
+try {
+javax.swing.UIManager.setLookAndFeel(javax.swing.UIManager.getCrossPlatformLookAndFeelClassName());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(e.getMessage());
+} else {
+throw e;
+}
+}
+fc.updateUI();
+try {
+javax.swing.UIManager.setLookAndFeel(lnf);
+} catch (e) {
+if (Clazz.exceptionOf(e,"javax.swing.UnsupportedLookAndFeelException")){
+System.out.println(e.getMessage());
+} else {
+throw e;
+}
+}
+}} else {
+fc.updateUI();
+}}, "javax.swing.JFileChooser");
+Clazz.overrideMethod(c$, "setImageInfo",
+function(qualityJPG, qualityPNG, imageType){
+this.qualityJ = qualityJPG;
+this.qualityP = qualityPNG;
+this.imageType = imageType;
+}, "~N,~N,~S");
+Clazz.overrideMethod(c$, "getFileNameFromDialog",
+function(v, dType, iFileName){
+this.vwr = v;
+this.dialogType = dType;
+this.inputFileName = iFileName;
+this.outputFileName = null;
+try {
+javax.swing.SwingUtilities.invokeAndWait(((Clazz.isClassDefined("J.dialog.Dialog$1") ? 0 : J.dialog.Dialog.$Dialog$1$ ()), Clazz.innerTypeInstance(J.dialog.Dialog$1, this, null)));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error(e.getMessage());
+} else {
+throw e;
+}
+}
+return this.outputFileName;
+}, "JV.Viewer,~S,~S");
+c$.$Dialog$QualityListener$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.isJPEG = false;
+this.slider = null;
+Clazz.instantialize(this, arguments);}, J.dialog.Dialog, "QualityListener", null, javax.swing.event.ChangeListener);
+Clazz.makeConstructor(c$,
+function(isJPEG, slider){
+this.isJPEG = isJPEG;
+this.slider = slider;
+}, "~B,javax.swing.JSlider");
+Clazz.overrideMethod(c$, "stateChanged",
+function(arg0){
+var value = this.slider.getValue();
+if (this.isJPEG) {
+J.dialog.Dialog.qualityJPG = value;
+this.b$["J.dialog.Dialog"].qPanelJPEG.setBorder( new javax.swing.border.TitledBorder(J.i18n.GT.i(J.i18n.GT.$("JPEG Quality ({0})"), value)));
+} else {
+J.dialog.Dialog.qualityPNG = value;
+this.b$["J.dialog.Dialog"].qPanelPNG.setBorder( new javax.swing.border.TitledBorder(J.i18n.GT.i(J.i18n.GT.$("PNG Quality ({0})"), value)));
+}}, "javax.swing.event.ChangeEvent");
+/*eoif4*/})();
+};
+c$.$Dialog$ExportChoiceListener$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+Clazz.instantialize(this, arguments);}, J.dialog.Dialog, "ExportChoiceListener", null, java.awt.event.ItemListener);
+Clazz.overrideMethod(c$, "itemStateChanged",
+function(e){
+var source = e.getSource();
+var selectedFile = J.dialog.Dialog.imageChooser.getSelectedFile();
+if (selectedFile == null) selectedFile = this.b$["J.dialog.Dialog"].initialFile;
+var newFile = null;
+var name;
+var newExt = this.b$["J.dialog.Dialog"].extensions[source.getSelectedIndex()];
+if ((name = selectedFile.getName()) != null && name.endsWith("." + this.b$["J.dialog.Dialog"].extension)) {
+name = name.substring(0, name.length - this.b$["J.dialog.Dialog"].extension.length);
+name += newExt;
+this.b$["J.dialog.Dialog"].initialFile = newFile = new java.io.File(selectedFile.getParent(), name);
+}this.b$["J.dialog.Dialog"].extension = newExt;
+J.dialog.Dialog.imageChooser.resetChoosableFileFilters();
+J.dialog.Dialog.imageChooser.addChoosableFileFilter( new J.dialog.Dialog.TypeFilter(this.b$["J.dialog.Dialog"].extension));
+if (newFile != null) J.dialog.Dialog.imageChooser.setSelectedFile(newFile);
+this.b$["J.dialog.Dialog"].choice = source.getSelectedItem();
+}, "java.awt.event.ItemEvent");
+/*eoif4*/})();
+};
+c$.$Dialog$1$=function(){
+/*if5*/;(function(){
+var c$ = Clazz.declareAnonymous(J.dialog, "Dialog$1", null, Runnable);
+Clazz.overrideMethod(c$, "run",
+function(){
+if (this.b$["J.dialog.Dialog"].dialogType.equals("Load")) {
+this.b$["J.dialog.Dialog"].outputFileName = this.b$["J.dialog.Dialog"].getOpenFileNameFromDialog(this.b$["J.dialog.Dialog"].vwr.vwrOptions, this.b$["J.dialog.Dialog"].vwr, this.b$["J.dialog.Dialog"].inputFileName, null, null, false);
+return;
+}if (this.b$["J.dialog.Dialog"].dialogType.equals("Save")) {
+this.b$["J.dialog.Dialog"].outputFileName = this.b$["J.dialog.Dialog"].getSaveFileNameFromDialog(this.b$["J.dialog.Dialog"].vwr, this.b$["J.dialog.Dialog"].inputFileName, null);
+return;
+}if (this.b$["J.dialog.Dialog"].dialogType.startsWith("Save Image")) {
+this.b$["J.dialog.Dialog"].outputFileName = this.b$["J.dialog.Dialog"].getImageFileNameFromDialog(this.b$["J.dialog.Dialog"].vwr, this.b$["J.dialog.Dialog"].inputFileName, this.b$["J.dialog.Dialog"].imageType, this.b$["J.dialog.Dialog"].imageChoices, this.b$["J.dialog.Dialog"].imageExtensions, this.b$["J.dialog.Dialog"].qualityJ, this.b$["J.dialog.Dialog"].qualityP);
+return;
+}this.b$["J.dialog.Dialog"].outputFileName = null;
+});
+/*eoif5*/})();
+};
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.thisType = null;
+Clazz.instantialize(this, arguments);}, J.dialog.Dialog, "TypeFilter", javax.swing.filechooser.FileFilter);
+Clazz.makeConstructor(c$,
+function(type){
+Clazz.superConstructor (this, J.dialog.Dialog.TypeFilter, []);
+this.thisType = type.toLowerCase();
+}, "~S");
+Clazz.overrideMethod(c$, "accept",
+function(f){
+if (f.isDirectory() || this.thisType == null) {
+return true;
+}var ext = f.getName();
+var pt = ext.lastIndexOf(".");
+return (pt >= 0 && ext.substring(pt + 1).toLowerCase().equals(this.thisType));
+}, "java.io.File");
+Clazz.overrideMethod(c$, "getDescription",
+function(){
+return this.thisType.toUpperCase() + " (*." + this.thisType + ")";
+});
+/*eoif3*/})();
+c$.defaultChoice = 0;
+c$.qualityJPG = 75;
+c$.qualityPNG = 2;
+c$.imageChooser = null;
+c$.saveChooser = null;
+c$.openChooser = null;
+c$.haveTranslations = false;
+c$.isMac = System.getProperty("os.name", "").startsWith("Mac");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dialog/FileChooser.js b/config/plugins/visualizations/jmol/static/j2s/J/dialog/FileChooser.js
new file mode 100755
index 000000000000..2a86d8be3ba0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dialog/FileChooser.js
@@ -0,0 +1,31 @@
+Clazz.declarePackage("J.dialog");
+Clazz.load(["javax.swing.JFileChooser"], "J.dialog.FileChooser", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.dialogLocation = null;
+this.dialogSize = null;
+this.$dialog = null;
+Clazz.instantialize(this, arguments);}, J.dialog, "FileChooser", javax.swing.JFileChooser);
+Clazz.defineMethod(c$, "createDialog",
+function(parent){
+this.$dialog = Clazz.superCall(this, J.dialog.FileChooser, "createDialog", [parent]);
+if (this.$dialog != null) {
+if (this.dialogLocation != null) {
+this.$dialog.setLocation(this.dialogLocation);
+}if (this.dialogSize != null) {
+this.$dialog.setSize(this.dialogSize);
+}}return this.$dialog;
+}, "java.awt.Component");
+Clazz.defineMethod(c$, "setDialogLocation",
+function(p){
+this.dialogLocation = p;
+}, "java.awt.Point");
+Clazz.defineMethod(c$, "setDialogSize",
+function(d){
+this.dialogSize = d;
+}, "java.awt.Dimension");
+Clazz.defineMethod(c$, "getDialog",
+function(){
+return this.$dialog;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dialog/FilePreview.js b/config/plugins/visualizations/jmol/static/j2s/J/dialog/FilePreview.js
new file mode 100755
index 000000000000..72f1fe9e38f4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dialog/FilePreview.js
@@ -0,0 +1,125 @@
+Clazz.declarePackage("J.dialog");
+Clazz.load(["java.beans.PropertyChangeListener", "javax.swing.JPanel", ], "J.dialog.FilePreview", ["JU.PT", "javax.swing.Box", "$.JCheckBox", "J.i18n.GT", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.active = null;
+this.append = null;
+this.cartoons = null;
+this.chooser = null;
+this.display = null;
+this.vwr = null;
+Clazz.instantialize(this, arguments);}, J.dialog, "FilePreview", javax.swing.JPanel, java.beans.PropertyChangeListener);
+Clazz.makeConstructor(c$,
+function(vwr, fileChooser, allowAppend, vwrOptions){
+Clazz.superConstructor(this, J.dialog.FilePreview);
+this.vwr = vwr;
+this.chooser = fileChooser;
+var box = javax.swing.Box.createVerticalBox();
+this.active = new javax.swing.JCheckBox(J.i18n.GT.$("Preview"), false);
+this.active.addActionListener(((Clazz.isClassDefined("J.dialog.FilePreview$1") ? 0 : J.dialog.FilePreview.$FilePreview$1$ ()), Clazz.innerTypeInstance(J.dialog.FilePreview$1, this, null)));
+box.add(this.active);
+this.display = new J.dialog.FilePreview.FPPanel(vwrOptions);
+this.display.setPreferredSize( new java.awt.Dimension(80, 80));
+this.display.setMinimumSize( new java.awt.Dimension(50, 50));
+box.add(this.display);
+if (allowAppend) {
+this.append = new javax.swing.JCheckBox(J.i18n.GT.$("Append models"), false);
+box.add(this.append);
+this.cartoons = new javax.swing.JCheckBox(J.i18n.GT.$("PDB cartoons"), J.dialog.FilePreview.pdbCartoonChecked);
+this.cartoons.addActionListener(((Clazz.isClassDefined("J.dialog.FilePreview$2") ? 0 : J.dialog.FilePreview.$FilePreview$2$ ()), Clazz.innerTypeInstance(J.dialog.FilePreview$2, this, null)));
+box.add(this.cartoons);
+}this.add(box);
+fileChooser.setAccessory(this);
+fileChooser.addPropertyChangeListener(this);
+}, "JV.Viewer,javax.swing.JFileChooser,~B,java.util.Map");
+Clazz.defineMethod(c$, "doPreviewAction",
+function(selected){
+this.doUpdatePreview(selected ? this.chooser.getSelectedFile() : null);
+}, "~B");
+Clazz.defineMethod(c$, "isAppendSelected",
+function(){
+return (this.append != null && this.append.isSelected());
+});
+Clazz.defineMethod(c$, "isCartoonsSelected",
+function(){
+return J.dialog.FilePreview.pdbCartoonChecked = (this.cartoons != null && this.cartoons.isSelected());
+});
+Clazz.overrideMethod(c$, "propertyChange",
+function(evt){
+if (this.active.isSelected()) {
+var prop = evt.getPropertyName();
+if ("SelectedFileChangedProperty".equals(prop)) {
+this.doUpdatePreview(evt.getNewValue());
+}}}, "java.beans.PropertyChangeEvent");
+Clazz.defineMethod(c$, "doUpdatePreview",
+function(file){
+var script;
+if (file == null) {
+script = "zap";
+} else {
+var fileName = file.getAbsolutePath();
+var url = this.vwr.getLocalUrl(fileName);
+if (url != null) fileName = url;
+fileName = fileName.$replace('\\', '/');
+script = " \"" + fileName + "\"";
+if (fileName.indexOf(".spt") >= 0) {
+script = "script " + script;
+} else {
+script = JU.PT.rep(this.display.vwr.getP("defaultdropscript"), "\"%FILE\"", script + " 1");
+script = JU.PT.rep(script, "%ALLOWCARTOONS", "" + (this.isCartoonsSelected() && !this.isAppendSelected()));
+System.out.println(script);
+}}this.display.vwr.evalStringQuiet(script);
+}, "java.io.File");
+Clazz.defineMethod(c$, "setPreviewOptions",
+function(TF){
+if (this.append == null) return;
+this.append.setVisible(TF);
+this.cartoons.setVisible(TF);
+}, "~B");
+c$.$FilePreview$1$=function(){
+/*if5*/;(function(){
+var c$ = Clazz.declareAnonymous(J.dialog, "FilePreview$1", null, java.awt.event.ActionListener);
+Clazz.overrideMethod(c$, "actionPerformed",
+function(e){
+this.b$["J.dialog.FilePreview"].doPreviewAction(this.b$["J.dialog.FilePreview"].active.isSelected());
+}, "java.awt.event.ActionEvent");
+/*eoif5*/})();
+};
+c$.$FilePreview$2$=function(){
+/*if5*/;(function(){
+var c$ = Clazz.declareAnonymous(J.dialog, "FilePreview$2", null, java.awt.event.ActionListener);
+Clazz.overrideMethod(c$, "actionPerformed",
+function(e){
+if (this.b$["J.dialog.FilePreview"].active.isSelected()) {
+this.b$["J.dialog.FilePreview"].doUpdatePreview(this.b$["J.dialog.FilePreview"].chooser.getSelectedFile());
+}}, "java.awt.event.ActionEvent");
+/*eoif5*/})();
+};
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.currentSize = null;
+Clazz.instantialize(this, arguments);}, J.dialog.FilePreview, "FPPanel", javax.swing.JPanel);
+Clazz.prepareFields (c$, function(){
+this.currentSize = new java.awt.Dimension();
+});
+Clazz.makeConstructor(c$,
+function(info){
+Clazz.superConstructor (this, J.dialog.FilePreview.FPPanel, []);
+info.put("previewOnly", Boolean.TRUE);
+var display = info.get("display");
+info.put("display", this);
+this.vwr = new JV.Viewer(info);
+info.put("display", display);
+}, "java.util.Map");
+Clazz.overrideMethod(c$, "paint",
+function(g){
+this.getSize(this.currentSize);
+this.vwr.setScreenDimension(this.currentSize.width, this.currentSize.height);
+var rectClip = new java.awt.Rectangle();
+g.getClipBounds(rectClip);
+this.vwr.renderScreenImage(g, this.currentSize.width, this.currentSize.height);
+}, "java.awt.Graphics");
+/*eoif3*/})();
+c$.pdbCartoonChecked = true;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dssx/AnnotationParser.js b/config/plugins/visualizations/jmol/static/j2s/J/dssx/AnnotationParser.js
new file mode 100755
index 000000000000..8c4e5414c9f4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dssx/AnnotationParser.js
@@ -0,0 +1,429 @@
+Clazz.declarePackage("J.dssx");
+Clazz.load(["J.api.JmolAnnotationParser"], "J.dssx.AnnotationParser", ["java.util.Hashtable", "JU.AU", "$.BS", "$.Lst", "$.PT", "$.SB", "JM.Group", "JM.BioResolver", "JS.SV", "JU.BSUtil", "$.Logger"], function(){
+var c$ = Clazz.declareType(J.dssx, "AnnotationParser", null, J.api.JmolAnnotationParser);
+/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "getAnnotationKVPairs",
+function(a, match, dotPath, sb, pre, showDetail, isMappingOnly, type){
+var map = a.getMap();
+if (map == null || map.isEmpty()) return;
+if (map.containsKey("_map")) map = map.get("_map").getMap();
+var detailKey = this.getDataKey(type);
+if (showDetail && map.containsKey(detailKey)) {
+if (match == null || dotPath.indexOf(match) >= 0) sb.append(map.get(detailKey).asString()).append("\n");
+return;
+}for (var e, $e = map.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var key = e.getKey();
+if (key.equals(detailKey)) continue;
+if (key.equals("metadata")) sb.append("\n");
+var val = e.getValue();
+if (val.tok == 6) {
+if (type == 1073742189 && !showDetail) {
+sb.append(key).append("\n");
+} else {
+this.getAnnotationKVPairs(val, match, (dotPath.length == 0 ? "" : dotPath + ".") + key, sb, (pre.length == 0 ? "" : pre + "\t") + key, showDetail, isMappingOnly, type);
+}} else {
+var s = val.asString();
+if (match == null || s.indexOf(match) >= 0 || pre.indexOf(match) >= 0 || key.indexOf(match) >= 0 || dotPath.indexOf(match) >= 0) {
+if (showDetail && isMappingOnly) continue;
+if (pre.length > 0) sb.append(pre).append("\t");
+sb.append(key).append("=");
+sb.append(s).append("\n");
+}}}
+}, "JS.SV,~S,~S,JU.SB,~S,~B,~B,~N");
+Clazz.defineMethod(c$, "getDataKey",
+function(type){
+switch (type) {
+case 1073741925:
+return "mappings";
+case 1073742189:
+return "outliers";
+}
+return null;
+}, "~N");
+Clazz.overrideMethod(c$, "catalogStructureUnits",
+function(viewer, map0, modelAtomIndices, resMap, object, modelMap){
+var note = "Use within(rna3d, TYPE) where TYPE is one of: ";
+var data = map0.getMap();
+if (data == null) return null;
+try {
+map0.mapPut("_map", JS.SV.newV(6, data));
+var list = new JU.Lst();
+var set = data.entrySet();
+var sv;
+var map;
+for (var e, $e = set.iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+sv = e.getValue();
+var structures = sv.getList();
+if (structures != null) {
+var key = e.getKey();
+note += "\"" + key + "\" ";
+var svPath = JS.SV.newS(key);
+for (var j = structures.size(); --j >= 0; ) {
+var struc = structures.get(j);
+map = struc.getMap();
+sv = map.get("units");
+map.put("_isres", JS.SV.vT);
+var units = (sv == null || sv.tok == 7 ? sv.getList() : sv.tok == 4 ? new JU.Lst() : null);
+if (units != null) {
+if (sv.tok == 4) {
+var svl = JU.PT.split(sv.asString(), ",");
+for (var i = svl.length; --i >= 0; ) units.addLast(JS.SV.newS(svl[i].trim()));
+
+}if (units.size() > 0) {
+var bsAtoms = new JU.BS();
+map.put("_atoms", JS.SV.getVariable(bsAtoms));
+map.put("_path", svPath);
+list.addLast(struc);
+for (var k = units.size(); --k >= 0; ) {
+this.catalogUnit(viewer, null, units.get(k).asString(), 0, bsAtoms, modelAtomIndices, resMap, null, modelMap);
+}
+}}}
+}}
+map0.mapPut("_list", JS.SV.newV(7, list));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.info(e + " while cataloging structures");
+return null;
+} else {
+throw e;
+}
+}
+return note;
+}, "JV.Viewer,JS.SV,~A,java.util.Map,~O,java.util.Map");
+Clazz.overrideMethod(c$, "catalogValidations",
+function(viewer, map0, modelAtomIndices, resMap, atomMap, modelMap){
+var data = map0.getMap();
+if (data == null) return null;
+var retProperties = new JU.Lst();
+var nModels = modelAtomIndices.length - 1;
+try {
+data = this.getMainItem(data).getMap();
+map0.mapPut("_map", JS.SV.newV(6, data));
+var list = new JU.Lst();
+map0.mapPut("_list", JS.SV.newV(7, list));
+var set = data.entrySet();
+var sv;
+var map;
+for (var e, $e = set.iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var floats = JU.AU.newFloat2(nModels);
+for (var m = nModels; --m >= 0; ) floats[m] = Clazz.newFloatArray (modelAtomIndices[m + 1] - modelAtomIndices[m], 0);
+
+sv = e.getValue();
+var outliers = sv.getList();
+if (outliers == null) {
+map = sv.getMap();
+if (map != null && (sv = map.get("outliers")) != null) outliers = sv.getList();
+}if (outliers != null) {
+var hasUnit = false;
+var key = e.getKey();
+var svPath = JS.SV.newS(key);
+var isRes = false;
+for (var j = outliers.size(); --j >= 0; ) {
+var out = outliers.get(j);
+map = out.getMap();
+sv = map.get("units");
+var svv = map.get("value");
+var val = (svv == null ? 1 : JS.SV.fValue(svv));
+var units = (val == 0 || sv == null || sv.tok == 7 ? sv.getList() : sv.tok == 4 ? new JU.Lst() : null);
+if (units != null) {
+if (sv.tok == 4) {
+var svl = JU.PT.split(sv.asString(), ",");
+for (var i = svl.length; --i >= 0; ) units.addLast(JS.SV.newS(svl[i].trim()));
+
+}if (units.size() > 0) {
+var bsAtoms = new JU.BS();
+map.put("_atoms", JS.SV.getVariable(bsAtoms));
+map.put("_path", svPath);
+hasUnit = true;
+list.addLast(out);
+for (var k = units.size(); --k >= 0; ) {
+var ret = this.catalogUnit(viewer, floats, units.get(k).asString(), val, bsAtoms, modelAtomIndices, resMap, atomMap, modelMap);
+if (ret) map.put("_isres", JS.SV.vT);
+isRes = new Boolean (isRes | ret).valueOf();
+}
+}}}
+if (hasUnit) {
+for (var m = nModels; --m >= 0; ) if (floats[m] != null) {
+retProperties.addLast(key);
+retProperties.addLast(floats[m]);
+retProperties.addLast(Integer.$valueOf(m));
+retProperties.addLast(Boolean.$valueOf(isRes));
+}
+}}}
+return retProperties;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.info(e + " while cataloging validations");
+return null;
+} else {
+throw e;
+}
+}
+}, "JV.Viewer,JS.SV,~A,java.util.Map,java.util.Map,java.util.Map");
+Clazz.defineMethod(c$, "getMainItem",
+function(data){
+for (var e, $e = data.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var key = e.getKey();
+if (!key.contains("metadata")) return e.getValue();
+}
+return null;
+}, "java.util.Map");
+Clazz.overrideMethod(c$, "initializeAnnotation",
+function(objAnn, type, modelIndex){
+var map = objAnn.getMap();
+var _list = map.get("_list");
+if (_list != null) return _list.getList();
+var dataKey = this.getDataKey(type);
+var main = this.getMainItem(map);
+map.put("_map", main);
+var noSingles = true;
+var _cat = new java.util.Hashtable();
+map.put("_cat", JS.SV.newV(6, _cat));
+var list = new JU.Lst();
+map.put("_list", _list = JS.SV.newV(7, list));
+for (var e, $e = main.getMap().entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
+var _dbName = e.getKey();
+var _dbMap = e.getValue();
+_cat.putAll(_dbMap.getMap());
+for (var e2, $e2 = _dbMap.getMap().entrySet().iterator (); $e2.hasNext()&& ((e2 = $e2.next ()) || true);) {
+var _domainName = e2.getKey();
+var _domainMap = e2.getValue();
+var _domainList = _domainMap.mapGet(dataKey);
+var _mapList = _domainList.getList();
+for (var i = _mapList.size(); --i >= 0; ) {
+var mapping = _mapList.get(i);
+list.addLast(mapping);
+var mmap = mapping.getMap();
+var _chain = mmap.get("chain_id");
+var start = mmap.get("start");
+var end = mmap.get("end");
+var res1 = 0;
+var res2 = 0;
+var rescode = "modelIndex=" + modelIndex + "&chain='" + _chain.value + "'";
+if (start != null && end != null) {
+res1 = start.mapGet("residue_number").intValue;
+res2 = end.mapGet("residue_number").intValue;
+rescode += "&seqid>=" + res1 + "&seqid<=" + res2;
+} else {
+res2 = 1;
+rescode += "&seqid>0";
+}var _atoms = (noSingles && res1 >= res2 ? JS.SV.getVariable( new JU.BS()) : _cat.get(rescode));
+if (_atoms == null) _cat.put(rescode, _atoms = JS.SV.newS(rescode));
+mmap.put("_atoms", _atoms);
+mmap.put("_path", JS.SV.newS(_dbName + "." + _domainName));
+mmap.put("domain", _domainMap);
+}
+}
+}
+return list;
+}, "JS.SV,~N,~N");
+Clazz.defineMethod(c$, "findAnnotationAtoms",
+function(vwr, name, _list, key, bs){
+if (_list == null) return;
+System.out.println("Checking " + name + " for " + key);
+var data = vwr.extractProperty(_list, "[" + key + "]", -1);
+var list = null;
+if (Clazz.instanceOf(data,"JU.Lst")) {
+list = data;
+} else if (Clazz.instanceOf(data,"JS.SV")) {
+list = (data).getList();
+}if (list == null) return;
+for (var i = 0, n = list.size(); i < n; i++) {
+var o = list.get(i);
+var mapping = (Clazz.instanceOf(o,"JS.SV") ? (o).getMap() : o);
+if (mapping == null) return;
+bs.or(this.setAnnotationAtoms(vwr, mapping, i));
+}
+}, "JV.Viewer,~S,JU.Lst,~S,JU.BS");
+Clazz.defineMethod(c$, "setAnnotationAtoms",
+function(vwr, mapping, i){
+var _atoms = mapping.get("_atoms");
+if (_atoms.tok != 10) {
+var bs2 = vwr.getAtomBitSet(_atoms.value);
+if (i >= 0) JU.Logger.info("#" + (i + 1) + " found " + bs2.cardinality() + " atoms for " + _atoms.value);
+_atoms.tok = 10;
+_atoms.value = bs2;
+}return _atoms.value;
+}, "JV.Viewer,java.util.Map,~N");
+Clazz.defineMethod(c$, "catalogUnit",
+function(viewer, vals, unitID, val, bsAtoms, modelAtomIndices, resMap, atomMap, modelMap){
+var s = JU.PT.split(unitID + (vals == null ? "||||" : "|||"), "|");
+if (s.length < 8 || s[1].length == 0 || s[2].length == 0 || s[3].length == 0 || s[4].length == 0) return false;
+var sm = (s[1].length == 0 ? "1" : s[1]);
+var m = (modelMap == null ? JU.PT.parseInt(sm) - 1 : -1);
+var im = (m >= 0 ? null : modelMap.get(sm));
+if (im != null) m = im.intValue();
+if (m >= modelAtomIndices.length) return false;
+var res = s[1] + "_" + viewer.getChainID(s[2], true) + "_" + s[4] + "_" + s[7].toLowerCase();
+var i0 = modelAtomIndices[m];
+var isRes = (atomMap == null || s[5].length == 0);
+if (isRes) {
+var a2 = resMap.get(res);
+if (a2 != null) for (var j = a2[1], j0 = a2[0]; --j >= j0; ) {
+bsAtoms.set(i0 + j);
+if (vals != null) vals[m][j] += Math.abs(val);
+}
+} else {
+if (s[5].charAt(0) == 'H') s[5] = this.getAttachedAtomForPDBH(s[3], s[5]);
+var atom = res + "_" + s[5] + "_" + s[6].toLowerCase();
+var ia = atomMap.get(atom);
+if (ia != null) {
+var j = ia.intValue();
+bsAtoms.set(i0 + j);
+if (vals != null) vals[m][j] += Math.abs(val);
+}}return isRes;
+}, "JV.Viewer,~A,~S,~N,JU.BS,~A,java.util.Map,java.util.Map,java.util.Map");
+Clazz.overrideMethod(c$, "getAtomBits",
+function(vwr, key, dbObj, annotationCache, type, modelIndex, bsModel){
+if (dbObj == null) return new JU.BS();
+var doCache = !key.contains("NOCACHE");
+if (!doCache) {
+key = JU.PT.rep(key, "NOCACHE", "").trim();
+}var bs = (doCache ? annotationCache.get(key) : null);
+if (bs != null) return bs;
+bs = new JU.BS();
+if (doCache) annotationCache.put(key, bs);
+try {
+var list = this.initializeAnnotation(dbObj, type, modelIndex);
+var pt = key.toLowerCase().indexOf(" where ");
+var path = JU.PT.rep((pt < 0 ? key : key.substring(0, pt)), " ", "");
+var newKey = (pt < 0 ? "" : key.substring(pt + 7).trim());
+if (path.indexOf(".") < 0) {
+path = " _path like '" + path + "*'";
+} else {
+path = " _path='" + path + "'";
+}newKey = "select * where " + (pt < 0 ? path : "(" + newKey + ") and (" + path + ")");
+JU.Logger.info("looking for " + newKey);
+this.findAnnotationAtoms(vwr, path, list, newKey, bs);
+bs.and(bsModel);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(e.toString() + " in AnnotationParser");
+bs.clearAll();
+} else {
+throw e;
+}
+}
+return bs;
+}, "JV.Viewer,~S,~O,java.util.Map,~N,~N,JU.BS");
+Clazz.overrideMethod(c$, "getAtomValidation",
+function(vwr, type, atom){
+var i = 0;
+var n = 0;
+var l = null;
+var map = null;
+var list = null;
+try {
+var ia = atom.i;
+l = new JU.Lst();
+list = (vwr.ms.getModelAuxiliaryInfo(atom.mi).get("validation")).mapGet("_list").getList();
+for (i = 0, n = list.size(); i < n; i++) {
+map = list.get(i).getMap();
+if (map.get("_path").value.equals(type) && (map.get("_atoms").value).get(ia)) {
+var v = map.get("value");
+l.addLast(v.tok == 3 ? v.value : Float.$valueOf(v.asFloat()));
+}}
+return l;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return null;
+} else {
+throw e;
+}
+}
+}, "JV.Viewer,~S,JM.Atom");
+Clazz.overrideMethod(c$, "getAnnotationInfo",
+function(vwr, a, match, type, modelIndex){
+var sb = new JU.SB();
+if ("".equals(match)) match = null;
+var isDetail = (match != null && (match.equals("all") || match.endsWith(" all")));
+if (isDetail) {
+var _list = this.initializeAnnotation(a, type, modelIndex);
+for (var i = _list.size(); --i >= 0; ) this.setAnnotationAtoms(vwr, _list.get(i).getMap(), -1);
+
+match = match.substring(0, Math.max(0, match.length - 4)).trim();
+}if ("".equals(match)) match = null;
+if (type == 1073742189 && !isDetail && match == null) return a.mapGet("_note").asString();
+var isMappingOnly = (match != null && match.indexOf(".") >= 0 && match.indexOf(".*") < 0);
+match = JU.PT.rep(match, "*", "");
+try {
+this.getAnnotationKVPairs(a, match, "", sb, "", isDetail, isMappingOnly, type);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+{
+System.out.println(e);
+}} else {
+throw e;
+}
+}
+return sb.toString();
+}, "JV.Viewer,JS.SV,~S,~N,~N");
+Clazz.defineMethod(c$, "getAttachedAtomForPDBH",
+function(group3, name){
+if (name.charAt(0) == 'H') {
+if (J.dssx.AnnotationParser.pdbAtomForH == null) {
+J.dssx.AnnotationParser.pdbAtomForH = new java.util.Hashtable();
+this.assignPDBH("", "N H H1 H2 H3 CB HB2 HB3 CD HD2 HD3 CG HG2 HG3 C2' H2'' H2' C5' H5'' H5' OXT HXT");
+for (var i = JM.BioResolver.pdbBondInfo.length; --i >= 1; ) {
+this.assignPDBH(JM.Group.group3Names[i], JM.BioResolver.pdbBondInfo[i]);
+}
+}var a = J.dssx.AnnotationParser.pdbAtomForH.get(name);
+if (a == null) a = J.dssx.AnnotationParser.pdbAtomForH.get(group3 + name);
+if (a != null) return a;
+}return name;
+}, "~S,~S");
+Clazz.defineMethod(c$, "assignPDBH",
+function(group3, sNames){
+var names = JU.PT.getTokens(JU.PT.rep(sNames, "@", " "));
+var a = null;
+for (var i = 0, n = names.length; i < n; i++) {
+var s = names[i];
+if (s.charAt(0) != 'H') {
+a = s;
+continue;
+}s = group3 + s;
+if (s.indexOf("?") >= 0) {
+s = s.substring(0, s.length - 1);
+J.dssx.AnnotationParser.pdbAtomForH.put(s + "1", a);
+J.dssx.AnnotationParser.pdbAtomForH.put(s + "2", a);
+J.dssx.AnnotationParser.pdbAtomForH.put(s + "3", a);
+} else {
+J.dssx.AnnotationParser.pdbAtomForH.put(s, a);
+}}
+}, "~S,~S");
+Clazz.overrideMethod(c$, "fixAtoms",
+function(modelIndex, dbObj, bsAddedMask, type, margin){
+var _list = this.initializeAnnotation(dbObj, type, modelIndex);
+for (var i = _list.size(); --i >= 0; ) {
+var m = _list.get(i).getMap();
+var _atoms = m.get("_atoms");
+if (_atoms != null && _atoms.tok == 10) JU.BSUtil.shiftBits(_atoms.value, bsAddedMask, _list.get(i).mapGet("_isres") != null, (_atoms.value).length() + margin);
+}
+}, "~N,JS.SV,JU.BS,~N,~N");
+Clazz.overrideMethod(c$, "getBasePairs",
+function(vwr, modelIndex){
+}, "JV.Viewer,~N");
+Clazz.overrideMethod(c$, "calculateDSSRStructure",
+function(vwr, bsAtoms){
+return null;
+}, "JV.Viewer,JU.BS");
+Clazz.overrideMethod(c$, "fixDSSRJSONMap",
+function(map){
+return null;
+}, "java.util.Map");
+Clazz.overrideMethod(c$, "getHBonds",
+function(ms, modelIndex, vHBonds, doReport){
+return null;
+}, "JM.ModelSet,~N,JU.Lst,~B");
+Clazz.overrideMethod(c$, "getAtomicDSSRData",
+function(ms, modelIndex, dssrData, dataType){
+}, "JM.ModelSet,~N,~A,~S");
+Clazz.overrideMethod(c$, "setGroup1",
+function(ms, modelIndex){
+}, "JM.ModelSet,~N");
+Clazz.overrideMethod(c$, "getDSSRFrame",
+function(dssrNT){
+return null;
+}, "java.util.Map");
+c$.pdbAtomForH = null;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dssx/Bridge.js b/config/plugins/visualizations/jmol/static/j2s/J/dssx/Bridge.js
new file mode 100755
index 000000000000..d19ea4a6edf0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dssx/Bridge.js
@@ -0,0 +1,51 @@
+Clazz.declarePackage("J.dssx");
+Clazz.load(null, "J.dssx.Bridge", ["JU.Escape"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.a = null;
+this.b = null;
+this.ladder = null;
+this.isAntiparallel = false;
+Clazz.instantialize(this, arguments);}, J.dssx, "Bridge", null);
+Clazz.makeConstructor(c$,
+function(a, b, htLadders){
+this.a = a;
+this.b = b;
+this.ladder = Clazz.newIntArray (2, 2, 0);
+this.ladder[0][0] = this.ladder[0][1] = Math.min(a.i, b.i);
+this.ladder[1][0] = this.ladder[1][1] = Math.max(a.i, b.i);
+this.addLadder(htLadders);
+}, "JM.Atom,JM.Atom,java.util.Map");
+Clazz.defineMethod(c$, "addBridge",
+function(bridge, htLadders){
+if (bridge.isAntiparallel != this.isAntiparallel || !this.canAdd(bridge) || !bridge.canAdd(this)) return false;
+this.extendLadder(bridge.ladder[0][0], bridge.ladder[1][0]);
+this.extendLadder(bridge.ladder[0][1], bridge.ladder[1][1]);
+bridge.ladder = this.ladder;
+if (bridge.ladder !== this.ladder) {
+htLadders.remove(bridge.ladder);
+this.addLadder(htLadders);
+}return true;
+}, "J.dssx.Bridge,java.util.Map");
+Clazz.defineMethod(c$, "addLadder",
+function(htLadders){
+htLadders.put(this.ladder, (this.isAntiparallel ? Boolean.TRUE : Boolean.FALSE));
+}, "java.util.Map");
+Clazz.defineMethod(c$, "canAdd",
+function(bridge){
+var index1 = bridge.a.i;
+var index2 = bridge.b.i;
+return (this.isAntiparallel ? (index1 >= this.ladder[0][1] && index2 <= this.ladder[1][0] || index1 <= this.ladder[0][0] && index2 >= this.ladder[1][1]) : (index1 <= this.ladder[0][0] && index2 <= this.ladder[1][0] || index1 >= this.ladder[0][1] && index2 >= this.ladder[1][1]));
+}, "J.dssx.Bridge");
+Clazz.defineMethod(c$, "extendLadder",
+function(index1, index2){
+if (this.ladder[0][0] > index1) this.ladder[0][0] = index1;
+if (this.ladder[0][1] < index1) this.ladder[0][1] = index1;
+if (this.ladder[1][0] > index2) this.ladder[1][0] = index2;
+if (this.ladder[1][1] < index2) this.ladder[1][1] = index2;
+}, "~N,~N");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return (this.isAntiparallel ? "a " : "p ") + this.a + " - " + this.b + "\t" + JU.Escape.e(this.ladder);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSP.js b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSP.js
new file mode 100755
index 000000000000..d0add9efe685
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSP.js
@@ -0,0 +1,366 @@
+Clazz.declarePackage("J.dssx");
+Clazz.load(null, "J.dssx.DSSP", ["java.util.Hashtable", "JU.AU", "$.BS", "$.Lst", "$.PT", "$.SB", "J.c.STR", "J.dssx.Bridge", "J.i18n.GT", "JM.HBond", "JU.Escape", "$.Logger", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.bioPolymers = null;
+this.vHBonds = null;
+this.done = null;
+this.doReport = false;
+this.dsspIgnoreHydrogens = false;
+this.setStructure = false;
+this.labels = null;
+this.bsBad = null;
+this.bioPolymerCount = 0;
+this.htBridges = null;
+this.htLadders = null;
+this.bridgesA = null;
+this.bridgesP = null;
+this.isDSSP2 = false;
+this.sheetOffsets = null;
+Clazz.instantialize(this, arguments);}, J.dssx, "DSSP", null);
+Clazz.prepareFields (c$, function(){
+this.sheetOffsets = Clazz.newArray(-1, [ Clazz.newIntArray(-1, [0, -1, 1, 0, 1, 0, 0, -1]), Clazz.newIntArray(-1, [0, 0, 0, 0, 1, -1, 1, -1])]);
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.defineMethod(c$, "calculateDssp",
+function(objBioPolymers, bioPolymerCount, objVHBonds, doReport, dsspIgnoreHydrogens, setStructure, version){
+this.bioPolymers = objBioPolymers;
+this.bioPolymerCount = bioPolymerCount;
+this.vHBonds = objVHBonds;
+this.doReport = doReport;
+this.dsspIgnoreHydrogens = dsspIgnoreHydrogens;
+this.setStructure = setStructure;
+this.isDSSP2 = (version > 1);
+var bsAmino = new JU.BS();
+for (var i = 0; i < bioPolymerCount; i++) if (Clazz.instanceOf(this.bioPolymers[i],"JM.AminoPolymer")) bsAmino.set(i);
+
+if (bsAmino.isEmpty()) return "";
+var m = this.bioPolymers[0].model;
+var sb = new JU.SB();
+sb.append("Jmol ").append(JV.Viewer.getJmolVersion()).append(" DSSP analysis for model ").append(m.ms.getModelNumberDotted(m.modelIndex)).append(" - ").append(m.ms.getModelTitle(m.modelIndex)).append("\n");
+if (m.modelIndex == 0) sb.append("\nW. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637\n\nWe thank Wolfgang Kabsch and Chris Sander for writing the DSSP software,\nand we thank the CMBI for maintaining it to the extent that it was easy to\nre-engineer in Java for our purposes. \n\nSecond generation DSSP 2.0 is ").append(this.isDSSP2 ? "" : "NOT ").append("used in this analysis. See Int. J. Mol. Sci. 2014, 15, 7841-7864; doi:10.3390/ijms15057841.\n");
+if (setStructure && m.modelIndex == 0) sb.append("\nAll bioshapes have been deleted and must be regenerated.\n");
+if (m.altLocCount > 0) sb.append("\nNote: This model contains alternative locations. Use 'CONFIGURATION 1' to be consistent with CMBI DSSP.\n");
+this.labels = Clazz.newCharArray (bioPolymerCount, '\0');
+this.done = new Array(bioPolymerCount);
+this.bsBad = new JU.BS();
+var haveWarned = false;
+for (var i = bsAmino.nextSetBit(0); i >= 0; i = bsAmino.nextSetBit(i + 1)) {
+var ap = this.bioPolymers[i];
+if (!haveWarned && (ap.monomers[0]).getExplicitNH() != null) {
+if (dsspIgnoreHydrogens) sb.append(J.i18n.GT.o(J.i18n.GT.$("NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.\nUse {0} to not use this approximation.\n\n"), "SET dsspCalculateHydrogenAlways FALSE"));
+ else sb.append(J.i18n.GT.o(J.i18n.GT.$("NOTE: Backbone amide hydrogen positions are present and will be used. Results may differ significantly from standard DSSP analysis.\nUse {0} to ignore these hydrogen positions.\n\n"), "SET dsspCalculateHydrogenAlways TRUE"));
+haveWarned = true;
+}ap.recalculateLeadMidpointsAndWingVectors();
+var n = ap.monomerCount;
+this.labels[i] = Clazz.newCharArray (n, '\0');
+this.done[i] = new JU.BS();
+for (var j = 0; j < n; j++) if ((ap.monomers[j]).getCarbonylOxygenAtom() == null) this.bsBad.set(ap.monomers[j].leadAtomIndex);
+
+}
+var min = this.getDualHydrogenBondArray();
+this.bridgesA = new JU.Lst();
+this.bridgesP = new JU.Lst();
+this.htBridges = new java.util.Hashtable();
+this.htLadders = new java.util.Hashtable();
+this.getBridges(min);
+this.getSheetStructures();
+var reports = new Array(bioPolymerCount);
+for (var i = bsAmino.nextSetBit(0); i >= 0; i = bsAmino.nextSetBit(i + 1)) if (min[i] != null) reports[i] = this.findHelixes(i, min[i]);
+
+if (doReport) {
+var sbSummary = new JU.SB();
+sb.append("\n------------------------------\n");
+for (var i = bsAmino.nextSetBit(0); i >= 0; i = bsAmino.nextSetBit(i + 1)) if (this.labels[i] != null) {
+var ap = this.bioPolymers[i];
+sbSummary.append(this.dumpSummary(ap, this.labels[i]));
+sb.append(reports[i]).append(this.dumpTags(ap, "$.1: " + String.valueOf(this.labels[i]), this.bsBad, 2));
+}
+if (this.bsBad.nextSetBit(0) >= 0) sb.append("\nNOTE: '!' indicates a residue that is missing a backbone carbonyl oxygen atom.\n");
+sb.append("\n").append("SUMMARY:" + sbSummary);
+}return sb.toString();
+}, "~A,~N,~O,~B,~B,~B,~N");
+Clazz.defineMethod(c$, "getDualHydrogenBondArray",
+function(){
+var min = JU.AU.newInt4(this.bioPolymerCount);
+for (var i = 0; i < this.bioPolymerCount; i++) {
+if (!(Clazz.instanceOf(this.bioPolymers[i],"JM.AminoPolymer"))) continue;
+var n = this.bioPolymers[i].monomerCount;
+min[i] = Clazz.newIntArray (n, 2, 3, 0);
+for (var j = 0; j < n; ++j) {
+min[i][j][0][1] = min[i][j][1][1] = -2147483648;
+min[i][j][0][2] = min[i][j][1][2] = 0;
+}
+}
+for (var i = 0; i < this.bioPolymerCount; i++) if (min[i] != null) for (var j = 0; j < this.bioPolymerCount; j++) if (min[j] != null) this.bioPolymers[i].calcRasmolHydrogenBonds(this.bioPolymers[j], null, null, null, 2, min[i], false, this.dsspIgnoreHydrogens);
+
+
+return min;
+});
+Clazz.defineMethod(c$, "getBridges",
+function(min){
+var atoms = this.bioPolymers[0].model.ms.at;
+var bridge = null;
+var htTemp = new java.util.Hashtable();
+for (var p1 = 0; p1 < min.length; p1++) if (Clazz.instanceOf(this.bioPolymers[p1],"JM.AminoPolymer")) {
+var ap1 = (this.bioPolymers[p1]);
+var n = min[p1].length - 1;
+for (var a = 1; a < n; a++) {
+var ia = ap1.monomers[a].leadAtomIndex;
+if (this.bsBad.get(ia)) continue;
+for (var p2 = p1; p2 < min.length; p2++) if (Clazz.instanceOf(this.bioPolymers[p2],"JM.AminoPolymer")) for (var b = (p1 == p2 ? a + 3 : 1); b < min[p2].length - 1; b++) {
+var ap2 = this.bioPolymers[p2];
+var ib = ap2.monomers[b].leadAtomIndex;
+if (this.bsBad.get(ib)) continue;
+if ((bridge = this.getBridge(min, p1, a, p2, b, this.bridgesP, atoms[ia], atoms[ib], ap1, ap2, htTemp, false)) != null) {
+} else if ((bridge = this.getBridge(min, p1, a, p2, b, this.bridgesA, atoms[ia], atoms[ib], ap1, ap2, htTemp, true)) != null) {
+bridge.isAntiparallel = true;
+} else {
+continue;
+}if (JU.Logger.debugging) JU.Logger.debug("Bridge found " + bridge);
+this.done[p1].set(a);
+this.done[p2].set(b);
+this.htBridges.put(ia + "-" + ib, bridge);
+}
+
+}
+}
+}, "~A");
+Clazz.defineMethod(c$, "getBridge",
+function(min, p1, a, p2, b, bridges, atom1, atom2, ap1, ap2, htTemp, isAntiparallel){
+var b1 = null;
+var b2 = null;
+var ipt = 0;
+var offsets = (isAntiparallel ? this.sheetOffsets[1] : this.sheetOffsets[0]);
+if ((b1 = this.isHbonded(a + offsets[0], b + offsets[1], p1, p2, min)) != null && (b2 = this.isHbonded(b + offsets[2], a + offsets[3], p2, p1, min)) != null || (b1 = this.isHbonded(a + offsets[ipt = 4], b + offsets[5], p1, p2, min)) != null && (b2 = this.isHbonded(b + offsets[6], a + offsets[7], p2, p1, min)) != null) {
+var bridge = new J.dssx.Bridge(atom1, atom2, this.htLadders);
+bridges.addLast(bridge);
+if (this.vHBonds != null) {
+var type = (isAntiparallel ? 14336 : 6144);
+this.addHbond(ap1.monomers[a + offsets[ipt]], ap2.monomers[b + offsets[++ipt]], b1[2], type, htTemp);
+this.addHbond(ap2.monomers[b + offsets[++ipt]], ap1.monomers[a + offsets[++ipt]], b2[2], type, htTemp);
+}return bridge;
+}return null;
+}, "~A,~N,~N,~N,~N,JU.Lst,JM.Atom,JM.Atom,JM.AminoPolymer,JM.AminoPolymer,java.util.Map,~B");
+Clazz.defineMethod(c$, "addHbond",
+function(donor, acceptor, iEnergy, type, htTemp){
+var nitrogen = (donor).getNitrogenAtom();
+var oxygen = (acceptor).getCarbonylOxygenAtom();
+if (htTemp != null) {
+var key = nitrogen.i + " " + oxygen.i;
+if (htTemp.containsKey(key)) return;
+htTemp.put(key, Boolean.TRUE);
+}this.vHBonds.addLast( new JM.HBond(nitrogen, oxygen, type, 1, 0, iEnergy / 1000));
+}, "JM.Monomer,JM.Monomer,~N,~N,java.util.Map");
+Clazz.defineMethod(c$, "getSheetStructures",
+function(){
+if (this.bridgesA.size() == 0 && this.bridgesP.size() == 0) return;
+this.createLadders(this.bridgesA, true);
+this.createLadders(this.bridgesP, false);
+var bsEEE = new JU.BS();
+var bsB = new JU.BS();
+for (var ladder, $ladder = this.htLadders.keySet().iterator (); $ladder.hasNext()&& ((ladder = $ladder.next ()) || true);) {
+if (ladder[0][0] == ladder[0][1] && ladder[1][0] == ladder[1][1]) {
+bsB.set(ladder[0][0]);
+bsB.set(ladder[1][0]);
+} else {
+bsEEE.setBits(ladder[0][0], ladder[0][1] + 1);
+bsEEE.setBits(ladder[1][0], ladder[1][1] + 1);
+}}
+var bsSheet = new JU.BS();
+var bsBridge = new JU.BS();
+for (var i = this.bioPolymers.length; --i >= 0; ) {
+if (!(Clazz.instanceOf(this.bioPolymers[i],"JM.AminoPolymer"))) continue;
+bsSheet.clearAll();
+bsBridge.clearAll();
+var ap = this.bioPolymers[i];
+for (var iStart = 0; iStart < ap.monomerCount; ) {
+var index = ap.monomers[iStart].leadAtomIndex;
+if (bsEEE.get(index)) {
+var iEnd = iStart + 1;
+while (iEnd < ap.monomerCount && bsEEE.get(ap.monomers[iEnd].leadAtomIndex)) iEnd++;
+
+bsSheet.setBits(iStart, iEnd);
+iStart = iEnd;
+} else {
+if (bsB.get(index)) bsBridge.set(iStart);
+++iStart;
+}}
+if (this.doReport) {
+this.setTag(this.labels[i], bsBridge, 'B');
+this.setTag(this.labels[i], bsSheet, 'E');
+}if (this.setStructure) {
+ap.setStructureBS(0, 3, J.c.STR.SHEET, bsSheet, false);
+}this.done[i].or(bsSheet);
+this.done[i].or(bsBridge);
+}
+});
+Clazz.defineMethod(c$, "createLadders",
+function(bridges, isAntiparallel){
+var dir = (isAntiparallel ? -1 : 1);
+var n = bridges.size();
+for (var i = 0; i < n; i++) this.checkBridge(bridges.get(i), isAntiparallel, 1, dir);
+
+for (var i = 0; i < n; i++) this.checkBulge(bridges.get(i), isAntiparallel, 1);
+
+}, "JU.Lst,~B");
+Clazz.defineMethod(c$, "checkBridge",
+function(bridge, isAntiparallel, n1, n2){
+var b = this.htBridges.get(bridge.a.getOffsetResidueAtom("\0", n1) + "-" + bridge.b.getOffsetResidueAtom("\0", n2));
+return (b != null && bridge.addBridge(b, this.htLadders));
+}, "J.dssx.Bridge,~B,~N,~N");
+Clazz.defineMethod(c$, "checkBulge",
+function(bridge, isAntiparallel, dir){
+var dir1 = (isAntiparallel ? -1 : 1);
+for (var i = 0; i < 3; i++) for (var j = (i == 0 ? 1 : 0); j < 6; j++) {
+this.checkBridge(bridge, isAntiparallel, i * dir, j * dir1);
+if (j > i) this.checkBridge(bridge, isAntiparallel, j * dir, i * dir1);
+}
+
+}, "J.dssx.Bridge,~B,~N");
+Clazz.defineMethod(c$, "dumpSummary",
+function(ap, labels){
+var a = ap.monomers[0].getLeadAtom();
+var id = a.getChainID();
+var prefix = (id == 0 ? "" : a.getChainIDStr() + ":");
+var sb = new JU.SB();
+var lastChar = '\u0000';
+var insCode1 = '\u0000';
+var insCode2 = '\u0000';
+var firstResno = -1;
+var lastResno = -1;
+var n = ap.monomerCount;
+var m = ap.monomers;
+for (var i = 0; i <= n; i++) {
+if (i == n || labels[i] != lastChar) {
+if (lastChar != '\0') sb.appendC('\n').appendC(lastChar).append(" : ").append(prefix).appendI(firstResno).append(insCode1 == '\0' ? "" : String.valueOf(insCode1)).append("_").append(prefix).appendI(lastResno).append(insCode2 == '\0' ? "" : String.valueOf(insCode2));
+if (i == n) break;
+lastChar = labels[i];
+firstResno = m[i].getResno();
+insCode1 = m[i].getInsertionCode();
+}lastResno = m[i].getResno();
+insCode2 = m[i].getInsertionCode();
+}
+return sb.toString();
+}, "JM.AminoPolymer,~A");
+Clazz.defineMethod(c$, "dumpTags",
+function(ap, lines, bsBad, mode){
+var prefix = ap.monomers[0].getLeadAtom().getChainID() + "." + (ap.bioPolymerIndexInModel + 1);
+lines = JU.PT.rep(lines, "$", prefix);
+var iFirst = ap.monomers[0].getResno();
+var pre = "\n" + prefix;
+var sb = new JU.SB();
+var sb0 = new JU.SB().append(pre + ".8: ");
+var sb1 = new JU.SB().append(pre + ".7: ");
+var sb2 = new JU.SB().append(pre + ".6: ");
+var sb3 = new JU.SB().append(pre + ".0: ");
+var i = iFirst;
+var n = ap.monomerCount;
+for (var ii = 0; ii < n; ii++) {
+i = ap.monomers[ii].getResno();
+sb0.append(i % 100 == 0 ? "" + ((Clazz.doubleToInt(i / 100)) % 100) : " ");
+sb1.append(i % 10 == 0 ? "" + ((Clazz.doubleToInt(i / 10)) % 10) : " ");
+sb2.appendI(i % 10);
+sb3.appendC(bsBad.get(ap.monomers[ii].leadAtomIndex) ? '!' : ap.monomers[ii].getGroup1());
+}
+if ((mode & 1) == 1) sb.appendSB(sb0).appendSB(sb1).appendSB(sb2);
+sb.append("\n");
+sb.append(lines);
+if ((mode & 2) == 2) {
+sb.appendSB(sb3);
+sb.append("\n\n");
+}return sb.toString().$replace('\0', '.');
+}, "JM.AminoPolymer,~S,JU.BS,~N");
+Clazz.defineMethod(c$, "isHbonded",
+function(indexDonor, indexAcceptor, pDonor, pAcceptor, min){
+if (indexDonor < 0 || indexAcceptor < 0) return null;
+var min1 = min[pDonor];
+var min2 = min[pAcceptor];
+if (indexDonor >= min1.length || indexAcceptor >= min2.length) return null;
+return (min1[indexDonor][0][0] == pAcceptor && min1[indexDonor][0][1] == indexAcceptor ? min1[indexDonor][0] : min1[indexDonor][1][0] == pAcceptor && min1[indexDonor][1][1] == indexAcceptor ? min1[indexDonor][1] : null);
+}, "~N,~N,~N,~N,~A");
+Clazz.defineMethod(c$, "findHelixes",
+function(iPolymer, min){
+var ap = this.bioPolymers[iPolymer];
+if (JU.Logger.debugging) for (var j = 0; j < ap.monomerCount; j++) JU.Logger.debug(iPolymer + "." + ap.monomers[j].getResno() + "\t" + JU.Escape.e(min[j]));
+
+var bsTurn = new JU.BS();
+var line3;
+var line4;
+var line5;
+if (this.isDSSP2) {
+line5 = this.findHelixes2(0, iPolymer, 5, min, J.c.STR.HELIXPI, 12288, bsTurn, true);
+line4 = this.findHelixes2(2, iPolymer, 4, min, J.c.STR.HELIXALPHA, 10240, bsTurn, false);
+line3 = this.findHelixes2(4, iPolymer, 3, min, J.c.STR.HELIX310, 8192, bsTurn, false);
+} else {
+line4 = this.findHelixes2(2, iPolymer, 4, min, J.c.STR.HELIXALPHA, 10240, bsTurn, true);
+line3 = this.findHelixes2(4, iPolymer, 3, min, J.c.STR.HELIX310, 8192, bsTurn, false);
+line5 = this.findHelixes2(0, iPolymer, 5, min, J.c.STR.HELIXPI, 12288, bsTurn, false);
+}if (this.setStructure) ap.setStructureBS(0, 6, J.c.STR.TURN, bsTurn, false);
+if (this.doReport) {
+this.setTag(this.labels[iPolymer], bsTurn, 'T');
+return this.dumpTags(ap, "$.5: " + line5 + "\n" + "$.4: " + line4 + "\n" + "$.3: " + line3, this.bsBad, 1);
+}return "";
+}, "~N,~A");
+Clazz.defineMethod(c$, "findHelixes2",
+function(mmtfType, iPolymer, pitch, min, subtype, type, bsTurn, isFirst){
+var ap = this.bioPolymers[iPolymer];
+var bsStart = new JU.BS();
+var bsNNN = new JU.BS();
+var bsX = new JU.BS();
+var bsStop = new JU.BS();
+var bsHelix = new JU.BS();
+var bsDone = this.done[iPolymer];
+var warning = "";
+var n = ap.monomerCount;
+for (var i = pitch; i < n; ++i) {
+var i0 = i - pitch;
+var bpt = 0;
+if (min[i][0][0] == iPolymer && min[i][0][1] == i0 || min[i][bpt = 1][0] == iPolymer && min[i][1][1] == i0) {
+var ia = ap.monomers[i0].leadAtomIndex;
+var ipt = this.bsBad.nextSetBit(ia);
+var m = ap.monomers[i];
+if (ipt >= ia && ipt <= m.leadAtomIndex) continue;
+bsStart.set(i0);
+bsNNN.setBits(i0 + 1, i);
+bsStop.set(i);
+ipt = bsDone.nextSetBit(i0);
+var isClear = (ipt < 0 || ipt >= i);
+var addH = false;
+if (i0 > 0 && bsStart.get(i0 - 1) && (isFirst || isClear)) {
+bsHelix.setBits(i0, i);
+if (!isClear) warning += " WARNING! Bridge to helix at " + ap.monomers[ipt];
+addH = true;
+} else if (isClear || bsDone.nextClearBit(ipt) < i) {
+addH = true;
+}if (bsStop.get(i0)) bsX.set(i0);
+if (addH && this.vHBonds != null) {
+this.addHbond(m, ap.monomers[i0], min[i][bpt][2], type, null);
+}}}
+var taglines;
+if (this.doReport) {
+taglines = Clazz.newCharArray (n, '\0');
+this.setTag(taglines, bsNNN, String.fromCharCode(48 + pitch));
+this.setTag(taglines, bsStart, '>');
+this.setTag(taglines, bsStop, '<');
+this.setTag(taglines, bsX, 'X');
+} else {
+taglines = null;
+}bsDone.or(bsHelix);
+bsNNN.andNot(bsDone);
+bsTurn.or(bsNNN);
+bsTurn.andNot(bsHelix);
+if (this.setStructure) ap.setStructureBS(0, mmtfType, subtype, bsHelix, false);
+if (this.doReport) {
+this.setTag(this.labels[iPolymer], bsHelix, String.fromCharCode(68 + pitch));
+return String.valueOf(taglines) + warning;
+}return "";
+}, "~N,~N,~N,~A,J.c.STR,~N,JU.BS,~B");
+Clazz.defineMethod(c$, "setTag",
+function(tags, bs, ch){
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) tags[i] = ch;
+
+}, "~A,JU.BS,~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR0.js b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR0.js
new file mode 100755
index 000000000000..d665941700b2
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR0.js
@@ -0,0 +1,5 @@
+Clazz.declarePackage("J.dssx");
+(function(){
+var c$ = Clazz.declareType(J.dssx, "DSSR0", null);
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR1.js b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR1.js
new file mode 100755
index 000000000000..816d2cfb3ad7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/dssx/DSSR1.js
@@ -0,0 +1,279 @@
+Clazz.declarePackage("J.dssx");
+Clazz.load(["J.dssx.AnnotationParser"], "J.dssx.DSSR1", ["JU.BS", "$.Lst", "$.P3", "$.PT", "JM.HBond", "JM.BasePair", "JU.Escape", "$.Logger"], function(){
+var c$ = Clazz.declareType(J.dssx, "DSSR1", J.dssx.AnnotationParser);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.dssx.DSSR1, []);
+});
+Clazz.overrideMethod(c$, "calculateDSSRStructure",
+function(vwr, bsAtoms){
+var bs = vwr.ms.getModelBS(bsAtoms == null ? vwr.bsA() : bsAtoms, true);
+var s = "";
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) s += this.getDSSRForModel(vwr, i) + "\n";
+
+return s;
+}, "JV.Viewer,JU.BS");
+Clazz.defineMethod(c$, "getDSSRForModel",
+function(vwr, modelIndex){
+var info = null;
+var out = null;
+while (true) {
+if (!vwr.ms.am[modelIndex].isBioModel) break;
+info = vwr.ms.getModelAuxiliaryInfo(modelIndex);
+if (info.containsKey("dssr")) break;
+var bs = vwr.restrictToModel(vwr.ms.getAtoms(2097166, null), modelIndex);
+if (bs.nextClearBit(0) < 0) {
+info = null;
+break;
+}try {
+var name = vwr.setLoadFormat(false, "=dssrModel/", '=', false);
+name = JU.PT.rep(name, "%20", " ");
+JU.Logger.info("fetching " + name + "[pdb data]");
+var data = vwr.getPdbAtomData(bs, null, false, false);
+var modelNumber = vwr.getModelNumber(vwr.ms.getModelBS(bs, false).nextSetBit(0));
+var s = " " + modelNumber;
+data = "MODEL" + s.substring(s.length - 9) + "\n" + data + "ENDMDL\n";
+data = vwr.getFileAsString3(name + data, false, null);
+var x = vwr.parseJSONMap(data);
+if (x != null) {
+info.put("dssr", x);
+this.setGroup1(vwr.ms, modelIndex);
+this.fixDSSRJSONMap(x);
+this.setBioPolymers(vwr.ms.am[modelIndex], false);
+}} catch (e) {
+info = null;
+out = "" + e;
+}
+break;
+}
+return (info != null ? JU.PT.rep(JU.Escape.escapeMap((info.get("dssr")).get("counts")), ",", ",\n") : out == null ? "model has no nucleotides" : out);
+}, "JV.Viewer,~N");
+Clazz.overrideMethod(c$, "fixDSSRJSONMap",
+function(map){
+var s = "";
+try {
+this.fixIndices(map, "kissingLoops", "hairpin");
+this.fixIndices(map, "coaxStacks", "stem");
+if (map.containsKey("counts")) s += "_M.dssr.counts = " + map.get("counts").toString() + "\n";
+if (map.containsKey("dbn")) s += "_M.dssr.dbn = " + map.get("dbn").toString();
+} catch (e) {
+}
+return s;
+}, "java.util.Map");
+Clazz.defineMethod(c$, "fixIndices",
+function(map, key, root){
+var indices = root + "_indices";
+var original = root + "s";
+var lst = map.get(key);
+if (lst != null) {
+var hpins = map.get(original);
+for (var i = lst.size(); --i >= 0; ) {
+var kmap = lst.get(i);
+var khlist = kmap.get(indices);
+var n = khlist.size();
+if (n > 0) {
+var khpins = new JU.Lst();
+kmap.put(original, khpins);
+for (var j = n; --j >= 0; ) khpins.addLast(hpins.get((khlist.get(j)).intValue() - 1));
+
+}}
+}}, "java.util.Map,~S,~S");
+Clazz.overrideMethod(c$, "getBasePairs",
+function(vwr, modelIndex){
+var ms = vwr.ms;
+var info = ms.getInfo(modelIndex, "dssr");
+var pairs = (info == null ? null : info.get("pairs"));
+var singles = (info == null ? null : info.get("ssSegments"));
+if (pairs == null && singles == null) {
+this.setBioPolymers(vwr.ms.am[modelIndex], true);
+return;
+}var bsAtoms = ms.am[modelIndex].bsAtoms;
+try {
+var bs = new JU.BS();
+var atoms = ms.at;
+if (pairs != null) for (var i = pairs.size(); --i >= 0; ) {
+var map = pairs.get(i);
+var unit1 = map.get("nt1");
+var unit2 = map.get("nt2");
+var a1 = ms.getSequenceBits(unit1, bsAtoms, bs).nextSetBit(0);
+bs.clearAll();
+var a2 = ms.getSequenceBits(unit2, bsAtoms, bs).nextSetBit(0);
+bs.clearAll();
+JM.BasePair.add(map, this.setRes(atoms[a1]), this.setRes(atoms[a2]));
+}
+if (singles != null) for (var i = singles.size(); --i >= 0; ) {
+var map = singles.get(i);
+var units = map.get("nts_long");
+ms.getSequenceBits(units, bsAtoms, bs);
+for (var j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1)) this.setRes(atoms[j]);
+
+}
+} catch (e) {
+JU.Logger.error("Exception " + e + " in DSSRParser.getBasePairs");
+}
+}, "JV.Viewer,~N");
+Clazz.defineMethod(c$, "setBioPolymers",
+function(m, b){
+var n = m.getBioPolymerCount();
+for (var i = n; --i >= 0; ) {
+var bp = m.bioPolymers[i];
+if (bp.isNucleic()) (bp).isDssrSet = b;
+}
+}, "JM.BioModel,~B");
+Clazz.defineMethod(c$, "setRes",
+function(atom){
+if (atom.group.getBioPolymerLength() == 0) return null;
+var m = atom.group;
+(m.bioPolymer).isDssrSet = true;
+return m;
+}, "JM.Atom");
+Clazz.overrideMethod(c$, "getAtomBits",
+function(vwr, key, dbObj, annotationCache, type, modelIndex, bsModel){
+if (dbObj == null) return new JU.BS();
+var doCache = !key.contains("NOCACHE");
+if (!doCache) {
+key = JU.PT.rep(key, "NOCACHE", "").trim();
+}var bs = null;
+bs = new JU.BS();
+if (doCache) annotationCache.put(key, bs);
+try {
+key = JU.PT.rep(key, "[where", "[select * where");
+key = JU.PT.rep(key, "[WHERE", "[select * where");
+var ext = "";
+var n = -2147483648;
+var pt = key.toLowerCase().indexOf("[select");
+if (pt >= 0) {
+ext = key.substring(pt);
+key = key.substring(0, pt);
+pt = ext.lastIndexOf("]..");
+if (pt >= 0 && (n = JU.PT.parseInt(ext.substring(pt + 3))) != -2147483648) ext = ext.substring(0, pt + 1);
+}pt = key.toLowerCase().indexOf(" where ");
+if (pt < 0) {
+key = key.toLowerCase();
+pt = (n == -2147483648 ? key.lastIndexOf('.') : -1);
+var haveIndex = false;
+if (pt >= 0 && (haveIndex = (n = JU.PT.parseInt(key.substring(pt + 1))) != -2147483648)) key = key.substring(0, pt);
+pt = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".indexOf(".." + key) + 2;
+var len = key.length;
+if (pt < 2) return bs;
+var ptLast = (haveIndex ? pt + len : 2147483647);
+while (pt >= 2 && pt < ptLast && len > 0) {
+if (key.indexOf(".") < 0 && "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".substring(pt + len, pt + len + 2).equals("..")) {
+key = "[select (" + key + ")]";
+}dbObj = vwr.extractProperty(dbObj, key, -1);
+pt += len + 1;
+if (ext.length > 0) {
+dbObj = vwr.extractProperty(dbObj, ext, -1);
+ext = "";
+}var pt1 = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".indexOf(".", pt);
+key = "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*..".substring(pt, pt1);
+len = key.length;
+}
+} else {
+key = key.substring(0, pt).trim() + "[select * " + key.substring(pt + 1) + "]" + ext;
+dbObj = vwr.extractProperty(dbObj, key, -1);
+}if (n != -2147483648 && Clazz.instanceOf(dbObj,"JU.Lst")) {
+if (n <= 0) n += (dbObj).size();
+dbObj = (dbObj).get(n - 1);
+}bs.or(vwr.ms.getAtoms(1086324744, dbObj.toString()));
+bs.and(bsModel);
+} catch (e) {
+System.out.println(e.toString() + " in AnnotationParser");
+bs.clearAll();
+}
+return bs;
+}, "JV.Viewer,~S,~O,java.util.Map,~N,~N,JU.BS");
+Clazz.overrideMethod(c$, "getHBonds",
+function(ms, modelIndex, vHBonds, doReport){
+var info = ms.getInfo(modelIndex, "dssr");
+var list;
+if (info == null || (list = info.get("hbonds")) == null) return "no DSSR hydrogen-bond data";
+var bsAtoms = ms.am[modelIndex].bsAtoms;
+var unit1 = null;
+var unit2 = null;
+var a1 = 0;
+var a2 = 0;
+try {
+var bs = new JU.BS();
+for (var i = list.size(); --i >= 0; ) {
+var map = list.get(i);
+unit1 = map.get("atom1_id");
+a1 = ms.getSequenceBits(unit1, bsAtoms, bs).nextSetBit(0);
+if (a1 < 0) {
+JU.Logger.error("Atom " + unit1 + " was not found");
+continue;
+}unit2 = map.get("atom2_id");
+bs.clearAll();
+a2 = ms.getSequenceBits(unit2, bsAtoms, bs).nextSetBit(0);
+if (a2 < 0) {
+JU.Logger.error("Atom " + unit2 + " was not found");
+continue;
+}bs.clearAll();
+var energy = 0;
+vHBonds.addLast( new JM.HBond(ms.at[a1], ms.at[a2], 2048, 1, 0, energy));
+}
+} catch (e) {
+}
+return "DSSR reports " + list.size() + " hydrogen bonds";
+}, "JM.ModelSet,~N,JU.Lst,~B");
+Clazz.overrideMethod(c$, "setGroup1",
+function(ms, modelIndex){
+var info = ms.getInfo(modelIndex, "dssr");
+var list;
+if (info == null || (list = info.get("nts")) == null) return;
+var m = ms.am[modelIndex];
+var bsAtoms = m.bsAtoms;
+var atoms = ms.at;
+var bs = new JU.BS();
+for (var i = list.size(); --i >= 0; ) {
+var map = list.get(i);
+var ch = (map.get("nt_code")).charAt(0);
+var unit1 = map.get("nt_id");
+ms.bioModelset.getAllSequenceBits(unit1, bsAtoms, bs);
+var pt = bs.nextSetBit(0);
+if (pt < 0) continue;
+if ("ACGTU".indexOf(ch) < 0) atoms[pt].group.group1 = ch;
+atoms[pt].group.dssrNT = map;
+bs.clearAll();
+}
+}, "JM.ModelSet,~N");
+Clazz.overrideMethod(c$, "getAtomicDSSRData",
+function(ms, modelIndex, dssrData, dataType){
+var info = ms.getInfo(modelIndex, "dssr");
+var list;
+if (info == null || (list = info.get(dataType)) == null) return;
+var bsAtoms = ms.am[modelIndex].bsAtoms;
+try {
+var bs = new JU.BS();
+for (var i = list.size(); --i >= 0; ) {
+var map = list.get(i);
+bs.clearAll();
+ms.getSequenceBits(map.toString(), bsAtoms, bs);
+for (var j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1)) dssrData[j] = i;
+
+}
+} catch (e) {
+}
+}, "JM.ModelSet,~N,~A,~S");
+Clazz.overrideMethod(c$, "getDSSRFrame",
+function(nt){
+var frame = nt.get("frame");
+if (frame == null) return null;
+var oxyz = new Array(4);
+for (var i = 4; --i >= 0; ) oxyz[i] = new JU.P3();
+
+this.getPoint(frame, "origin", oxyz[0]);
+this.getPoint(frame, "x_axis", oxyz[1]);
+this.getPoint(frame, "y_axis", oxyz[2]);
+this.getPoint(frame, "z_axis", oxyz[3]);
+return oxyz;
+}, "java.util.Map");
+Clazz.defineMethod(c$, "getPoint",
+function(frame, item, pt){
+var xyz = frame.get(item);
+pt.x = xyz.get(0).floatValue();
+pt.y = xyz.get(1).floatValue();
+pt.z = xyz.get(2).floatValue();
+}, "java.util.Map,~S,JU.P3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/Export3D.js b/config/plugins/visualizations/jmol/static/j2s/J/export/Export3D.js
new file mode 100755
index 000000000000..d3a40aff9c4c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/Export3D.js
@@ -0,0 +1,397 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.api.JmolRendererInterface", "JU.P3"], "J.export.Export3D", ["J.api.Interface", "J.g3d.HermiteRenderer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.exporter = null;
+this.privateKey = 0;
+this.gdata = null;
+this.colix = 0;
+this.hermite3d = null;
+this.width = 0;
+this.height = 0;
+this.slab = 0;
+this.depth = 0;
+this.exportName = null;
+this.webGL = false;
+this.isCartesian = false;
+this.ptA = null;
+this.ptB = null;
+this.ptC = null;
+this.ptD = null;
+Clazz.instantialize(this, arguments);}, J["export"], "Export3D", null, J.api.JmolRendererInterface);
+Clazz.prepareFields (c$, function(){
+this.ptA = new JU.P3();
+this.ptB = new JU.P3();
+this.ptC = new JU.P3();
+this.ptD = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.overrideMethod(c$, "isWebGL",
+function(){
+return this.webGL;
+});
+Clazz.overrideMethod(c$, "initializeExporter",
+function(vwr, privateKey, gdata, params){
+this.exportName = params.get("type");
+this.webGL = this.exportName.equals("JS");
+if ((this.exporter = J.api.Interface.getOption("export." + (this.webGL ? "" : "_") + this.exportName + "Exporter", vwr, "export")) == null) return null;
+this.exporter.export3D = this;
+this.isCartesian = (this.exporter.exportType == 1);
+this.gdata = gdata;
+gdata.setNewWindowParametersForExport();
+this.slab = gdata.slab;
+this.width = gdata.width;
+this.height = gdata.height;
+this.privateKey = privateKey;
+return (this.initializeOutput(vwr, privateKey, params) ? this.exporter : null);
+}, "JV.Viewer,~N,JU.GData,java.util.Map");
+Clazz.overrideMethod(c$, "initializeOutput",
+function(vwr, privateKey, params){
+return this.exporter.initializeOutput(vwr, privateKey, this.gdata, params);
+}, "JV.Viewer,~N,java.util.Map");
+Clazz.overrideMethod(c$, "getExportType",
+function(){
+return this.exporter.exportType;
+});
+Clazz.overrideMethod(c$, "getExportName",
+function(){
+return this.exportName;
+});
+Clazz.overrideMethod(c$, "finalizeOutput",
+function(){
+return this.exporter.finalizeOutput();
+});
+Clazz.overrideMethod(c$, "setSlab",
+function(slabValue){
+this.gdata.setSlab(slabValue);
+this.slab = this.gdata.slab;
+}, "~N");
+Clazz.overrideMethod(c$, "setSlabAndZShade",
+function(slabValue, depthValue, zSlab, zDepth, zPower){
+this.gdata.setSlab(slabValue);
+this.slab = this.gdata.slab;
+this.gdata.setDepth(depthValue);
+this.depth = this.gdata.depth;
+}, "~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "renderBackground",
+function(me){
+if (!this.isCartesian) this.gdata.renderBackground(me);
+}, "J.api.JmolRendererInterface");
+Clazz.overrideMethod(c$, "drawAtom",
+function(atom, radius){
+this.exporter.drawAtom(atom, radius);
+}, "JM.Atom,~N");
+Clazz.overrideMethod(c$, "drawRect",
+function(x, y, z, zSlab, rWidth, rHeight){
+if (this.webGL) {
+return;
+}if (zSlab != 0 && this.gdata.isClippedZ(zSlab)) return;
+var w = rWidth - 1;
+var h = rHeight - 1;
+var xRight = x + w;
+var yBottom = y + h;
+if (y >= 0 && y < this.height) this.drawHLine(x, y, z, w);
+if (yBottom >= 0 && yBottom < this.height) this.drawHLine(x, yBottom, z, w);
+if (x >= 0 && x < this.width) this.drawVLine(x, y, z, h);
+if (xRight >= 0 && xRight < this.width) this.drawVLine(xRight, y, z, h);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "drawHLine",
+function(x, y, z, w){
+var argbCurrent = this.gdata.getColorArgbOrGray(this.colix);
+if (w < 0) {
+x += w;
+w = -w;
+}for (var i = 0; i <= w; i++) {
+this.exporter.drawTextPixel(argbCurrent, x + i, y, z);
+}
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "drawVLine",
+function(x, y, z, h){
+var argbCurrent = this.gdata.getColorArgbOrGray(this.colix);
+if (h < 0) {
+y += h;
+h = -h;
+}for (var i = 0; i <= h; i++) {
+this.exporter.drawTextPixel(argbCurrent, x, y + i, z);
+}
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawFilledCircle",
+function(colixRing, colixFill, diameter, x, y, z){
+if (!this.gdata.isClippedZ(z)) this.exporter.drawFilledCircle(colixRing, colixFill, diameter, x, y, z);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "drawCircle",
+function(colix, diameter, x, y, z, doFill){
+if (!this.gdata.isClippedZ(z)) this.exporter.drawCircle(x, y, z, diameter, colix, doFill);
+}, "~N,~N,~N,~N,~N,~B");
+Clazz.overrideMethod(c$, "fillSphereXYZ",
+function(diameter, x, y, z){
+this.ptA.set(x, y, z);
+this.fillSphereBits(diameter, this.ptA);
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "fillSphereI",
+function(diameter, center){
+this.ptA.set(center.x, center.y, center.z);
+this.fillSphereBits(diameter, this.ptA);
+}, "~N,JU.P3i");
+Clazz.overrideMethod(c$, "fillSphereBits",
+function(diameter, center){
+if (diameter != 0) this.exporter.fillSphere(this.colix, diameter, center);
+}, "~N,JU.P3");
+Clazz.overrideMethod(c$, "fillTextRect",
+function(x, y, z, zSlab, widthFill, heightFill){
+if (this.isCartesian || this.gdata.isClippedZ(zSlab)) return;
+z = this.exporter.fixScreenZ(z);
+this.ptA.set(x, y, z);
+this.ptB.set(x + widthFill, y, z);
+this.ptC.set(x + widthFill, y + heightFill, z);
+this.ptD.set(x, y + heightFill, z);
+this.fillQuadrilateral(this.ptA, this.ptB, this.ptC, this.ptD, false);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawString",
+function(str, font3d, xBaseline, yBaseline, z, zSlab, bgcolix){
+if (str != null && !this.gdata.isClippedZ(zSlab)) this.drawStringNoSlab(str, font3d, xBaseline, yBaseline, z, bgcolix);
+}, "~S,JU.Font,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawStringNoSlab",
+function(str, font3d, xBaseline, yBaseline, z, bgcolix){
+if (str == null) return;
+z = Math.max(this.slab, z);
+if (font3d == null) font3d = this.gdata.getFont3DCurrent();
+ else this.gdata.setFont(font3d);
+this.exporter.plotText(xBaseline, yBaseline, z, this.colix, str, font3d);
+}, "~S,JU.Font,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawImage",
+function(objImage, x, y, z, zSlab, bgcolix, width, height){
+if (this.isCartesian || objImage == null || width == 0 || height == 0 || this.gdata.isClippedZ(zSlab)) return;
+z = Math.max(this.slab, z);
+this.exporter.plotImage(x, y, z, objImage, bgcolix, width, height);
+}, "~O,~N,~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawPixel",
+function(x, y, z){
+this.plotPixelClipped(x, y, z);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "plotPixelClipped",
+function(x, y, z){
+if (this.isClipped(x, y, z)) return;
+this.exporter.drawPixel(this.colix, x, y, z, 1);
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "plotPixelClippedP3i",
+function(screen){
+if (this.isClipped(screen.x, screen.y, screen.z)) return;
+this.exporter.drawPixel(this.colix, screen.x, screen.y, screen.z, 1);
+}, "JU.P3i");
+Clazz.overrideMethod(c$, "drawPoints",
+function(count, coordinates, scale){
+for (var i = count * 3; i > 0; ) {
+var z = coordinates[--i];
+var y = coordinates[--i];
+var x = coordinates[--i];
+if (this.isClipped(x, y, z)) continue;
+this.exporter.drawPixel(this.colix, x, y, z, scale);
+}
+}, "~N,~A,~N");
+Clazz.overrideMethod(c$, "drawDashedLineBits",
+function(run, rise, pointA, pointB){
+this.exporter.fillCylinderScreenMad(this.colix, 2, this.exporter.lineWidthMad, pointA, pointB);
+}, "~N,~N,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "drawLineXYZ",
+function(x1, y1, z1, x2, y2, z2){
+this.ptA.set(x1, y1, z1);
+this.ptB.set(x2, y2, z2);
+this.exporter.fillCylinderScreenMad(this.colix, 2, this.exporter.lineWidthMad, this.ptA, this.ptB);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "drawLine",
+function(colixA, colixB, xA, yA, zA, xB, yB, zB){
+this.fillCylinderXYZ(colixA, colixB, 2, this.exporter.lineWidthMad, xA, yA, zA, xB, yB, zB);
+}, "~N,~N,~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "drawLineBits",
+function(colixA, colixB, pointA, pointB){
+this.fillCylinderBits2(colixA, colixB, 2, this.exporter.lineWidthMad, pointA, pointB);
+}, "~N,~N,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "drawLineAB",
+function(pointA, pointB){
+this.exporter.fillCylinderScreenMad(this.colix, 2, this.exporter.lineWidthMad, pointA, pointB);
+}, "JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "drawBond",
+function(atomA, atomB, colixA, colixB, endcaps, mad, bondOrder){
+if (mad == 1) mad = this.exporter.lineWidthMad;
+this.exporter.drawCylinder(atomA, atomB, colixA, colixB, endcaps, mad, bondOrder);
+}, "JU.P3,JU.P3,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "fillCylinderXYZ",
+function(colixA, colixB, endcaps, mad, xA, yA, zA, xB, yB, zB){
+this.ptA.set(xA, yA, zA);
+this.ptB.set(xB, yB, zB);
+this.exporter.drawCylinder(this.ptA, this.ptB, colixA, colixB, endcaps, mad, 1);
+}, "~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "fillCylinderScreen3I",
+function(endcaps, diameter, pointA, pointB, pt0f, pt1f, radius){
+if (diameter <= 0) return;
+this.exporter.fillCylinderScreen(this.colix, endcaps, diameter, pointA, pointB, pt0f, pt1f, radius);
+}, "~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");
+Clazz.overrideMethod(c$, "fillCylinder",
+function(endcaps, diameter, pointA, pointB){
+if (diameter <= 0) return;
+this.ptA.set(pointA.x, pointA.y, pointA.z);
+this.ptB.set(pointB.x, pointB.y, pointB.z);
+this.exporter.fillCylinderScreenMad(this.colix, endcaps, diameter, this.ptA, this.ptB);
+}, "~N,~N,JU.P3i,JU.P3i");
+Clazz.overrideMethod(c$, "fillCylinderBits",
+function(endcaps, diameter, pointA, pointB){
+if (diameter == 0) return;
+if (this.isCartesian) {
+this.exporter.fillCylinderScreen(this.colix, endcaps, diameter, pointA, pointB, null, null, 0);
+} else {
+this.exporter.fillCylinderScreenMad(this.colix, endcaps, diameter, pointA, pointB);
+}}, "~N,~N,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "fillConeScreen3f",
+function(endcap, screenDiameter, pointBase, screenTip, isBarb){
+this.exporter.fillConeScreen(this.colix, endcap, screenDiameter, pointBase, screenTip, isBarb);
+}, "~N,~N,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "drawHermite4",
+function(tension, s0, s1, s2, s3){
+this.hermite3d.renderHermiteRope(false, tension, 0, 0, 0, s0, s1, s2, s3);
+}, "~N,JU.P3,JU.P3,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "fillHermite",
+function(tension, diameterBeg, diameterMid, diameterEnd, s0, s1, s2, s3){
+this.hermite3d.renderHermiteRope(true, tension, diameterBeg, diameterMid, diameterEnd, s0, s1, s2, s3);
+}, "~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "drawTriangle3C",
+function(screenA, colixA, screenB, colixB, screenC, colixC, check){
+if ((check & 1) == 1) this.drawLine(colixA, colixB, screenA.x, screenA.y, screenA.z, screenB.x, screenB.y, screenB.z);
+if ((check & 2) == 2) this.drawLine(colixB, colixC, screenB.x, screenB.y, screenB.z, screenC.x, screenC.y, screenC.z);
+if ((check & 4) == 4) this.drawLine(colixA, colixC, screenA.x, screenA.y, screenA.z, screenC.x, screenC.y, screenC.z);
+}, "JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");
+Clazz.defineMethod(c$, "drawLineBits",
+function(screenA, screenB, colixA, colixB){
+this.exporter.drawCylinder(screenA, screenB, colixA, colixB, 2, this.exporter.lineWidthMad, 1);
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.overrideMethod(c$, "fillCylinderBits2",
+function(colixA, colixB, endcaps, mad, screenA, screenB){
+this.exporter.drawCylinder(screenA, screenB, colixA, colixB, endcaps, mad, 1);
+}, "~N,~N,~N,~N,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "fillTriangle3CNBits",
+function(pA, colixA, nA, pB, colixB, nB, pC, colixC, nC, twoSided){
+if (colixA != colixB || colixB != colixC) {
+return;
+}this.exporter.fillTriangle(colixA, pA, pB, pC, twoSided);
+}, "JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "fillTriangle3CN",
+function(pointA, colixA, normixA, pointB, colixB, normixB, pointC, colixC, normixC){
+}, "JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");
+Clazz.overrideMethod(c$, "fillTriangleTwoSided",
+function(normix, a, b, c){
+this.exporter.fillTriangle(this.colix, a, b, c, true);
+}, "~N,JU.P3,JU.P3,JU.P3");
+Clazz.overrideMethod(c$, "fillTriangle3f",
+function(pointA, pointB, pointC, setNoisy){
+this.exporter.fillTriangle(this.colix, pointA, pointB, pointC, false);
+}, "JU.P3,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "fillTriangle3i",
+function(screenA, screenB, screenC, ptA0, ptB0, ptC0, doShade){
+this.exporter.fillTriangle(this.colix, screenA, screenB, screenC, true);
+}, "JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");
+Clazz.overrideMethod(c$, "fillQuadrilateral",
+function(pointA, pointB, pointC, pointD, isSolid){
+this.exporter.fillTriangle(this.colix, pointA, pointB, pointC, false);
+this.exporter.fillTriangle(this.colix, pointA, pointC, pointD, false);
+}, "JU.P3,JU.P3,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "drawSurface",
+function(meshSurface, colix){
+this.exporter.drawSurface(meshSurface, colix);
+}, "JU.MeshSurface,~N");
+Clazz.overrideMethod(c$, "fillEllipsoid",
+function(center, points, x, y, z, diameter, mToEllipsoidal, coef, mDeriv, selectedOctant, octantPoints){
+this.exporter.fillEllipsoid(center, points, this.colix, x, y, z, diameter, mToEllipsoidal, coef, mDeriv, octantPoints);
+}, "JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");
+Clazz.overrideMethod(c$, "drawEllipse",
+function(ptAtom, ptX, ptY, fillArc, wireframeOnly){
+return this.exporter.drawEllipse(ptAtom, ptX, ptY, this.colix, fillArc);
+}, "JU.P3,JU.P3,JU.P3,~B,~B");
+Clazz.overrideMethod(c$, "isAntialiased",
+function(){
+return false;
+});
+Clazz.overrideMethod(c$, "checkTranslucent",
+function(isAlphaTranslucent){
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "haveTranslucentObjects",
+function(){
+return true;
+});
+Clazz.overrideMethod(c$, "setC",
+function(colix){
+this.colix = colix;
+this.gdata.setC(colix);
+return true;
+}, "~N");
+Clazz.overrideMethod(c$, "isInDisplayRange",
+function(x, y){
+return (this.isCartesian || this.gdata.isInDisplayRange(x, y));
+}, "~N,~N");
+Clazz.defineMethod(c$, "clipCode",
+function(x, y, z){
+return (this.isCartesian ? this.gdata.clipCode(z) : this.gdata.clipCode3(x, y, z));
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "isClippedXY",
+function(diameter, x, y){
+return (!this.isCartesian && this.gdata.isClippedXY(diameter, x, y));
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "isClipped",
+function(x, y, z){
+return (this.gdata.isClippedZ(z) || this.isClipped(x, y));
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "isClipped",
+function(x, y){
+return (!this.isCartesian && this.gdata.isClipped(x, y));
+}, "~N,~N");
+Clazz.defineMethod(c$, "getPrivateKey",
+function(){
+return this.privateKey;
+});
+Clazz.overrideMethod(c$, "volumeRender4",
+function(diam, x, y, z){
+this.fillSphereXYZ(diam, x, y, z);
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "renderCrossHairs",
+function(minMax, screenWidth, screenHeight, navigationOffset, navigationDepthPercent){
+}, "~A,~N,~N,JU.P3,~N");
+Clazz.overrideMethod(c$, "volumeRender",
+function(TF){
+}, "~B");
+Clazz.overrideMethod(c$, "addRenderer",
+function(tok){
+if (tok == 553648143) this.hermite3d = new J.g3d.HermiteRenderer().set(this, this.gdata);
+}, "~N");
+Clazz.overrideMethod(c$, "plotImagePixel",
+function(argb, x, y, z, shade, bgargb, width, height, pbuf, p, transpLog){
+if (this.webGL) return;
+z = Math.max(this.slab, z);
+if (shade != 0) {
+var a = (shade == 8 ? 0xFF : ((8 - shade) << 4) + (8 - shade));
+argb = (argb & 0xFFFFFF) | (a << 24);
+}this.exporter.drawTextPixel(argb, x, y, z);
+}, "~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");
+Clazz.overrideMethod(c$, "drawHermite7",
+function(fill, border, tension, s0, s1, s2, s3, s4, s5, s6, s7, aspectRatio, colixBack){
+if (colixBack == 0 || this.webGL) {
+this.hermite3d.renderHermiteRibbon(fill, border, tension, s0, s1, s2, s3, s4, s5, s6, s7, aspectRatio, 0);
+return;
+}this.hermite3d.renderHermiteRibbon(fill, border, tension, s0, s1, s2, s3, s4, s5, s6, s7, aspectRatio, 1);
+var colix = this.colix;
+this.setC(colixBack);
+this.hermite3d.renderHermiteRibbon(fill, border, tension, s0, s1, s2, s3, s4, s5, s6, s7, aspectRatio, -1);
+this.setC(colix);
+}, "~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");
+Clazz.overrideMethod(c$, "renderAllStrings",
+function(jr){
+if (this.webGL) {
+return;
+}this.gdata.renderAllStrings(this);
+}, "~O");
+Clazz.overrideMethod(c$, "drawLinePixels",
+function(sA, sB, z, zslab){
+return;
+}, "JU.P3i,JU.P3i,~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/JSExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/JSExporter.js
new file mode 100755
index 000000000000..d249754bdfbe
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/JSExporter.js
@@ -0,0 +1,127 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__CartesianExporter", "java.util.Hashtable", "J.export.Export3D", "$.___Exporter"], "J.export.JSExporter", ["J.export.UseTable"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.htSpheresRendered = null;
+this.htObjects = null;
+this.html5Applet = null;
+this.useTable = null;
+this.ret = null;
+Clazz.instantialize(this, arguments);}, J["export"], "JSExporter", J["export"].__CartesianExporter);
+Clazz.prepareFields (c$, function(){
+this.htSpheresRendered = new java.util.Hashtable();
+this.htObjects = new java.util.Hashtable();
+this.ret = new Array(1);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"].JSExporter, []);
+});
+Clazz.defineMethod(c$, "jsInitExport",
+function(applet){
+}, "~O");
+Clazz.defineMethod(c$, "jsEndExport",
+function(applet){
+}, "~O");
+Clazz.defineMethod(c$, "jsCylinder",
+function(applet, id, isNew, pt1, pt2, o){
+}, "~O,~S,~B,JU.P3,JU.P3,~A");
+Clazz.defineMethod(c$, "jsSphere",
+function(applet, id, isNew, pt, o){
+}, "~O,~S,~B,JU.T3,~A");
+Clazz.defineMethod(c$, "jsSurface",
+function(applet, vertices, normals, indices, nVertices, nPolygons, nFaces, bsPolygons, faceVertexMax, color, vertexColors, polygonColors){
+}, "~O,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,~A,~A");
+Clazz.defineMethod(c$, "jsTriangle",
+function(applet, color, pt1, pt2, pt3){
+}, "~O,~N,JU.T3,JU.T3,JU.T3");
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.html5Applet = this.vwr.html5Applet;
+this.useTable = new J["export"].UseTable("JS");
+this.htSpheresRendered.clear();
+this.htObjects.clear();
+this.jsInitExport(this.html5Applet);
+});
+Clazz.overrideMethod(c$, "outputFooter",
+function(){
+this.jsEndExport(this.html5Applet);
+this.htSpheresRendered.clear();
+this.htObjects.clear();
+this.useTable = null;
+});
+Clazz.overrideMethod(c$, "outputSphere",
+function(ptCenter, radius, colix, checkRadius){
+var iRad = Math.round(radius * 100);
+var check = J["export"].___Exporter.round(ptCenter) + (checkRadius ? " " + iRad : "");
+if (this.htSpheresRendered.get(check) != null) return;
+this.htSpheresRendered.put(check, Boolean.TRUE);
+var found = this.useTable.getDefRet("S" + colix + "_" + iRad, this.ret);
+var o;
+if (found) o = this.htObjects.get(this.ret[0]);
+ else this.htObjects.put(this.ret[0], o = Clazz.newArray(-1, [this.getColor(colix), Float.$valueOf(radius)]));
+this.jsSphere(this.html5Applet, this.ret[0], !found, ptCenter, o);
+}, "JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY, checkRadius){
+if (ptX != null) return false;
+var length = pt1.distance(pt2);
+var found = this.useTable.getDefRet("C" + colix + "_" + Math.round(length * 100) + "_" + radius + "_" + endcaps, this.ret);
+var o;
+if (found) o = this.htObjects.get(this.ret[0]);
+ else this.htObjects.put(this.ret[0], o = Clazz.newArray(-1, [this.getColor(colix), Float.$valueOf(length), Float.$valueOf(radius)]));
+this.jsCylinder(this.html5Applet, this.ret[0], !found, pt1, pt2, o);
+return true;
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(center, points, colix){
+}, "JU.P3,~A,~N");
+Clazz.overrideMethod(c$, "outputCone",
+function(ptBase, ptTip, radius, colix){
+this.outputCylinder(null, ptBase, ptTip, colix, 0, radius, null, null, false);
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "getColor",
+function(colix){
+return Integer.$valueOf(this.gdata.getColorArgbOrGray(colix));
+}, "~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, vertexColixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+var vertexColors = this.getColors(vertexColixes);
+var polygonColors = this.getColors(polygonColixes);
+this.jsSurface(this.html5Applet, vertices, normals, indices, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, this.gdata.getColorArgbOrGray(colix), vertexColors, polygonColors);
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+this.jsTriangle(this.html5Applet, this.gdata.getColorArgbOrGray(colix), pt1, pt2, pt3);
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(pt, argb){
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "outputFace",
+function(is, coordMap, faceVertexMax){
+}, "~A,~A,~N");
+Clazz.defineMethod(c$, "output",
+function(pt){
+}, "JU.T3");
+Clazz.overrideMethod(c$, "plotImage",
+function(x, y, z, image, bgcolix, width, height){
+}, "~N,~N,~N,~O,~N,~N,~N");
+Clazz.overrideMethod(c$, "plotText",
+function(x, y, z, colix, text, font3d){
+}, "~N,~N,~N,~N,~S,JU.Font");
+Clazz.defineMethod(c$, "getColors",
+function(colixes){
+if (colixes == null) return null;
+var colors = Clazz.newIntArray (colixes.length, 0);
+for (var i = colors.length; --i >= 0; ) {
+colors[i] = this.gdata.getColorArgbOrGray(colixes[i]);
+}
+return colors;
+}, "~A");
+{
+{
+Jmol && Jmol.GLmol && Jmol.GLmol.extendJSExporter(J.export.JSExporter.prototype);
+}}});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/MeshData.js b/config/plugins/visualizations/jmol/static/j2s/J/export/MeshData.js
new file mode 100755
index 000000000000..4ad6b98b72fb
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/MeshData.js
@@ -0,0 +1,87 @@
+Clazz.declarePackage("J.export");
+Clazz.load(null, "J.export.MeshData", ["JU.AU", "$.P3", "$.V3", "JU.MeshSurface"], function(){
+var c$ = Clazz.declareType(J["export"], "MeshData", null);
+c$.getCircleData = Clazz.defineMethod(c$, "getCircleData",
+function(){
+var ndeg = 10;
+var n = Clazz.doubleToInt(360 / ndeg);
+var vertexCount = n + 1;
+var faces = JU.AU.newInt2(n);
+for (var i = 0; i < n; i++) {
+faces[i] = Clazz.newIntArray(-1, [i, (i + 1) % n, n]);
+}
+var vertexes = new Array(vertexCount);
+var normals = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, y, 0);
+normals[i] = JU.P3.new3(0, 0, 1);
+}
+vertexes[n] = JU.P3.new3(0, 0, 0);
+normals[n] = JU.P3.new3(0, 0, 1);
+return JU.MeshSurface.newMesh(false, vertexes, 0, faces, normals, 0);
+});
+c$.getTriangleData = Clazz.defineMethod(c$, "getTriangleData",
+function(pt1, pt2, pt3){
+var vertexes = Clazz.newArray(-1, [pt1, pt2, pt3]);
+var v1 = JU.V3.newVsub(pt3, pt1);
+var v2 = JU.V3.newVsub(pt2, pt1);
+v2.cross(v2, v1);
+v2.normalize();
+var normals = Clazz.newArray(-1, [v2, v2, v2]);
+var faces = Clazz.newArray(-1, [ Clazz.newIntArray(-1, [0, 1, 2])]);
+return JU.MeshSurface.newMesh(false, vertexes, 0, faces, normals, 0);
+}, "JU.T3,JU.T3,JU.T3");
+c$.getConeData = Clazz.defineMethod(c$, "getConeData",
+function(){
+var ndeg = 10;
+var n = Clazz.doubleToInt(360 / ndeg);
+var vertices = new Array(n + 1);
+var faces = JU.AU.newInt2(n);
+for (var i = 0; i < n; i++) faces[i] = Clazz.newIntArray(-1, [i, (i + 1) % n, n]);
+
+var d = ndeg / 180. * 3.141592653589793;
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * d));
+var y = (Math.sin(i * d));
+vertices[i] = JU.P3.new3(x, y, 0);
+}
+vertices[n] = JU.P3.new3(0, 0, 1);
+return JU.MeshSurface.newMesh(false, vertices, 0, faces, vertices, 0);
+});
+c$.getCylinderData = Clazz.defineMethod(c$, "getCylinderData",
+function(inSide){
+var ndeg = 10;
+var vertexCount = Clazz.doubleToInt(360 / ndeg) * 2;
+var n = Clazz.doubleToInt(vertexCount / 2);
+var faces = JU.AU.newInt2(vertexCount);
+var fpt = -1;
+for (var i = 0; i < n; i++) {
+if (inSide) {
+faces[++fpt] = Clazz.newIntArray(-1, [i + n, (i + 1) % n, i]);
+faces[++fpt] = Clazz.newIntArray(-1, [i + n, (i + 1) % n + n, (i + 1) % n]);
+} else {
+faces[++fpt] = Clazz.newIntArray(-1, [i, (i + 1) % n, i + n]);
+faces[++fpt] = Clazz.newIntArray(-1, [(i + 1) % n, (i + 1) % n + n, i + n]);
+}}
+var vertexes = new Array(vertexCount);
+var normals = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, y, 0);
+normals[i] = JU.P3.new3(x, y, 0);
+}
+for (var i = 0; i < n; i++) {
+var x = (Math.cos((i + 0.5) * ndeg / 180 * 3.141592653589793));
+var y = (Math.sin((i + 0.5) * ndeg / 180 * 3.141592653589793));
+vertexes[i + n] = JU.P3.new3(x, y, 1);
+normals[i + n] = normals[i];
+}
+if (inSide) for (var i = 0; i < n; i++) normals[i].scale(-1);
+
+return JU.MeshSurface.newMesh(false, vertexes, 0, faces, normals, 0);
+}, "~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/UseTable.js b/config/plugins/visualizations/jmol/static/j2s/J/export/UseTable.js
new file mode 100755
index 000000000000..2c1316400f41
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/UseTable.js
@@ -0,0 +1,28 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["java.util.Hashtable"], "J.export.UseTable", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.iObj = 0;
+this.keyword = null;
+this.term = '\0';
+Clazz.instantialize(this, arguments);}, J["export"], "UseTable", java.util.Hashtable);
+Clazz.makeConstructor(c$,
+function(keyword){
+Clazz.superConstructor (this, J["export"].UseTable, []);
+this.keyword = keyword;
+this.term = keyword.charAt(keyword.length - 1);
+}, "~S");
+Clazz.defineMethod(c$, "getDef",
+function(key){
+if (this.containsKey(key)) return this.keyword + this.get(key) + this.term;
+var id = "_" + (this.iObj++);
+this.put(key, id);
+return id;
+}, "~S");
+Clazz.defineMethod(c$, "getDefRet",
+function(key, ret){
+if ((ret[0] = this.get(key)) != null) return true;
+this.put(key, ret[0] = "_" + key.charAt(0) + (this.iObj++));
+return false;
+}, "~S,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_IdtfExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_IdtfExporter.js
new file mode 100755
index 000000000000..734d3ecf4530
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_IdtfExporter.js
@@ -0,0 +1,532 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__CartesianExporter", "java.util.Hashtable", "JU.AU", "$.M4", "$.P3", "$.SB"], "J.export._IdtfExporter", ["JU.Lst", "$.Quat", "JU.C", "$.Geodesic", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.haveSphere = false;
+this.haveCylinder = false;
+this.haveCylinderIn = false;
+this.haveCone = false;
+this.haveCircle = false;
+this.ptMin = null;
+this.ptMax = null;
+this.iObj = 0;
+this.htDefs = null;
+this.m = null;
+this.models = null;
+this.resources = null;
+this.modifiers = null;
+this.htNodes = null;
+this.cylinderMatrix = null;
+this.sbTemp = null;
+this.triangleFace = null;
+Clazz.instantialize(this, arguments);}, J["export"], "_IdtfExporter", J["export"].__CartesianExporter);
+Clazz.prepareFields (c$, function(){
+this.ptMin = JU.P3.new3(1e10, 1e10, 1e10);
+this.ptMax = JU.P3.new3(-1.0E10, -1.0E10, -1.0E10);
+this.htDefs = new java.util.Hashtable();
+this.m = new JU.M4();
+this.models = new JU.SB();
+this.resources = new JU.SB();
+this.modifiers = new JU.SB();
+this.htNodes = new java.util.Hashtable();
+this.cylinderMatrix = new JU.M4();
+this.triangleFace = JU.AU.newInt2(1);
+{
+this.triangleFace[0] = Clazz.newIntArray(-1, [0, 1, 2]);
+}});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._IdtfExporter, []);
+this.commentChar = "% ";
+});
+Clazz.defineMethod(c$, "output",
+function(pt){
+this.output(pt, this.sbTemp, true);
+}, "JU.T3");
+Clazz.defineMethod(c$, "output",
+function(pt, sb, checkpt){
+if (checkpt) this.checkPoint(pt);
+sb.append(J["export"].___Exporter.round(pt.x)).append(" ").append(J["export"].___Exporter.round(pt.y)).append(" ").append(J["export"].___Exporter.round(pt.z)).append(" ");
+}, "JU.T3,JU.SB,~B");
+Clazz.defineMethod(c$, "checkPoint",
+function(pt){
+if (pt.x < this.ptMin.x) this.ptMin.x = pt.x;
+if (pt.y < this.ptMin.y) this.ptMin.y = pt.y;
+if (pt.z < this.ptMin.z) this.ptMin.z = pt.z;
+if (pt.x > this.ptMax.x) this.ptMax.x = pt.x;
+if (pt.y > this.ptMax.y) this.ptMax.y = pt.y;
+if (pt.z > this.ptMax.z) this.ptMax.z = pt.z;
+}, "JU.T3");
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.output("FILE_FORMAT \"IDTF\"\nFORMAT_VERSION 100\n");
+this.m.setIdentity();
+this.m.setToM3(this.tm.matrixRotate);
+this.m.rotate2(this.referenceCenter, this.tempP1);
+this.m.m03 = -this.tempP1.x;
+this.m.m13 = -this.tempP1.y;
+this.m.m23 = -this.tempP1.z;
+this.m.m33 = 1;
+this.output("NODE \"GROUP\" {\n");
+this.output("NODE_NAME \"Jmol\"\n");
+this.output("PARENT_LIST {\nPARENT_COUNT 1\n");
+this.output("PARENT 0 {\n");
+this.output(this.getParentItem("", this.m));
+this.output("}}}\n");
+});
+Clazz.overrideMethod(c$, "finalizeOutput",
+function(){
+this.finalizeOutput2();
+return this.getAuxiliaryFileData();
+});
+Clazz.defineMethod(c$, "getAuxiliaryFileData",
+function(){
+var fName = this.fileName.substring(this.fileName.lastIndexOf("/") + 1);
+fName = fName.substring(fName.lastIndexOf("\\") + 1);
+var name = fName + ".";
+name = name.substring(0, name.indexOf("."));
+return "% Created by: Jmol " + JV.Viewer.getJmolVersion() + "\n% Creation date: " + this.getExportDate() + "\n% File created: " + this.fileName + " (" + this.getByteCount() + " bytes)\n\n" + "\n\\documentclass[12pt,letter]{article}" + "\n\\usepackage{hyperref}" + "\n\\usepackage{media9}" + "\n\\usepackage{verbatim}" + "\n\\pagestyle{empty}" + "\n\\begin{document}" + "\n \\begin{center}" + "\n \\addmediapath{./} % here you can set the path where is been saved the u3d file" + "\n \\includemedia[" + "\n label=" + name + "," + "\n width=0.9\\textwidth," + "\n height=0.9\\textheight," + "\n activate=pageopen," + "\n deactivate=pageclose," + "\n 3Dtoolbar=false," + "\n 3Dnavpane=false," + "\n 3Dmenu," + "\n 3Droo=" + this.cameraDistance + "," + "\n 3Dcoo= 0.0 0.0 0.0," + "\n 3Dc2c=0.0 0.0 1.0," + "\n 3Daac=" + this.apertureAngle + "," + "\n 3Droll=0.0," + "\n 3Dbg=" + this.rgbFractionalFromColix(this.backgroundColix) + ", % to set the background color for 3D vwr; white = 1 1 1; so, you need to do the proportion: '255:1=[RGB]:x'" + "\n transparent=false," + "\n 3Dlights=Headlamp," + "\n 3Drender=Solid," + "\n 3Dpartsattrs=restore," + "\n ]{}{" + name + ".u3d}" + "\n% \\\\" + "\n%\\movieref[3Dcalculate]{" + name + "}{Click here!}" + "\n\\end{center}" + "\n\\end{document}" + "\n\\begin{comment}" + this.vwr.getWrappedStateScript() + "\n\\end{comment}";
+});
+Clazz.defineMethod(c$, "getParentItem",
+function(name, m){
+var sb = new JU.SB();
+sb.append("PARENT_NAME \"" + name + "\"\n");
+sb.append("PARENT_TM {\n");
+sb.append(m.m00 + " " + m.m10 + " " + m.m20 + " 0.0\n");
+sb.append(m.m01 + " " + m.m11 + " " + m.m21 + " 0.0\n");
+sb.append(m.m02 + " " + m.m12 + " " + m.m22 + " 0.0\n");
+sb.append(m.m03 + " " + m.m13 + " " + m.m23 + " " + m.m33 + "\n");
+sb.append("}\n");
+return sb.toString();
+}, "~S,JU.M4");
+Clazz.defineMethod(c$, "addColix",
+function(colix, haveColors){
+var key = "_" + colix;
+if (this.htDefs.containsKey(key)) return;
+var color = (haveColors ? "1.0 1.0 1.0" : this.rgbFractionalFromColix(colix));
+this.htDefs.put(key, Boolean.TRUE);
+this.resources.append("RESOURCE_LIST \"SHADER\" {\n");
+this.resources.append("RESOURCE_COUNT 1\n");
+this.resources.append("RESOURCE 0 {\n");
+this.resources.append("RESOURCE_NAME \"Shader" + key + "\"\n");
+this.resources.append("ATTRIBUTE_USE_VERTEX_COLOR \"FALSE\"\n");
+this.resources.append("SHADER_MATERIAL_NAME \"Mat" + key + "\"\n");
+this.resources.append("SHADER_ACTIVE_TEXTURE_COUNT 0\n");
+this.resources.append("}}\n");
+this.resources.append("RESOURCE_LIST \"MATERIAL\" {\n");
+this.resources.append("RESOURCE_COUNT 1\n");
+this.resources.append("RESOURCE 0 {\n");
+this.resources.append("RESOURCE_NAME \"Mat" + key + "\"\n");
+this.resources.append("MATERIAL_AMBIENT " + color + "\n");
+this.resources.append("MATERIAL_DIFFUSE " + color + "\n");
+this.resources.append("MATERIAL_SPECULAR 0.0 0.0 0.0\n");
+this.resources.append("MATERIAL_EMISSIVE 0.0 0.0 0.0\n");
+this.resources.append("MATERIAL_REFLECTIVITY 0.00000\n");
+this.resources.append("MATERIAL_OPACITY " + J["export"].___Exporter.opacityFractionalFromColix(colix) + "\n");
+this.resources.append("}}\n");
+}, "~N,~B");
+Clazz.defineMethod(c$, "addShader",
+function(key, colix){
+this.modifiers.append("MODIFIER \"SHADING\" {\n");
+this.modifiers.append("MODIFIER_NAME \"" + key + "\"\n");
+this.modifiers.append("PARAMETERS {\n");
+this.modifiers.append("SHADER_LIST_COUNT 1\n");
+this.modifiers.append("SHADING_GROUP {\n");
+this.modifiers.append("SHADER_LIST 0 {\n");
+this.modifiers.append("SHADER_COUNT 1\n");
+this.modifiers.append("SHADER_NAME_LIST {\n");
+this.modifiers.append("SHADER 0 NAME: \"Shader_" + colix + "\"\n");
+this.modifiers.append("}}}}}\n");
+}, "~S,~N");
+Clazz.overrideMethod(c$, "outputFooter",
+function(){
+this.htDefs = null;
+this.outputNodes();
+this.output(this.models.toString());
+this.output(this.resources.toString());
+this.output("RESOURCE_LIST \"VIEW\" {\n");
+this.output("\tRESOURCE_COUNT 1\n");
+this.output("\tRESOURCE 0 {\n");
+this.output("\t\tRESOURCE_NAME \"View0\"\n");
+this.output("\t\tVIEW_PASS_COUNT 1\n");
+this.output("\t\tVIEW_ROOT_NODE_LIST {\n");
+this.output("\t\t\tROOT_NODE 0 {\n");
+this.output("\t\t\t\tROOT_NODE_NAME \"\"\n");
+this.output("\t\t\t}\n");
+this.output("\t\t}\n");
+this.output("\t}\n");
+this.output("}\n\n");
+this.output(this.modifiers.toString());
+});
+Clazz.defineMethod(c$, "outputNodes",
+function(){
+for (var entry, $entry = this.htNodes.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
+var key = entry.getKey();
+var v = entry.getValue();
+this.output("NODE \"MODEL\" {\n");
+this.output("NODE_NAME \"" + key + "\"\n");
+System.out.println("output idtf " + key);
+var n = v.size();
+this.output("PARENT_LIST {\nPARENT_COUNT " + n + "\n");
+for (var i = 0; i < n; i++) {
+this.output("PARENT " + i + " {\n");
+this.output(v.get(i));
+this.output("}\n");
+}
+this.output("}\n");
+var i = key.indexOf("_");
+if (i > 0) {
+key = key.substring(0, i);
+}if (key.equals("Ellipse")) {
+key = "Circle";
+}this.output("RESOURCE_NAME \"" + key + "_Mesh\"\n}\n");
+}
+});
+Clazz.defineMethod(c$, "outputEllipsoid",
+function(center, points, colix){
+var a = JU.Quat.getQuaternionFrame(center, points[1], points[3]).toAxisAngle4f();
+var sx = points[1].distance(center);
+var sy = points[3].distance(center);
+var sz = points[5].distance(center);
+this.setSphereMatrix(center, sx, sy, sz, a, this.sphereMatrix);
+this.outputEllipsoid(center, this.sphereMatrix, colix);
+}, "JU.P3,~A,~N");
+Clazz.defineMethod(c$, "outputEllipsoid",
+function(center, sphereMatrix, colix){
+if (!this.haveSphere) {
+this.models.append(this.getSphereResource());
+this.haveSphere = true;
+}this.checkPoint(center);
+this.addColix(colix, false);
+var key = "Sphere_" + colix;
+var v = this.htNodes.get(key);
+if (v == null) {
+v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+}v.addLast(this.getParentItem("Jmol", sphereMatrix));
+}, "JU.T3,JU.M4,~N");
+Clazz.defineMethod(c$, "getSphereResource",
+function(){
+var sb = new JU.SB();
+sb.append("RESOURCE_LIST \"MODEL\" {\n").append("RESOURCE_COUNT 1\n").append("RESOURCE 0 {\n").append("RESOURCE_NAME \"Sphere_Mesh\"\n").append("MODEL_TYPE \"MESH\"\n").append("MESH {\n");
+var vertexCount = JU.Geodesic.getVertexCount(2);
+var f = JU.Geodesic.getFaceVertexes(2);
+var nFaces = Clazz.doubleToInt(f.length / 3);
+var faces = Clazz.newIntArray (nFaces, 3, 0);
+for (var i = 0, p = 0; i < nFaces; i++) for (var j = 0; j < 3; j++) faces[i][j] = f[p++];
+
+
+var vertexes = new Array(vertexCount);
+for (var i = 0; i < vertexCount; i++) vertexes[i] = JU.Geodesic.getVertexVector(i);
+
+return this.getMeshData("Sphere", faces, vertexes, vertexes);
+});
+Clazz.defineMethod(c$, "getMeshData",
+function(type, indices, vertexes, normals){
+var nFaces = indices.length;
+var vertexCount = vertexes.length;
+var normalCount = normals.length;
+var sb = new JU.SB();
+this.getMeshHeader(type, nFaces, vertexCount, normalCount, 0, sb);
+var sb1 = new JU.SB();
+for (var i = 0; i < indices.length; i++) {
+sb1.appendI(indices[i][0]).append(" ");
+sb1.appendI(indices[i][1]).append(" ");
+sb1.appendI(indices[i][2]).append(" ");
+}
+sb.append("MESH_FACE_POSITION_LIST { ");
+sb.appendSB(sb1);
+sb.append("}\n");
+sb.append("MESH_FACE_NORMAL_LIST { ");
+sb.appendSB(sb1);
+sb.append("}\n");
+sb.append("MESH_FACE_SHADING_LIST { ");
+for (var i = 0; i < nFaces; i++) sb.append("0 ");
+
+sb.append("}\n");
+sb.append("MODEL_POSITION_LIST { ");
+for (var i = 0; i < vertexCount; i++) this.output(vertexes[i], sb, false);
+
+sb.append("}\n");
+sb.append("MODEL_NORMAL_LIST { ");
+for (var i = 0; i < normalCount; i++) this.output(normals[i], sb, false);
+
+sb.append("}\n}}}\n");
+return sb.toString();
+}, "~S,~A,~A,~A");
+Clazz.defineMethod(c$, "getMeshHeader",
+function(type, nFaces, vertexCount, normalCount, colorCount, sb){
+sb.append("RESOURCE_LIST \"MODEL\" {\n").append("RESOURCE_COUNT 1\n").append("RESOURCE 0 {\n").append("RESOURCE_NAME \"").append(type).append("_Mesh\"\n").append("MODEL_TYPE \"MESH\"\n").append("MESH {\n").append("FACE_COUNT ").appendI(nFaces).append("\n").append("MODEL_POSITION_COUNT ").appendI(vertexCount).append("\n").append("MODEL_NORMAL_COUNT ").appendI(normalCount).append("\n").append("MODEL_DIFFUSE_COLOR_COUNT ").appendI(colorCount).append("\n").append("MODEL_SPECULAR_COLOR_COUNT 0\n").append("MODEL_TEXTURE_COORD_COUNT 0\n").append("MODEL_BONE_COUNT 0\n").append("MODEL_SHADING_COUNT 1\n").append("MODEL_SHADING_DESCRIPTION_LIST {\n").append("SHADING_DESCRIPTION 0 {\n").append("TEXTURE_LAYER_COUNT 0\n").append("SHADER_ID 0\n}}\n");
+}, "~S,~N,~N,~N,~N,JU.SB");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY, checkRadius){
+if (ptX != null) {
+if (endcaps == 2) {
+this.outputEllipse(ptCenter, pt1, ptX, ptY, colix);
+this.tempP3.add2(ptCenter, ptCenter);
+this.tempP3.sub(ptX);
+this.outputEllipse(ptCenter, pt2, this.tempP3, ptY, colix);
+}} else if (endcaps == 3) {
+this.outputSphere(pt1, radius * 1.01, colix, true);
+this.outputSphere(pt2, radius * 1.01, colix, true);
+} else if (endcaps == 2) {
+this.outputCircle(pt1, pt2, colix, radius);
+this.outputCircle(pt2, pt1, colix, radius);
+}if (!this.haveCylinder) {
+this.models.append(this.getCylinderResource(false));
+this.haveCylinder = true;
+}if (ptX != null && endcaps == 0 && !this.haveCylinderIn) {
+this.models.append(this.getCylinderResource(true));
+this.haveCylinderIn = true;
+}this.checkPoint(pt1);
+this.checkPoint(pt2);
+this.addColix(colix, false);
+var n = (ptX != null && endcaps == 0 ? 2 : 1);
+for (var i = 0; i < n; i++) {
+var key = "Cylinder" + (i == 0 ? "_" : "In_") + colix;
+var v = this.htNodes.get(key);
+if (v == null) {
+v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+}if (ptX == null) this.cylinderMatrix.setToM3(this.getRotationMatrix(pt1, pt2, radius));
+ else this.cylinderMatrix.setToM3(this.getRotationMatrix(ptCenter, pt2, radius, ptX, ptY));
+this.cylinderMatrix.m03 = pt1.x;
+this.cylinderMatrix.m13 = pt1.y;
+this.cylinderMatrix.m23 = pt1.z;
+this.cylinderMatrix.m33 = 1;
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+radius *= 0.95;
+}
+return true;
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3,~B");
+Clazz.defineMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+if (doFill) {
+this.outputCircle(pt1, pt2, colix, radius);
+return;
+}}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.defineMethod(c$, "outputEllipse",
+function(ptCenter, ptZ, ptX, ptY, colix){
+if (!this.haveCircle) {
+this.models.append(this.getCircleResource());
+this.haveCircle = true;
+this.cylinderMatrix = new JU.M4();
+}this.addColix(colix, false);
+var key = "Ellipse_" + colix;
+var v = this.htNodes.get(key);
+if (v == null) {
+v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+}this.checkPoint(ptCenter);
+this.cylinderMatrix.setToM3(this.getRotationMatrix(ptCenter, ptZ, 1, ptX, ptY));
+this.cylinderMatrix.m03 = ptZ.x;
+this.cylinderMatrix.m13 = ptZ.y;
+this.cylinderMatrix.m23 = ptZ.z;
+this.cylinderMatrix.m33 = 1;
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+return true;
+}, "JU.P3,JU.P3,JU.P3,JU.P3,~N");
+Clazz.defineMethod(c$, "outputCircle",
+function(ptCenter, ptPerp, colix, radius){
+if (!this.haveCircle) {
+this.models.append(this.getCircleResource());
+this.haveCircle = true;
+this.cylinderMatrix = new JU.M4();
+}this.addColix(colix, false);
+var key = "Circle_" + colix;
+var v = this.htNodes.get(key);
+if (v == null) {
+v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+}this.checkPoint(ptCenter);
+this.cylinderMatrix.setToM3(this.getRotationMatrix(ptCenter, ptPerp, radius));
+this.cylinderMatrix.m03 = ptCenter.x;
+this.cylinderMatrix.m13 = ptCenter.y;
+this.cylinderMatrix.m23 = ptCenter.z;
+this.cylinderMatrix.m33 = 1;
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "getCylinderResource",
+function(inSide){
+var ndeg = 10;
+var vertexCount = Clazz.doubleToInt(360 / ndeg) * 2;
+var n = Clazz.doubleToInt(vertexCount / 2);
+var faces = JU.AU.newInt2(vertexCount);
+var fpt = -1;
+for (var i = 0; i < n; i++) {
+if (inSide) {
+faces[++fpt] = Clazz.newIntArray(-1, [i + n, (i + 1) % n, i]);
+faces[++fpt] = Clazz.newIntArray(-1, [i + n, (i + 1) % n + n, (i + 1) % n]);
+} else {
+faces[++fpt] = Clazz.newIntArray(-1, [i, (i + 1) % n, i + n]);
+faces[++fpt] = Clazz.newIntArray(-1, [(i + 1) % n, (i + 1) % n + n, i + n]);
+}}
+var vertexes = new Array(vertexCount);
+var normals = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, y, 0);
+normals[i] = JU.P3.new3(x, y, 0);
+}
+for (var i = 0; i < n; i++) {
+var x = (Math.cos((i + 0.5) * ndeg / 180 * 3.141592653589793));
+var y = (Math.sin((i + 0.5) * ndeg / 180 * 3.141592653589793));
+vertexes[i + n] = JU.P3.new3(x, y, 1);
+normals[i + n] = normals[i];
+}
+if (inSide) for (var i = 0; i < n; i++) normals[i].scale(-1);
+
+return this.getMeshData(inSide ? "CylinderIn" : "Cylinder", faces, vertexes, normals);
+}, "~B");
+Clazz.overrideMethod(c$, "outputFace",
+function(face, map, faceVertexMax){
+this.sbTemp.append(" " + map[face[0]] + " " + map[face[1]] + " " + map[face[2]]);
+if (faceVertexMax == 4 && face.length == 4) {
+this.sbTemp.append(" " + map[face[0]] + " " + map[face[2]] + " " + map[face[3]]);
+}}, "~A,~A,~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+this.addColix(colix, polygonColixes != null || colixes != null);
+if (polygonColixes != null) {
+return;
+}var sbFaceCoordIndices = this.sbTemp = new JU.SB();
+var map = Clazz.newIntArray (nVertices, 0);
+var nCoord = this.getCoordinateMap(vertices, map, null);
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+var sbFaceNormalIndices = this.sbTemp = new JU.SB();
+var vNormals = null;
+if (normals != null) {
+vNormals = new JU.Lst();
+map = this.getNormalMap(normals, nVertices, null, vNormals);
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+}map = null;
+var sbColorIndexes = new JU.SB();
+if (colorList != null) {
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+sbColorIndexes.append(" " + htColixes.get(Short.$valueOf(colixes[indices[i][0]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][1]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][2]])));
+if (faceVertexMax == 4 && indices[i].length == 4) sbColorIndexes.append(" " + htColixes.get(Short.$valueOf(colixes[indices[i][0]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][2]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][3]])));
+}
+}var sbCoords = this.sbTemp = new JU.SB();
+this.outputVertices(vertices, nVertices, offset);
+var sbNormals = new JU.SB();
+var nNormals = 0;
+if (normals != null) {
+nNormals = vNormals.size();
+for (var i = 0; i < nNormals; i++) sbNormals.append(vNormals.get(i));
+
+vNormals = null;
+}var sbColors = new JU.SB();
+var nColors = 0;
+if (colorList != null) {
+nColors = colorList.size();
+for (var i = 0; i < nColors; i++) {
+var c = colorList.get(i).shortValue();
+sbColors.append(this.rgbFractionalFromColix(c)).append(" ").append(J["export"].___Exporter.translucencyFractionalFromColix(c)).append(" ");
+}
+}var key = "mesh" + (++this.iObj);
+this.addMeshData(key, nTriangles, nCoord, nNormals, nColors, sbFaceCoordIndices, sbFaceNormalIndices, sbColorIndexes, sbCoords, sbNormals, sbColors);
+var v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+this.cylinderMatrix.setIdentity();
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.defineMethod(c$, "addMeshData",
+function(key, nFaces, nCoord, nNormals, nColors, sbFaceCoordIndices, sbFaceNormalIndices, sbColorIndices, sbCoords, sbNormals, sbColors){
+this.getMeshHeader(key, nFaces, nCoord, nNormals, nColors, this.models);
+this.models.append("MESH_FACE_POSITION_LIST { ").appendSB(sbFaceCoordIndices).append(" }\n").append("MESH_FACE_NORMAL_LIST { ").appendSB(sbFaceNormalIndices).append(" }\n");
+this.models.append("MESH_FACE_SHADING_LIST { ");
+for (var i = 0; i < nFaces; i++) this.models.append("0 ");
+
+this.models.append("}\n");
+if (nColors > 0) this.models.append("MESH_FACE_DIFFUSE_COLOR_LIST { ").appendSB(sbColorIndices).append(" }\n");
+this.models.append("MODEL_POSITION_LIST { ").appendSB(sbCoords).append(" }\n").append("MODEL_NORMAL_LIST { ").appendSB(sbNormals).append(" }\n");
+if (nColors > 0) this.models.append("MODEL_DIFFUSE_COLOR_LIST { ").appendSB(sbColors).append(" }\n");
+this.models.append("}}}\n");
+}, "~S,~N,~N,~N,~N,JU.SB,JU.SB,JU.SB,JU.SB,JU.SB,JU.SB");
+Clazz.overrideMethod(c$, "outputCone",
+function(ptBase, ptTip, radius, colix){
+if (!this.haveCone) {
+this.models.append(this.getConeResource());
+this.haveCone = true;
+}this.checkPoint(ptBase);
+this.checkPoint(ptTip);
+this.addColix(colix, false);
+var key = "Cone_" + colix;
+var v = this.htNodes.get(key);
+if (v == null) {
+v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+}this.cylinderMatrix.setToM3(this.getRotationMatrix(ptBase, ptTip, radius));
+this.cylinderMatrix.m03 = ptBase.x;
+this.cylinderMatrix.m13 = ptBase.y;
+this.cylinderMatrix.m23 = ptBase.z;
+this.cylinderMatrix.m33 = 1;
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "getConeResource",
+function(){
+var m = J["export"].___Exporter.getConeMesh(null, null, 0);
+return this.getMeshData("Cone", m.pis, m.vs, m.vs);
+});
+Clazz.defineMethod(c$, "getCircleResource",
+function(){
+var ndeg = 10;
+var n = Clazz.doubleToInt(360 / ndeg);
+var vertexCount = n + 1;
+var faces = JU.AU.newInt2(n);
+for (var i = 0; i < n; i++) faces[i] = Clazz.newIntArray(-1, [i, (i + 1) % n, n]);
+
+var vertexes = new Array(vertexCount);
+var normals = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, y, 0);
+normals[i] = JU.P3.new3(0, 0, 1);
+}
+vertexes[n] = JU.P3.new3(0, 0, 0);
+normals[n] = JU.P3.new3(0, 0, 1);
+return this.getMeshData("Circle", faces, vertexes, normals);
+});
+Clazz.overrideMethod(c$, "outputSphere",
+function(center, radius, colix, checkRadius){
+this.setSphereMatrix(center, radius, radius, radius, null, this.sphereMatrix);
+this.outputEllipsoid(center, this.sphereMatrix, colix);
+}, "JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(pt, argb){
+var colix = JU.C.getColix(argb);
+this.outputSphere(pt, 0.02, colix, true);
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+this.addColix(colix, false);
+var key = "T" + (++this.iObj);
+this.models.append(this.getTriangleResource(key, pt1, pt2, pt3));
+var v = new JU.Lst();
+this.htNodes.put(key, v);
+this.addShader(key, colix);
+if (this.cylinderMatrix == null) this.cylinderMatrix = new JU.M4();
+this.cylinderMatrix.setIdentity();
+v.addLast(this.getParentItem("Jmol", this.cylinderMatrix));
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.defineMethod(c$, "getTriangleResource",
+function(key, pt1, pt2, pt3){
+var vertexes = Clazz.newArray(-1, [pt1, pt2, pt3]);
+this.tempV1.sub2(pt3, pt1);
+this.tempV2.sub2(pt2, pt1);
+this.tempV2.cross(this.tempV2, this.tempV1);
+this.tempV2.normalize();
+var normals = Clazz.newArray(-1, [this.tempV2, this.tempV2, this.tempV2]);
+return this.getMeshData(key, this.triangleFace, vertexes, normals);
+}, "~S,JU.T3,JU.T3,JU.T3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_MayaExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_MayaExporter.js
new file mode 100755
index 000000000000..70563863c63d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_MayaExporter.js
@@ -0,0 +1,127 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__CartesianExporter"], "J.export._MayaExporter", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nBalls = 0;
+this.nCyl = 0;
+this.name = null;
+this.id = null;
+Clazz.instantialize(this, arguments);}, J["export"], "_MayaExporter", J["export"].__CartesianExporter);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._MayaExporter, []);
+this.commentChar = "// ";
+});
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.output("// Maya ASCII 8.5 scene\n");
+this.output("// Name: ball_stripped.ma\n");
+this.output("// Last modified: Thu, Jul 5, 2007 10:25:55 PM\n");
+this.output("// Codeset: UTF-8\n");
+this.output("requires maya \"8.5\";\n");
+this.output("currentUnit -l centimeter -a degree -t film;\n");
+this.output("fileInfo \"application\" \"maya\";\n");
+this.output("fileInfo \"product\" \"Maya Unlimited 8.5\";\n");
+this.output("fileInfo \"version\" \"8.5\";\n");
+this.output("fileInfo \"cutIdentifier\" \"200612170012-692032\";\n");
+this.output("fileInfo \"osv\" \"Mac OS X 10.4.9\"; \n");
+});
+Clazz.defineMethod(c$, "addAttr",
+function(){
+this.output(" setAttr -k off \".v\";\n");
+this.output(" setAttr \".vir\" yes;\n");
+this.output(" setAttr \".vif\" yes;\n");
+this.output(" setAttr \".tw\" yes;\n");
+this.output(" setAttr \".covm[0]\" 0 1 1;\n");
+this.output(" setAttr \".cdvm[0]\" 0 1 1;\n");
+});
+Clazz.defineMethod(c$, "addConnect",
+function(){
+this.output(" connectAttr \"make" + this.name + ".os\" \"" + this.id + ".cr\";\n");
+this.output("connectAttr \"" + this.id + ".iog\" \":initialShadingGroup.dsm\" -na;\n");
+});
+Clazz.defineMethod(c$, "setAttr",
+function(attr, val){
+this.output(" setAttr \"." + attr + "\" " + val + ";\n");
+}, "~S,~N");
+Clazz.defineMethod(c$, "setAttr",
+function(attr, val){
+this.output(" setAttr \"." + attr + "\" " + val + ";\n");
+}, "~S,~N");
+Clazz.defineMethod(c$, "setAttr",
+function(attr, pt){
+this.output(" setAttr \"." + attr + "\" -type \"double3\" " + pt.x + " " + pt.y + " " + pt.z + ";\n");
+}, "~S,JU.T3");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY, checkRadius){
+if (ptX != null) return false;
+this.nCyl++;
+this.name = "nurbsCylinder" + this.nCyl;
+this.id = "nurbsCylinderShape" + this.nCyl;
+this.output(" createNode transform -n \"" + this.name + "\";\n");
+var length = pt1.distance(pt2);
+this.tempV1.ave(pt2, pt1);
+this.setAttr("t", this.tempV1);
+this.tempV1.sub(pt1);
+this.tempV2.setT(this.tempV1);
+this.tempV2.normalize();
+var r = this.tempV1.length();
+var rX = (Math.acos(this.tempV1.y / r) * 57.29577951308232);
+if (this.tempV1.x < 0) rX += 180;
+var rY = (Math.atan2(this.tempV1.x, this.tempV1.z) * 57.29577951308232);
+this.tempV2.set(rX, rY, 0);
+this.setAttr("r", this.tempV2);
+this.output(" createNode nurbsSurface -n \"" + this.id + "\" -p \"" + this.name + "\";\n");
+this.addAttr();
+this.output("createNode makeNurbCylinder -n \"make" + this.name + "\";\n");
+this.output(" setAttr \".ax\" -type \"double3\" 0 1 0;\n");
+this.setAttr("r", radius);
+this.setAttr("s", 4);
+this.setAttr("hr", length / radius);
+this.addConnect();
+return true;
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "outputSphere",
+function(pt, radius, colix, checkRadius){
+this.nBalls++;
+this.name = "nurbsSphere" + this.nBalls;
+this.id = "nurbsSphereShape" + this.nBalls;
+this.output("createNode transform -n \"" + this.name + "\";\n");
+this.setAttr("t", pt);
+this.output("createNode nurbsSurface -n \"" + this.id + "\" -p \"" + this.name + "\";\n");
+this.addAttr();
+this.output("createNode makeNurbSphere -n \"make" + this.name + "\";\n");
+this.output(" setAttr \".ax\" -type \"double3\" 0 1 0;\n");
+this.setAttr("r", radius);
+this.setAttr("s", 4);
+this.setAttr("nsp", 3);
+this.addConnect();
+}, "JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "drawTextPixel",
+function(argb, x, y, z){
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(pt, argb){
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCone",
+function(ptBase, ptTip, radius, colix){
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(center, points, colix){
+}, "JU.P3,~A,~N");
+Clazz.overrideMethod(c$, "outputFace",
+function(is, coordMap, faceVertexMax){
+}, "~A,~A,~N");
+Clazz.defineMethod(c$, "output",
+function(pt){
+}, "JU.T3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_ObjExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_ObjExporter.js
new file mode 100755
index 000000000000..8512a6efd0d0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_ObjExporter.js
@@ -0,0 +1,503 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__CartesianExporter", "java.util.HashSet", "JU.P3"], "J.export._ObjExporter", ["java.util.Hashtable", "JU.AU", "$.BS", "$.CU", "$.Lst", "$.M4", "$.PT", "$.Quat", "$.SB", "$.V3", "J.export.MeshData", "JU.Escape", "$.Logger", "$.MeshSurface", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.surfacesOnly = false;
+this.normalizeUV = true;
+this.mtlout = null;
+this.objFileRootName = null;
+this.nMtlBytes = 0;
+this.textures = null;
+this.textureFiles = null;
+this.sphereNum = 1;
+this.cylinderNum = 1;
+this.ellipseNum = 1;
+this.circleNum = 1;
+this.ellipsoidNum = 1;
+this.coneNum = 1;
+this.triangleNum = 1;
+this.surfaceNum = 1;
+this.currentVertexOrigin = 1;
+this.currentNormalOrigin = 1;
+this.currentTextureOrigin = 1;
+this.ptTemp = null;
+Clazz.instantialize(this, arguments);}, J["export"], "_ObjExporter", J["export"].__CartesianExporter);
+Clazz.prepareFields (c$, function(){
+this.textures = new java.util.HashSet();
+this.ptTemp = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._ObjExporter, []);
+this.debugPrint("_WavefrontObjExporter CTOR");
+this.commentChar = "# ";
+});
+Clazz.defineMethod(c$, "debugPrint",
+function(string){
+if (false) {
+JU.Logger.debug(string);
+}}, "~S");
+Clazz.overrideMethod(c$, "outputFace",
+function(face, map, faceVertexMax){
+}, "~A,~A,~N");
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+this.debugPrint("outputCircle");
+if (this.surfacesOnly) {
+this.debugPrint(" Not done owing to surfacesOnly");
+return;
+}if (doFill) {
+this.outputCircle1(pt1, pt2, colix, radius);
+}}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCone",
+function(ptBase, ptTip, radius, colix){
+this.debugPrint("outputCone");
+if (this.surfacesOnly) {
+this.debugPrint(" Not done owing to surfacesOnly");
+return;
+}this.outputCone1(ptBase, ptTip, radius, colix);
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY, checkRadius){
+if (false) {
+this.debugPrint("outputCylinder: colix=" + String.format("%04x", [Short.$valueOf(colix)]));
+this.debugPrint(" ptCenter=" + ptCenter);
+this.debugPrint(" pt1=" + pt1);
+this.debugPrint(" endcaps=" + endcaps + " NONE=" + 0 + " FLAT=" + 2 + " SPHERICAL=" + 3);
+this.debugPrint(" radius=" + radius);
+this.debugPrint(" pt2=" + pt2);
+this.debugPrint(" ptX=" + ptX);
+this.debugPrint(" ptY=" + ptY);
+}if (this.surfacesOnly) {
+this.debugPrint(" Not done owing to surfacesOnly");
+return true;
+}if (ptX != null) {
+if (endcaps == 2) {
+this.outputEllipse1(ptCenter, pt1, ptX, ptY, colix);
+this.tempP3.add2(ptCenter, ptCenter);
+this.tempP3.sub(ptX);
+this.outputEllipse1(ptCenter, pt2, this.tempP3, ptY, colix);
+}} else if (endcaps == 3) {
+this.outputSphere(pt1, radius * 1.01, colix, true);
+this.outputSphere(pt2, radius * 1.01, colix, true);
+} else if (endcaps == 2) {
+this.outputCircle1(pt1, pt2, colix, radius);
+this.outputCircle1(pt2, pt1, colix, radius);
+}this.outputCylinder1(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY);
+return true;
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3,~B");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(center, points, colix){
+if (false) {
+this.debugPrint("outputEllipsoid: colix=" + String.format("%04x", [Short.$valueOf(colix)]));
+this.debugPrint(" center=" + center);
+this.debugPrint(" points[0]=" + points[0]);
+this.debugPrint(" points[1]=" + points[1]);
+this.debugPrint(" points[2]=" + points[2]);
+}if (this.surfacesOnly) {
+this.debugPrint(" Not done owing to surfacesOnly");
+return;
+}var a = JU.Quat.getQuaternionFrame(center, points[1], points[3]).toAxisAngle4f();
+var sx = points[1].distance(center);
+var sy = points[3].distance(center);
+var sz = points[5].distance(center);
+this.outputEllipsoid1(center, sx, sy, sz, a, colix);
+}, "JU.P3,~A,~N");
+Clazz.overrideMethod(c$, "outputSphere",
+function(center, radius, colix, checkRadius){
+if (false) {
+this.debugPrint("outputSphere: colix=" + String.format("%04x", [Short.$valueOf(colix)]));
+this.debugPrint(" center.getClass().getName()=" + center.getClass().getName());
+this.debugPrint(" center=" + center);
+this.debugPrint(" center.x=" + center.x);
+this.debugPrint(" center.y=" + center.y);
+this.debugPrint(" center.z=" + center.z);
+this.debugPrint(" radius=" + radius);
+}if (this.surfacesOnly) {
+this.debugPrint(" Not done owing to surfacesOnly");
+return;
+}this.outputEllipsoid1(center, radius, radius, radius, null, colix);
+}, "JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(pt, argb){
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+if (this.surfacesOnly) {
+return;
+}this.outputTriangle1(pt1, pt2, pt3, colix);
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.debugPrint("outputHeader");
+this.output("#obj Created by Jmol " + JV.Viewer.getJmolVersion() + "\n");
+});
+Clazz.defineMethod(c$, "output",
+function(pt){
+this.debugPrint("output");
+}, "JU.T3");
+Clazz.overrideMethod(c$, "drawSurface",
+function(meshSurface, colix){
+if (JU.Logger.debugging) {
+this.debugPrint("outputSurface");
+this.debugPrint(" nVertices=" + meshSurface.vc);
+if (meshSurface.normals == null) {
+this.debugPrint(" no vertex normals");
+} else {
+this.debugPrint(" nNormals=" + meshSurface.vc);
+}if (meshSurface.vcs == null) {
+this.debugPrint(" no vertex colors");
+} else {
+this.debugPrint(" nColixes=" + meshSurface.vc);
+}this.debugPrint(" number of triangles or quads=" + meshSurface.pc);
+if (meshSurface.pcs == null) {
+this.debugPrint(" no face colors");
+} else {
+this.debugPrint(" nPolygonColixes=" + meshSurface.pc);
+}if (meshSurface.bsPolygons == null) {
+this.debugPrint(" all polygons used");
+} else {
+this.debugPrint(" number of polygons used=" + meshSurface.bsPolygons.cardinality());
+}this.debugPrint(" solid color=" + this.gdata.getColorArgbOrGray(colix));
+}var bsPolygons = meshSurface.bsPolygons;
+var nPolygons = meshSurface.pc;
+if (meshSurface.normals != null) meshSurface.normalCount = meshSurface.vc;
+var isAll = (bsPolygons == null);
+var faces = JU.AU.newInt2(isAll ? nPolygons : bsPolygons.cardinality());
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0, ipt = 0; i >= 0; i = isAll ? i - 1 : bsPolygons.nextSetBit(i + 1)) {
+var polygon = meshSurface.pis[i];
+faces[ipt++] = (meshSurface.haveQuads ? polygon : Clazz.newIntArray(-1, [polygon[0], polygon[1], polygon[2]]));
+}
+var data = JU.MeshSurface.newMesh(false, meshSurface.vs, meshSurface.vc, faces, meshSurface.normals, 0);
+data.vcs = meshSurface.vcs;
+var name = "Surface" + this.surfaceNum++;
+var isSolidColor = (colix != 0);
+this.addTexture(colix, isSolidColor ? null : name);
+var dim = null;
+if (isSolidColor) {
+this.debugPrint("outputSurface: coloring solid");
+this.debugPrint(" Omitting texture map");
+} else {
+var nFaces = faces.length;
+var width = Clazz.doubleToInt(Math.ceil(Math.sqrt(nFaces)));
+var height = Clazz.doubleToInt(nFaces / width);
+if (nFaces % width != 0) {
+height++;
+}dim = Clazz.newIntArray(-1, [width, height]);
+this.debugPrint(" width=" + width + " height=" + height + " size = " + (width * height));
+var file = this.createTextureFile(name, data, dim);
+if (file == null || file.getByteCount() == 0) {
+System.out.println("Error creating texture file: " + name);
+this.textureFiles.addLast("Error creating texture file: " + name);
+return;
+}this.textureFiles.addLast(file.getByteCount() + " (" + width + "x" + height + ") " + name);
+var shortName = file.getName();
+this.outputMtl(" map_Kd " + shortName + "\n");
+this.outputMtl(" map_Ka " + shortName + "\n");
+}var matrix = JU.M4.newM4(null);
+matrix.setTranslation(JU.V3.newV(meshSurface.offset));
+var bsValid = new JU.BS();
+this.addMesh(name, data, matrix, null, colix, dim, bsValid);
+}, "JU.MeshSurface,~N");
+Clazz.overrideMethod(c$, "initializeOutput",
+function(vwr, privateKey, gdata, params){
+this.debugPrint("initializeOutput: + output");
+var retVal = this.initOutput(vwr, privateKey, gdata, params);
+if (!retVal) {
+this.debugPrint("End initializeOutput (error in super):");
+return false;
+}if (this.fileName == null) {
+throw new NullPointerException("Cannot output two files (OBJ and MTL) to string");
+}var dot = this.fileName.lastIndexOf(".");
+if (dot < 0) {
+this.debugPrint("End initializeOutput (Error creating .mtl file):");
+return false;
+}this.objFileRootName = this.fileName.substring(0, dot);
+try {
+var mtlFileName = this.objFileRootName + ".mtl";
+this.mtlout = vwr.openExportChannel(privateKey, mtlFileName, true);
+} catch (ex) {
+if (Clazz.exceptionOf(ex, Exception)){
+this.debugPrint("End initializeOutput (" + ex.getMessage() + "):");
+return false;
+} else {
+throw ex;
+}
+}
+this.outputMtl("# Created by Jmol " + JV.Viewer.getJmolVersion() + "\n");
+this.output("\nmtllib " + this.mtlout.getName() + "\n");
+this.textureFiles = new JU.Lst();
+this.debugPrint("End initializeOutput:");
+return true;
+}, "JV.Viewer,~N,JU.GData,java.util.Map");
+Clazz.overrideMethod(c$, "finalizeOutput",
+function(){
+this.debugPrint("finalizeOutput");
+var retVal = this.finalizeOutput2();
+var ret = this.mtlout.closeChannel();
+if (ret != null) {
+JU.Logger.info(ret);
+ret = "ERROR EXPORTING MTL FILE: " + ret;
+if (retVal.startsWith("OK")) return ret;
+return retVal + " and " + ret;
+}retVal += ", " + this.nMtlBytes + " " + this.mtlout.getFileName();
+for (var string, $string = this.textureFiles.iterator (); $string.hasNext()&& ((string = $string.next ()) || true);) {
+retVal += ", " + string;
+}
+this.debugPrint(retVal);
+this.debugPrint("End finalizeOutput:");
+return retVal;
+});
+Clazz.defineMethod(c$, "outputMtl",
+function(data){
+this.nMtlBytes += data.length;
+this.mtlout.append(data);
+}, "~S");
+Clazz.defineMethod(c$, "getTextureName",
+function(colix){
+return "k" + JU.Escape.getHexColorFromRGB(this.gdata.getColorArgbOrGray(colix));
+}, "~N");
+Clazz.defineMethod(c$, "outputCircle1",
+function(ptCenter, ptPerp, colix, radius){
+var data = J["export"].MeshData.getCircleData();
+var matrix = new JU.M4();
+this.addTexture(colix, null);
+var name = "Circle" + this.circleNum++;
+matrix.setToM3(this.getRotationMatrix(ptCenter, ptPerp, radius));
+matrix.m03 = ptCenter.x;
+matrix.m13 = ptCenter.y;
+matrix.m23 = ptCenter.z;
+matrix.m33 = 1;
+this.addMesh(name, data, matrix, matrix, colix, null, null);
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "outputCone1",
+function(ptBase, ptTip, radius, colix){
+var data = J["export"].MeshData.getConeData();
+var matrix = new JU.M4();
+this.addTexture(colix, null);
+var name = "Cone" + this.coneNum++;
+matrix.setToM3(this.getRotationMatrix(ptBase, ptTip, radius));
+matrix.m03 = ptBase.x;
+matrix.m13 = ptBase.y;
+matrix.m23 = ptBase.z;
+matrix.m33 = 1;
+this.addMesh(name, data, matrix, matrix, colix, null, null);
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "outputEllipse1",
+function(ptCenter, ptZ, ptX, ptY, colix){
+var data = J["export"].MeshData.getCircleData();
+var matrix = new JU.M4();
+this.addTexture(colix, null);
+var name = "Ellipse" + this.ellipseNum++;
+matrix.setToM3(this.getRotationMatrix(ptCenter, ptZ, 1, ptX, ptY));
+matrix.m03 = ptZ.x;
+matrix.m13 = ptZ.y;
+matrix.m23 = ptZ.z;
+matrix.m33 = 1;
+this.addMesh(name, data, matrix, matrix, colix, null, null);
+return true;
+}, "JU.P3,JU.P3,JU.P3,JU.P3,~N");
+Clazz.defineMethod(c$, "outputEllipsoid1",
+function(center, rx, ry, rz, a, colix){
+var data = JU.MeshSurface.getSphereData(3);
+this.addTexture(colix, null);
+var name;
+if (Clazz.instanceOf(center,"JM.Atom")) {
+var atom = center;
+name = JU.PT.replaceAllCharacters(atom.getAtomName(), " \t", "") + "_Atom";
+} else if (rx == ry && rx == rz) {
+name = "Sphere" + this.sphereNum++;
+} else {
+name = "Ellipsoid" + this.ellipsoidNum++;
+}this.setSphereMatrix(center, rx, ry, rz, a, this.sphereMatrix);
+this.addMesh(name, data, this.sphereMatrix, this.sphereMatrix, colix, null, null);
+}, "JU.T3,~N,~N,~N,JU.A4,~N");
+Clazz.defineMethod(c$, "outputCylinder1",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY){
+var data = J["export"].MeshData.getCylinderData(false);
+var matrix = new JU.M4();
+this.addTexture(colix, null);
+var name = "Cylinder" + this.cylinderNum++;
+var n = (ptX != null && endcaps == 0 ? 2 : 1);
+for (var i = 0; i < n; i++) {
+if (ptX == null) matrix.setToM3(this.getRotationMatrix(pt1, pt2, radius));
+ else matrix.setToM3(this.getRotationMatrix(ptCenter, pt2, radius, ptX, ptY));
+matrix.m03 = pt1.x;
+matrix.m13 = pt1.y;
+matrix.m23 = pt1.z;
+matrix.m33 = 1;
+}
+this.addMesh(name, data, matrix, matrix, colix, null, null);
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3");
+Clazz.defineMethod(c$, "outputTriangle1",
+function(pt1, pt2, pt3, colix){
+var data = J["export"].MeshData.getTriangleData(pt1, pt2, pt3);
+this.addTexture(colix, null);
+var name = "Triangle" + this.triangleNum++;
+var matrix = JU.M4.newM4(null);
+this.addMesh(name, data, matrix, matrix, colix, null, null);
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.defineMethod(c$, "addTexture",
+function(colix, name){
+var scolix = Short.$valueOf(colix);
+if (name == null && this.textures.contains(scolix)) {
+return;
+}this.textures.add(scolix);
+var sb = new JU.SB();
+sb.append("\nnewmtl " + (name == null ? this.getTextureName(colix) : name) + "\n");
+sb.append(" Ns 163\n");
+sb.append(" Tr " + J["export"].___Exporter.opacityFractionalFromColix(colix) + "\n");
+sb.append(" Ni 0.001\n");
+sb.append(" illum 2\n");
+sb.append(" Ka 0.20 0.20 0.20\n");
+sb.append(" Kd " + this.rgbFractionalFromColix(colix) + "\n");
+sb.append(" Ks 0.25 0.25 0.25\n");
+this.outputMtl(sb.toString());
+}, "~N,~S");
+Clazz.defineMethod(c$, "addMesh",
+function(name, data, matrix, matrix1, colix, dim, bsValid){
+if (this.surfacesOnly) {
+if (name == null || !name.startsWith("Surface")) {
+return;
+}}this.output("\ng " + name + "\n");
+this.output("usemtl " + (dim == null ? this.getTextureName(colix) : name) + "\n");
+var faces = data.getFaces();
+var nFaces = faces.length;
+if (bsValid != null) for (var face, $face = 0, $$face = faces; $face < $$face.length && ((face = $$face[$face]) || true); $face++) for (var i, $i = 0, $$i = face; $i < $$i.length && ((i = $$i[$i]) || true); $i++) bsValid.set(i);
+
+
+var vertices = data.getVertices();
+var nVertices = data.vc;
+var map = Clazz.newIntArray (nVertices, 0);
+var nCoord = this.getCoordinateMap(vertices, map, bsValid);
+this.output("# Number of vertices: " + nCoord + "\n");
+this.outputList(vertices, nVertices, matrix, "v ", bsValid);
+nVertices = nCoord;
+var normals = data.normals;
+var nNormals = data.normalCount;
+var map2 = null;
+var vNormals = null;
+if (normals != null) {
+vNormals = new JU.Lst();
+map2 = this.getNormalMap(normals, nNormals, bsValid, vNormals);
+nNormals = vNormals.size();
+this.output("# Number of normals: " + nNormals + "\n");
+for (var i = 0; i < nNormals; i++) this.output("vn " + vNormals.get(i));
+
+}if (dim != null) {
+this.output("# Number of texture coordinates: " + nFaces + "\n");
+var width = dim[0];
+var height = dim[1];
+var u;
+var v;
+for (var row = 0, iFace = 0; row < height; row++) {
+v = row + .5;
+if (this.normalizeUV) v /= height;
+for (var col = 0; col < width; col++) {
+u = col + .5;
+if (this.normalizeUV) u /= width;
+this.output("vt " + u + " " + v + "\n");
+if (++iFace == nFaces) break;
+}
+}
+if (!this.normalizeUV) {
+this.output("vt 0.0 0.0\n");
+this.output("vt " + width + " " + height + "\n");
+}}this.output("# Number of faces: " + nFaces + "\n");
+for (var i = 0; i < nFaces; i++) if (dim != null) this.outputFace2(faces[i], i, map, map2);
+ else this.outputFace1(faces[i], map, map2);
+
+if (dim != null) this.currentTextureOrigin += nFaces;
+this.currentVertexOrigin += nVertices;
+this.currentNormalOrigin += nNormals;
+}, "~S,JU.MeshSurface,JU.M4,JU.M4,~N,~A,JU.BS");
+Clazz.defineMethod(c$, "outputList",
+function(pts, nPts, m, prefix, bsValid){
+for (var i = 0; i < nPts; i++) {
+if (bsValid != null && !bsValid.get(i)) continue;
+this.ptTemp.setT(pts[i]);
+if (m != null) m.rotTrans(this.ptTemp);
+this.output(prefix + this.ptTemp.x + " " + this.ptTemp.y + " " + this.ptTemp.z + "\n");
+}
+}, "~A,~N,JU.M4,~S,JU.BS");
+Clazz.defineMethod(c$, "outputFace1",
+function(face, map, map2){
+this.output("f");
+for (var i, $i = 0, $$i = face; $i < $$i.length && ((i = $$i[$i]) || true); $i++) this.output(" " + ((map == null ? i : map[i]) + this.currentVertexOrigin) + "//" + ((map2 == null ? i : map2[i]) + this.currentNormalOrigin));
+
+this.output("\n");
+}, "~A,~A,~A");
+Clazz.defineMethod(c$, "outputFace2",
+function(face, vt, map, map2){
+this.output("f");
+for (var i, $i = 0, $$i = face; $i < $$i.length && ((i = $$i[$i]) || true); $i++) {
+this.output(" " + ((map == null ? i : map[i]) + this.currentVertexOrigin) + "/" + (this.currentTextureOrigin + vt) + "/" + ((map2 == null ? i : map2[i]) + this.currentNormalOrigin));
+}
+this.output("\n");
+}, "~A,~N,~A,~A");
+Clazz.defineMethod(c$, "createTextureFile",
+function(name, data, dim){
+this.debugPrint("createTextureFile: " + name);
+var colixes = (data.pcs == null ? data.vcs : data.pcs);
+if (colixes == null || colixes.length == 0) {
+this.debugPrint("createTextureFile: Array problem");
+this.debugPrint(" colixes=" + colixes + " data=" + data);
+if (colixes != null) {
+this.debugPrint(" colixes.length=" + colixes.length);
+}return null;
+}var nUsed = data.pis.length;
+if (nUsed <= 0) {
+this.debugPrint("createTextureFile: nFaces = 0");
+return null;
+}var width = dim[0];
+var height = dim[1];
+var textureType = "png";
+var row = height - 1;
+var col = 0;
+var sum = new JU.P3();
+var w = width * 3;
+var h = height * 3;
+var bytes = (textureType.equals("tga") ? Clazz.newByteArray (h, w * 3, 0) : null);
+var rgbbuf = (bytes == null ? Clazz.newIntArray (h * w, 0) : null);
+var ptTemp = new JU.P3();
+for (var i = 0; i < data.pis.length; i++) {
+var rgb;
+if (data.pcs == null) {
+var face = data.pis[i];
+sum.set(0, 0, 0);
+for (var iVertex, $iVertex = 0, $$iVertex = face; $iVertex < $$iVertex.length && ((iVertex = $$iVertex[$iVertex]) || true); $iVertex++) sum.add(JU.CU.colorPtFromInt(this.gdata.getColorArgbOrGray(colixes[iVertex]), ptTemp));
+
+sum.scale(1.0 / face.length);
+rgb = JU.CU.colorPtToFFRGB(sum);
+} else {
+rgb = this.gdata.getColorArgbOrGray(colixes[i]);
+}if (bytes == null) {
+for (var j = 0; j < 3; j++) for (var k = 0; k < 3; k++) rgbbuf[(row * 3 + k) * w + col * 3 + j] = rgb;
+
+
+} else {
+}if ((col = (col + 1) % width) == 0) row--;
+}
+try {
+var params = new java.util.Hashtable();
+var fname = this.fileName;
+if (rgbbuf != null) {
+params.put("rgbbuf", rgbbuf);
+params.put("fileName", this.objFileRootName + "_" + name + "." + textureType);
+params.put("type", textureType);
+params.put("width", Integer.$valueOf(w));
+params.put("height", Integer.$valueOf(h));
+fname = this.fileName = this.vwr.outputToFile(params);
+}this.debugPrint("End createTextureFile: " + fname);
+return params.get("outputChannel");
+} catch (ex) {
+if (Clazz.exceptionOf(ex, Exception)){
+this.debugPrint("End createTextureFile (" + ex.getMessage() + "):");
+return null;
+} else {
+throw ex;
+}
+}
+}, "~S,JU.MeshSurface,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_PovrayExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_PovrayExporter.js
new file mode 100755
index 000000000000..f6d4429e9d4c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_PovrayExporter.js
@@ -0,0 +1,245 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__RayTracerExporter"], "J.export._PovrayExporter", ["JU.Measure", "$.P4", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.haveMacros = false;
+Clazz.instantialize(this, arguments);}, J["export"], "_PovrayExporter", J["export"].__RayTracerExporter);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._PovrayExporter, []);
+this.commentChar = "// ";
+});
+Clazz.overrideMethod(c$, "finalizeOutput",
+function(){
+this.finalizeOutput2();
+return this.getAuxiliaryFileData();
+});
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.initVars();
+this.output("// ******************************************************\n");
+this.output("// Created by Jmol " + JV.Viewer.getJmolVersion() + "\n");
+this.output("//\n");
+this.output("// This script was generated on " + this.getExportDate() + "\n");
+this.output("// ******************************************************\n");
+try {
+this.output(this.vwr.getWrappedStateScript());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+this.output("\n");
+this.output(this.getJmolPerspective());
+this.output("\n");
+this.output("// ******************************************************\n");
+this.output("// Declare the resolution, camera, and light sources.\n");
+this.output("// ******************************************************\n");
+this.output("\n");
+this.output("// NOTE: if you plan to render at a different resolution,\n");
+this.output("// be sure to update the following two lines to maintain\n");
+this.output("// the correct aspect ratio.\n\n");
+this.output("#declare Width = " + this.screenWidth + ";\n");
+this.output("#declare Height = " + this.screenHeight + ";\n");
+this.output("#declare minScreenDimension = " + this.minScreenDimension + ";\n");
+this.output("#declare showAtoms = true;\n");
+this.output("#declare showBonds = true;\n");
+this.output("#declare noShadows = true;\n");
+this.output("camera{\n");
+var offsetX;
+var offsetY;
+var f;
+if (this.wasPerspective) {
+offsetX = this.vwr.tm.getTranslationXPercent() / 100 * this.screenWidth;
+offsetY = this.vwr.tm.getTranslationYPercent() / 100 * this.screenHeight;
+f = 1 / this.vwr.tm.getPerspectiveFactor((this.vwr.tm.getCameraDepth() - 0.5) * this.vwr.getScreenDim());
+this.output(" perspective\n");
+this.output(" angle " + this.apertureAngle + "\n");
+this.output(" right < " + this.screenWidth + ", 0, 0>\n");
+this.output(" up < 0, " + -this.screenHeight + ", 0 >\n");
+} else {
+offsetX = offsetY = f = 0;
+this.output(" orthographic\n");
+this.output(" right < " + -this.screenWidth + ", 0, 0>\n");
+this.output(" up < 0, " + this.screenHeight + ", 0 >\n");
+}this.output(" sky < 0, -1, 0 >\n");
+this.output(" location < " + (this.screenWidth / 2 + offsetX) + ", " + (this.screenHeight / 2 + offsetY) + ", 0>\n");
+this.output(" look_at < " + (this.screenWidth / 2 + f * offsetX) + ", " + (this.screenHeight / 2 + f * offsetY) + ", 1000 >\n");
+this.output("}\n");
+this.output("\n");
+this.output("background { color rgb <" + this.rgbFractionalFromColix(this.backgroundColix) + "> }\n");
+this.output("\n");
+var distance = Math.max(this.screenWidth, this.screenHeight);
+this.output("light_source { <" + this.lightSource.x * distance + "," + this.lightSource.y * distance + ", " + (-1 * this.lightSource.z * distance) + "> " + " rgb <0.6,0.6,0.6> }\n");
+this.output("\n");
+this.output("\n");
+this.output("// ***********************************************\n");
+this.output("// macros for common shapes\n");
+this.output("// ***********************************************\n");
+this.output("\n");
+this.writeMacros();
+});
+Clazz.defineMethod(c$, "writeMacros",
+function(){
+this.output("#default { finish {\n" + " ambient " + this.gdata.getAmbientPercent() / 100 + "\n" + " diffuse " + this.gdata.getDiffusePercent() / 100 + "\n" + " specular " + this.gdata.getSpecularPercent() / 100 + "\n" + " roughness .00001\n metallic\n phong 0.9\n phong_size 120\n}}" + "\n\n");
+this.output("#macro check_shadow()\n #if (noShadows)\n no_shadow \n #end\n#end\n\n");
+this.output("#declare slabZ = " + this.slabZ + ";\n" + "#declare depthZ = " + this.depthZ + ";\n" + "#declare dzSlab = 10;\n" + "#declare dzDepth = dzSlab;\n" + "#declare dzStep = 0.001;\n\n");
+this.output("#macro clip()\n clipped_by { box {<0,0,slabZ>,} }\n#end\n\n");
+this.output("#macro circleCap(Z,RADIUS,R,G,B,T)\n// cap for lower clip\n #local cutDiff = Z - slabZ;\n #local cutRadius2 = (RADIUS*RADIUS) - (cutDiff*cutDiff);\n #if (cutRadius2 > 0)\n #local cutRadius = sqrt(cutRadius2);\n #if (dzSlab > 0)\n #declare dzSlab = dzSlab - dzStep;\n #end\n cylinder{,,cutRadius\n pigment{rgbt}\n translucentFinish(T)\n check_shadow()}\n #end\n// cap for upper clip\n #declare cutDiff = Z - depthZ;\n #declare cutRadius2 = (RADIUS*RADIUS) - (cutDiff*cutDiff);\n #if (cutRadius2 > 0)\n #local cutRadius = sqrt(cutRadius2);\n #if (dzDepth > 0)\n #declare dzDepth = dzDepth - dzStep;\n #end\n cylinder{,,cutRadius\n pigment{rgbt}\n translucentFinish(T)\n check_shadow()}\n #end\n#end\n\n");
+this.writeMacrosFinish();
+this.writeMacrosAtom();
+this.writeMacrosBond();
+});
+Clazz.defineMethod(c$, "writeMacrosFinish",
+function(){
+this.output("#macro translucentFinish(T)\n" + " #local shineFactor = T;\n" + " #if (T <= 0.25)\n" + " #declare shineFactor = (1.0-4*T);\n" + " #end\n" + " #if (T > 0.25)\n" + " #declare shineFactor = 0;\n" + " #end\n" + " finish {\n" + " ambient " + this.gdata.getAmbientPercent() / 100 + "\n" + " diffuse " + this.gdata.getDiffusePercent() / 100 + "\n" + " specular " + this.gdata.getSpecularPercent() / 100 + "\n" + " roughness .00001\n" + " metallic shineFactor\n" + " phong 0.9*shineFactor\n" + " phong_size 120*shineFactor\n}" + "#end\n\n");
+});
+Clazz.defineMethod(c$, "writeMacrosAtom",
+function(){
+this.output("#macro a(X,Y,Z,RADIUS,R,G,B,T)\n sphere{,RADIUS\n pigment{rgbt}\n translucentFinish(T)\n clip()\n check_shadow()}\n" + (this.isSlabEnabled ? " circleCap(Z,RADIUS,R,G,B,T)\n" : "") + "#end\n\n");
+this.output("#macro q(XX,YY,ZZ,XY,XZ,YZ,X,Y,Z,J,R,G,B,T)\n quadric{,,,J\n pigment{rgbt}\n translucentFinish(T)\n clip()\n check_shadow()}\n#end\n\n");
+});
+Clazz.defineMethod(c$, "writeMacrosBond",
+function(){
+this.output("#macro b(X1,Y1,Z1,RADIUS1,X2,Y2,Z2,RADIUS2,R,G,B,T)\n cone{,RADIUS1,,RADIUS2\n pigment{rgbt}\n translucentFinish(T)\n clip()\n check_shadow()}\n#end\n\n");
+this.output("#macro c(X1,Y1,Z1,RADIUS1,X2,Y2,Z2,RADIUS2,R,G,B,T)\n cone{,RADIUS1,,RADIUS2 open\n pigment{rgbt}\n translucentFinish(T)\n clip()\n check_shadow()}\n#end\n\n");
+});
+Clazz.defineMethod(c$, "writeMacros2",
+function(){
+this.output("#macro r(X1,Y1,Z1,X2,Y2,Z2,X3,Y3,Z3,R,G,B,T)\n triangle{,,\n pigment{rgbt}\n translucentFinish(T)\n clip()\n check_shadow()}\n#end\n\n");
+this.output("#macro p(X,Y,Z,R,G,B,T)\n box{,\n pigment{rgbt}\n clip()\n check_shadow()}\n#end\n\n");
+this.output("#macro barb(X1,Y1,Z1,RADIUS1,X2,Y2,Z2,RADIUS2,R,G,B,T,X3,Y3,Z3,W3)\n cone{,RADIUS1,,RADIUS2\n pigment{rgbt}\n translucentFinish(T)\n clip()\n clipped_by{plane{,W3}}\n check_shadow()}\n#end\n\n");
+this.haveMacros = true;
+});
+Clazz.defineMethod(c$, "getTriad",
+function(pt){
+if (Float.isNaN(pt.x)) return "0,0,0";
+return pt.x + "," + pt.y + "," + pt.z;
+}, "JU.T3");
+Clazz.defineMethod(c$, "getTriad",
+function(i){
+return i[0] + "," + i[1] + "," + i[2];
+}, "~A");
+Clazz.defineMethod(c$, "color4",
+function(colix){
+return this.rgbFractionalFromColix(colix) + "," + J["export"].___Exporter.translucencyFractionalFromColix(colix);
+}, "~N");
+Clazz.defineMethod(c$, "getAuxiliaryFileData",
+function(){
+var fName = this.fileName.substring(this.fileName.lastIndexOf("/") + 1);
+fName = fName.substring(fName.lastIndexOf("\\") + 1);
+return "; Created by: Jmol " + JV.Viewer.getJmolVersion() + "\n; Creation date: " + this.getExportDate() + "\n; File created: " + this.fileName + " (" + this.getByteCount() + " bytes)\n\n" + (this.commandLineOptions != null ? this.commandLineOptions : "\n; Jmol state: (embedded in input file)\nInput_File_Name=" + fName + "\nOutput_to_File=true" + "\nOutput_File_Type=N" + "\nOutput_File_Name=" + fName + ".png" + "\nWidth=" + this.screenWidth + "\nHeight=" + this.screenHeight + "\nAntialias=true" + "\nAntialias_Threshold=0.1" + "\nDisplay=true" + "\nPause_When_Done=true" + "\nWarning_Level=5" + "\nVerbose=false" + "\n");
+});
+Clazz.defineMethod(c$, "output",
+function(pt){
+this.output(", <" + this.getTriad(pt) + ">");
+}, "JU.T3");
+Clazz.overrideMethod(c$, "outputCircle",
+function(x, y, z, radius, colix, doFill){
+this.output((doFill ? "b(" : "c(") + x + "," + y + "," + z + "," + radius + "," + x + "," + y + "," + (z + 1) + "," + (radius + (doFill ? 0 : 2)) + "," + this.color4(colix) + ")\n");
+}, "~N,~N,~N,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCone",
+function(screenBase, screenTip, radius, colix, isBarb){
+if (isBarb) {
+if (!this.haveMacros) this.writeMacros2();
+this.tempP1.set(screenBase.x, screenTip.y, 12345.6789);
+var plane = JU.Measure.getPlaneThroughPoints(screenBase, screenTip, this.tempP1, this.tempV1, this.tempV2, new JU.P4());
+this.output("barb(" + this.getTriad(screenBase) + "," + radius + "," + this.getTriad(screenTip) + ",0" + "," + this.color4(colix) + "," + plane.x + "," + plane.y + "," + plane.z + "," + -plane.w + ")\n");
+} else {
+this.output("b(" + this.getTriad(screenBase) + "," + radius + "," + this.getTriad(screenTip) + ",0" + "," + this.color4(colix) + ")\n");
+}}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(screenA, screenB, radius, colix, withCaps){
+var color = this.color4(colix);
+this.output((withCaps ? "b(" : "c(") + this.getTriad(screenA) + "," + radius + "," + this.getTriad(screenB) + "," + radius + "," + color + ")\n");
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCylinderConical",
+function(screenA, screenB, radius1, radius2, colix){
+this.output("b(" + this.getTriad(screenA) + "," + radius1 + "," + this.getTriad(screenB) + "," + radius2 + "," + this.color4(colix) + ")\n");
+}, "JU.P3,JU.P3,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(center, radius, coef, colix){
+var s = coef[0] + "," + coef[1] + "," + coef[2] + "," + coef[3] + "," + coef[4] + "," + coef[5] + "," + coef[6] + "," + coef[7] + "," + coef[8] + "," + coef[9] + "," + this.color4(colix);
+this.output("q(" + s + ")\n");
+}, "JU.P3,~N,~A,~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+if (polygonColixes != null) {
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+this.output("polygon { 4\n");
+for (var j = 0; j <= 3; j++) this.outputVertex(vertices[indices[i][j % 3]], offset);
+
+this.output("\n");
+this.output("pigment{rgbt<" + this.color4(colix = polygonColixes[i]) + ">}\n");
+this.output(" translucentFinish(" + J["export"].___Exporter.translucencyFractionalFromColix(colix) + ")\n");
+this.output(" check_shadow()\n");
+this.output(" clip()\n");
+this.output("}\n");
+}
+return;
+}this.output("mesh2 {\n");
+this.output("vertex_vectors { " + nVertices);
+for (var i = 0; i < nVertices; i++) this.outputVertex(vertices[i], offset);
+
+this.output("\n}\n");
+var haveNormals = (normals != null);
+if (haveNormals) {
+this.output("normal_vectors { " + nVertices);
+for (var i = 0; i < nVertices; i++) {
+J["export"].___Exporter.setTempVertex(vertices[i], offset, this.tempP2);
+this.output(this.getScreenNormal(this.tempP2, normals[i], 1));
+this.output("\n");
+}
+this.output("\n}\n");
+}if (colixes != null) {
+var nColix = colorList.size();
+this.output("texture_list { " + nColix);
+var finish = ">} translucentFinish(" + J["export"].___Exporter.translucencyFractionalFromColix(colixes[0]) + ")}";
+for (var i = 0; i < nColix; i++) this.output("\n, texture{pigment{rgbt<" + this.color4(colorList.get(i).shortValue()) + finish);
+
+this.output("\n}\n");
+}this.output("face_indices { " + nTriangles);
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+this.output(", <" + this.getTriad(indices[i]) + ">");
+if (colixes != null) {
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][0]])));
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][1]])));
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][2]])));
+}if (faceVertexMax == 4 && indices[i].length == 4) {
+this.output(", <" + indices[i][0] + "," + indices[i][2] + "," + indices[i][3] + ">");
+if (colixes != null) {
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][0]])));
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][2]])));
+this.output("," + htColixes.get(Short.$valueOf(colixes[indices[i][3]])));
+}}this.output("\n");
+}
+this.output("\n}\n");
+if (colixes == null) {
+this.output("pigment{rgbt<" + this.color4(colix) + ">}\n");
+this.output(" translucentFinish(" + J["export"].___Exporter.translucencyFractionalFromColix(colix) + ")\n");
+}this.output(" check_shadow()\n");
+this.output(" clip()\n");
+this.output("}\n");
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.overrideMethod(c$, "outputSphere",
+function(x, y, z, radius, colix){
+this.output("a(" + x + "," + y + "," + z + "," + radius + "," + this.color4(colix) + ")\n");
+}, "~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(x, y, z, argb){
+if (!this.haveMacros) this.writeMacros2();
+var tr = ((argb >> 24) & 0xFF);
+tr = (255 - tr) / 255;
+this.output("p(" + x + "," + y + "," + z + "," + this.rgbFractionalFromArgb(argb) + "," + tr + ")\n");
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(ptA, ptB, ptC, colix){
+if (!this.haveMacros) this.writeMacros2();
+this.output("r(" + this.getTriad(ptA) + "," + this.getTriad(ptB) + "," + this.getTriad(ptC) + "," + this.color4(colix) + ")\n");
+}, "JU.T3,JU.T3,JU.T3,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_StlExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_StlExporter.js
new file mode 100755
index 000000000000..d117ec8d3bff
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_StlExporter.js
@@ -0,0 +1,147 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export._VrmlExporter", "JU.M4"], "J.export._StlExporter", ["java.io.ByteArrayOutputStream", "JU.Lst", "$.Measure", "$.OC", "JU.Logger", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isDebug = false;
+this.header = null;
+this.oc = null;
+this.bos = null;
+this.m4 = null;
+this.lstMatrix = null;
+this.m4a = null;
+this.nTri = 0;
+Clazz.instantialize(this, arguments);}, J["export"], "_StlExporter", J["export"]._VrmlExporter);
+Clazz.prepareFields (c$, function(){
+this.m4a = new JU.M4();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor(this, J["export"]._StlExporter);
+this.useTable = null;
+this.lineWidthMad = 20;
+this.noColor = true;
+this.isDebug = JU.Logger.debugging;
+if (!this.isDebug) {
+this.oc = new JU.OC();
+this.oc.setBigEndian(false);
+this.oc.setParams(null, null, false, this.bos = new java.io.ByteArrayOutputStream());
+}});
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.header = ("solid model generated by Jmol " + JV.Viewer.getJmolVersion() + " ").substring(0, 80);
+if (this.isDebug) {
+this.out.append(this.header);
+this.out.append("\n");
+} else {
+this.oc.write(this.header.getBytes(), 0, 80);
+this.oc.write( Clazz.newByteArray (4, 0), 0, 4);
+}this.lstMatrix = new JU.Lst();
+this.m4 = new JU.M4();
+this.m4.setIdentity();
+this.lstMatrix.addLast(this.m4);
+this.outputInitialTransform();
+});
+Clazz.overrideMethod(c$, "pushMatrix",
+function(){
+this.lstMatrix.addLast(this.m4);
+this.m4 = JU.M4.newM4(this.m4);
+});
+Clazz.overrideMethod(c$, "popMatrix",
+function(){
+this.m4 = this.lstMatrix.removeItemAt(this.lstMatrix.size() - 1);
+});
+Clazz.defineMethod(c$, "output",
+function(data){
+}, "~S");
+Clazz.overrideMethod(c$, "outputChildStart",
+function(){
+});
+Clazz.overrideMethod(c$, "outputChildClose",
+function(){
+});
+Clazz.overrideMethod(c$, "outputRotation",
+function(a){
+this.m4a.setToAA(a);
+this.m4.mul(this.m4a);
+}, "JU.A4");
+Clazz.overrideMethod(c$, "outputAttrPt",
+function(attr, pt){
+this.outputAttr(attr, pt.x, pt.y, pt.z);
+}, "~S,JU.T3");
+Clazz.overrideMethod(c$, "outputAttr",
+function(attr, x, y, z){
+this.m4a.setIdentity();
+if (attr === "scale") {
+this.m4a.m00 = x;
+this.m4a.m11 = y;
+this.m4a.m22 = z;
+} else if (attr === "translation") {
+this.m4a.m03 = x;
+this.m4a.m13 = y;
+this.m4a.m23 = z;
+}this.m4.mul(this.m4a);
+}, "~S,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputGeometry",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, bsPolygons, faceVertexMax, colorList, htColixes, offset){
+for (var i = 0; i < nPolygons; i++) {
+if (bsPolygons != null && !bsPolygons.get(i)) continue;
+var face = indices[i];
+this.writeFacet(vertices, face, 0, 1, 2);
+if (faceVertexMax == 4 && face.length >= 4 && face[2] != face[3]) this.writeFacet(vertices, face, 2, 3, 0);
+}
+}, "~A,~A,~A,~A,~A,~N,~N,JU.BS,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.defineMethod(c$, "writeFacet",
+function(vertices, face, i, j, k){
+this.tempQ1.setT(vertices[face[i]]);
+this.tempQ2.setT(vertices[face[j]]);
+this.tempQ3.setT(vertices[face[k]]);
+this.m4.rotTrans(this.tempQ1);
+this.m4.rotTrans(this.tempQ2);
+this.m4.rotTrans(this.tempQ3);
+JU.Measure.calcNormalizedNormal(this.tempQ1, this.tempQ2, this.tempQ3, this.tempV1, this.tempV2);
+if (Float.isNaN(this.tempV1.x)) {
+return;
+}this.writePoint("facet normal", this.tempV1);
+this.writePoint("outer loop\nvertex", this.tempQ1);
+this.writePoint("vertex", this.tempQ2);
+this.writePoint("vertex", this.tempQ3);
+if (this.isDebug) {
+this.out.append("endloop\nendfacet\n");
+} else {
+this.oc.writeByteAsInt(0);
+this.oc.writeByteAsInt(0);
+}this.nTri++;
+}, "~A,~A,~N,~N,~N");
+Clazz.overrideMethod(c$, "finalizeOutput",
+function(){
+if (this.isDebug) {
+this.out.append("endsolid model\n");
+} else {
+var b = this.bos.toByteArray();
+b[80] = (this.nTri & 0xff);
+b[81] = ((this.nTri >> 8) & 0xff);
+b[82] = ((this.nTri >> 16) & 0xff);
+b[83] = ((this.nTri >> 24) & 0xff);
+this.out.write(b, 0, b.length);
+}return this.finalizeOutput2();
+});
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "plotText",
+function(x, y, z, colix, text, font3d){
+}, "~N,~N,~N,~N,~S,JU.Font");
+Clazz.defineMethod(c$, "writePoint",
+function(s, p){
+if (this.isDebug) this.out.append(s);
+this.writeFloat(p.x);
+this.writeFloat(p.y);
+this.writeFloat(p.z);
+if (this.isDebug) this.out.append("\n");
+}, "~S,JU.T3");
+Clazz.defineMethod(c$, "writeFloat",
+function(f){
+if (this.isDebug) this.out.append(" " + f);
+ else this.oc.writeInt(Float.floatToIntBits(f));
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_TachyonExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_TachyonExporter.js
new file mode 100755
index 000000000000..f5cec55f0e55
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_TachyonExporter.js
@@ -0,0 +1,227 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__RayTracerExporter", "$.UseTable"], "J.export._TachyonExporter", ["JU.SB", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.lighting = null;
+this.phong = null;
+this.textures = null;
+this.textureCode = null;
+Clazz.instantialize(this, arguments);}, J["export"], "_TachyonExporter", J["export"].__RayTracerExporter);
+Clazz.prepareFields (c$, function(){
+this.textures = new J["export"].UseTable(" ");
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._TachyonExporter, []);
+this.commentChar = "# ";
+});
+Clazz.overrideMethod(c$, "initializeOutput",
+function(vwr, privateKey, gdata, params){
+this.getLightingInfo();
+return this.initOutput(vwr, privateKey, gdata, params);
+}, "JV.Viewer,~N,JU.GData,java.util.Map");
+Clazz.defineMethod(c$, "getLightingInfo",
+function(){
+this.lighting = " AMBIENT " + J["export"].___Exporter.round(this.gdata.getAmbientPercent() / 100) + " DIFFUSE " + J["export"].___Exporter.round(this.gdata.getDiffusePercent() / 100) + " SPECULAR " + J["export"].___Exporter.round(this.gdata.getSpecularPercent() / 100);
+this.phong = " Phong Plastic 0.5 Phong_size " + this.gdata.getSpecularExponent();
+});
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.initVars();
+this.output("# ******************************************************\n");
+this.output("# Created by Jmol " + JV.Viewer.getJmolVersion() + "\n");
+this.output("#\n");
+this.output("# This script was generated on " + this.getExportDate() + "\n");
+this.output("#\n");
+this.output("# Requires Tachyon version 0.98.7 or newer\n");
+this.output("#\n");
+this.output("# Default tachyon rendering command for this scene:\n");
+this.output("# tachyon -aasamples 12 %s -format TARGA -o %s.tga\n");
+this.output("#\n");
+this.output("# ******************************************************\n");
+this.output("\n");
+this.output(this.getJmolPerspective());
+this.output("\n");
+this.output("Begin_Scene\n");
+this.output("Resolution " + this.screenWidth + " " + this.screenHeight + "\n");
+this.output("Shader_Mode Medium\n");
+this.output(" Trans_VMD\n");
+this.output(" Fog_VMD\n");
+this.output("End_Shader_Mode\n");
+this.output("Camera\n");
+this.output(" Zoom 3.0\n");
+this.output(" Aspectratio 1\n");
+this.output(" Antialiasing 12\n");
+this.output(" Raydepth 8\n");
+this.output(" Center " + this.triad(Clazz.doubleToInt(this.screenWidth / 2), Clazz.doubleToInt(this.screenHeight / 2), 0) + "\n");
+this.output(" Viewdir 0 0 1\n");
+this.output(" Updir 0 1 0\n");
+this.output("End_Camera\n");
+this.output("Directional_Light Direction " + J["export"].___Exporter.round(this.lightSource) + " Color 1 1 1\n");
+this.output("\n");
+this.output("Background " + this.rgbFractionalFromColix(this.backgroundColix) + "\n");
+this.output("\n");
+});
+Clazz.overrideMethod(c$, "outputFooter",
+function(){
+this.output("End_Scene\n");
+});
+Clazz.defineMethod(c$, "output",
+function(pt){
+this.output(this.triad(pt));
+}, "JU.T3");
+Clazz.defineMethod(c$, "triad",
+function(x, y, z){
+return Clazz.floatToInt(x) + " " + Clazz.floatToInt(-y) + " " + Clazz.floatToInt(z);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "triad",
+function(pt){
+if (Float.isNaN(pt.x)) return "0 0 0";
+return this.triad(pt.x, pt.y, pt.z);
+}, "JU.T3");
+Clazz.defineMethod(c$, "outputTextureCode",
+function(){
+this.output(this.textureCode);
+this.output("\n");
+});
+Clazz.defineMethod(c$, "outputTexture",
+function(colix, useTexDef){
+this.outputTexture2(this.rgbFractionalFromColix(colix), J["export"].___Exporter.opacityFractionalFromColix(colix), useTexDef);
+}, "~N,~B");
+Clazz.defineMethod(c$, "outputTexture",
+function(argb, useTexDef){
+this.outputTexture2(this.rgbFractionalFromArgb(argb), J["export"].___Exporter.opacityFractionalFromArgb(argb), useTexDef);
+}, "~N,~B");
+Clazz.defineMethod(c$, "outputTexture2",
+function(rgb, opacity, useTexDef){
+this.textureCode = (useTexDef ? this.textures.getDef("t" + rgb + opacity) : null);
+if (useTexDef && this.textureCode.startsWith(" ")) return;
+var sb = new JU.SB();
+sb.append(this.lighting);
+sb.append(" Opacity " + opacity);
+sb.append(this.phong);
+sb.append(" Color " + rgb);
+sb.append(" TexFunc 0\n");
+if (!useTexDef) {
+this.textureCode = "Texture " + sb;
+return;
+}this.output("TexDef " + this.textureCode);
+this.output(sb.toString());
+this.textureCode = " " + this.textureCode;
+}, "~S,~S,~B");
+Clazz.overrideMethod(c$, "outputCircle",
+function(x, y, z, radius, colix, doFill){
+this.tempV1.set(0, 0, -1);
+this.outputRing(x, y, z, this.tempV1, radius, colix, doFill);
+}, "~N,~N,~N,~N,~N,~B");
+Clazz.defineMethod(c$, "outputRing",
+function(x, y, z, tempV1, radius, colix, doFill){
+this.outputTexture(colix, true);
+this.output("Ring Center ");
+this.output(this.triad(x, y, z));
+this.output(" Normal " + this.triad(tempV1));
+this.output(" Inner " + J["export"].___Exporter.round((doFill ? 0 : radius * 0.95)));
+this.output(" Outer " + J["export"].___Exporter.round(radius));
+this.outputTextureCode();
+}, "~N,~N,~N,JU.V3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCone",
+function(screenBase, screenTip, radius, colix, isBarb){
+this.tm.unTransformPoint(screenBase, this.tempP1);
+this.tm.unTransformPoint(screenTip, this.tempP2);
+radius = this.vwr.tm.unscaleToScreen(screenBase.z, radius);
+var matRotateScale = this.getRotationMatrix(this.tempP1, this.tempP2, radius);
+this.export3D.drawSurface(J["export"].___Exporter.getConeMesh(this.tempP1, matRotateScale, colix), colix);
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(screenA, screenB, radius, colix, withCaps){
+this.outputTexture(colix, true);
+this.output("FCylinder Base ");
+this.output(this.triad(screenA));
+this.output(" Apex ");
+this.output(this.triad(screenB));
+this.output(" Rad " + J["export"].___Exporter.round(radius));
+this.outputTextureCode();
+if (withCaps && radius > 1) {
+this.tempV1.sub2(screenA, screenB);
+this.outputRing(Clazz.floatToInt(screenA.x), Clazz.floatToInt(screenA.y), Clazz.floatToInt(screenA.z), this.tempV1, radius, colix, true);
+this.tempV1.scale(-1);
+this.outputRing(Clazz.floatToInt(screenB.x), Clazz.floatToInt(screenB.y), Clazz.floatToInt(screenB.z), this.tempV1, radius, colix, true);
+}}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "fillConicalCylinder",
+function(screenA, screenB, madBond, colix, endcaps){
+var diameter = Clazz.floatToInt(this.vwr.tm.scaleToScreen(Clazz.floatToInt((screenA.z + screenB.z) / 2), madBond));
+this.fillCylinderScreenMad(colix, endcaps, diameter, screenA, screenB);
+}, "JU.P3,JU.P3,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputCylinderConical",
+function(screenA, screenB, radius1, radius2, colix){
+}, "JU.P3,JU.P3,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(center, radius, coef, colix){
+this.tm.transformPt3f(center, this.tempP1);
+this.outputSphere(this.tempP1.x, this.tempP1.y, this.tempP1.z, radius, colix);
+}, "JU.P3,~N,~A,~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+if (polygonColixes != null) {
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+J["export"].___Exporter.setTempVertex(vertices[indices[i][0]], offset, this.tempP1);
+J["export"].___Exporter.setTempVertex(vertices[indices[i][1]], offset, this.tempP2);
+J["export"].___Exporter.setTempVertex(vertices[indices[i][2]], offset, this.tempP3);
+this.tm.transformPt3f(this.tempP1, this.tempP1);
+this.tm.transformPt3f(this.tempP2, this.tempP2);
+this.tm.transformPt3f(this.tempP3, this.tempP3);
+this.outputTriangle(this.tempP1, this.tempP2, this.tempP3, colix);
+}
+return;
+}this.outputTexture(colixes == null ? colix : colixes[0], false);
+this.output("VertexArray Numverts " + nVertices + "\nCoords\n");
+for (var i = 0; i < nVertices; i++) this.outputVertex(vertices[i], offset);
+
+this.output("\nNormals\n");
+for (var i = 0; i < nVertices; i++) {
+J["export"].___Exporter.setTempVertex(vertices[i], offset, this.tempP1);
+this.output(this.triad(this.getScreenNormal(this.tempP1, normals[i], 10)) + "\n");
+}
+var rgb = (colixes == null ? this.rgbFractionalFromColix(colix) : null);
+this.output("\nColors\n");
+for (var i = 0; i < nVertices; i++) {
+this.output((colixes == null ? rgb : this.rgbFractionalFromColix(colixes[i])) + "\n");
+}
+this.outputTextureCode();
+this.output("\nTriMesh " + nTriangles + "\n");
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+this.output(indices[i][0] + " " + indices[i][1] + " " + indices[i][2] + "\n");
+if (faceVertexMax == 4 && indices[i].length == 4) this.output(indices[i][0] + " " + indices[i][2] + " " + indices[i][3] + "\n");
+}
+this.output("\nEnd_VertexArray\n");
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.overrideMethod(c$, "outputSphere",
+function(x, y, z, radius, colix){
+this.outputTexture(colix, true);
+this.output("Sphere Center ");
+this.output(this.triad(x, y, z));
+this.output(" Rad " + J["export"].___Exporter.round(radius));
+this.outputTextureCode();
+}, "~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(x, y, z, argb){
+this.outputTexture(argb, true);
+this.output("Sphere Center ");
+this.output(this.triad(x, y, z));
+this.output(" Rad 1");
+this.outputTextureCode();
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(ptA, ptB, ptC, colix){
+this.outputTexture(colix, true);
+this.output("TRI");
+this.output(" V0 " + this.triad(ptA));
+this.output(" V1 " + this.triad(ptB));
+this.output(" V2 " + this.triad(ptC));
+this.outputTextureCode();
+}, "JU.T3,JU.T3,JU.T3,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_VrmlExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_VrmlExporter.js
new file mode 100755
index 000000000000..a6d3997fbf86
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_VrmlExporter.js
@@ -0,0 +1,552 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export.__CartesianExporter", "java.util.Hashtable", "JU.P3"], "J.export._VrmlExporter", ["JU.A4", "$.AU", "$.Lst", "$.Measure", "$.PT", "$.Quat", "J.export.UseTable", "JU.Geodesic", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.useTable = null;
+this.htSpheresRendered = null;
+this.plateVertices = null;
+this.plateIndices = null;
+this.plateColixes = null;
+this.tempQ1 = null;
+this.tempQ2 = null;
+this.tempQ3 = null;
+this.oneFace = null;
+this.threeVertices = null;
+this.fontSize = 0;
+this.fontFace = null;
+this.fontStyle = null;
+this.fontChild = null;
+Clazz.instantialize(this, arguments);}, J["export"], "_VrmlExporter", J["export"].__CartesianExporter);
+Clazz.prepareFields (c$, function(){
+this.htSpheresRendered = new java.util.Hashtable();
+this.tempQ1 = new JU.P3();
+this.tempQ2 = new JU.P3();
+this.tempQ3 = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J["export"]._VrmlExporter, []);
+this.useTable = new J["export"].UseTable("USE ");
+this.commentChar = "# ";
+this.canCapCylinders = true;
+this.solidOnly = true;
+});
+Clazz.defineMethod(c$, "output",
+function(pt){
+this.output(J["export"].___Exporter.round(pt));
+}, "JU.T3");
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.output("#VRML V2.0 utf8 Generated by Jmol " + JV.Viewer.getJmolVersion() + "\n");
+this.output("WorldInfo { \n");
+this.output(" title " + JU.PT.esc(this.vwr.ms.modelSetName) + "\n");
+this.output(" info [ \"Generated by Jmol " + JV.Viewer.getJmolVersion() + " \", \n");
+this.output(" \"http://www.jmol.org \", \n");
+this.output(" \"Creation date: " + this.getExportDate() + " \" ]\n");
+this.output("} \n");
+this.output("NavigationInfo { type \"EXAMINE\" } \n");
+this.output("Background { skyColor [" + this.rgbFractionalFromColix(this.backgroundColix) + "] } \n");
+var angle = this.getViewpoint();
+this.output("Viewpoint{fieldOfView " + angle);
+this.output(" position ");
+this.cameraPosition.scale(this.exportScale);
+this.output(this.cameraPosition);
+this.output(" orientation ");
+this.output(this.tempP1);
+this.output(" " + -this.viewpoint.angle);
+this.output("\n jump TRUE description \"v1\"\n}\n\n");
+this.output(this.getJmolPerspective());
+this.outputInitialTransform();
+this.output("\n");
+});
+Clazz.defineMethod(c$, "outputInitialTransform",
+function(){
+this.pushMatrix();
+this.outputAttr("scale", this.exportScale, this.exportScale, this.exportScale);
+this.outputCloseTag();
+this.outputChildStart();
+this.pushMatrix();
+this.tempP1.setT(this.center);
+this.tempP1.scale(-1);
+this.outputAttrPt("translation", this.tempP1);
+this.outputCloseTag();
+this.outputChildStart();
+});
+Clazz.defineMethod(c$, "getViewpoint",
+function(){
+this.viewpoint.setM(this.vwr.tm.matrixRotate);
+this.tempP1.set(this.viewpoint.x, this.viewpoint.y, (this.viewpoint.angle == 0 ? 1 : this.viewpoint.z));
+return (this.apertureAngle * 3.141592653589793 / 180);
+});
+Clazz.overrideMethod(c$, "outputFooter",
+function(){
+this.useTable = null;
+this.output("\n]}\n");
+this.output("]}");
+});
+Clazz.defineMethod(c$, "outputAppearance",
+function(colix, isText){
+var def = this.getDef((isText ? "T" : "") + colix);
+this.output("appearance ");
+if (def.charAt(0) == '_') {
+var color = this.rgbFractionalFromColix(colix);
+this.output(" DEF " + def + " Appearance{material Material{diffuseColor ");
+if (isText) this.output(" 0 0 0 specularColor 0 0 0 ambientIntensity 0.0 shininess 0.0 emissiveColor " + color + " }}");
+ else this.output(color + " transparency " + J["export"].___Exporter.translucencyFractionalFromColix(colix) + "}}");
+return;
+}this.output(def);
+}, "~N,~B");
+Clazz.defineMethod(c$, "pushMatrix",
+function(){
+this.output("Transform{");
+});
+Clazz.defineMethod(c$, "popMatrix",
+function(){
+this.output("}\n");
+});
+Clazz.defineMethod(c$, "outputAttrPt",
+function(attr, pt){
+this.output(" " + attr + " " + pt.x + " " + pt.y + " " + pt.z);
+}, "~S,JU.T3");
+Clazz.defineMethod(c$, "outputAttr",
+function(attr, x, y, z){
+this.output(" " + attr + " " + J["export"].___Exporter.round(x) + " " + J["export"].___Exporter.round(y) + " " + J["export"].___Exporter.round(z));
+}, "~S,~N,~N,~N");
+Clazz.defineMethod(c$, "outputRotation",
+function(a){
+this.output(" rotation " + a.x + " " + a.y + " " + a.z + " " + a.angle);
+}, "JU.A4");
+Clazz.defineMethod(c$, "outputTransRot",
+function(pt1, pt2, x, y, z){
+this.tempV1.ave(pt2, pt1);
+this.outputAttrPt("translation", this.tempV1);
+this.tempV1.sub(pt1);
+this.tempV1.normalize();
+this.tempV2.set(x, y, z);
+this.tempV2.add(this.tempV1);
+this.outputRotation(JU.A4.newVA(this.tempV2, 3.141592653589793));
+}, "JU.P3,JU.P3,~N,~N,~N");
+Clazz.defineMethod(c$, "outputQuaternionFrame",
+function(ptCenter, ptX, ptY, ptZ, xScale, yScale, zScale){
+this.tempQ1.setT(ptX);
+this.tempQ2.setT(ptY);
+var a = JU.Quat.getQuaternionFrame(ptCenter, this.tempQ1, this.tempQ2).toAxisAngle4f();
+if (!Float.isNaN(a.x)) {
+this.tempQ1.set(a.x, a.y, a.z);
+this.outputRotation(a);
+}var sx = (ptX.distance(ptCenter) * xScale);
+var sy = (ptY.distance(ptCenter) * yScale);
+var sz = (ptZ.distance(ptCenter) * zScale);
+this.outputAttr("scale", sx, sy, sz);
+}, "JU.P3,JU.P3,JU.P3,JU.P3,~N,~N,~N");
+Clazz.defineMethod(c$, "outputChildShapeStart",
+function(){
+this.outputChildStart();
+this.outputShapeStart();
+});
+Clazz.defineMethod(c$, "outputChildStart",
+function(){
+this.output(" children[");
+});
+Clazz.defineMethod(c$, "outputShapeStart",
+function(){
+this.output(" Shape{geometry ");
+});
+Clazz.defineMethod(c$, "outputDefChildFaceSet",
+function(child){
+if (child != null) this.output("DEF " + child + " ");
+this.outputFaceSetStart();
+}, "~S");
+Clazz.defineMethod(c$, "outputFaceSetStart",
+function(){
+this.output("IndexedFaceSet {");
+});
+Clazz.defineMethod(c$, "outputFaceSetClose",
+function(){
+this.output("}\n");
+});
+Clazz.defineMethod(c$, "outputUseChildClose",
+function(child){
+this.output(child);
+}, "~S");
+Clazz.defineMethod(c$, "outputChildShapeClose",
+function(){
+this.outputShapeClose();
+this.outputChildClose();
+});
+Clazz.defineMethod(c$, "outputChildClose",
+function(){
+this.output("]");
+});
+Clazz.defineMethod(c$, "outputShapeClose",
+function(){
+this.output("}");
+});
+Clazz.defineMethod(c$, "outputCloseTag",
+function(){
+});
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+if (doFill) {
+this.pushMatrix();
+this.tempV1.ave(pt1, pt2);
+this.outputAttr("translation", this.tempV1.x, this.tempV1.y, this.tempV1.z);
+this.output(" children [ Billboard{axisOfRotation 0 0 0 children [ Transform{rotation 1 0 0 1.5708");
+var height = (pt1.distance(pt2));
+this.outputAttr("scale", radius, height, radius);
+this.outputCylinderChildScaled(colix, 2);
+this.output("}] }]\n");
+this.popMatrix();
+return;
+}var child = this.getDef("C" + colix + "_" + radius);
+this.pushMatrix();
+this.outputTransRot(pt1, pt2, 0, 0, 1);
+this.outputAttr("scale", radius, radius, radius);
+this.output(" children [");
+if (child.charAt(0) == '_') {
+this.output("DEF " + child);
+this.output(" Billboard{axisOfRotation 0 0 0 children [ Transform{children[");
+this.output(" Shape{");
+this.output("geometry Extrusion{beginCap FALSE convex FALSE endCap FALSE creaseAngle 1.57");
+this.output(" crossSection [");
+var rpd = 0.017453292;
+var scale = 0.02 / radius;
+for (var i = 0; i <= 360; i += 10) {
+this.output(J["export"].___Exporter.round(Math.cos(i * rpd) * scale) + " ");
+this.output(J["export"].___Exporter.round(Math.sin(i * rpd) * scale) + " ");
+}
+this.output("] spine [");
+for (var i = 0; i <= 360; i += 10) {
+this.output(J["export"].___Exporter.round(Math.cos(i * rpd)) + " ");
+this.output(J["export"].___Exporter.round(Math.sin(i * rpd)) + " 0 ");
+}
+this.output("]");
+this.output("}");
+this.outputAppearance(colix, false);
+this.output("}");
+this.output("]} ]}");
+} else {
+this.output(child);
+}this.output("]");
+this.popMatrix();
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputCone",
+function(ptBase, ptTip, radius, colix){
+var height = (ptBase.distance(ptTip));
+this.pushMatrix();
+this.outputTransRot(ptBase, ptTip, 0, 1, 0);
+this.outputAttr("scale", radius, height, radius);
+this.outputCloseTag();
+this.outputChildShapeStart();
+var child = this.getDef("c");
+if (child.charAt(0) == '_') {
+this.outputDefChildFaceSet(child);
+this.outputConeGeometry(true);
+this.outputFaceSetClose();
+} else {
+this.outputUseChildClose(child);
+}this.outputAppearance(colix, false);
+this.outputChildShapeClose();
+this.popMatrix();
+}, "JU.P3,JU.P3,~N,~N");
+Clazz.defineMethod(c$, "outputConeGeometry",
+function(addBase){
+var ndeg = 10;
+var n = Clazz.doubleToInt(360 / ndeg);
+var vertexCount = n + (addBase ? 2 : 1);
+var faces = JU.AU.newInt2(n * (addBase ? 2 : 1));
+for (var i = 0, fpt = 0; i < n; i++) {
+faces[fpt++] = Clazz.newIntArray(-1, [i, (i + n - 1) % n, n]);
+if (addBase) faces[fpt++] = Clazz.newIntArray(-1, [i, (i + 1) % n, n + 1]);
+}
+var vertexes = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, -0.5, y);
+}
+vertexes[n++] = JU.P3.new3(0, 0.5, 0);
+if (addBase) vertexes[n++] = JU.P3.new3(0, -0.5, 0);
+this.outputGeometry(vertexes, null, null, faces, null, vertexCount, faces.length, null, 3, null, null, null);
+}, "~B");
+Clazz.overrideMethod(c$, "outputCylinder",
+function(ptCenter, pt1, pt2, colix, endcaps, radius, ptX, ptY, checkRadius){
+var height = (pt1.distance(pt2));
+if (radius < 0.01 || height == 0) return false;
+this.pushMatrix();
+if (ptX == null) {
+this.outputTransRot(pt1, pt2, 0, 1, 0);
+this.outputAttr("scale", radius, height, radius);
+} else {
+this.outputAttrPt("translation", ptCenter);
+this.outputQuaternionFrame(ptCenter, ptY, pt1, ptX, 2, 2, 2);
+pt1.set(0, 0, -0.5);
+pt2.set(0, 0, 0.5);
+}this.outputCloseTag();
+this.outputCylinderChildScaled(colix, endcaps);
+this.popMatrix();
+if (radius > 0.1) switch (endcaps) {
+case 3:
+this.outputSphere(pt1, radius * 1.01, colix, checkRadius);
+case 5:
+case 4:
+this.outputSphere(pt2, radius * 1.01, colix, checkRadius);
+break;
+case 2:
+break;
+}
+return true;
+}, "JU.P3,JU.P3,JU.P3,~N,~N,~N,JU.P3,JU.P3,~B");
+Clazz.defineMethod(c$, "outputCylinderChildScaled",
+function(colix, endcaps){
+this.outputChildShapeStart();
+var child = this.getDef("C" + "_" + endcaps);
+if (child.charAt(0) == '_') {
+this.outputDefChildFaceSet(child);
+this.outputCylinderGeometry(endcaps);
+this.outputFaceSetClose();
+} else {
+this.outputUseChildClose(child);
+}this.outputAppearance(colix, false);
+this.outputChildShapeClose();
+}, "~N,~N");
+Clazz.defineMethod(c$, "outputCylinderGeometry",
+function(endcaps){
+var ndeg = 10;
+var n = Clazz.doubleToInt(360 / ndeg);
+var vertexCount = n * 2;
+var addEndcaps = false;
+switch (endcaps) {
+case 3:
+case 5:
+case 4:
+case 2:
+vertexCount += 2;
+addEndcaps = true;
+break;
+}
+var faces = JU.AU.newInt2(n * (addEndcaps ? 4 : 2));
+for (var i = 0, fpt = 0; i < n; i++) {
+faces[fpt++] = Clazz.newIntArray(-1, [i, (i + 1) % n, i + n]);
+faces[fpt++] = Clazz.newIntArray(-1, [(i + 1) % n, (i + 1) % n + n, i + n]);
+if (addEndcaps) {
+faces[fpt++] = Clazz.newIntArray(-1, [i, (i + n - 1) % n, vertexCount - 2]);
+faces[fpt++] = Clazz.newIntArray(-1, [i + n, (i + n + 1) % n + n, vertexCount - 1]);
+}}
+var vertexes = new Array(vertexCount);
+for (var i = 0; i < n; i++) {
+var x = (Math.cos(i * ndeg / 180. * 3.141592653589793));
+var y = (Math.sin(i * ndeg / 180. * 3.141592653589793));
+vertexes[i] = JU.P3.new3(x, 0.5, y);
+}
+for (var i = 0; i < n; i++) {
+var x = (Math.cos((i + 0.5) * ndeg / 180 * 3.141592653589793));
+var y = (Math.sin((i + 0.5) * ndeg / 180 * 3.141592653589793));
+vertexes[i + n] = JU.P3.new3(x, -0.5, y);
+}
+if (addEndcaps) {
+vertexes[vertexCount - 2] = JU.P3.new3(0, 0.5, 0);
+vertexes[vertexCount - 1] = JU.P3.new3(0, -0.5, 0);
+}this.outputGeometry(vertexes, null, null, faces, null, vertexCount, faces.length, null, 3, null, null, null);
+}, "~N");
+Clazz.overrideMethod(c$, "outputSphere",
+function(ptCenter, radius, colix, checkRadius){
+var check = J["export"].___Exporter.round(ptCenter) + (checkRadius ? " " + Clazz.floatToInt(radius * 100) : "");
+if (this.htSpheresRendered.get(check) != null) return;
+this.htSpheresRendered.put(check, Boolean.TRUE);
+this.outputSphereChildScaled(ptCenter, radius, null, colix);
+}, "JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputEllipsoid",
+function(ptCenter, points, colix){
+this.outputSphereChildScaled(ptCenter, 1.0, points, colix);
+}, "JU.P3,~A,~N");
+Clazz.defineMethod(c$, "outputSphereChildScaled",
+function(ptCenter, radius, points, colix){
+this.pushMatrix();
+this.outputAttrPt("translation", ptCenter);
+if (points == null) this.outputAttr("scale", radius, radius, radius);
+ else this.outputQuaternionFrame(ptCenter, points[1], points[3], points[5], 1, 1, 1);
+this.outputCloseTag();
+this.outputChildShapeStart();
+var child = this.getDef("S");
+if (child.charAt(0) == '_') {
+this.outputDefChildFaceSet(child);
+this.outputSphereGeometry();
+this.outputFaceSetClose();
+} else {
+this.outputUseChildClose(child);
+}this.outputAppearance(colix, false);
+this.outputChildShapeClose();
+this.popMatrix();
+}, "JU.P3,~N,~A,~N");
+Clazz.defineMethod(c$, "outputSphereGeometry",
+function(){
+var vertices = JU.Geodesic.getVertexVectors();
+var nVertices = 162;
+var faceList = JU.Geodesic.getFaceVertexes(2);
+var nFaces = Clazz.doubleToInt(faceList.length / 3);
+var indices = Clazz.newIntArray (nFaces, 3, 0);
+for (var i = 0, p = 0; i < nFaces; i++) for (var j = 0; j < 3; j++) indices[i][j] = faceList[p++];
+
+
+this.outputGeometry(vertices, null, null, indices, null, nVertices, nFaces, null, 3, null, null, null);
+});
+Clazz.overrideMethod(c$, "outputSolidPlate",
+function(tempP1, tempP2, tempP3, colix){
+if (this.plateVertices == null) {
+this.plateVertices = new Array(6);
+for (var i = 0; i < 6; i++) this.plateVertices[i] = new JU.P3();
+
+this.plateIndices = Clazz.newArray(-1, [ Clazz.newIntArray(-1, [0, 1, 2]), Clazz.newIntArray(-1, [5, 4, 3]), Clazz.newIntArray(-1, [0, 3, 1]), Clazz.newIntArray(-1, [1, 3, 4]), Clazz.newIntArray(-1, [1, 4, 2]), Clazz.newIntArray(-1, [2, 4, 5]), Clazz.newIntArray(-1, [2, 5, 0]), Clazz.newIntArray(-1, [0, 5, 3])]);
+}JU.Measure.calcNormalizedNormal(tempP1, tempP2, tempP3, this.tempV1, this.tempV2);
+this.tempV1.scale(0.2);
+this.plateVertices[0].setT(tempP1);
+this.plateVertices[1].setT(tempP2);
+this.plateVertices[2].setT(tempP3);
+for (var i = 0; i < 3; i++) this.plateVertices[i].add(this.tempV1);
+
+this.tempV1.scale(-2);
+for (var i = 3; i < 6; i++) this.plateVertices[i].add2(this.plateVertices[i - 3], this.tempV1);
+
+this.outputSurface(this.plateVertices, null, null, this.plateIndices, this.plateColixes, 6, 8, 8, null, 3, colix, null, null, null);
+}, "JU.P3,JU.P3,JU.P3,~N");
+Clazz.overrideMethod(c$, "outputSurface",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, nTriangles, bsPolygons, faceVertexMax, colix, colorList, htColixes, offset){
+this.outputShapeStart();
+this.outputDefChildFaceSet(null);
+this.outputGeometry(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, bsPolygons, faceVertexMax, colorList, htColixes, offset);
+this.outputFaceSetClose();
+this.outputAppearance(colix, false);
+this.outputShapeClose();
+}, "~A,~A,~A,~A,~A,~N,~N,~N,JU.BS,~N,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.defineMethod(c$, "outputGeometry",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, bsPolygons, faceVertexMax, colorList, htColixes, offset){
+if (polygonColixes == null) this.output(" creaseAngle 0.5 \n");
+ else this.output(" colorPerVertex FALSE\n");
+this.output("coord Coordinate {\npoint [\n");
+this.outputVertices(vertices, nVertices, offset);
+this.output(" ]\n");
+this.output(" }\n");
+this.output(" coordIndex [\n");
+var map = Clazz.newIntArray (nVertices, 0);
+this.getCoordinateMap(vertices, map, null);
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+this.output(" ]\n");
+if (normals != null) {
+var vNormals = new JU.Lst();
+map = this.getNormalMap(normals, nVertices, null, vNormals);
+this.output(" solid FALSE\n normalPerVertex TRUE\n normal Normal {\n vector [\n");
+this.outputNormals(vNormals);
+this.output(" ]\n");
+this.output(" }\n");
+this.output(" normalIndex [\n");
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+this.output(" ]\n");
+}map = null;
+if (colorList != null) {
+this.output(" color Color { color [\n");
+this.outputColors(colorList);
+this.output(" ] } \n");
+this.output(" colorIndex [\n");
+this.outputColorIndices(indices, nPolygons, bsPolygons, faceVertexMax, htColixes, colixes, polygonColixes);
+this.output(" ]\n");
+}}, "~A,~A,~A,~A,~A,~N,~N,JU.BS,~N,JU.Lst,java.util.Map,JU.P3");
+Clazz.overrideMethod(c$, "outputFace",
+function(face, map, faceVertexMax){
+this.output(map[face[0]] + " " + map[face[1]] + " " + map[face[2]] + " -1\n");
+if (faceVertexMax == 4 && face.length == 4) this.output(map[face[0]] + " " + map[face[2]] + " " + map[face[3]] + " -1\n");
+}, "~A,~A,~N");
+Clazz.defineMethod(c$, "outputNormals",
+function(vNormals){
+var n = vNormals.size();
+for (var i = 0; i < n; i++) {
+this.output(vNormals.get(i));
+}
+}, "JU.Lst");
+Clazz.defineMethod(c$, "outputColors",
+function(colorList){
+var nColors = colorList.size();
+for (var i = 0; i < nColors; i++) {
+var color = this.rgbFractionalFromColix(colorList.get(i).shortValue());
+this.output(" ");
+this.output(color);
+this.output("\n");
+}
+}, "JU.Lst");
+Clazz.defineMethod(c$, "outputColorIndices",
+function(indices, nPolygons, bsPolygons, faceVertexMax, htColixes, colixes, polygonColixes){
+var isAll = (bsPolygons == null);
+var i0 = (isAll ? nPolygons - 1 : bsPolygons.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsPolygons.nextSetBit(i + 1))) {
+if (polygonColixes == null) {
+this.output(htColixes.get(Short.$valueOf(colixes[indices[i][0]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][1]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][2]])) + " -1\n");
+if (faceVertexMax == 4 && indices[i].length == 4) this.output(htColixes.get(Short.$valueOf(colixes[indices[i][0]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][2]])) + " " + htColixes.get(Short.$valueOf(colixes[indices[i][3]])) + " -1\n");
+} else {
+this.output(htColixes.get(Short.$valueOf(polygonColixes[i])) + "\n");
+}}
+}, "~A,~N,JU.BS,~N,java.util.Map,~A,~A");
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+this.output("Shape{geometry IndexedFaceSet{ ");
+this.outputTriangleGeometry(pt1, pt2, pt3, colix);
+this.output("}\n");
+this.outputAppearance(colix, false);
+this.output("}\n");
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.defineMethod(c$, "outputTriangleGeometry",
+function(pt1, pt2, pt3, colix){
+if (this.oneFace == null) {
+this.oneFace = Clazz.newArray(-1, [ Clazz.newIntArray(-1, [0, 1, 2])]);
+this.threeVertices = Clazz.newArray(-1, [this.tempP1, this.tempP2, this.tempP3]);
+}this.threeVertices[0].setT(pt1);
+this.threeVertices[1].setT(pt2);
+this.threeVertices[2].setT(pt3);
+this.outputGeometry(this.threeVertices, null, null, this.oneFace, null, 3, 1, null, 3, null, null, null);
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.overrideMethod(c$, "outputTextPixel",
+function(pt, argb){
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "plotText",
+function(x, y, z, colix, text, font3d){
+this.pushMatrix();
+this.tempP3.set(x, y, this.fixScreenZ(z));
+this.tm.unTransformPoint(this.tempP3, this.tempP1);
+this.outputAttrPt("translation", this.tempP1);
+this.setFont(colix, text, font3d);
+this.outputChildStart();
+if (this.fontChild.charAt(0) == '_') {
+this.output("DEF " + this.fontChild + " Billboard{");
+this.outputAttr("axisOfRotation", 0, 0, 0);
+this.outputChildStart();
+this.pushMatrix();
+this.outputChildShapeStart();
+this.output("Text{fontStyle ");
+var fontstyle = this.getDef("F" + this.fontFace + this.fontStyle);
+if (fontstyle.charAt(0) == '_') {
+this.output("DEF " + fontstyle + " FontStyle{size " + this.fontSize + " family \"" + this.fontFace + "\" style \"" + this.fontStyle + "\"}");
+} else {
+this.output(fontstyle);
+}this.output(" string " + JU.PT.esc(text) + "}");
+this.outputAppearance(colix, true);
+this.outputChildShapeClose();
+this.popMatrix();
+this.outputChildClose();
+this.output("}");
+} else {
+this.output(this.fontChild);
+}this.outputChildClose();
+this.popMatrix();
+}, "~N,~N,~N,~N,~S,JU.Font");
+Clazz.defineMethod(c$, "setFont",
+function(colix, text, font3d){
+this.fontStyle = font3d.fontStyle.toUpperCase();
+this.fontFace = font3d.fontFace.toUpperCase();
+this.fontFace = (this.fontFace.equals("MONOSPACED") ? "TYPEWRITER" : this.fontFace.equals("SERIF") ? "SERIF" : "Arial");
+this.fontSize = font3d.fontSize * 0.015;
+this.fontChild = this.getDef("T" + colix + this.fontFace + this.fontStyle + this.fontSize + "_" + text);
+}, "~N,~S,JU.Font");
+Clazz.defineMethod(c$, "getDef",
+function(key){
+return (this.useTable == null ? "_" : this.useTable.getDef(key));
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/export/_X3dExporter.js b/config/plugins/visualizations/jmol/static/j2s/J/export/_X3dExporter.js
new file mode 100755
index 000000000000..9c0dadd9a2c3
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/export/_X3dExporter.js
@@ -0,0 +1,231 @@
+Clazz.declarePackage("J.export");
+Clazz.load(["J.export._VrmlExporter"], "J.export._X3dExporter", ["JU.Lst", "$.PT", "J.export.UseTable", "JV.Viewer"], function(){
+var c$ = Clazz.declareType(J["export"], "_X3dExporter", J["export"]._VrmlExporter);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor(this, J["export"]._X3dExporter);
+this.useTable = new J["export"].UseTable("USE='");
+});
+Clazz.overrideMethod(c$, "outputHeader",
+function(){
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+this.output("\n");
+});
+Clazz.overrideMethod(c$, "outputAttr",
+function(attr, x, y, z){
+this.output(" " + attr + "='" + J["export"].___Exporter.round(x) + " " + J["export"].___Exporter.round(y) + " " + J["export"].___Exporter.round(z) + "'");
+}, "~S,~N,~N,~N");
+Clazz.overrideMethod(c$, "outputRotation",
+function(a){
+this.output(" rotation='" + a.x + " " + a.y + " " + a.z + " " + a.angle + "'");
+}, "JU.A4");
+Clazz.overrideMethod(c$, "outputFooter",
+function(){
+this.useTable = null;
+this.popMatrix();
+this.popMatrix();
+this.output(" \n");
+this.output(" \n");
+});
+Clazz.overrideMethod(c$, "outputAppearance",
+function(colix, isText){
+var def = this.getDef((isText ? "T" : "") + colix);
+this.output("");
+this.outputFaceSetStart();
+});
+Clazz.overrideMethod(c$, "outputChildStart",
+function(){
+});
+Clazz.overrideMethod(c$, "outputChildClose",
+function(){
+});
+Clazz.overrideMethod(c$, "outputDefChildFaceSet",
+function(child){
+if (child != null) this.output("DEF='" + child + "'");
+}, "~S");
+Clazz.overrideMethod(c$, "outputFaceSetStart",
+function(){
+this.output("\n");
+});
+Clazz.overrideMethod(c$, "outputUseChildClose",
+function(child){
+this.output(child + "/>");
+}, "~S");
+Clazz.overrideMethod(c$, "outputChildShapeClose",
+function(){
+this.outputShapeClose();
+});
+Clazz.overrideMethod(c$, "outputShapeClose",
+function(){
+this.output(" \n");
+});
+Clazz.overrideMethod(c$, "outputCloseTag",
+function(){
+this.output(">\n");
+});
+Clazz.overrideMethod(c$, "outputTriangle",
+function(pt1, pt2, pt3, colix){
+this.output("\n");
+this.output("");
+this.output(" \n");
+this.outputAppearance(colix, false);
+this.output("\n \n");
+}, "JU.T3,JU.T3,JU.T3,~N");
+Clazz.overrideMethod(c$, "outputCircle",
+function(pt1, pt2, radius, colix, doFill){
+if (doFill) {
+this.pushMatrix();
+this.output("translation='");
+this.tempV1.ave(this.tempP3, pt1);
+this.output(this.tempV1);
+this.output("'>");
+this.pushMatrix();
+this.output("rotation='1 0 0 1.5708'");
+var height = pt1.distance(pt2);
+this.outputAttr("scale", radius, height, radius);
+this.output(">");
+this.outputCylinderChildScaled(colix, 2);
+this.popMatrix();
+this.output(" ");
+this.popMatrix();
+return;
+}var child = this.getDef("C" + colix + "_" + radius);
+this.pushMatrix();
+this.outputTransRot(this.tempP3, pt1, 0, 0, 1);
+this.tempP3.set(1, 1, 1);
+this.tempP3.scale(radius);
+this.outputAttr("scale", this.tempP3.x, this.tempP3.y, this.tempP3.z);
+this.output(">\n");
+this.pushMatrix();
+this.output(" \n");
+this.popMatrix();
+}, "JU.P3,JU.P3,~N,~N,~B");
+Clazz.overrideMethod(c$, "outputGeometry",
+function(vertices, normals, colixes, indices, polygonColixes, nVertices, nPolygons, bsPolygons, faceVertexMax, colorList, htColixes, offset){
+this.output(" creaseAngle='0.5'\n");
+if (polygonColixes != null) this.output(" colorPerVertex='false'\n");
+this.output("coordIndex='\n");
+var map = Clazz.newIntArray (nVertices, 0);
+this.getCoordinateMap(vertices, map, null);
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+this.output("'\n");
+var vNormals = null;
+if (normals != null) {
+vNormals = new JU.Lst();
+map = this.getNormalMap(normals, nVertices, null, vNormals);
+this.output(" solid='false'\n normalPerVertex='true'\n normalIndex='\n");
+this.outputIndices(indices, map, nPolygons, bsPolygons, faceVertexMax);
+this.output("'\n");
+}map = null;
+if (colorList != null) {
+this.output(" colorIndex='\n");
+this.outputColorIndices(indices, nPolygons, bsPolygons, faceVertexMax, htColixes, colixes, polygonColixes);
+this.output("'\n");
+}this.output(">\n");
+this.output("= 0 || text.indexOf("= 0) return J.g3d.TextRenderer.plotByCharacter(x, y, z, argb, bgargb, text, font3d, g3d, jr, antialias);
+var offset = font3d.getAscent();
+y -= offset;
+var text3d = J.g3d.TextRenderer.getPlotText3D(x, y, g3d, text, font3d, antialias);
+if (text3d.isInvalid) return text3d.width;
+if (antialias) argb = J.g3d.Graphics3D.fixTextImageRGB(argb);
+var textHeight = text3d.height;
+var textWidth = text3d.width;
+var tmap = text3d.tmap;
+var g = g3d;
+var width = g.width;
+var height = g.height;
+var zbuf = g.zbuf;
+var p = g.pixel;
+var tLog = g.translucencyLog;
+if (jr != null || (x < 0 || x + text3d.width > width || y < 0 || y + text3d.height > height) && (jr = g3d) != null) {
+for (var off = 0, i = 0; i < textHeight; i++) {
+for (var j = 0; j < textWidth; j++) {
+var shade = tmap[off++];
+if (shade != 0) jr.plotImagePixel(argb, x + j, y + i, z, shade, bgargb, width, height, zbuf, p, tLog);
+}
+}
+} else {
+for (var i = 0, off = 0, pbufOffset = y * width + x; i < textHeight; i++, pbufOffset += (width - textWidth)) for (var j = 0; j < textWidth; j++) p.addImagePixel(tmap[off++], tLog, pbufOffset++, z, argb, bgargb);
+
+
+}return text3d.width;
+}, "~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");
+c$.plotByCharacter = Clazz.defineMethod(c$, "plotByCharacter",
+function(x, y, z, argb, bgargb, text, font3d, g3d, jmolRenderer, antialias){
+var w = 0;
+var len = text.length;
+var suboffset = Math.round(font3d.getHeight() * 0.25);
+var supoffset = -Math.round(font3d.getHeight() * 0.3);
+var argb0 = 0;
+for (var i = 0; i < len; i++) {
+if (text.charAt(i) == '<') {
+if (i + 5 < len && text.substring(i, i + 6).equals("", i);
+if (pt < 0) continue;
+argb = JU.CU.getArgbFromString(text.substring(i + 7, pt).trim());
+i = pt;
+continue;
+}if (i + 7 < len && text.substring(i, i + 8).equals("")) {
+i += 7;
+argb = argb0;
+continue;
+}if (i + 4 < len && text.substring(i, i + 5).equals("")) {
+i += 4;
+y += suboffset;
+continue;
+}if (i + 4 < len && text.substring(i, i + 5).equals("")) {
+i += 4;
+y += supoffset;
+continue;
+}if (i + 5 < len && text.substring(i, i + 6).equals("")) {
+i += 5;
+y -= suboffset;
+continue;
+}if (i + 5 < len && text.substring(i, i + 6).equals("")) {
+i += 5;
+y -= supoffset;
+continue;
+}}var width = J.g3d.TextRenderer.plot(x + w, y, z, argb, bgargb, text.substring(i, i + 1), font3d, g3d, jmolRenderer, antialias);
+w += width;
+}
+return w;
+}, "~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");
+c$.getPlotText3D = Clazz.defineMethod(c$, "getPlotText3D",
+function(x, y, g3d, text, font3d, antialias){
+J.g3d.TextRenderer.working = true;
+var ht = (antialias ? J.g3d.TextRenderer.htFont3dAntialias : J.g3d.TextRenderer.htFont3d);
+var htForThisFont = ht.get(font3d);
+var text3d = null;
+var newFont = false;
+var newText = false;
+if (htForThisFont != null) {
+text3d = htForThisFont.get(text);
+} else {
+htForThisFont = new java.util.Hashtable();
+newFont = true;
+}if (text3d == null) {
+text3d = new J.g3d.TextRenderer(text, font3d);
+newText = true;
+}text3d.isInvalid = (text3d.width == 0 || x + text3d.width <= 0 || x >= g3d.width || y + text3d.height <= 0 || y >= g3d.height);
+if (text3d.isInvalid) return text3d;
+if (newFont) ht.put(font3d, htForThisFont);
+if (newText) {
+text3d.setTranslucency(text, font3d, g3d);
+htForThisFont.put(text, text3d);
+}J.g3d.TextRenderer.working = false;
+return text3d;
+}, "~N,~N,J.g3d.Graphics3D,~S,JU.Font,~B");
+Clazz.defineMethod(c$, "setTranslucency",
+function(text, font3d, g3d){
+var pixels = g3d.apiPlatform.getTextPixels(text, font3d, g3d.platform.getGraphicsForTextOrImage(this.mapWidth, this.height), g3d.platform.offscreenImage, this.mapWidth, this.height, this.ascent);
+if (pixels == null) return;
+this.tmap = Clazz.newByteArray (this.size, 0);
+for (var i = pixels.length; --i >= 0; ) {
+var p = pixels[i] & 0xFF;
+if (p != 0) {
+this.tmap[i] = J.g3d.TextRenderer.translucency[p >> 5];
+}}
+}, "~S,JU.Font,J.g3d.Graphics3D");
+c$.translucency = Clazz.newByteArray(-1, [7, 6, 5, 4, 3, 2, 1, 8]);
+c$.working = false;
+c$.htFont3d = new java.util.Hashtable();
+c$.htFont3dAntialias = new java.util.Hashtable();
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/g3d/TextString.js b/config/plugins/visualizations/jmol/static/j2s/J/g3d/TextString.js
new file mode 100755
index 000000000000..97e13368a446
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/g3d/TextString.js
@@ -0,0 +1,28 @@
+Clazz.declarePackage("J.g3d");
+Clazz.load(["JU.P3i"], "J.g3d.TextString", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.text = null;
+this.font = null;
+this.argb = 0;
+this.bgargb = 0;
+Clazz.instantialize(this, arguments);}, J.g3d, "TextString", JU.P3i, java.util.Comparator);
+Clazz.defineMethod(c$, "setText",
+function(text, font, argb, bgargb, x, y, z){
+this.text = text;
+this.font = font;
+this.argb = argb;
+this.bgargb = bgargb;
+this.x = x;
+this.y = y;
+this.z = z;
+}, "~S,JU.Font,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "compare",
+function(a, b){
+return (a == null || b == null ? 0 : a.z > b.z ? -1 : a.z < b.z ? 1 : 0);
+}, "J.g3d.TextString,J.g3d.TextString");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return this.asString() + " " + this.text;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/g3d/TriangleRenderer.js b/config/plugins/visualizations/jmol/static/j2s/J/g3d/TriangleRenderer.js
new file mode 100755
index 000000000000..856d72a79e9c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/g3d/TriangleRenderer.js
@@ -0,0 +1,244 @@
+Clazz.declarePackage("J.g3d");
+Clazz.load(["J.g3d.G3DRenderer", "$.PrecisionRenderer", "JU.Rgb16"], "J.g3d.TriangleRenderer", ["JU.GData"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.g3d = null;
+this.ax = null;
+this.ay = null;
+this.az = null;
+this.aa = null;
+this.bb = null;
+this.axW = null;
+this.azW = null;
+this.axE = null;
+this.azE = null;
+this.rgb16sW = null;
+this.rgb16sE = null;
+this.rgb16sGouraud = null;
+this.rgb16t1 = null;
+this.rgb16t2 = null;
+Clazz.instantialize(this, arguments);}, J.g3d, "TriangleRenderer", J.g3d.PrecisionRenderer, J.g3d.G3DRenderer);
+Clazz.prepareFields (c$, function(){
+this.ax = Clazz.newIntArray (3, 0);
+this.ay = Clazz.newIntArray (3, 0);
+this.az = Clazz.newIntArray (3, 0);
+this.aa = Clazz.newFloatArray (64, 0);
+this.bb = Clazz.newFloatArray (64, 0);
+this.axW = Clazz.newIntArray (64, 0);
+this.azW = Clazz.newIntArray (64, 0);
+this.axE = Clazz.newIntArray (64, 0);
+this.azE = Clazz.newIntArray (64, 0);
+this.rgb16t1 = new JU.Rgb16();
+this.rgb16t2 = new JU.Rgb16();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.g3d.TriangleRenderer, []);
+});
+Clazz.overrideMethod(c$, "set",
+function(g3d, gdata){
+try {
+this.rgb16sW = new Array(64);
+this.rgb16sE = new Array(64);
+for (var i = 64; --i >= 0; ) {
+this.rgb16sW[i] = new JU.Rgb16();
+this.rgb16sE[i] = new JU.Rgb16();
+}
+this.g3d = g3d;
+this.rgb16sGouraud = new Array(3);
+for (var i = 3; --i >= 0; ) this.rgb16sGouraud[i] = new JU.Rgb16();
+
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+return this;
+}, "J.api.JmolRendererInterface,JU.GData");
+Clazz.defineMethod(c$, "reallocRgb16s",
+function(rgb16s, n){
+var t = new Array(n);
+System.arraycopy(rgb16s, 0, t, 0, rgb16s.length);
+for (var i = rgb16s.length; i < n; ++i) t[i] = new JU.Rgb16();
+
+return t;
+}, "~A,~N");
+Clazz.defineMethod(c$, "setGouraud",
+function(rgbA, rgbB, rgbC){
+this.rgb16sGouraud[0].setInt(rgbA);
+this.rgb16sGouraud[1].setInt(rgbB);
+this.rgb16sGouraud[2].setInt(rgbC);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "fillTriangle",
+function(screenA, screenB, screenC, useGouraud){
+this.ax[0] = screenA.x;
+this.ax[1] = screenB.x;
+this.ax[2] = screenC.x;
+this.ay[0] = screenA.y;
+this.ay[1] = screenB.y;
+this.ay[2] = screenC.y;
+this.az[0] = screenA.z;
+this.az[1] = screenB.z;
+this.az[2] = screenC.z;
+if (this.az[0] <= 1 || this.az[1] <= 1 || this.az[2] <= 1) return;
+var cc0 = this.g3d.clipCode3(this.ax[0], this.ay[0], this.az[0]);
+var cc1 = this.g3d.clipCode3(this.ax[1], this.ay[1], this.az[1]);
+var cc2 = this.g3d.clipCode3(this.ax[2], this.ay[2], this.az[2]);
+var c = (cc0 | cc1 | cc2);
+var isClipped = (c != 0);
+if (isClipped) {
+if (c == -1 || (cc0 & cc1 & cc2) != 0) {
+return;
+}}var iMinY = 0;
+if (this.ay[1] < this.ay[iMinY]) iMinY = 1;
+if (this.ay[2] < this.ay[iMinY]) iMinY = 2;
+var iMidY = (iMinY + 1) % 3;
+var iMaxY = (iMinY + 2) % 3;
+if (this.ay[iMidY] > this.ay[iMaxY]) {
+var t = iMidY;
+iMidY = iMaxY;
+iMaxY = t;
+}var yMin = this.ay[iMinY];
+var yMid = this.ay[iMidY];
+var yMax = this.ay[iMaxY];
+var nLines = yMax - yMin + 1;
+if (nLines > this.g3d.height * 3) return;
+if (nLines > this.axW.length) {
+var n = (nLines + 31) & -32;
+this.axW = Clazz.newIntArray (n, 0);
+this.azW = Clazz.newIntArray (n, 0);
+this.axE = Clazz.newIntArray (n, 0);
+this.azE = Clazz.newIntArray (n, 0);
+this.aa = Clazz.newFloatArray (n, 0);
+this.bb = Clazz.newFloatArray (n, 0);
+this.rgb16sW = this.reallocRgb16s(this.rgb16sW, n);
+this.rgb16sE = this.reallocRgb16s(this.rgb16sE, n);
+}var gouraudW;
+var gouraudE;
+if (useGouraud) {
+gouraudW = this.rgb16sW;
+gouraudE = this.rgb16sE;
+} else {
+gouraudW = gouraudE = null;
+}var dyMidMin = yMid - yMin;
+if (dyMidMin == 0) {
+if (this.ax[iMidY] < this.ax[iMinY]) {
+var t = iMidY;
+iMidY = iMinY;
+iMinY = t;
+}this.generateRaster(nLines, iMinY, iMaxY, this.axW, this.azW, 0, gouraudW);
+this.generateRaster(nLines, iMidY, iMaxY, this.axE, this.azE, 0, gouraudE);
+} else if (yMid == yMax) {
+if (this.ax[iMaxY] < this.ax[iMidY]) {
+var t = iMidY;
+iMidY = iMaxY;
+iMaxY = t;
+}this.generateRaster(nLines, iMinY, iMidY, this.axW, this.azW, 0, gouraudW);
+this.generateRaster(nLines, iMinY, iMaxY, this.axE, this.azE, 0, gouraudE);
+} else {
+var dxMaxMin = this.ax[iMaxY] - this.ax[iMinY];
+var roundFactor;
+roundFactor = JU.GData.roundInt(Clazz.doubleToInt(nLines / 2));
+if (dxMaxMin < 0) roundFactor = -roundFactor;
+var axSplit = this.ax[iMinY] + Clazz.doubleToInt((dxMaxMin * dyMidMin + roundFactor) / nLines);
+if (axSplit < this.ax[iMidY]) {
+this.generateRaster(nLines, iMinY, iMaxY, this.axW, this.azW, 0, gouraudW);
+this.generateRaster(dyMidMin + 1, iMinY, iMidY, this.axE, this.azE, 0, gouraudE);
+this.generateRaster(nLines - dyMidMin, iMidY, iMaxY, this.axE, this.azE, dyMidMin, gouraudE);
+} else {
+this.generateRaster(dyMidMin + 1, iMinY, iMidY, this.axW, this.azW, 0, gouraudW);
+this.generateRaster(nLines - dyMidMin, iMidY, iMaxY, this.axW, this.azW, dyMidMin, gouraudW);
+this.generateRaster(nLines, iMinY, iMaxY, this.axE, this.azE, 0, gouraudE);
+}}this.g3d.setZMargin(5);
+var pass2Row = this.g3d.pass2Flag01;
+var pass2Off = 1 - pass2Row;
+var xW;
+var i = 0;
+if (yMin < 0) {
+nLines += yMin;
+i -= yMin;
+yMin = 0;
+}if (yMin + nLines > this.g3d.height) nLines = this.g3d.height - yMin;
+if (useGouraud) {
+if (isClipped) {
+for (; --nLines >= pass2Row; ++yMin, ++i) {
+var pixelCount = this.axE[i] - (xW = this.axW[i]) + pass2Off;
+if (pixelCount > 0) this.g3d.plotPixelsClippedRaster(pixelCount, xW, yMin, this.azW[i], this.azE[i], this.rgb16sW[i], this.rgb16sE[i]);
+}
+} else {
+for (; --nLines >= pass2Row; ++yMin, ++i) {
+var pixelCount = this.axE[i] - (xW = this.axW[i]) + pass2Off;
+if (pass2Row == 1 && pixelCount < 0) {
+pixelCount = 1;
+xW--;
+}if (pixelCount > 0) this.g3d.plotPixelsUnclippedRaster(pixelCount, xW, yMin, this.azW[i], this.azE[i], this.rgb16sW[i], this.rgb16sE[i]);
+}
+}} else {
+if (isClipped) {
+for (; --nLines >= pass2Row; ++yMin, ++i) {
+var pixelCount = this.axE[i] - (xW = this.axW[i]) + pass2Off;
+if (pixelCount > 0) this.g3d.plotPixelsClippedRasterBits(pixelCount, xW, yMin, this.azW[i], this.azE[i], null, null, this.aa[i], this.bb[i]);
+}
+} else {
+for (; --nLines >= pass2Row; ++yMin, ++i) {
+var pixelCount = this.axE[i] - (xW = this.axW[i]) + pass2Off;
+if (pass2Row == 1 && pixelCount < 0) {
+pixelCount = 1;
+xW--;
+}if (pixelCount > 0) this.g3d.plotPixelsUnclippedRasterBits(pixelCount, xW, yMin, null, null, this.aa[i], this.bb[i]);
+}
+}}this.g3d.setZMargin(0);
+}, "JU.P3i,JU.P3i,JU.P3i,~B");
+Clazz.defineMethod(c$, "generateRaster",
+function(dy, iN, iS, axRaster, azRaster, iRaster, gouraud){
+var xN = this.ax[iN];
+var xS = this.ax[iS];
+var dx = xS - xN;
+var xCurrent = xN;
+var xIncrement;
+var width;
+var errorTerm;
+if (dx >= 0) {
+xIncrement = 1;
+width = dx;
+errorTerm = 0;
+} else {
+xIncrement = -1;
+width = -dx;
+errorTerm = 1 - dy;
+}var xMajorIncrement;
+var xMajorError;
+if (width <= dy) {
+xMajorIncrement = 0;
+xMajorError = width;
+} else {
+xMajorIncrement = JU.GData.roundInt(Clazz.doubleToInt(dx / dy));
+xMajorError = width % dy;
+}this.setRastAB(this.ay[iN], this.az[iN], this.ay[iS], this.az[iS]);
+var a0 = this.a;
+var b0 = this.b;
+var isEast = (axRaster === this.axE);
+for (var y = 0, zy = this.ay[iN], lastY = dy - 1, i = iRaster; y <= lastY; ++i, ++y, ++zy) {
+if (i == 0 || i > iRaster) {
+axRaster[i] = (y == lastY ? this.ax[iS] : xCurrent);
+azRaster[i] = this.getZCurrent(a0, b0, zy);
+if (isEast) {
+this.setRastAB(this.axW[i], this.azW[i], axRaster[i], azRaster[i]);
+this.aa[i] = this.a;
+this.bb[i] = this.b;
+}}xCurrent += xMajorIncrement;
+errorTerm += xMajorError;
+if (errorTerm > 0) {
+xCurrent += xIncrement;
+errorTerm -= dy;
+}}
+if (gouraud != null) {
+var rgb16Base = this.rgb16t1;
+rgb16Base.setRgb(this.rgb16sGouraud[iN]);
+var rgb16Increment = this.rgb16t2;
+rgb16Increment.diffDiv(this.rgb16sGouraud[iS], rgb16Base, dy);
+for (var i = iRaster, iMax = iRaster + dy; i < iMax; ++i) gouraud[i].setAndIncrement(rgb16Base, rgb16Increment);
+
+}}, "~N,~N,~N,~A,~A,~N,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/g3d/package.html b/config/plugins/visualizations/jmol/static/j2s/J/g3d/package.html
new file mode 100755
index 000000000000..dd367deda1a7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/g3d/package.html
@@ -0,0 +1,61 @@
+
+
+
+
+
+
+
+
+ Provides a software implementation of complete 3D graphics engine
+ for rendering molecules and associated shapes.
+ basic shapes.
+
+
+ This package implements all graphics primitives used by Jmol. The
+ graphics engine does not use Java3D or OpenGL. It requires no specialized
+ graphics hardware. This allows Jmol and the JmolApplet to run on any
+ machine that has a JVM.
+
+
+ It is a software implementation of a graphics z-buffer. An int[] called
+ pbuf (for pixel buffer) is used to hold ARGB values for pixels. A short[]
+ called zbuf holds the z-depth value.
+
+
+ Shape primitives are provided for drawing spheres, cylinders, triangles, etc.
+ Shading primitives provide lighting/shading support
+
+
+ Related Documentation
+
+ Makes use of javax.vecmath classes.
+
+
+
+
+
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/geodesic/EnvelopeCalculation.js b/config/plugins/visualizations/jmol/static/j2s/J/geodesic/EnvelopeCalculation.js
new file mode 100755
index 000000000000..1952b2cdd9da
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/geodesic/EnvelopeCalculation.js
@@ -0,0 +1,359 @@
+Clazz.declarePackage("J.geodesic");
+Clazz.load(["J.api.JmolEnvCalc", "JU.P3", "J.atomdata.AtomData"], "J.geodesic.EnvelopeCalculation", ["JU.AU", "$.BS", "$.V3", "J.atomdata.RadiusData", "JU.BSUtil", "$.Geodesic", "$.Normix"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.geodesicMap = null;
+this.mapT = null;
+this.mads = null;
+this.atomData = null;
+this.vwr = null;
+this.ac = 0;
+this.maxRadius = 0;
+this.modelZeroBased = false;
+this.disregardNeighbors = false;
+this.bsMySelected = null;
+this.dotsConvexMaps = null;
+this.dotsConvexMax = 0;
+this.geodesicCount = 0;
+this.bsSurface = null;
+this.radiusP = 0;
+this.diameterP = 0;
+this.bsTemp = null;
+this.bsIgnore = null;
+this.onlySelectedDots = false;
+this.isSurface = false;
+this.multiModel = false;
+this.currentPoints = null;
+this.indexI = 0;
+this.centerI = null;
+this.radiusI = 0;
+this.radiiIP2 = 0;
+this.pointT = null;
+this.centerT = null;
+this.vertexTest = null;
+this.neighborCount = 0;
+this.neighborIndices = null;
+this.neighborCenters = null;
+this.neighborPlusProbeRadii2 = null;
+this.neighborRadii2 = null;
+Clazz.instantialize(this, arguments);}, J.geodesic, "EnvelopeCalculation", null, J.api.JmolEnvCalc);
+Clazz.prepareFields (c$, function(){
+this.atomData = new J.atomdata.AtomData();
+this.pointT = new JU.P3();
+this.vertexTest = new Array(12);
+{
+for (var i = 0; i < 12; i++) this.vertexTest[i] = new JU.P3();
+
+}this.neighborIndices = Clazz.newIntArray (16, 0);
+this.neighborCenters = new Array(16);
+this.neighborPlusProbeRadii2 = Clazz.newFloatArray (16, 0);
+this.neighborRadii2 = Clazz.newFloatArray (16, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.overrideMethod(c$, "set",
+function(vwr, ac, mads){
+this.vwr = vwr;
+this.ac = ac;
+this.mads = mads;
+this.geodesicCount = JU.Geodesic.getVertexCount(3);
+this.geodesicMap = JU.BS.newN(this.geodesicCount);
+this.mapT = JU.BS.newN(this.geodesicCount);
+J.geodesic.EnvelopeCalculation.EMPTY_SET = JU.BSUtil.emptySet;
+return this;
+}, "J.atomdata.AtomDataServer,~N,~A");
+Clazz.defineMethod(c$, "getDotsConvexMaps",
+function(){
+return this.dotsConvexMaps;
+});
+Clazz.defineMethod(c$, "getDotsConvexMax",
+function(){
+return this.dotsConvexMax;
+});
+Clazz.defineMethod(c$, "allocDotsConvexMaps",
+function(max){
+if (this.dotsConvexMax >= max) return;
+this.dotsConvexMax = max;
+this.dotsConvexMaps = new Array(max);
+}, "~N");
+Clazz.overrideMethod(c$, "getBsSurfaceClone",
+function(){
+return JU.BSUtil.copy(this.bsSurface);
+});
+Clazz.defineMethod(c$, "setMads",
+function(mads){
+this.mads = mads;
+}, "~A");
+Clazz.defineMethod(c$, "setFromBits",
+function(index, bs){
+this.geodesicMap.setBits(0, this.geodesicCount);
+for (var iDot = this.geodesicCount; --iDot >= 0; ) if (!bs.get(iDot)) this.geodesicMap.clear(iDot);
+
+if (this.dotsConvexMaps == null) this.dotsConvexMaps = new Array(this.ac);
+var map;
+if (this.geodesicMap.isEmpty()) map = J.geodesic.EnvelopeCalculation.EMPTY_SET;
+ else map = JU.BSUtil.copy(this.geodesicMap);
+if (index >= this.dotsConvexMaps.length) return;
+this.dotsConvexMaps[index] = map;
+this.dotsConvexMax = Math.max(this.dotsConvexMax, index);
+}, "~N,JU.BS");
+Clazz.defineMethod(c$, "newSet",
+function(){
+this.dotsConvexMax = 0;
+this.dotsConvexMaps = null;
+this.radiusP = this.diameterP = 0;
+this.mads = null;
+});
+Clazz.defineMethod(c$, "reCalculate",
+function(bs, m){
+if (this.atomData.radiusData != null) {
+this.calculate(null, this.maxRadius, bs, this.bsIgnore, this.disregardNeighbors, this.onlySelectedDots, this.isSurface, this.multiModel);
+return;
+}if (this.dotsConvexMaps == null || this.dotsConvexMax == 0) return;
+var pt = new JU.V3();
+if (this.bsTemp == null) this.bsTemp = JU.Normix.newVertexBitSet();
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (i >= this.dotsConvexMax) return;
+var map = this.dotsConvexMaps[i];
+if (map == null || map.isEmpty()) continue;
+var bsNew = new JU.BS();
+for (var j = map.nextSetBit(0); j >= 0; j = map.nextSetBit(j + 1)) {
+pt.setT(JU.Geodesic.getVertexVector(j));
+m.rotate(pt);
+bsNew.set(JU.Normix.getNormixV(pt, this.bsTemp));
+}
+this.dotsConvexMaps[i] = bsNew;
+}
+}, "JU.BS,JU.M3");
+Clazz.overrideMethod(c$, "calculate",
+function(rd, maxRadius, bsSelected, bsIgnore, disregardNeighbors, onlySelectedDots, isSurface, multiModel){
+if (rd == null) {
+rd = this.atomData.radiusData;
+if (rd == null) return;
+} else {
+this.atomData.radiusData = rd;
+this.bsIgnore = bsIgnore;
+this.onlySelectedDots = onlySelectedDots;
+this.multiModel = multiModel;
+this.isSurface = isSurface;
+}if (rd.value == 3.4028235E38) rd.value = 3.0;
+this.atomData.modelIndex = (multiModel ? -1 : 0);
+this.modelZeroBased = !multiModel;
+this.vwr.fillAtomData(this.atomData, 1 | (this.mads == null ? 2 : 0));
+this.ac = this.atomData.ac;
+if (this.mads != null) for (var i = 0; i < this.ac; i++) this.atomData.atomRadius[i] = this.mads[i] / 1000;
+
+this.bsMySelected = (onlySelectedDots && bsSelected != null ? JU.BSUtil.copy(bsSelected) : bsIgnore != null ? JU.BSUtil.setAll(this.ac) : null);
+JU.BSUtil.andNot(this.bsMySelected, bsIgnore);
+this.disregardNeighbors = disregardNeighbors;
+this.maxRadius = maxRadius;
+this.bsSurface = new JU.BS();
+var isAll = (bsSelected == null);
+var iter = this.vwr.getSelectedAtomIterator(this.bsMySelected, false, this.modelZeroBased, false);
+this.checkNewDotsArray();
+var i0 = (isAll ? this.ac - 1 : bsSelected.nextSetBit(0));
+for (var i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i + 1))) if (bsIgnore == null || !bsIgnore.get(i)) {
+this.setAtomI(i);
+this.getNeighbors(iter);
+this.calcConvexMap(isSurface);
+}
+iter.release();
+this.currentPoints = null;
+this.setDotsConvexMax();
+}, "J.atomdata.RadiusData,~N,JU.BS,JU.BS,~B,~B,~B,~B");
+Clazz.defineMethod(c$, "getRadius",
+function(atomIndex){
+return this.atomData.atomRadius[atomIndex];
+}, "~N");
+Clazz.overrideMethod(c$, "getPoints",
+function(){
+if (this.dotsConvexMaps == null) {
+this.calculate( new J.atomdata.RadiusData(null, 3.0, J.atomdata.RadiusData.EnumType.ABSOLUTE, null), 3.4028235E38, this.bsMySelected, null, false, false, false, false);
+}if (this.currentPoints != null) return this.currentPoints;
+var nPoints = 0;
+var dotCount = 42;
+for (var i = this.dotsConvexMax; --i >= 0; ) if (this.dotsConvexMaps[i] != null) nPoints += this.dotsConvexMaps[i].cardinalityN(dotCount);
+
+var points = new Array(nPoints);
+if (nPoints == 0) return points;
+nPoints = 0;
+for (var i = this.dotsConvexMax; --i >= 0; ) if (this.dotsConvexMaps[i] != null) {
+var iDot = this.dotsConvexMaps[i].size();
+if (iDot > dotCount) iDot = dotCount;
+while (--iDot >= 0) if (this.dotsConvexMaps[i].get(iDot)) {
+var pt = new JU.P3();
+pt.scaleAdd2(this.atomData.atomRadius[i], JU.Geodesic.getVertexVector(iDot), this.atomData.xyz[i]);
+points[nPoints++] = pt;
+}
+}
+this.currentPoints = points;
+return points;
+});
+Clazz.defineMethod(c$, "setDotsConvexMax",
+function(){
+if (this.dotsConvexMaps == null) this.dotsConvexMax = 0;
+ else {
+var i;
+for (i = this.ac; --i >= 0 && this.dotsConvexMaps[i] == null; ) {
+}
+this.dotsConvexMax = i + 1;
+}});
+Clazz.defineMethod(c$, "getAppropriateRadius",
+function(atomIndex){
+return (this.mads != null ? (atomIndex >= this.mads.length ? 0 : this.mads[atomIndex] / 1000) : this.atomData.atomRadius[atomIndex]);
+}, "~N");
+Clazz.defineMethod(c$, "setAtomI",
+function(indexI){
+this.indexI = indexI;
+this.centerI = this.atomData.xyz[indexI];
+this.radiusI = this.atomData.atomRadius[indexI];
+this.radiiIP2 = this.radiusI + this.radiusP;
+this.radiiIP2 *= this.radiiIP2;
+}, "~N");
+Clazz.defineMethod(c$, "calcConvexMap",
+function(isSurface){
+this.calcConvexBits();
+var map;
+if (this.geodesicMap.isEmpty()) map = J.geodesic.EnvelopeCalculation.EMPTY_SET;
+ else {
+this.bsSurface.set(this.indexI);
+if (isSurface) {
+this.addIncompleteFaces(this.geodesicMap);
+this.addIncompleteFaces(this.geodesicMap);
+}map = JU.BSUtil.copy(this.geodesicMap);
+}this.dotsConvexMaps[this.indexI] = map;
+}, "~B");
+Clazz.defineMethod(c$, "addIncompleteFaces",
+function(points){
+this.mapT.clearAll();
+var faces = JU.Geodesic.getFaceVertexes(3);
+var len = faces.length;
+var maxPt = -1;
+for (var f = 0; f < len; ) {
+var p1 = faces[f++];
+var p2 = faces[f++];
+var p3 = faces[f++];
+var ok1 = points.get(p1);
+var ok2 = points.get(p2);
+var ok3 = points.get(p3);
+if (!(ok1 || ok2 || ok3) || ok1 && ok2 && ok3) continue;
+if (!ok1) {
+this.mapT.set(p1);
+if (maxPt < p1) maxPt = p1;
+}if (!ok2) {
+this.mapT.set(p2);
+if (maxPt < p2) maxPt = p2;
+}if (!ok3) {
+this.mapT.set(p3);
+if (maxPt < p3) maxPt = p3;
+}}
+for (var i = 0; i <= maxPt; i++) {
+if (this.mapT.get(i)) points.set(i);
+}
+}, "JU.BS");
+Clazz.defineMethod(c$, "calcConvexBits",
+function(){
+this.geodesicMap.setBits(0, this.geodesicCount);
+var combinedRadii = this.radiusI + this.radiusP;
+if (this.neighborCount == 0) return;
+var faceTest;
+var p1;
+var p2;
+var p3;
+var faces = JU.Geodesic.getFaceVertexes(3);
+var p4 = J.geodesic.EnvelopeCalculation.power4[2];
+var ok1;
+var ok2;
+var ok3;
+this.mapT.clearAll();
+for (var i = 0; i < 12; i++) {
+this.vertexTest[i].scaleAdd2(combinedRadii, JU.Geodesic.getVertexVector(i), this.centerI);
+}
+for (var f = 0; f < 20; f++) {
+faceTest = 0;
+p1 = faces[3 * p4 * (4 * f + 0)];
+p2 = faces[3 * p4 * (4 * f + 1)];
+p3 = faces[3 * p4 * (4 * f + 2)];
+for (var j = 0; j < this.neighborCount; j++) {
+var maxDist = this.neighborPlusProbeRadii2[j];
+this.centerT = this.neighborCenters[j];
+ok1 = this.vertexTest[p1].distanceSquared(this.centerT) >= maxDist;
+ok2 = this.vertexTest[p2].distanceSquared(this.centerT) >= maxDist;
+ok3 = this.vertexTest[p3].distanceSquared(this.centerT) >= maxDist;
+if (!ok1) this.geodesicMap.clear(p1);
+if (!ok2) this.geodesicMap.clear(p2);
+if (!ok3) this.geodesicMap.clear(p3);
+if (!ok1 && !ok2 && !ok3) {
+faceTest = -1;
+break;
+}}
+var kFirst = f * 12 * p4;
+var kLast = kFirst + 12 * p4;
+for (var k = kFirst; k < kLast; k++) {
+var vect = faces[k];
+if (this.mapT.get(vect) || !this.geodesicMap.get(vect)) continue;
+switch (faceTest) {
+case -1:
+this.geodesicMap.clear(vect);
+break;
+case 0:
+for (var j = 0; j < this.neighborCount; j++) {
+var maxDist = this.neighborPlusProbeRadii2[j];
+this.centerT = this.neighborCenters[j];
+this.pointT.scaleAdd2(combinedRadii, JU.Geodesic.getVertexVector(vect), this.centerI);
+if (this.pointT.distanceSquared(this.centerT) < maxDist) this.geodesicMap.clear(vect);
+}
+break;
+case 1:
+}
+this.mapT.set(vect);
+}
+}
+});
+Clazz.defineMethod(c$, "checkNewDotsArray",
+function(){
+if (this.dotsConvexMaps == null) {
+this.dotsConvexMaps = new Array(this.ac);
+} else if (this.dotsConvexMaps.length != this.ac) {
+var a = new Array(this.ac);
+for (var i = 0; i < this.ac && i < this.dotsConvexMaps.length; i++) a[i] = this.dotsConvexMaps[i];
+
+this.dotsConvexMaps = a;
+}});
+Clazz.defineMethod(c$, "getNeighbors",
+function(iter){
+this.neighborCount = 0;
+if (this.disregardNeighbors) return null;
+this.vwr.setIteratorForAtom(iter, this.indexI, this.radiusI + this.diameterP + this.maxRadius);
+while (iter.hasNext()) {
+var indexN = iter.next();
+var neighborRadius = this.atomData.atomRadius[indexN];
+if (this.centerI.distance(this.atomData.xyz[indexN]) > this.radiusI + this.radiusP + this.radiusP + neighborRadius) continue;
+if (this.neighborCount == this.neighborIndices.length) {
+this.neighborIndices = JU.AU.doubleLengthI(this.neighborIndices);
+this.neighborCenters = JU.AU.doubleLength(this.neighborCenters);
+this.neighborPlusProbeRadii2 = JU.AU.doubleLengthF(this.neighborPlusProbeRadii2);
+this.neighborRadii2 = JU.AU.doubleLengthF(this.neighborRadii2);
+}this.neighborCenters[this.neighborCount] = this.atomData.xyz[indexN];
+this.neighborIndices[this.neighborCount] = indexN;
+var r = neighborRadius + this.radiusP;
+this.neighborPlusProbeRadii2[this.neighborCount] = r * r;
+this.neighborRadii2[this.neighborCount] = neighborRadius * neighborRadius;
+++this.neighborCount;
+}
+return iter;
+}, "J.api.AtomIndexIterator");
+Clazz.defineMethod(c$, "deleteAtoms",
+function(firstAtomDeleted, nAtomsDeleted){
+this.dotsConvexMaps = JU.AU.deleteElements(this.dotsConvexMaps, firstAtomDeleted, nAtomsDeleted);
+this.dotsConvexMax = this.dotsConvexMaps.length;
+if (this.mads != null) this.mads = JU.AU.deleteElements(this.mads, firstAtomDeleted, nAtomsDeleted);
+this.atomData.atomRadius = JU.AU.deleteElements(this.atomData.atomRadius, firstAtomDeleted, nAtomsDeleted);
+this.atomData.xyz = JU.AU.deleteElements(this.atomData.xyz, firstAtomDeleted, nAtomsDeleted);
+this.atomData.ac -= nAtomsDeleted;
+this.ac = this.atomData.ac;
+}, "~N,~N");
+c$.EMPTY_SET = null;
+c$.power4 = Clazz.newIntArray(-1, [1, 4, 16, 64, 256]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/i18n/GT.js b/config/plugins/visualizations/jmol/static/j2s/J/i18n/GT.js
new file mode 100755
index 000000000000..f5a47063edd8
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/i18n/GT.js
@@ -0,0 +1,186 @@
+Clazz.declarePackage("J.i18n");
+Clazz.load(["J.api.Translator", "java.text.MessageFormat", "java.util.Hashtable", "JU.PT", "J.i18n.Language", "$.Resource"], "J.i18n.GT", ["JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.resources = null;
+this.resourceCount = 0;
+this.doTranslate = true;
+this.language = null;
+Clazz.instantialize(this, arguments);}, J.i18n, "GT", null, J.api.Translator);
+/*LV!1824 unnec constructor*/Clazz.makeConstructor(c$,
+function(vr, langCode){
+{
+}this.resources = null;
+this.resourceCount = 0;
+J.i18n.GT.$getTextWrapper = this;
+if (langCode != null && langCode.length == 0) langCode = "none";
+if (langCode != null) this.language = langCode;
+if ("none".equals(this.language)) this.language = null;
+if (this.language == null) this.language = J.i18n.Resource.getLanguage();
+if (this.language == null) this.language = "en";
+var la = this.language;
+var la_co = null;
+var la_co_va = null;
+var i = this.language.indexOf("_");
+if (i >= 0) {
+la = la.substring(0, i);
+la_co = this.language;
+if ((i = la_co.indexOf("_", ++i)) >= 0) {
+la_co = la_co.substring(0, i);
+la_co_va = this.language;
+}}if ((this.language = this.getSupported(la_co_va)) == null && (this.language = this.getSupported(la_co)) == null && (this.language = this.getSupported(la)) == null) {
+this.language = "en";
+System.out.println(this.language + " not supported -- using en");
+return;
+}la_co_va = null;
+la_co = null;
+switch (this.language.length) {
+default:
+la_co_va = this.language;
+la_co = this.language.substring(0, 5);
+la = this.language.substring(0, 2);
+break;
+case 5:
+la_co = this.language;
+la = this.language.substring(0, 2);
+break;
+case 2:
+la = this.language;
+break;
+}
+la_co = this.getSupported(la_co);
+la = this.getSupported(la);
+if (la === la_co || "en_US".equals(la)) la = null;
+if (la_co === la_co_va) la_co = null;
+if ("en_US".equals(la_co)) return;
+if (J.i18n.GT.allowDebug && JU.Logger.debugging) JU.Logger.debug("Instantiating gettext wrapper for " + this.language + " using files for language:" + la + " country:" + la_co + " variant:" + la_co_va);
+if (!J.i18n.GT.$ignoreApplicationBundle) this.addBundles(vr, "Jmol", la_co_va, null, null);
+this.addBundles(vr, "JmolApplet", la_co_va, null, null);
+if (!J.i18n.GT.$ignoreApplicationBundle) this.addBundles(vr, "Jmol", null, la_co, null);
+this.addBundles(vr, "JmolApplet", null, la_co, null);
+if (!J.i18n.GT.$ignoreApplicationBundle) this.addBundles(vr, "Jmol", null, null, la);
+this.addBundles(vr, "JmolApplet", null, null, la);
+}, "JV.Viewer,~S");
+Clazz.overrideMethod(c$, "translate",
+function(s){
+return J.i18n.GT.$(s);
+}, "~S");
+c$.getLanguageList = Clazz.defineMethod(c$, "getLanguageList",
+function(gt){
+if (J.i18n.GT.languageList == null) {
+if (gt == null) gt = J.i18n.GT.getTextWrapper();
+gt.createLanguageList();
+}return J.i18n.GT.languageList;
+}, "J.i18n.GT");
+c$.getLanguage = Clazz.defineMethod(c$, "getLanguage",
+function(){
+return J.i18n.GT.getTextWrapper().language;
+});
+c$.ignoreApplicationBundle = Clazz.defineMethod(c$, "ignoreApplicationBundle",
+function(){
+J.i18n.GT.$ignoreApplicationBundle = true;
+});
+c$.setDoTranslate = Clazz.defineMethod(c$, "setDoTranslate",
+function(TF){
+var b = J.i18n.GT.getDoTranslate();
+J.i18n.GT.getTextWrapper().doTranslate = TF;
+return b;
+}, "~B");
+c$.getDoTranslate = Clazz.defineMethod(c$, "getDoTranslate",
+function(){
+return J.i18n.GT.getTextWrapper().doTranslate;
+});
+c$.$ = Clazz.defineMethod(c$, "$",
+function(string){
+return J.i18n.GT.getTextWrapper().getString(string);
+}, "~S");
+c$.o = Clazz.defineMethod(c$, "o",
+function(s, o){
+if (Clazz.instanceOf(o,Array)) {
+if ((o).length != 1) return java.text.MessageFormat.format(s, o);
+o = (o)[0];
+}return JU.PT.rep(s, "{0}", o.toString());
+}, "~S,~O");
+c$.i = Clazz.defineMethod(c$, "i",
+function(s, n){
+return JU.PT.rep(s, "{0}", "" + n);
+}, "~S,~N");
+c$.escapeHTML = Clazz.defineMethod(c$, "escapeHTML",
+function(msg){
+var ch;
+for (var i = msg.length; --i >= 0; ) if ((ch = msg.charAt(i)).charCodeAt(0) > 0x7F) {
+msg = msg.substring(0, i) + "&#" + ((ch).charCodeAt(0)) + ";" + msg.substring(i + 1);
+}
+return msg;
+}, "~S");
+c$.getTextWrapper = Clazz.defineMethod(c$, "getTextWrapper",
+function(){
+return (J.i18n.GT.$getTextWrapper == null ? J.i18n.GT.$getTextWrapper = new J.i18n.GT(null, null) : J.i18n.GT.$getTextWrapper);
+});
+Clazz.defineMethod(c$, "createLanguageList",
+function(){
+var wasTranslating = this.doTranslate;
+this.doTranslate = false;
+J.i18n.GT.languageList = J.i18n.Language.getLanguageList();
+this.doTranslate = wasTranslating;
+});
+Clazz.defineMethod(c$, "getSupported",
+function(code){
+if (code == null) return null;
+var s = J.i18n.GT.htLanguages.get(code);
+if (s != null) return (s.length == 0 ? null : s);
+s = J.i18n.Language.getSupported(J.i18n.GT.getLanguageList(this), code);
+J.i18n.GT.htLanguages.put(code, (s == null ? "" : s));
+return s;
+}, "~S");
+Clazz.defineMethod(c$, "addBundles",
+function(vwr, type, la_co_va, la_co, la){
+try {
+var className = "J.translation." + type + ".";
+if (la_co_va != null) this.addBundle(vwr, className, la_co_va);
+if (la_co != null) this.addBundle(vwr, className, la_co);
+if (la != null) this.addBundle(vwr, className, la);
+} catch (exception) {
+if (Clazz.exceptionOf(exception, Exception)){
+if (J.i18n.GT.allowDebug) JU.Logger.errorEx("Some exception occurred!", exception);
+this.resources = null;
+this.resourceCount = 0;
+} else {
+throw exception;
+}
+}
+}, "JV.Viewer,~S,~S,~S,~S");
+Clazz.defineMethod(c$, "addBundle",
+function(vwr, className, name){
+var resource = J.i18n.Resource.getResource(vwr, className, name);
+if (resource != null) {
+if (this.resources == null) {
+this.resources = new Array(8);
+this.resourceCount = 0;
+}this.resources[this.resourceCount] = resource;
+this.resourceCount++;
+if (J.i18n.GT.allowDebug) JU.Logger.debug("GT adding " + className);
+}}, "JV.Viewer,~S,~S");
+Clazz.defineMethod(c$, "getString",
+function(s){
+var trans = null;
+if (this.doTranslate) {
+for (var bundle = 0; bundle < this.resourceCount; bundle++) {
+trans = this.resources[bundle].getString(s);
+if (trans != null) {
+s = trans;
+break;
+}}
+if (this.resourceCount > 0 && trans == null && J.i18n.GT.allowDebug && JU.Logger.debugging) JU.Logger.debug("No trans, using default: " + s);
+}if (trans == null) {
+if (s.startsWith("[")) s = s.substring(s.indexOf("]") + 1);
+ else if (s.endsWith("]")) s = s.substring(0, s.indexOf("["));
+}return s;
+}, "~S");
+c$.$ignoreApplicationBundle = false;
+c$.$getTextWrapper = null;
+c$.languageList = null;
+c$.allowDebug = false;
+c$.vwr = null;
+c$.htLanguages = new java.util.Hashtable();
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/i18n/Language.js b/config/plugins/visualizations/jmol/static/j2s/J/i18n/Language.js
new file mode 100755
index 000000000000..45640dcbe94c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/i18n/Language.js
@@ -0,0 +1,29 @@
+Clazz.declarePackage("J.i18n");
+Clazz.load(null, "J.i18n.Language", ["J.i18n.GT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.code = null;
+this.language = null;
+this.nativeLanguage = null;
+this.display = false;
+Clazz.instantialize(this, arguments);}, J.i18n, "Language", null);
+Clazz.makeConstructor(c$,
+function(code, language, nativeLanguage, display){
+this.code = code;
+this.language = language;
+this.nativeLanguage = nativeLanguage;
+this.display = display;
+}, "~S,~S,~S,~B");
+c$.getLanguageList = Clazz.defineMethod(c$, "getLanguageList",
+function(){
+return Clazz.newArray(-1, [ new J.i18n.Language("ar", J.i18n.GT.$("Arabic"), "العربية", false), new J.i18n.Language("ast", J.i18n.GT.$("Asturian"), "Asturian", false), new J.i18n.Language("az", J.i18n.GT.$("Azerbaijani"), "azÉ™rbaycan dili", false), new J.i18n.Language("bs", J.i18n.GT.$("Bosnian"), "bosanski jezik", false), new J.i18n.Language("ca", J.i18n.GT.$("Catalan"), "Català ", true), new J.i18n.Language("cs", J.i18n.GT.$("Czech"), "ÄŒeÅ¡tina", true), new J.i18n.Language("da", J.i18n.GT.$("Danish"), "Dansk", true), new J.i18n.Language("de", J.i18n.GT.$("German"), "Deutsch", true), new J.i18n.Language("el", J.i18n.GT.$("Greek"), "Ελληνικά", false), new J.i18n.Language("en_AU", J.i18n.GT.$("Australian English"), "Australian English", false), new J.i18n.Language("en_GB", J.i18n.GT.$("British English"), "British English", true), new J.i18n.Language("en_US", J.i18n.GT.$("American English"), "American English", true), new J.i18n.Language("es", J.i18n.GT.$("Spanish"), "Español", true), new J.i18n.Language("et", J.i18n.GT.$("Estonian"), "Eesti", false), new J.i18n.Language("eu", J.i18n.GT.$("Basque"), "Euskara", true), new J.i18n.Language("fi", J.i18n.GT.$("Finnish"), "Suomi", true), new J.i18n.Language("fo", J.i18n.GT.$("Faroese"), "Føroyskt", false), new J.i18n.Language("fr", J.i18n.GT.$("French"), "Français", true), new J.i18n.Language("fy", J.i18n.GT.$("Frisian"), "Frysk", false), new J.i18n.Language("gl", J.i18n.GT.$("Galician"), "Galego", false), new J.i18n.Language("hr", J.i18n.GT.$("Croatian"), "Hrvatski", false), new J.i18n.Language("hu", J.i18n.GT.$("Hungarian"), "Magyar", true), new J.i18n.Language("hy", J.i18n.GT.$("Armenian"), "Õ€Õ¡ÕµÕ¥Ö€Õ¥Õ¶", false), new J.i18n.Language("id", J.i18n.GT.$("Indonesian"), "Indonesia", true), new J.i18n.Language("it", J.i18n.GT.$("Italian"), "Italiano", true), new J.i18n.Language("ja", J.i18n.GT.$("Japanese"), "日本語", true), new J.i18n.Language("jv", J.i18n.GT.$("Javanese"), "Basa Jawa", false), new J.i18n.Language("ko", J.i18n.GT.$("Korean"), "í•œêµì–´", true), new J.i18n.Language("ms", J.i18n.GT.$("Malay"), "Bahasa Melayu", true), new J.i18n.Language("nb", J.i18n.GT.$("Norwegian Bokmal"), "Norsk BokmÃ¥l", false), new J.i18n.Language("nl", J.i18n.GT.$("Dutch"), "Nederlands", true), new J.i18n.Language("oc", J.i18n.GT.$("Occitan"), "Occitan", false), new J.i18n.Language("pl", J.i18n.GT.$("Polish"), "Polski", false), new J.i18n.Language("pt", J.i18n.GT.$("Portuguese"), "Português", false), new J.i18n.Language("pt_BR", J.i18n.GT.$("Brazilian Portuguese"), "Português brasileiro", true), new J.i18n.Language("ru", J.i18n.GT.$("Russian"), "РуÑÑкий", true), new J.i18n.Language("sl", J.i18n.GT.$("Slovenian"), "SlovenÅ¡Äina", false), new J.i18n.Language("sr", J.i18n.GT.$("Serbian"), "ÑрпÑки језик", false), new J.i18n.Language("sv", J.i18n.GT.$("Swedish"), "Svenska", true), new J.i18n.Language("ta", J.i18n.GT.$("Tamil"), "தமிழà¯", false), new J.i18n.Language("te", J.i18n.GT.$("Telugu"), "తెలà±à°—à±", false), new J.i18n.Language("tr", J.i18n.GT.$("Turkish"), "Türkçe", true), new J.i18n.Language("ug", J.i18n.GT.$("Uyghur"), "UyÆ£urqÉ™", false), new J.i18n.Language("uk", J.i18n.GT.$("Ukrainian"), "УкраїнÑька", true), new J.i18n.Language("uz", J.i18n.GT.$("Uzbek"), "O'zbek", false), new J.i18n.Language("zh_CN", J.i18n.GT.$("Simplified Chinese"), "简体ä¸æ–‡", true), new J.i18n.Language("zh_TW", J.i18n.GT.$("Traditional Chinese"), "ç¹é«”ä¸æ–‡", true)]);
+});
+c$.getSupported = Clazz.defineMethod(c$, "getSupported",
+function(list, code){
+for (var i = list.length; --i >= 0; ) if (list[i].code.equalsIgnoreCase(code)) return list[i].code;
+
+for (var i = list.length; --i >= 0; ) if (list[i].code.startsWith(code)) return list[i].code;
+
+return null;
+}, "~A,~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/i18n/Resource.js b/config/plugins/visualizations/jmol/static/j2s/J/i18n/Resource.js
new file mode 100755
index 000000000000..46bcdb59f091
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/i18n/Resource.js
@@ -0,0 +1,87 @@
+Clazz.declarePackage("J.i18n");
+Clazz.load(null, "J.i18n.Resource", ["java.util.Hashtable", "JU.PT", "$.Rdr", "J.translation.PO", "JU.Logger", "JV.FileManager"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.resource = null;
+this.resourceMap = null;
+Clazz.instantialize(this, arguments);}, J.i18n, "Resource", null);
+Clazz.makeConstructor(c$,
+function(resource, className){
+if (className == null) this.resourceMap = resource;
+ else this.resource = resource;
+}, "~O,~S");
+c$.getResource = Clazz.defineMethod(c$, "getResource",
+function(vwr, className, name){
+try {
+var br = JV.FileManager.getBufferedReaderForResource(vwr, new J.translation.PO(), "J/translation/", (className.indexOf("Applet") >= 0 ? "JmolApplet/" : "Jmol/") + name + ".po");
+var data = new Array(1);
+JU.Rdr.readAllAsString(br, 2147483647, false, data, 0);
+var poData = data[0];
+return J.i18n.Resource.getResourceFromPO(poData);
+} catch (e) {
+if (Clazz.exceptionOf(e,"java.io.IOException")){
+return null;
+} else {
+throw e;
+}
+}
+}, "JV.Viewer,~S,~S");
+Clazz.defineMethod(c$, "getString",
+function(string){
+try {
+return (this.resource == null ? this.resourceMap.get(string) : this.resource.getString(string));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return null;
+} else {
+throw e;
+}
+}
+}, "~S");
+c$.getLanguage = Clazz.defineMethod(c$, "getLanguage",
+function(){
+var language = null;
+{
+language = Jmol.featureDetection.getDefaultLanguage().replace(/-/g,'_');
+}return language;
+});
+c$.getResourceFromPO = Clazz.defineMethod(c$, "getResourceFromPO",
+function(data){
+if (data == null || data.length == 0) return null;
+var map = new java.util.Hashtable();
+try {
+var lines = JU.PT.split(data, "\n");
+var mode = 0;
+var msgstr = "";
+var msgid = "";
+for (var i = 0; i < lines.length; i++) {
+var line = lines[i];
+if (line.length <= 2) {
+if (mode == 2 && msgstr.length != 0 && msgid.length != 0) map.put(msgid, msgstr);
+mode = 0;
+} else if (line.indexOf("msgid") == 0) {
+mode = 1;
+msgid = J.i18n.Resource.fix(line);
+} else if (line.indexOf("msgstr") == 0) {
+mode = 2;
+msgstr = J.i18n.Resource.fix(line);
+} else if (mode == 1) {
+msgid += J.i18n.Resource.fix(line);
+} else if (mode == 2) {
+msgstr += J.i18n.Resource.fix(line);
+}}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+JU.Logger.info(map.size() + " translations loaded");
+return (map.size() == 0 ? null : new J.i18n.Resource(map, null));
+}, "~S");
+c$.fix = Clazz.defineMethod(c$, "fix",
+function(line){
+if (line.indexOf("\\\"") >= 0) line = JU.PT.rep(line, "\\\"", "\"");
+return JU.PT.rep(line.substring(line.indexOf("\"") + 1, line.lastIndexOf("\"")), "\\n", "\n");
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/image/AviCreator.js b/config/plugins/visualizations/jmol/static/j2s/J/image/AviCreator.js
new file mode 100755
index 000000000000..d05c362326b0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/image/AviCreator.js
@@ -0,0 +1,11 @@
+Clazz.declarePackage("J.image");
+Clazz.load(["J.api.JmolMovieCreatorInterface"], "J.image.AviCreator", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.errorMsg = null;
+Clazz.instantialize(this, arguments);}, J.image, "AviCreator", null, J.api.JmolMovieCreatorInterface);
+Clazz.overrideMethod(c$, "createMovie",
+function(vwr, files, width, height, fps, fileName){
+return this.errorMsg;
+}, "JV.Viewer,~A,~N,~N,~N,~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/inchi/InChIJS.js b/config/plugins/visualizations/jmol/static/j2s/J/inchi/InChIJS.js
new file mode 100755
index 000000000000..7e54bf549f8f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/inchi/InChIJS.js
@@ -0,0 +1,52 @@
+Clazz.declarePackage("J.inchi");
+Clazz.load(["J.api.JmolInChI"], "J.inchi.InChIJS", ["JU.PT"], function(){
+var c$ = Clazz.declareType(J.inchi, "InChIJS", null, J.api.JmolInChI);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "getInchi",
+function(vwr, atoms, molData, options){
+if (atoms == null ? molData == null : atoms.isEmpty()) return "";
+var ret = "";
+try {
+if (options == null) options = "";
+options = JU.PT.rep(JU.PT.rep(options.$replace('-', ' '), " ", " ").trim(), " ", " -").toLowerCase();
+if (options.length > 0) options = "-" + options;
+if (molData == null) molData = vwr.getModelExtract(atoms, false, false, "MOL");
+if ((typeof(molData)=='string') && (molData).startsWith("InChI=")) {
+{
+ret = (Jmol.inchiToInchiKey ? Jmol.inchiToInchiKey(molData) : "");
+}return ret;
+}var haveKey = (options.indexOf("key") >= 0);
+if (haveKey) {
+options = options.$replace("inchikey", "key");
+}if (options.indexOf("fixedh?") >= 0) {
+var fxd = this.getInchi(vwr, atoms, molData, options.$replace('?', ' '));
+options = JU.PT.rep(options, "-fixedh?", "");
+if (haveKey) options = JU.PT.rep(options, "-key", "");
+var inchi = this.getInchi(vwr, atoms, molData, options);
+if (fxd != null && fxd.length > inchi.length) inchi = fxd;
+return (haveKey ? this.getInchi(vwr, atoms, inchi, "-key") : inchi);
+}{
+ret = (Jmol.molfileToInChI ? Jmol.molfileToInChI(molData,
+options) : "");
+}} catch (e) {
+{
+e = (e.getMessage$ ? e.getMessage$() : e);
+}System.err.println("InChIJS exception: " + e);
+}
+return ret;
+}, "JV.Viewer,JU.BS,~O,~S");
+{
+var wasmPath = "/_WASM";
+var es6Path = "/_ES6";
+try {
+{
+var j2sPath = Jmol._applets.master._j2sFullPath;
+//
+Jmol.inchiPath = j2sPath + wasmPath;
+//
+var importPath = j2sPath + es6Path;
+//
+import(importPath + "/molfile-to-inchi.js");
+}} catch (t) {
+}
+}});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/io/DOMReader.js b/config/plugins/visualizations/jmol/static/j2s/J/io/DOMReader.js
new file mode 100755
index 000000000000..0a97d816a72a
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/io/DOMReader.js
@@ -0,0 +1,34 @@
+Clazz.declarePackage("J.io");
+(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.fm = null;
+this.vwr = null;
+this.aDOMNode = null;
+this.atomSetCollection = null;
+this.htParams = null;
+Clazz.instantialize(this, arguments);}, J.io, "DOMReader", null);
+Clazz.prepareFields (c$, function(){
+this.aDOMNode = new Array(1);
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.defineMethod(c$, "set",
+function(fileManager, vwr, DOMNode, htParams){
+this.fm = fileManager;
+this.vwr = vwr;
+this.aDOMNode[0] = DOMNode;
+this.htParams = htParams;
+}, "JV.FileManager,JV.Viewer,~O,java.util.Map");
+Clazz.defineMethod(c$, "run",
+function(){
+var info = null;
+{
+}if (info != null) this.htParams.put("nameSpaceInfo", info);
+this.vwr.zap(false, true, false);
+this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollectionFromDOM(this.aDOMNode, this.htParams);
+if ((typeof(this.atomSetCollection)=='string')) return;
+this.fm.setFileInfo( Clazz.newArray(-1, ["JSNode"]));
+});
+})();
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/io/FileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/io/FileReader.js
new file mode 100755
index 000000000000..455184498917
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/io/FileReader.js
@@ -0,0 +1,92 @@
+Clazz.declarePackage("J.io");
+Clazz.load(null, "J.io.FileReader", ["java.io.BufferedReader", "JU.AU", "$.PT", "$.Rdr", "J.api.Interface", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.fileNameIn = null;
+this.fullPathNameIn = null;
+this.nameAsGivenIn = null;
+this.fileTypeIn = null;
+this.atomSetCollection = null;
+this.readerOrDocument = null;
+this.htParams = null;
+this.isAppend = false;
+this.bytesOrStream = null;
+Clazz.instantialize(this, arguments);}, J.io, "FileReader", null);
+Clazz.makeConstructor(c$,
+function(vwr, fileName, fullPathName, nameAsGiven, type, reader, htParams, isAppend){
+this.vwr = vwr;
+this.fileNameIn = (fileName == null ? fullPathName : fileName);
+this.fullPathNameIn = (fullPathName == null ? this.fileNameIn : fullPathName);
+this.nameAsGivenIn = (nameAsGiven == null ? this.fileNameIn : nameAsGiven);
+this.fileTypeIn = type;
+if (reader != null) {
+if (JU.AU.isAB(reader) || Clazz.instanceOf(reader,"java.io.BufferedInputStream")) {
+this.bytesOrStream = reader;
+reader = null;
+} else if (Clazz.instanceOf(reader,"java.io.Reader") && !(Clazz.instanceOf(reader,"java.io.BufferedReader"))) {
+reader = new java.io.BufferedReader(reader);
+}}this.readerOrDocument = reader;
+this.htParams = htParams;
+this.isAppend = isAppend;
+}, "JV.Viewer,~S,~S,~S,~S,~O,java.util.Map,~B");
+Clazz.defineMethod(c$, "run",
+function(){
+if (!this.isAppend && this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
+var errorMessage = null;
+var t = null;
+if (this.fullPathNameIn.contains("#_DOCACHE_")) this.readerOrDocument = J.io.FileReader.getChangeableReader(this.vwr, this.nameAsGivenIn, this.fullPathNameIn);
+if (this.readerOrDocument == null) {
+t = this.vwr.fm.getUnzippedReaderOrStreamFromName(this.fullPathNameIn, this.bytesOrStream, true, false, false, true, this.htParams);
+if (t == null || (typeof(t)=='string')) {
+errorMessage = (t == null ? "error opening:" + this.nameAsGivenIn : t);
+if (!errorMessage.startsWith("NOTE:")) JU.Logger.error("file ERROR: " + this.fullPathNameIn + "\n" + errorMessage);
+this.atomSetCollection = errorMessage;
+return;
+}if (Clazz.instanceOf(t,"java.io.BufferedReader")) {
+this.readerOrDocument = t;
+} else if (Clazz.instanceOf(t,"javajs.api.ZInputStream")) {
+var name = this.fullPathNameIn;
+var subFileList = null;
+name = name.$replace('\\', '/');
+if (name.indexOf("|") >= 0 && !name.endsWith(".zip")) {
+subFileList = JU.PT.split(name, "|");
+name = subFileList[0];
+}if (subFileList != null) this.htParams.put("subFileList", subFileList);
+var zis = t;
+var zipDirectory = this.vwr.fm.getZipDirectory(name, true, true);
+this.atomSetCollection = t = this.vwr.fm.getJzu().getAtomSetCollectionOrBufferedReaderFromZip(this.vwr, zis, name, zipDirectory, this.htParams, 1, false);
+try {
+zis.close();
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+}}if (Clazz.instanceOf(t,"java.io.BufferedInputStream")) this.readerOrDocument = (J.api.Interface.getInterface("JU.BinaryDocument", this.vwr, "file")).setStream(t, !this.htParams.containsKey("isLittleEndian"));
+if (this.readerOrDocument != null) {
+this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollectionReader(this.fullPathNameIn, this.fileTypeIn, this.readerOrDocument, this.htParams);
+if (!((typeof(this.atomSetCollection)=='string'))) this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollection(this.atomSetCollection);
+try {
+if (Clazz.instanceOf(this.readerOrDocument,"java.io.BufferedReader")) (this.readerOrDocument).close();
+ else if (Clazz.instanceOf(this.readerOrDocument,"javajs.api.GenericBinaryDocument")) (this.readerOrDocument).close();
+} catch (e) {
+if (Clazz.exceptionOf(e,"java.io.IOException")){
+} else {
+throw e;
+}
+}
+}if ((typeof(this.atomSetCollection)=='string')) return;
+if (!this.isAppend && !this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
+this.vwr.fm.setFileInfo( Clazz.newArray(-1, [this.fullPathNameIn, this.fileNameIn, this.nameAsGivenIn]));
+});
+c$.getChangeableReader = Clazz.defineMethod(c$, "getChangeableReader",
+function(vwr, nameAsGivenIn, fullPathNameIn){
+return JU.Rdr.getBR(vwr.getLigandModel(nameAsGivenIn, fullPathNameIn, "_file", null));
+}, "JV.Viewer,~S,~S");
+Clazz.defineMethod(c$, "getAtomSetCollection",
+function(){
+return this.atomSetCollection;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/io/FilesReader.js b/config/plugins/visualizations/jmol/static/j2s/J/io/FilesReader.js
new file mode 100755
index 000000000000..bbb7153d4c66
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/io/FilesReader.js
@@ -0,0 +1,56 @@
+Clazz.declarePackage("J.io");
+Clazz.load(["J.api.JmolFilesReaderInterface"], "J.io.FilesReader", ["JU.Rdr", "J.api.Interface", "J.io.FileReader", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.fm = null;
+this.vwr = null;
+this.fullPathNamesIn = null;
+this.namesAsGivenIn = null;
+this.fileTypesIn = null;
+this.atomSetCollection = null;
+this.dataReaders = null;
+this.htParams = null;
+this.isAppend = false;
+Clazz.instantialize(this, arguments);}, J.io, "FilesReader", null, J.api.JmolFilesReaderInterface);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set",
+function(fileManager, vwr, name, nameAsGiven, types, readers, htParams, isAppend){
+this.fm = fileManager;
+this.vwr = vwr;
+this.fullPathNamesIn = name;
+this.namesAsGivenIn = nameAsGiven;
+this.fileTypesIn = types;
+this.dataReaders = readers;
+this.htParams = htParams;
+this.isAppend = isAppend;
+}, "JV.FileManager,JV.Viewer,~A,~A,~A,~A,java.util.Map,~B");
+Clazz.overrideMethod(c$, "run",
+function(){
+if (!this.isAppend && this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
+var getReadersOnly = !this.vwr.displayLoadErrors;
+this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollectionReaders(this, this.fullPathNamesIn, this.fileTypesIn, this.htParams, getReadersOnly);
+this.dataReaders = null;
+if (getReadersOnly && !((typeof(this.atomSetCollection)=='string'))) {
+this.atomSetCollection = this.vwr.getModelAdapter().getAtomSetCollectionFromSet(this.atomSetCollection, null, this.htParams);
+}if ((typeof(this.atomSetCollection)=='string')) {
+JU.Logger.error("file ERROR: " + this.atomSetCollection);
+return;
+}if (!this.isAppend && !this.vwr.displayLoadErrors) this.vwr.zap(false, true, false);
+this.fm.setFileInfo( Clazz.newArray(-1, [this.dataReaders == null ? this.fullPathNamesIn[0] : "String[]"]));
+});
+Clazz.overrideMethod(c$, "getBufferedReaderOrBinaryDocument",
+function(i, forceBinary){
+if (this.dataReaders != null) return (forceBinary ? null : this.dataReaders[i].getBufferedReader());
+var name = this.fullPathNamesIn[i];
+if (name.contains("#_DOCACHE_")) return J.io.FileReader.getChangeableReader(this.vwr, this.namesAsGivenIn[i], name);
+var t = this.fm.getUnzippedReaderOrStreamFromName(name, null, false, forceBinary, false, true, this.htParams);
+if (Clazz.instanceOf(t,"java.io.BufferedInputStream") && JU.Rdr.isZipS(t)) {
+var zipDirectory = this.fm.getZipDirectory(name, true, true);
+t = this.fm.getBufferedInputStreamOrErrorMessageFromName(name, this.fullPathNamesIn[i], false, false, null, false, true);
+t = this.fm.getJzu().getAtomSetCollectionOrBufferedReaderFromZip(this.vwr, t, name, zipDirectory, this.htParams, 1, true);
+}return (Clazz.instanceOf(t,"java.io.BufferedInputStream") ? (J.api.Interface.getInterface("JU.BinaryDocument", this.vwr, "file")).setStream(t, true) : Clazz.instanceOf(t,"java.io.BufferedReader") || Clazz.instanceOf(t,"javajs.api.GenericBinaryDocument") ? t : t == null ? "error opening:" + this.namesAsGivenIn[i] : t);
+}, "~N,~B");
+Clazz.overrideMethod(c$, "getAtomSetCollection",
+function(){
+return this.atomSetCollection;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/io/JmolUtil.js b/config/plugins/visualizations/jmol/static/j2s/J/io/JmolUtil.js
new file mode 100755
index 000000000000..b9b67c369669
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/io/JmolUtil.js
@@ -0,0 +1,251 @@
+Clazz.declarePackage("J.io");
+Clazz.load(null, "J.io.JmolUtil", ["java.net.URL", "java.util.Hashtable", "JU.AU", "$.Lst", "$.OC", "$.PT", "$.Rdr", "J.adapter.smarter.AtomSetCollection", "J.api.Interface", "JU.Logger", "JV.FileManager", "$.Viewer"], function(){
+var c$ = Clazz.declareType(J.io, "JmolUtil", null);
+/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "getImage",
+function(vwr, fullPathNameOrBytes, echoName, forceSync){
+var image = null;
+var info = null;
+var apiPlatform = vwr.apiPlatform;
+var createImage = false;
+var fullPathName = "" + fullPathNameOrBytes;
+if ((typeof(fullPathNameOrBytes)=='string')) {
+var isBMP = fullPathName.toUpperCase().endsWith("BMP");
+if (forceSync || fullPathName.indexOf("|") > 0 || isBMP) {
+var ret = vwr.fm.getFileAsBytes(fullPathName, null);
+if (!JU.AU.isAB(ret)) return "" + ret;
+if (JV.Viewer.isJS) info = Clazz.newArray(-1, [echoName, fullPathNameOrBytes, ret]);
+ else image = apiPlatform.createImage(ret);
+} else if (JU.OC.urlTypeIndex(fullPathName) >= 0) {
+if (JV.Viewer.isJS) info = Clazz.newArray(-1, [echoName, fullPathNameOrBytes, null]);
+ else try {
+image = apiPlatform.createImage( new java.net.URL(Clazz.castNullAs("java.net.URL"), fullPathName, null));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return "bad URL: " + fullPathName;
+} else {
+throw e;
+}
+}
+} else {
+createImage = true;
+}} else if (JV.Viewer.isJS) {
+info = Clazz.newArray(-1, [echoName, JU.Rdr.guessMimeTypeForBytes(fullPathNameOrBytes), fullPathNameOrBytes]);
+} else {
+createImage = true;
+}if (createImage) image = apiPlatform.createImage("\1close".equals(fullPathNameOrBytes) ? "\1close" + echoName : fullPathNameOrBytes);
+ else if (info != null) image = apiPlatform.createImage(info);
+{
+return image;
+}}, "JV.Viewer,~O,~S,~B");
+Clazz.defineMethod(c$, "getAtomSetCollectionOrBufferedReaderFromZip",
+function(vwr, is, fileName, zipDirectory, htParams, subFilePtr, asBufferedReader){
+var adapter = vwr.getModelAdapter();
+var doCombine = (subFilePtr == 1);
+htParams.put("zipSet", fileName);
+var subFileList = htParams.get("subFileList");
+if (subFileList == null) subFileList = this.getSpartanSubfiles(zipDirectory);
+var subFileName = (subFileList == null || subFilePtr >= subFileList.length ? htParams.get("SubFileName") : subFileList[subFilePtr]);
+if (subFileName != null && (subFileName.startsWith("/") || subFileName.startsWith("\\"))) subFileName = subFileName.substring(1);
+var selectedFile = 0;
+if (subFileName == null && htParams.containsKey("modelNumber")) {
+selectedFile = (htParams.get("modelNumber")).intValue();
+if (selectedFile > 0 && doCombine) htParams.remove("modelNumber");
+}var manifest = htParams.get("manifest");
+var useFileManifest = (manifest == null);
+if (useFileManifest) manifest = (zipDirectory.length > 0 ? zipDirectory[0] : "");
+var haveManifest = (manifest.length > 0);
+if (haveManifest) {
+if (JU.Logger.debugging) JU.Logger.debug("manifest for " + fileName + ":\n" + manifest);
+}var ignoreErrors = (manifest.indexOf("IGNORE_ERRORS") >= 0);
+var selectAll = (manifest.indexOf("IGNORE_MANIFEST") >= 0);
+var exceptFiles = (manifest.indexOf("EXCEPT_FILES") >= 0);
+if (selectAll || subFileName != null) haveManifest = false;
+if (useFileManifest && haveManifest) {
+var path = JV.FileManager.getManifestScriptPath(manifest);
+if (path != null) {
+return "NOTE: file recognized as a script file: " + fileName + path + "\n";
+}}var vCollections = new JU.Lst();
+var htCollections = (haveManifest ? new java.util.Hashtable() : null);
+var nFiles = 0;
+try {
+var spartanData = (this.isSpartanZip(zipDirectory) ? vwr.fm.spartanUtil().getData(is, zipDirectory) : null);
+var zpt = vwr.getJzt();
+var ret;
+if (spartanData != null) {
+var reader = JU.Rdr.getBR(spartanData.toString());
+if (asBufferedReader) return reader;
+ret = adapter.getAtomSetCollectionFromReader(fileName, reader, htParams);
+if ((typeof(ret)=='string')) return ret;
+if (Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection")) {
+var atomSetCollection = ret;
+if (atomSetCollection.errorMessage != null) {
+if (ignoreErrors) return null;
+return atomSetCollection.errorMessage;
+}return atomSetCollection;
+}if (ignoreErrors) return null;
+return "unknown reader error";
+}if (Clazz.instanceOf(is,"java.io.BufferedInputStream")) is = JU.Rdr.getPngZipStream(is, true);
+var zis = zpt.newZipInputStream(is);
+var ze;
+if (haveManifest) manifest = '|' + manifest.$replace('\r', '|').$replace('\n', '|') + '|';
+while ((ze = zis.getNextEntry()) != null && (selectedFile <= 0 || vCollections.size() < selectedFile)) {
+if (ze.isDirectory()) continue;
+var thisEntry = ze.getName();
+if (subFileName != null && !thisEntry.equals(subFileName)) continue;
+if (subFileName != null) htParams.put("subFileName", subFileName);
+if (thisEntry.startsWith("JmolManifest") || haveManifest && exceptFiles == manifest.indexOf("|" + thisEntry + "|") >= 0) continue;
+var bytes = JU.Rdr.getLimitedStreamBytes(zis, ze.getSize());
+if (JU.Rdr.isGzipB(bytes)) bytes = JU.Rdr.getLimitedStreamBytes(zpt.getUnGzippedInputStream(bytes), -1);
+if (JU.Rdr.isZipB(bytes) || JU.Rdr.isPngZipB(bytes)) {
+var bis = JU.Rdr.getBIS(bytes);
+var zipDir2 = zpt.getZipDirectoryAndClose(bis, "JmolManifest");
+bis = JU.Rdr.getBIS(bytes);
+var atomSetCollections = this.getAtomSetCollectionOrBufferedReaderFromZip(vwr, bis, fileName + "|" + thisEntry, zipDir2, htParams, ++subFilePtr, asBufferedReader);
+if ((typeof(atomSetCollections)=='string')) {
+if (ignoreErrors) continue;
+return atomSetCollections;
+} else if (Clazz.instanceOf(atomSetCollections,"J.adapter.smarter.AtomSetCollection") || Clazz.instanceOf(atomSetCollections,"JU.Lst")) {
+if (haveManifest && !exceptFiles) htCollections.put(thisEntry, atomSetCollections);
+ else vCollections.addLast(atomSetCollections);
+} else if (Clazz.instanceOf(atomSetCollections,"java.io.BufferedReader")) {
+if (doCombine) zis.close();
+return atomSetCollections;
+} else {
+if (ignoreErrors) continue;
+zis.close();
+return "unknown zip reader error";
+}} else if (JU.Rdr.isPickleB(bytes)) {
+var bis = JU.Rdr.getBIS(bytes);
+if (doCombine) zis.close();
+return bis;
+} else {
+var sData;
+if (JU.Rdr.isCompoundDocumentB(bytes)) {
+var jd = J.api.Interface.getInterface("JU.CompoundDocument", vwr, "file");
+jd.setDocStream(zpt, JU.Rdr.getBIS(bytes));
+sData = jd.getAllDataFiles("Molecule", "Input").toString();
+} else {
+sData = JU.Rdr.fixUTF(bytes);
+}var reader = JU.Rdr.getBR(sData);
+if (asBufferedReader) {
+if (doCombine) zis.close();
+return reader;
+}var fname = fileName + "|" + ze.getName();
+ret = adapter.getAtomSetCollectionFromReader(fname, reader, htParams);
+if (!(Clazz.instanceOf(ret,"J.adapter.smarter.AtomSetCollection"))) {
+if (ignoreErrors) continue;
+zis.close();
+return "" + ret;
+}if (haveManifest && !exceptFiles) htCollections.put(thisEntry, ret);
+ else vCollections.addLast(ret);
+var a = ret;
+if (a.errorMessage != null) {
+if (ignoreErrors) continue;
+zis.close();
+return a.errorMessage;
+}}}
+if (doCombine) zis.close();
+if (haveManifest && !exceptFiles) {
+var list = JU.PT.split(manifest, "|");
+for (var i = 0; i < list.length; i++) {
+var file = list[i];
+if (file.length == 0 || file.indexOf("#") == 0) continue;
+if (htCollections.containsKey(file)) vCollections.addLast(htCollections.get(file));
+ else if (JU.Logger.debugging) JU.Logger.debug("manifested file " + file + " was not found in " + fileName);
+}
+}if (!doCombine) return vCollections;
+var result = (vCollections.size() == 1 && Clazz.instanceOf(vCollections.get(0),"J.adapter.smarter.AtomSetCollection") ? vCollections.get(0) : new J.adapter.smarter.AtomSetCollection("Array", null, null, vCollections));
+if (result.errorMessage != null) {
+if (ignoreErrors) return null;
+return result.errorMessage;
+}if (nFiles == 1) selectedFile = 1;
+if (selectedFile > 0 && selectedFile <= vCollections.size()) return vCollections.get(selectedFile - 1);
+return result;
+} catch (e$$) {
+if (Clazz.exceptionOf(e$$, Exception)){
+var e = e$$;
+{
+if (ignoreErrors) return null;
+JU.Logger.error("" + e);
+return "" + e;
+}
+} else if (Clazz.exceptionOf(e$$, Error)){
+var er = e$$;
+{
+JU.Logger.errorEx(null, er);
+return "" + er;
+}
+} else {
+throw e$$;
+}
+}
+}, "JV.Viewer,java.io.InputStream,~S,~A,java.util.Map,~N,~B");
+Clazz.defineMethod(c$, "getCachedPngjBytes",
+function(fm, pathName){
+if (pathName.startsWith("file:///")) pathName = "file:" + pathName.substring(7);
+JU.Logger.info("JmolUtil checking PNGJ cache for " + pathName);
+var shortName = this.shortSceneFilename(pathName);
+if (fm.pngjCache == null && !this.clearAndCachePngjFile(fm, Clazz.newArray(-1, [pathName, null]))) return null;
+var cache = fm.pngjCache;
+var isMin = (pathName.indexOf(".min.") >= 0);
+if (!isMin) {
+var cName = fm.getCanonicalName(JU.Rdr.getZipRoot(pathName));
+if (!cache.containsKey(cName) && !this.clearAndCachePngjFile(fm, Clazz.newArray(-1, [pathName, null]))) return null;
+if (pathName.indexOf("|") < 0) shortName = cName;
+}if (cache.containsKey(shortName)) {
+JU.Logger.info("FileManager using memory cache " + shortName);
+return fm.pngjCache.get(shortName);
+}if (!isMin || !this.clearAndCachePngjFile(fm, Clazz.newArray(-1, [pathName, null]))) return null;
+JU.Logger.info("FileManager using memory cache " + shortName);
+return cache.get(shortName);
+}, "JV.FileManager,~S");
+Clazz.defineMethod(c$, "clearAndCachePngjFile",
+function(fm, data){
+fm.pngjCache = new java.util.Hashtable();
+if (data == null || data[0] == null) return false;
+data[0] = JU.Rdr.getZipRoot(data[0]);
+var shortName = this.shortSceneFilename(data[0]);
+var cache = fm.pngjCache;
+try {
+data[1] = fm.vwr.getJzt().cacheZipContents(JU.Rdr.getPngZipStream(fm.getBufferedInputStreamOrErrorMessageFromName(data[0], null, false, false, null, false, true), true), shortName, cache, false);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return false;
+} else {
+throw e;
+}
+}
+if (data[1] == null) return false;
+var bytes = data[1].getBytes();
+cache.put(fm.getCanonicalName(data[0]), bytes);
+if (shortName.indexOf("_scene_") >= 0) {
+cache.put(this.shortSceneFilename(data[0]), bytes);
+bytes = cache.remove(shortName + "|state.spt");
+if (bytes != null) cache.put(this.shortSceneFilename(data[0] + "|state.spt"), bytes);
+}return true;
+}, "JV.FileManager,~A");
+Clazz.defineMethod(c$, "shortSceneFilename",
+function(pathName){
+var pt = pathName.indexOf("_scene_") + 7;
+if (pt < 7) return pathName;
+var s = "";
+if (pathName.endsWith("|state.spt")) {
+var pt1 = pathName.indexOf('.', pt);
+if (pt1 < 0) return pathName;
+s = pathName.substring(pt, pt1);
+}var pt2 = pathName.lastIndexOf("|");
+return pathName.substring(0, pt) + s + (pt2 > 0 ? pathName.substring(pt2) : "");
+}, "~S");
+Clazz.defineMethod(c$, "getSpartanSubfiles",
+function(zipDirectory){
+var name = (zipDirectory.length < 2 ? null : zipDirectory[1]);
+return (name == null || zipDirectory.length != 2 || !name.endsWith(".spardir/") ? null : Clazz.newArray(-1, ["", JU.PT.trim(name, "/")]));
+}, "~A");
+Clazz.defineMethod(c$, "isSpartanZip",
+function(zipDirectory){
+for (var i = 1; i < zipDirectory.length; i++) if (zipDirectory[i].endsWith(".spardir/") || zipDirectory[i].indexOf("_spartandir") >= 0) return true;
+
+return false;
+}, "~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jsv/JDXMOLParser.js b/config/plugins/visualizations/jmol/static/j2s/J/jsv/JDXMOLParser.js
new file mode 100755
index 000000000000..e79e4693aa3b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jsv/JDXMOLParser.js
@@ -0,0 +1,293 @@
+Clazz.declarePackage("J.jsv");
+Clazz.load(["J.api.JmolJDXMOLParser"], "J.jsv.JDXMOLParser", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.PT", "$.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.line = null;
+this.lastModel = "";
+this.thisModelID = null;
+this.baseModel = null;
+this.vibScale = 0;
+this.piUnitsX = null;
+this.piUnitsY = null;
+this.loader = null;
+this.modelIdList = "";
+this.peakIndex = null;
+this.peakFilePath = null;
+Clazz.instantialize(this, arguments);}, J.jsv, "JDXMOLParser", null, J.api.JmolJDXMOLParser);
+/*LV!1824 unnec constructor*/Clazz.overrideMethod(c$, "set",
+function(loader, filePath, htParams){
+this.loader = loader;
+this.peakFilePath = filePath;
+this.peakIndex = Clazz.newIntArray (1, 0);
+if (htParams != null) {
+htParams.remove("modelNumber");
+if (htParams.containsKey("zipSet")) {
+this.peakIndex = htParams.get("peakIndex");
+if (this.peakIndex == null) {
+this.peakIndex = Clazz.newIntArray (1, 0);
+htParams.put("peakIndex", this.peakIndex);
+}if (!htParams.containsKey("subFileName")) this.peakFilePath = JU.PT.split(filePath, "|")[0];
+}}return this;
+}, "J.api.JmolJDXMOLReader,~S,java.util.Map");
+Clazz.overrideMethod(c$, "getAttribute",
+function(line, tag){
+var attr = JU.PT.getQuotedAttribute(line, tag);
+return (attr == null ? "" : attr);
+}, "~S,~S");
+Clazz.overrideMethod(c$, "getRecord",
+function(key){
+if (this.line == null || this.line.indexOf(key) < 0) return null;
+var s = this.line;
+while (s.indexOf(">") < 0) s += " " + this.readLine();
+
+return this.line = s;
+}, "~S");
+Clazz.overrideMethod(c$, "readModels",
+function(){
+if (!this.findRecord("Models")) return false;
+this.line = "";
+this.thisModelID = "";
+var isFirst = true;
+while (true) {
+this.line = this.loader.discardLinesUntilNonBlank();
+if (this.getRecord("") < 0) s += " " + this.readLine();
+
+s = s.trim();
+}s = JU.PT.replaceAllCharacters(s, "()<>", " ").trim();
+if (s.length == 0) break;
+var pt = s.indexOf("'");
+if (pt >= 0) {
+var pt2 = s.indexOf("'", pt + 1);
+s = s.substring(0, pt) + JU.PT.rep(s.substring(pt + 1, pt2), ",", ";") + s.substring(pt2 + 1);
+}JU.Logger.info("Peak Assignment: " + s);
+var tokens = JU.PT.split(s, ",");
+list.addLast(tokens);
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Error reading peak assignments at " + this.line + ": " + e);
+} else {
+throw e;
+}
+}
+return list;
+}, "~N,~B");
+Clazz.overrideMethod(c$, "setACDAssignments",
+function(model, mytype, peakCount, acdlist, molFile){
+try {
+if (peakCount >= 0) this.peakIndex = Clazz.newIntArray(-1, [peakCount]);
+var isMS = (mytype.indexOf("MASS") == 0);
+var file = " file=" + JU.PT.esc(this.peakFilePath.$replace('\\', '/'));
+model = " model=" + JU.PT.esc(model + " (assigned)");
+this.piUnitsX = "";
+this.piUnitsY = "";
+var dx = this.getACDPeakWidth(mytype) / 2;
+var htSets = new java.util.Hashtable();
+var list = new JU.Lst();
+var zzcMap = null;
+var ptx;
+var pta;
+var nAtoms = 0;
+if (isMS) {
+zzcMap = new java.util.Hashtable();
+var tokens = JU.PT.split(molFile, "M ZZC");
+for (var i = tokens.length; --i >= 1; ) {
+var ab = JU.PT.getTokens(tokens[i]);
+nAtoms = Math.max(nAtoms, JU.PT.parseInt(ab[0]));
+zzcMap.put(ab[1], ab[0]);
+}
+ptx = 4;
+pta = 0;
+} else if (mytype.indexOf("NMR") >= 0) {
+ptx = 0;
+pta = 3;
+} else {
+ptx = 0;
+pta = 2;
+}var nPeaks = acdlist.size();
+for (var i = 0; i < nPeaks; i++) {
+var data = acdlist.get(i);
+var x = JU.PT.parseFloat(data[ptx]);
+var a = data[pta];
+if (isMS) a = this.fixACDAtomList(a, zzcMap, nAtoms);
+ else a = a.$replace(';', ',');
+if (a.indexOf("select") >= 0) {
+var pt = a.indexOf("select atomno=");
+if (pt < 0) continue;
+a = JU.PT.split(a.substring(pt + 14), " ")[0];
+}var title = (isMS ? "m/z=" + Math.round(x) + ": " + data[2] + " (" + data[1] + ")" : pta == 2 ? "" + (Math.round(x * 10) / 10) : null);
+this.getStringInfo(file, title, mytype, model, a, htSets, "" + x, list, " atoms=\"%ATOMS%\" xMin=\"" + (x - dx) + "\" xMax=\"" + (x + dx) + "\">");
+}
+return this.setPeakData(list, 0);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return 0;
+} else {
+throw e;
+}
+}
+}, "~S,~S,~N,JU.Lst,~S");
+Clazz.defineMethod(c$, "fixACDAtomList",
+function(atoms, zzcMap, nAtoms){
+atoms = atoms.trim();
+var tokens = JU.PT.getTokens(atoms.$replace(';', ' '));
+var bs = new JU.BS();
+var isM = false;
+for (var i = 0; i < tokens.length; i++) {
+var a = tokens[i];
+isM = (a.indexOf("M") >= 0);
+if (isM) a = "1-" + nAtoms;
+var pt = a.indexOf('-');
+if (pt >= 0) {
+var i1 = JU.PT.parseInt(a.substring(0, pt));
+var i2 = JU.PT.parseInt(a.substring(pt + 1)) + 1;
+for (var k = i1; k < i2; k++) bs.set(isM ? k : JU.PT.parseInt(zzcMap.get("" + k)));
+
+} else {
+bs.set(JU.PT.parseInt(zzcMap.get(a)));
+}}
+var s = bs.toJSON();
+return s.substring(1, s.length - 1);
+}, "~S,java.util.Map,~N");
+Clazz.defineMethod(c$, "getACDPeakWidth",
+function(type){
+return (type.indexOf("HNMR") >= 0 ? 0.05 : type.indexOf("CNMR") >= 0 ? 1 : type.indexOf("MASS") >= 0 ? 1 : 10);
+}, "~S");
+Clazz.overrideMethod(c$, "readPeaks",
+function(isSignals, peakCount){
+try {
+if (peakCount >= 0) this.peakIndex = Clazz.newIntArray(-1, [peakCount]);
+var offset = (isSignals ? 1 : 0);
+var tag1 = (isSignals ? "Signals" : "Peaks");
+var tag2 = (isSignals ? "= 0; j = bs.nextSetBit(j + 1)) s += "," + (j + offset);
+
+var na = bs.cardinality();
+nH += na;
+info = JU.PT.rep(info, "%ATOMS%", s.substring(1));
+info = JU.PT.rep(info, "%S%", (na == 1 ? "" : "s"));
+info = JU.PT.rep(info, "%NATOMS%", "" + na);
+}JU.Logger.info("adding PeakData " + info);
+this.loader.addPeakData(info);
+}
+this.loader.setSpectrumPeaks(nH, this.piUnitsX, this.piUnitsY);
+return n;
+}, "JU.Lst,~N");
+Clazz.defineMethod(c$, "getStringInfo",
+function(file, title, mytype, model, atoms, htSets, key, list, more){
+if ("HNMR".equals(mytype)) mytype = "1HNMR";
+ else if ("CNMR".equals(mytype)) mytype = "13CNMR";
+var type = (mytype == null ? "" : " type=" + JU.PT.esc(mytype));
+if (title == null) title = ("1HNMR".equals(mytype) ? "atom%S%: %ATOMS%; integration: %NATOMS%" : "");
+title = " title=" + JU.PT.esc(title);
+var stringInfo = "= 0) {
+this.line = this.loader.discardLinesUntilContains("");
+return;
+}this.modelIdList += key;
+this.baseModel = this.getAttribute(this.line, "baseModel");
+while (this.line.indexOf(">") < 0 && this.line.indexOf("type") < 0) this.readLine();
+
+var modelType = this.getAttribute(this.line, "type").toLowerCase();
+this.vibScale = JU.PT.parseFloat(this.getAttribute(this.line, "vibrationScale"));
+if (modelType.equals("xyzvib")) modelType = "xyz";
+ else if (modelType.length == 0) modelType = null;
+var sb = new JU.SB();
+while (this.readLine() != null && !this.line.contains("")) sb.append(this.line).appendC('\n');
+
+this.loader.processModelData(sb.toString(), this.thisModelID, modelType, this.baseModel, this.lastModel, NaN, this.vibScale, isFirst);
+}, "~B");
+Clazz.defineMethod(c$, "findRecord",
+function(tag){
+if (this.line == null) this.readLine();
+if (this.line != null && this.line.indexOf("<" + tag) < 0) this.line = this.loader.discardLinesUntilContains2("<" + tag, "##");
+return (this.line != null && this.line.indexOf("<" + tag) >= 0);
+}, "~S");
+Clazz.defineMethod(c$, "readLine",
+function(){
+return this.line = this.loader.rd();
+});
+Clazz.overrideMethod(c$, "setLine",
+function(s){
+this.line = s;
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jsv/JSpecView.js b/config/plugins/visualizations/jmol/static/j2s/J/jsv/JSpecView.js
new file mode 100755
index 000000000000..9292f409ffc6
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jsv/JSpecView.js
@@ -0,0 +1,134 @@
+Clazz.declarePackage("J.jsv");
+Clazz.load(["J.api.JmolJSpecView"], "J.jsv.JSpecView", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.PT", "JU.Escape", "$.Logger", "JV.FileManager"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+Clazz.instantialize(this, arguments);}, J.jsv, "JSpecView", null, J.api.JmolJSpecView);
+Clazz.overrideMethod(c$, "setViewer",
+function(vwr){
+this.vwr = vwr;
+}, "JV.Viewer");
+Clazz.overrideMethod(c$, "atomPicked",
+function(atomIndex){
+if (atomIndex < 0) return;
+var peak = this.getPeakAtomRecord(atomIndex);
+if (peak != null) this.sendJSpecView(peak + " src=\"JmolAtomSelect\"");
+}, "~N");
+Clazz.defineMethod(c$, "getPeakAtomRecord",
+function(atomIndex){
+var atoms = this.vwr.ms.at;
+var iModel = atoms[atomIndex].mi;
+var type = null;
+switch (atoms[atomIndex].getElementNumber()) {
+case 1:
+type = "1HNMR";
+break;
+case 6:
+type = "13CNMR";
+break;
+default:
+return null;
+}
+var peaks = this.vwr.ms.getInfo(iModel, "jdxAtomSelect_" + type);
+if (peaks == null) return null;
+this.vwr.ms.htPeaks = new java.util.Hashtable();
+var htPeaks = this.vwr.ms.htPeaks;
+for (var i = 0; i < peaks.size(); i++) {
+var peak = peaks.get(i);
+System.out.println("Jmol JSpecView.java peak=" + peak);
+var bsPeak = htPeaks.get(peak);
+System.out.println("Jmol JSpecView.java bspeak=" + bsPeak);
+if (bsPeak == null) {
+htPeaks.put(peak, bsPeak = new JU.BS());
+var satoms = JU.PT.getQuotedAttribute(peak, "atoms");
+var select = JU.PT.getQuotedAttribute(peak, "select");
+System.out.println("Jmol JSpecView.java satoms select " + satoms + " " + select);
+var script = "";
+if (satoms != null) script += "visible & (atomno=" + JU.PT.rep(satoms, ",", " or atomno=") + ")";
+ else if (select != null) script += "visible & (" + select + ")";
+System.out.println("Jmol JSpecView.java script : " + script);
+bsPeak.or(this.vwr.getAtomBitSet(script));
+}System.out.println("Jmol JSpecView bsPeak now : " + bsPeak + " " + atomIndex);
+if (bsPeak.get(atomIndex)) return peak;
+}
+return null;
+}, "~N");
+Clazz.defineMethod(c$, "sendJSpecView",
+function(peak){
+var msg = JU.PT.getQuotedAttribute(peak, "title");
+if (msg != null) this.vwr.scriptEcho(JU.Logger.debugging ? peak : msg);
+peak = this.vwr.fullName + "JSpecView: " + peak;
+JU.Logger.info("Jmol.JSpecView.sendJSpecView Jmol>JSV " + peak);
+this.vwr.sm.syncSend(peak, ">", 0);
+}, "~S");
+Clazz.overrideMethod(c$, "setModel",
+function(modelIndex){
+var syncMode = ("sync on".equals(this.vwr.ms.getInfoM("jmolscript")) ? 1 : this.vwr.sm.getSyncMode());
+if (syncMode != 1) return;
+var peak = this.vwr.ms.getInfo(modelIndex, "jdxModelSelect");
+if (peak != null) this.sendJSpecView(peak + " src=\"Jmol\"");
+}, "~N");
+Clazz.overrideMethod(c$, "getBaseModelIndex",
+function(modelIndex){
+var baseModel = this.vwr.ms.getInfo(modelIndex, "jdxBaseModel");
+if (baseModel != null) for (var i = this.vwr.ms.mc; --i >= 0; ) if (baseModel.equals(this.vwr.ms.getInfo(i, "jdxModelID"))) return i;
+
+return modelIndex;
+}, "~N");
+Clazz.overrideMethod(c$, "processSync",
+function(script, jsvMode){
+if (JU.Logger.debugging) JU.Logger.info("J.jsv.JSpecView jsvMode=" + jsvMode + " script=" + script);
+switch (jsvMode) {
+default:
+return null;
+case 0:
+this.vwr.sm.syncSend(this.vwr.fullName + "JSpecView" + script.substring(10), ">", 0);
+return null;
+case 77:
+case 28:
+case 35:
+this.vwr.sm.syncSend(this.vwr.fullName + "JSpecView:" + script, ">", 0);
+return null;
+case 21:
+if (this.vwr.isApplet) return null;
+return null;
+case 14:
+var filename = JU.PT.getQuotedAttribute(script, "file");
+var isSimulation = (filename != null && filename.startsWith(JV.FileManager.SIMULATION_PROTOCOL));
+var id = (!isSimulation || this.vwr.isApplet ? "" : JU.PT.getQuotedAttribute(filename.$replace('\'', '"'), "id"));
+if (isSimulation && !this.vwr.isApplet && (filename.startsWith(JV.FileManager.SIMULATION_PROTOCOL + "C13/MOL=") || filename.startsWith(JV.FileManager.SIMULATION_PROTOCOL + "H1/MOL="))) filename = null;
+ else filename = JU.PT.rep(filename, "#molfile", "");
+var modelID = (isSimulation ? "molfile" : JU.PT.getQuotedAttribute(script, "model"));
+var baseModel = JU.PT.getQuotedAttribute(script, "baseModel");
+var atoms = JU.PT.getQuotedAttribute(script, "atoms");
+var select = JU.PT.getQuotedAttribute(script, "select");
+var script2 = JU.PT.getQuotedAttribute(script, "script");
+if (id == null || id.length == 0) id = (modelID == null ? null : (filename == null ? "" : filename + "#") + modelID);
+if ("".equals(baseModel)) id += ".baseModel";
+var modelIndex = (id == null ? -3 : this.vwr.getModelIndexFromId(id));
+if (modelIndex == -2) return null;
+if (modelIndex != -1 || filename == null) {
+script = "";
+} else if (isSimulation && !this.vwr.isApplet) {
+return null;
+} else {
+if (isSimulation) filename += "#molfile";
+script = "load " + JU.PT.esc(filename);
+}if (id != null) script += ";model " + JU.PT.esc(id);
+if (atoms != null) script += ";select visible & (@" + JU.PT.rep(atoms, ",", " or @") + ")";
+ else if (select != null) script += ";select visible & (" + select + ")";
+if (script2 != null) script += ";" + script2;
+return script;
+case 7:
+var list = JU.Escape.unescapeStringArray(script.substring(7));
+var peaks = new JU.Lst();
+var type = "1HNMR";
+for (var i = 0; i < list.length; i++) {
+if (i == 0 && list[i].indexOf(JV.FileManager.SIMULATION_PROTOCOL + "C13/") >= 0) type = "13CNMR";
+peaks.addLast(list[i]);
+}
+this.vwr.ms.setInfo(this.vwr.am.cmi, "jdxAtomSelect_" + type, peaks);
+return null;
+}
+}, "~S,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/MeshDataServer.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/MeshDataServer.js
new file mode 100755
index 000000000000..ec87297a5f68
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/MeshDataServer.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.jvxl.api");
+Clazz.declareInterface(J.jvxl.api, "MeshDataServer", J.jvxl.api.VertexDataServer);
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/VertexDataServer.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/VertexDataServer.js
new file mode 100755
index 000000000000..a90d248928a1
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/api/VertexDataServer.js
@@ -0,0 +1,3 @@
+Clazz.declarePackage("J.jvxl.api");
+Clazz.declareInterface(J.jvxl.api, "VertexDataServer");
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingCubes.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingCubes.js
new file mode 100755
index 000000000000..9a88925ac9fc
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingCubes.js
@@ -0,0 +1,337 @@
+Clazz.declarePackage("J.jvxl.calc");
+Clazz.load(["JU.TriangleData", "JU.BS", "$.P3", "$.SB", "$.V3"], "J.jvxl.calc.MarchingCubes", ["J.jvxl.data.JvxlCoder"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.surfaceReader = null;
+this.volumeData = null;
+this.contourType = 0;
+this.isContoured = false;
+this.cutoff = 0;
+this.isCutoffAbsolute = false;
+this.isSquared = false;
+this.isXLowToHigh = false;
+this.cubeCountX = 0;
+this.cubeCountY = 0;
+this.cubeCountZ = 0;
+this.nY = 0;
+this.nZ = 0;
+this.yzCount = 0;
+this.colorDensity = false;
+this.integrateSquared = true;
+this.bsVoxels = null;
+this.bsExcludedVertices = null;
+this.bsExcludedTriangles = null;
+this.bsExcludedPlanes = null;
+this.edgeData = null;
+this.excludePartialCubes = true;
+this.isDensityRange = false;
+this.mode = 0;
+this.vertexValues = null;
+this.edgeCount = 0;
+this.voxelVertexVectors = null;
+this.edgeVectors = null;
+this.edgePointIndexes = null;
+this.isoPointIndexPlanes = null;
+this.yzPlanes = null;
+this.mappingPlane = null;
+this.allInside = false;
+this.$isInside = false;
+this.offset = null;
+this.voxelData = null;
+this.nTriangles = 0;
+this.bsValues = null;
+this.pt0 = null;
+this.pointA = null;
+this.edgeVertexPointers = null;
+this.edgeVertexPlanes = null;
+this.fReturn = null;
+this.linearOffsets = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.calc, "MarchingCubes", JU.TriangleData);
+Clazz.prepareFields (c$, function(){
+this.edgeData = new JU.SB();
+this.vertexValues = Clazz.newFloatArray (8, 0);
+this.voxelVertexVectors = new Array(8);
+this.edgeVectors = new Array(12);
+{
+for (var i = 12; --i >= 0; ) this.edgeVectors[i] = new JU.V3();
+
+}this.edgePointIndexes = Clazz.newIntArray (12, 0);
+this.bsValues = new JU.BS();
+this.pt0 = new JU.P3();
+this.pointA = new JU.P3();
+this.fReturn = Clazz.newFloatArray (1, 0);
+this.linearOffsets = Clazz.newIntArray (8, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.calc.MarchingCubes, []);
+});
+Clazz.makeConstructor(c$,
+function(surfaceReader, volumeData, params, bsVoxels){
+Clazz.superConstructor (this, J.jvxl.calc.MarchingCubes, []);
+this.excludePartialCubes = true;
+this.surfaceReader = surfaceReader;
+this.bsVoxels = bsVoxels;
+var bsExcluded = params.bsExcluded;
+this.bsExcludedVertices = (bsExcluded[0] == null ? bsExcluded[0] = new JU.BS() : bsExcluded[0]);
+this.bsExcludedPlanes = (bsExcluded[2] == null ? bsExcluded[2] = new JU.BS() : bsExcluded[2]);
+this.bsExcludedTriangles = (bsExcluded[3] == null ? bsExcluded[3] = new JU.BS() : bsExcluded[3]);
+this.mode = (volumeData.getVoxelData() != null || volumeData.mappingPlane != null ? 1 : bsVoxels != null ? 2 : 3);
+this.setParameters(volumeData, params);
+}, "J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");
+Clazz.defineMethod(c$, "setParameters",
+function(volumeData, params){
+this.volumeData = volumeData;
+this.colorDensity = params.colorDensity;
+this.isContoured = params.thePlane == null && params.isContoured && !this.colorDensity;
+this.cutoff = params.cutoff;
+this.isCutoffAbsolute = params.isCutoffAbsolute;
+this.isDensityRange = (params.cutoffRange != null);
+this.contourType = params.contourType;
+this.isSquared = params.isSquared;
+this.isXLowToHigh = params.isXLowToHigh;
+this.cubeCountX = volumeData.voxelCounts[0] - 1;
+this.cubeCountY = volumeData.voxelCounts[1] - 1;
+this.cubeCountZ = volumeData.voxelCounts[2] - 1;
+volumeData.getYzCount();
+if (params.mapLattice != null) {
+this.cubeCountX *= Math.abs(params.mapLattice.x);
+this.cubeCountY *= Math.abs(params.mapLattice.y);
+this.cubeCountZ *= Math.abs(params.mapLattice.z);
+}this.nY = this.cubeCountY + 1;
+this.nZ = this.cubeCountZ + 1;
+this.yzCount = this.nY * this.nZ;
+if (this.bsVoxels == null) this.bsVoxels = new JU.BS();
+this.edgeVertexPointers = (this.isXLowToHigh ? J.jvxl.calc.MarchingCubes.edgeVertexPointersLowToHigh : J.jvxl.calc.MarchingCubes.edgeVertexPointersHighToLow);
+this.edgeVertexPlanes = (this.isXLowToHigh ? J.jvxl.calc.MarchingCubes.edgeVertexPlanesLowToHigh : J.jvxl.calc.MarchingCubes.edgeVertexPlanesHighToLow);
+this.isoPointIndexPlanes = Clazz.newIntArray (2, this.yzCount, 3, 0);
+this.yzPlanes = (this.mode == 3 ? Clazz.newFloatArray (2, this.yzCount, 0) : null);
+this.setLinearOffsets();
+this.calcVoxelVertexVectors();
+}, "J.jvxl.data.VolumeData,J.jvxl.readers.Parameters");
+Clazz.defineMethod(c$, "calcVoxelVertexVectors",
+function(){
+for (var i = 8; --i >= 0; ) this.volumeData.transform(J.jvxl.calc.MarchingCubes.cubeVertexVectors[i], this.voxelVertexVectors[i] = new JU.V3());
+
+for (var i = 12; --i >= 0; ) this.edgeVectors[i].sub2(this.voxelVertexVectors[JU.TriangleData.edgeVertexes[i + i + 1]], this.voxelVertexVectors[JU.TriangleData.edgeVertexes[i + i]]);
+
+});
+Clazz.defineMethod(c$, "resetIndexPlane",
+function(plane){
+for (var i = 0; i < this.yzCount; i++) for (var j = 0; j < 3; j++) plane[i][j] = -2147483648;
+
+
+return plane;
+}, "~A");
+Clazz.defineMethod(c$, "getEdgeData",
+function(){
+if (this.cubeCountX < 0 || this.cubeCountY < 0 || this.cubeCountZ < 0) return "";
+this.mappingPlane = this.volumeData.mappingPlane;
+this.edgeCount = 0;
+var x0;
+var x1;
+var xStep;
+var ptStep;
+var pt;
+var ptX;
+if (this.isXLowToHigh) {
+x0 = 0;
+x1 = this.cubeCountX + (this.colorDensity ? 1 : 0);
+if (this.colorDensity) {
+x1 = this.cubeCountX + 1;
+ptX = this.yzCount - 1;
+} else {
+x1 = this.cubeCountX;
+ptX = (this.yzCount - 1) - this.nZ - 1;
+}xStep = 1;
+ptStep = this.yzCount;
+} else {
+if (this.colorDensity) {
+x0 = this.cubeCountX;
+ptX = (this.cubeCountX + 1) * this.yzCount - 1;
+} else {
+x0 = this.cubeCountX - 1;
+ptX = (this.cubeCountX * this.yzCount - 1) - this.nZ - 1;
+}x1 = -1;
+xStep = -1;
+ptStep = -this.yzCount;
+}pt = ptX;
+this.resetIndexPlane(this.isoPointIndexPlanes[1]);
+this.voxelData = null;
+var y1 = this.cubeCountY + (this.colorDensity ? 1 : 0);
+var z1 = this.cubeCountZ + (this.colorDensity ? 1 : 0);
+switch (this.mode) {
+case 3:
+this.getPlane(x0, false);
+break;
+case 1:
+this.voxelData = this.volumeData.getVoxelData();
+break;
+}
+this.allInside = (this.colorDensity && (this.cutoff == 0 || this.mode == 2 && this.bsVoxels.nextSetBit(0) < 0));
+var colorDensityAll = (this.colorDensity && this.cutoff == 0);
+var v = 0;
+for (var x = x0; x != x1; x += xStep, ptX += ptStep, pt = ptX) {
+if (this.mode == 3) {
+if (x + xStep <= x1) this.getPlane(x + xStep, true);
+}if (this.bsExcludedPlanes.get(x) && this.bsExcludedPlanes.get(x + xStep)) continue;
+if (this.colorDensity) {
+for (var y = y1; --y >= 0; ) for (var z = z1; --z >= 0; pt--) {
+v = this.getValue(x, y, z, pt, 0);
+if (colorDensityAll || this.$isInside) {
+this.addVertex(x, y, z, pt, v);
+}}
+
+continue;
+}var indexPlane = this.isoPointIndexPlanes[0];
+this.isoPointIndexPlanes[0] = this.isoPointIndexPlanes[1];
+this.isoPointIndexPlanes[1] = this.resetIndexPlane(indexPlane);
+var noValues = true;
+for (var y = y1; --y >= 0; pt--) {
+for (var z = z1; --z >= 0; pt--) {
+var insideMask = 0;
+for (var i = 8; --i >= 0; ) {
+v = this.getValue(x, y, z, pt, i);
+if (this.$isInside) insideMask |= JU.TriangleData.Pwr2[i];
+}
+if (noValues && !Float.isNaN(v)) noValues = false;
+if (insideMask == 0) {
+continue;
+}if (insideMask == 0xFF) {
+continue;
+}if (this.processOneCubical(insideMask, x, y, z, pt) && !this.isContoured && !this.colorDensity) {
+this.processTriangles(insideMask);
+}}
+}
+if (noValues) {
+this.bsExcludedPlanes.set(x);
+}}
+return this.edgeData.toString();
+});
+Clazz.defineMethod(c$, "getValue",
+function(x, y, z, pt, i){
+var v;
+this.offset = JU.TriangleData.cubeVertexOffsets[i];
+var pti = pt + this.linearOffsets[i];
+switch (this.mode) {
+case 3:
+v = this.vertexValues[i] = this.getValueArray(x + this.offset.x, y + this.offset.y, z + this.offset.z, pti, this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[i]]);
+this.$isInside = (this.allInside || this.bsVoxels.get(pti));
+break;
+case 2:
+this.$isInside = (this.allInside || this.bsVoxels.get(pti));
+v = this.vertexValues[i] = ((this.isDensityRange ? !this.$isInside : this.bsExcludedVertices.get(pti)) ? NaN : this.$isInside ? 1 : 0);
+break;
+default:
+case 1:
+if (this.mappingPlane == null) {
+v = this.vertexValues[i] = this.voxelData[x + this.offset.x][y + this.offset.y][z + this.offset.z];
+} else {
+this.volumeData.voxelPtToXYZ(x + this.offset.x, y + this.offset.y, z + this.offset.z, this.pt0);
+v = this.vertexValues[i] = this.volumeData.distanceToMappingPlane(this.pt0);
+}if (this.isSquared) this.vertexValues[i] *= this.vertexValues[i];
+this.$isInside = (this.allInside ? true : J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[i], this.cutoff, this.isCutoffAbsolute));
+if (this.$isInside) this.bsVoxels.set(pti);
+}
+return v;
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "getPlane",
+function(i, andSwap){
+if (i < 0 || i > this.cubeCountX) return;
+this.surfaceReader.getPlane(i);
+if (andSwap) {
+var plane = this.yzPlanes[0];
+this.yzPlanes[0] = this.yzPlanes[1];
+this.yzPlanes[1] = plane;
+}}, "~N,~B");
+Clazz.defineMethod(c$, "processTriangles",
+function(insideMask){
+var triangles = JU.TriangleData.triangleTable2[insideMask];
+for (var i = triangles.length; (i -= 4) >= 0; ) this.addTriangle(triangles[i], triangles[i + 1], triangles[i + 2], triangles[i + 3]);
+
+}, "~N");
+Clazz.defineMethod(c$, "addVertex",
+function(x, y, z, pti, value){
+this.volumeData.voxelPtToXYZ(x, y, z, this.pt0);
+if (this.surfaceReader.addVertexCopy(this.pt0, value, -4, true) < 0) this.bsExcludedVertices.set(pti);
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "addTriangle",
+function(ia, ib, ic, edgeType){
+if (!this.bsExcludedTriangles.get(this.nTriangles) && this.surfaceReader.addTriangleCheck(this.edgePointIndexes[ia], this.edgePointIndexes[ib], this.edgePointIndexes[ic], edgeType, 0, this.isCutoffAbsolute, 0) < 0) {
+this.bsExcludedTriangles.set(this.nTriangles);
+}this.nTriangles++;
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "getValueArray",
+function(x, y, z, pt, tempValues){
+var ptyz = pt % this.yzCount;
+this.bsValues.set(pt);
+var value = this.surfaceReader.getValue(x, y, z, ptyz);
+if (this.isSquared) value *= value;
+tempValues[ptyz] = value;
+if (J.jvxl.calc.MarchingCubes.isInside(value, this.cutoff, this.isCutoffAbsolute)) this.bsVoxels.set(pt);
+return value;
+}, "~N,~N,~N,~N,~A");
+c$.isInside = Clazz.defineMethod(c$, "isInside",
+function(voxelValue, max, isAbsolute){
+return ((max > 0 && (isAbsolute ? Math.abs(voxelValue) : voxelValue) >= max) || (max <= 0 && voxelValue <= max));
+}, "~N,~N,~B");
+Clazz.defineMethod(c$, "processOneCubical",
+function(insideMask, x, y, z, pt){
+var edgeMask = J.jvxl.calc.MarchingCubes.insideMaskTable[insideMask];
+var isNaN = false;
+for (var iEdge = 12; --iEdge >= 0; ) {
+var xEdge = JU.TriangleData.Pwr2[iEdge];
+if ((edgeMask & xEdge) == 0) continue;
+var iPlane = this.edgeVertexPlanes[iEdge];
+var iPt = (pt + this.linearOffsets[this.edgeVertexPointers[iEdge]]) % this.yzCount;
+var iType = J.jvxl.calc.MarchingCubes.edgeTypeTable[iEdge];
+var index = this.edgePointIndexes[iEdge] = this.isoPointIndexPlanes[iPlane][iPt][iType];
+if (index != -2147483648) {
+if (index == -1) isNaN = this.excludePartialCubes;
+continue;
+}var vertexA = JU.TriangleData.edgeVertexes[iEdge << 1];
+var vertexB = JU.TriangleData.edgeVertexes[(iEdge << 1) + 1];
+var valueA = this.vertexValues[vertexA];
+var valueB = this.vertexValues[vertexB];
+this.calcVertexPoint(x, y, z, vertexA, this.pointA);
+this.edgeCount++;
+var i = this.edgePointIndexes[iEdge] = this.isoPointIndexPlanes[iPlane][iPt][iType] = this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff, this.isCutoffAbsolute, x, y, z, JU.TriangleData.cubeVertexOffsets[vertexA], vertexA, vertexB, valueA, valueB, this.pointA, this.edgeVectors[iEdge], iType == this.contourType, this.fReturn);
+this.addEdgeData(i < 0 ? NaN : this.fReturn[0]);
+if (Float.isNaN(this.fReturn[0]) || i < 0) isNaN = this.excludePartialCubes;
+}
+return !isNaN;
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "addEdgeData",
+function(f){
+var ch = J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(f);
+this.edgeData.appendC(ch);
+}, "~N");
+Clazz.defineMethod(c$, "calcVertexPoint",
+function(x, y, z, vertex, pt){
+this.volumeData.voxelPtToXYZ(x, y, z, this.pt0);
+pt.add2(this.pt0, this.voxelVertexVectors[vertex]);
+}, "~N,~N,~N,~N,JU.P3");
+Clazz.defineMethod(c$, "setLinearOffsets",
+function(){
+this.linearOffsets[0] = 0;
+this.linearOffsets[1] = this.yzCount;
+this.linearOffsets[2] = this.yzCount + 1;
+this.linearOffsets[3] = 1;
+this.linearOffsets[4] = this.nZ;
+this.linearOffsets[5] = this.yzCount + this.nZ;
+this.linearOffsets[6] = this.yzCount + this.nZ + 1;
+this.linearOffsets[7] = this.nZ + 1;
+});
+Clazz.defineMethod(c$, "getLinearOffset",
+function(x, y, z, offset){
+return x * this.yzCount + y * this.nZ + z + this.linearOffsets[offset];
+}, "~N,~N,~N,~N");
+c$.yzPlanePts = Clazz.newIntArray(-1, [0, 1, 1, 0, 0, 1, 1, 0]);
+c$.edgeVertexPointersLowToHigh = Clazz.newIntArray(-1, [1, 1, 2, 0, 5, 5, 6, 4, 0, 1, 2, 3]);
+c$.edgeVertexPointersHighToLow = Clazz.newIntArray(-1, [0, 1, 3, 0, 4, 5, 7, 4, 0, 1, 2, 3]);
+c$.edgeVertexPlanesLowToHigh = Clazz.newIntArray(-1, [1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0]);
+c$.edgeVertexPlanesHighToLow = Clazz.newIntArray(-1, [1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1]);
+c$.cubeVertexVectors = Clazz.newArray(-1, [JU.V3.new3(0, 0, 0), JU.V3.new3(1, 0, 0), JU.V3.new3(1, 0, 1), JU.V3.new3(0, 0, 1), JU.V3.new3(0, 1, 0), JU.V3.new3(1, 1, 0), JU.V3.new3(1, 1, 1), JU.V3.new3(0, 1, 1)]);
+c$.edgeTypeTable = Clazz.newIntArray(-1, [0, 2, 0, 2, 0, 2, 0, 2, 1, 1, 1, 1]);
+c$.insideMaskTable = Clazz.newShortArray(-1, [0x0000, 0x0109, 0x0203, 0x030A, 0x0406, 0x050F, 0x0605, 0x070C, 0x080C, 0x0905, 0x0A0F, 0x0B06, 0x0C0A, 0x0D03, 0x0E09, 0x0F00, 0x0190, 0x0099, 0x0393, 0x029A, 0x0596, 0x049F, 0x0795, 0x069C, 0x099C, 0x0895, 0x0B9F, 0x0A96, 0x0D9A, 0x0C93, 0x0F99, 0x0E90, 0x0230, 0x0339, 0x0033, 0x013A, 0x0636, 0x073F, 0x0435, 0x053C, 0x0A3C, 0x0B35, 0x083F, 0x0936, 0x0E3A, 0x0F33, 0x0C39, 0x0D30, 0x03A0, 0x02A9, 0x01A3, 0x00AA, 0x07A6, 0x06AF, 0x05A5, 0x04AC, 0x0BAC, 0x0AA5, 0x09AF, 0x08A6, 0x0FAA, 0x0EA3, 0x0DA9, 0x0CA0, 0x0460, 0x0569, 0x0663, 0x076A, 0x0066, 0x016F, 0x0265, 0x036C, 0x0C6C, 0x0D65, 0x0E6F, 0x0F66, 0x086A, 0x0963, 0x0A69, 0x0B60, 0x05F0, 0x04F9, 0x07F3, 0x06FA, 0x01F6, 0x00FF, 0x03F5, 0x02FC, 0x0DFC, 0x0CF5, 0x0FFF, 0x0EF6, 0x09FA, 0x08F3, 0x0BF9, 0x0AF0, 0x0650, 0x0759, 0x0453, 0x055A, 0x0256, 0x035F, 0x0055, 0x015C, 0x0E5C, 0x0F55, 0x0C5F, 0x0D56, 0x0A5A, 0x0B53, 0x0859, 0x0950, 0x07C0, 0x06C9, 0x05C3, 0x04CA, 0x03C6, 0x02CF, 0x01C5, 0x00CC, 0x0FCC, 0x0EC5, 0x0DCF, 0x0CC6, 0x0BCA, 0x0AC3, 0x09C9, 0x08C0, 0x08C0, 0x09C9, 0x0AC3, 0x0BCA, 0x0CC6, 0x0DCF, 0x0EC5, 0x0FCC, 0x00CC, 0x01C5, 0x02CF, 0x03C6, 0x04CA, 0x05C3, 0x06C9, 0x07C0, 0x0950, 0x0859, 0x0B53, 0x0A5A, 0x0D56, 0x0C5F, 0x0F55, 0x0E5C, 0x015C, 0x0055, 0x035F, 0x0256, 0x055A, 0x0453, 0x0759, 0x0650, 0x0AF0, 0x0BF9, 0x08F3, 0x09FA, 0x0EF6, 0x0FFF, 0x0CF5, 0x0DFC, 0x02FC, 0x03F5, 0x00FF, 0x01F6, 0x06FA, 0x07F3, 0x04F9, 0x05F0, 0x0B60, 0x0A69, 0x0963, 0x086A, 0x0F66, 0x0E6F, 0x0D65, 0x0C6C, 0x036C, 0x0265, 0x016F, 0x0066, 0x076A, 0x0663, 0x0569, 0x0460, 0x0CA0, 0x0DA9, 0x0EA3, 0x0FAA, 0x08A6, 0x09AF, 0x0AA5, 0x0BAC, 0x04AC, 0x05A5, 0x06AF, 0x07A6, 0x00AA, 0x01A3, 0x02A9, 0x03A0, 0x0D30, 0x0C39, 0x0F33, 0x0E3A, 0x0936, 0x083F, 0x0B35, 0x0A3C, 0x053C, 0x0435, 0x073F, 0x0636, 0x013A, 0x0033, 0x0339, 0x0230, 0x0E90, 0x0F99, 0x0C93, 0x0D9A, 0x0A96, 0x0B9F, 0x0895, 0x099C, 0x069C, 0x0795, 0x049F, 0x0596, 0x029A, 0x0393, 0x0099, 0x0190, 0x0F00, 0x0E09, 0x0D03, 0x0C0A, 0x0B06, 0x0A0F, 0x0905, 0x080C, 0x070C, 0x0605, 0x050F, 0x0406, 0x030A, 0x0203, 0x0109, 0x0000]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingSquares.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingSquares.js
new file mode 100755
index 000000000000..6540033afc09
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/calc/MarchingSquares.js
@@ -0,0 +1,241 @@
+Clazz.declarePackage("J.jvxl.calc");
+Clazz.load(["JU.P3", "java.util.Hashtable"], "J.jvxl.calc.MarchingSquares", ["JU.AU", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.surfaceReader = null;
+this.volumeData = null;
+this.nContourSegments = 0;
+this.contourType = 0;
+this.thisContour = 0;
+this.valueMin = 0;
+this.valueMax = 0;
+this.pointA = null;
+this.pointB = null;
+this.contourFromZero = true;
+this.contoursDiscrete = null;
+this.contourVertexCount = 0;
+this.contourVertexes = null;
+if (!Clazz.isClassDefined("J.jvxl.calc.MarchingSquares.ContourVertex")) {
+J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$ ();
+}
+this.contourPlaneMinimumValue = 0;
+this.contourPlaneMaximumValue = 0;
+this.contourValuesUsed = null;
+this.ptTemp = null;
+this.triangleCount = 0;
+this.triangles = null;
+this.htPts = null;
+if (!Clazz.isClassDefined("J.jvxl.calc.MarchingSquares.Triangle")) {
+J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$ ();
+}
+Clazz.instantialize(this, arguments);}, J.jvxl.calc, "MarchingSquares", null);
+Clazz.prepareFields (c$, function(){
+this.pointA = new JU.P3();
+this.pointB = new JU.P3();
+this.contourVertexes = new Array(1000);
+this.ptTemp = new JU.P3();
+this.triangles = new Array(1000);
+this.htPts = new java.util.Hashtable();
+});
+Clazz.makeConstructor(c$,
+function(surfaceReader, volumeData, thePlane, contoursDiscrete, nContours, thisContour, contourFromZero){
+this.surfaceReader = surfaceReader;
+this.volumeData = volumeData;
+this.thisContour = thisContour;
+this.contoursDiscrete = contoursDiscrete;
+this.contourFromZero = contourFromZero;
+if (contoursDiscrete == null) {
+var i = 0;
+this.nContourSegments = (nContours == 0 ? 9 : nContours) + i;
+if (this.nContourSegments > 100) this.nContourSegments = 100;
+} else {
+nContours = contoursDiscrete.length;
+this.nContourSegments = nContours;
+this.contourFromZero = false;
+}}, "J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,JU.P4,~A,~N,~N,~B");
+Clazz.defineMethod(c$, "setMinMax",
+function(valueMin, valueMax){
+this.valueMin = valueMin;
+this.valueMax = valueMax;
+}, "~N,~N");
+Clazz.defineMethod(c$, "addContourVertex",
+function(vertexXYZ, value){
+if (this.contourVertexCount == this.contourVertexes.length) this.contourVertexes = JU.AU.doubleLength(this.contourVertexes);
+var vPt = this.surfaceReader.addVertexCopy(vertexXYZ, value, -2, true);
+this.contourVertexes[this.contourVertexCount++] = Clazz.innerTypeInstance(J.jvxl.calc.MarchingSquares.ContourVertex, this, null, vertexXYZ);
+return vPt;
+}, "JU.P3,~N");
+Clazz.defineMethod(c$, "setContourData",
+function(i, value){
+this.contourVertexes[i].setValue(value);
+}, "~N,~N");
+Clazz.defineMethod(c$, "calcContourPoint",
+function(cutoff, valueA, valueB, pt){
+return this.volumeData.calculateFractionalPoint(cutoff, this.pointA, this.pointB, valueA, valueB, pt);
+}, "~N,~N,~N,JU.P3");
+Clazz.defineMethod(c$, "addTriangle",
+function(iA, iB, iC, check, iContour){
+if (this.triangleCount == this.triangles.length) this.triangles = JU.AU.doubleLength(this.triangles);
+this.triangles[this.triangleCount++] = Clazz.innerTypeInstance(J.jvxl.calc.MarchingSquares.Triangle, this, null, iA, iB, iC, check, iContour);
+return 0;
+}, "~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "generateContourData",
+function(haveData, zeroOffset){
+JU.Logger.info("generateContours: " + this.nContourSegments + " segments");
+this.getVertexValues(haveData);
+this.createContours(this.valueMin, this.valueMax, zeroOffset);
+this.addAllTriangles();
+return this.contourVertexCount;
+}, "~B,~N");
+Clazz.defineMethod(c$, "getVertexValues",
+function(haveData){
+this.contourPlaneMinimumValue = 3.4028235E38;
+this.contourPlaneMaximumValue = -3.4028235E38;
+for (var i = 0; i < this.contourVertexCount; i++) {
+var c = this.contourVertexes[i];
+var value;
+if (haveData) {
+value = c.value;
+} else {
+value = this.volumeData.lookupInterpolatedVoxelValue(c, false);
+c.setValue(value);
+}if (value < this.contourPlaneMinimumValue) this.contourPlaneMinimumValue = value;
+if (value > this.contourPlaneMaximumValue) this.contourPlaneMaximumValue = value;
+}
+}, "~B");
+Clazz.defineMethod(c$, "createContours",
+function(min, max, zeroOffset){
+var diff = max - min;
+this.contourValuesUsed = Clazz.newFloatArray (this.nContourSegments, 0);
+for (var i = this.triangleCount; --i >= 0; ) this.triangles[i].check = 0;
+
+var minCutoff = -3.4028235E38;
+var cutoff = minCutoff;
+for (var i = 0; i < this.nContourSegments; i++) {
+cutoff = (this.contoursDiscrete != null ? this.contoursDiscrete[i] : this.contourFromZero ? min + (i * 1 / this.nContourSegments) * diff : i == 0 ? -3.4028235E38 : i == this.nContourSegments - 1 ? 3.4028235E38 : min + ((i - 1) * 1 / (this.nContourSegments - 1)) * diff);
+if (this.contoursDiscrete == null && Math.abs(cutoff) < zeroOffset) cutoff = (cutoff < 0 ? -zeroOffset : zeroOffset);
+this.contourValuesUsed[i] = cutoff;
+JU.Logger.info("#contour " + (i + 1) + " " + cutoff + " " + this.triangleCount);
+this.htPts.clear();
+for (var ii = this.triangleCount; --ii >= 0; ) {
+if (this.triangles[ii].isValid) this.checkContour(this.triangles[ii], i, cutoff);
+}
+if (this.thisContour > 0) {
+if (i + 1 == this.thisContour) minCutoff = cutoff;
+} else {
+}}
+if (this.contoursDiscrete != null) {
+minCutoff = this.contoursDiscrete[0];
+}this.valueMin = this.contourValuesUsed[0];
+this.valueMax = (this.contourValuesUsed.length == 0 ? this.valueMin : this.contourValuesUsed[this.contourValuesUsed.length - 1]);
+return true;
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "intercept",
+function(t, i, value){
+var iA = t.pts[i];
+var iB = t.pts[(i + 1) % 3];
+if (iA == 2147483647 || iB == 2147483647) return -1;
+var key = (iA < iB ? iA + "_" + iB : iB + "_" + iA);
+if (this.htPts.containsKey(key)) return this.htPts.get(key).intValue();
+var valueA = this.contourVertexes[iA].value;
+var valueB = this.contourVertexes[iB].value;
+var iPt = -1;
+if (valueA != valueB) {
+var f = (value - valueA) / (valueB - valueA);
+if (f >= 0 && f <= 1) {
+this.pointA.setT(this.contourVertexes[iA]);
+this.pointB.setT(this.contourVertexes[iB]);
+value = this.calcContourPoint(value, valueA, valueB, this.ptTemp);
+if (!Float.isNaN(value)) {
+iPt = this.addContourVertex(this.ptTemp, value);
+if (iPt < 0) return -1;
+this.contourVertexes[iPt].setValue(value);
+} else {
+}}}this.htPts.put(key, Integer.$valueOf(iPt));
+return iPt;
+}, "J.jvxl.calc.MarchingSquares.Triangle,~N,~N");
+Clazz.defineMethod(c$, "checkContour",
+function(t, i, value){
+if (this.thisContour > 0 && i + 1 != this.thisContour) return;
+var ipt0 = this.intercept(t, 0, value);
+var ipt1 = this.intercept(t, 1, value);
+var ipt2 = this.intercept(t, 2, value);
+var pts = t.pts;
+var mode = 0;
+if (ipt0 >= 0) {
+mode += 1;
+}if (ipt1 >= 0) {
+mode += 2;
+}if (ipt2 >= 0) {
+mode += 4;
+}switch (mode) {
+case 3:
+this.addTriangle(pts[0], ipt0, ipt1, 2 | (t.check & 1), i);
+this.addTriangle(ipt0, pts[1], ipt1, 4 | (t.check & 3), i);
+this.addTriangle(pts[0], ipt1, pts[2], (t.check & 6), i);
+break;
+case 5:
+this.addTriangle(pts[0], ipt0, ipt2, 2 | (t.check & 5), i);
+this.addTriangle(ipt0, pts[1], ipt2, 4 | (t.check & 1), i);
+this.addTriangle(ipt2, pts[1], pts[2], (t.check & 6), i);
+break;
+case 6:
+this.addTriangle(pts[0], pts[1], ipt2, (t.check & 5), i);
+this.addTriangle(ipt2, pts[1], ipt1, 4 | (t.check & 2), i);
+this.addTriangle(ipt2, ipt1, pts[2], 1 | (t.check & 6), i);
+break;
+default:
+return;
+}
+t.isValid = false;
+}, "J.jvxl.calc.MarchingSquares.Triangle,~N,~N");
+Clazz.defineMethod(c$, "getMinMax",
+function(){
+return Clazz.newFloatArray(-1, [this.valueMin, this.valueMax]);
+});
+Clazz.defineMethod(c$, "addAllTriangles",
+function(){
+for (var i = 0; i < this.triangleCount; i++) if (this.triangles[i].isValid) {
+var t = this.triangles[i];
+this.surfaceReader.addTriangleCheck(t.pts[0], t.pts[1], t.pts[2], t.check, t.contourIndex, false, -1);
+}
+});
+c$.$MarchingSquares$ContourVertex$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.value = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.calc.MarchingSquares, "ContourVertex", JU.P3);
+Clazz.makeConstructor(c$,
+function(vertexXYZ){
+Clazz.superConstructor (this, J.jvxl.calc.MarchingSquares.ContourVertex, []);
+this.setT(vertexXYZ);
+}, "JU.P3");
+Clazz.defineMethod(c$, "setValue",
+function(value){
+this.value = value;
+}, "~N");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return this.value + " " + this.x + " " + this.y + " " + this.z;
+});
+/*eoif4*/})();
+};
+c$.$MarchingSquares$Triangle$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.pts = null;
+this.check = 0;
+this.isValid = true;
+this.contourIndex = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.calc.MarchingSquares, "Triangle", null);
+Clazz.makeConstructor(c$,
+function(iA, iB, iC, check, contourIndex){
+this.pts = Clazz.newIntArray(-1, [iA, iB, iC]);
+this.check = check;
+this.contourIndex = contourIndex;
+}, "~N,~N,~N,~N,~N");
+/*eoif4*/})();
+};
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlCoder.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlCoder.js
new file mode 100755
index 000000000000..aa084a0b5a48
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlCoder.js
@@ -0,0 +1,698 @@
+Clazz.declarePackage("J.jvxl.data");
+Clazz.load(null, "J.jvxl.data.JvxlCoder", ["JU.BS", "$.Lst", "$.P3", "$.PT", "$.SB", "J.api.Interface", "J.jvxl.data.VolumeData", "JU.BSUtil", "$.C", "$.Escape", "$.Logger", "JV.Viewer"], function(){
+var c$ = Clazz.declareType(J.jvxl.data, "JvxlCoder", null);
+c$.jvxlGetFile = Clazz.defineMethod(c$, "jvxlGetFile",
+function(jvxlData, meshData, title, msg, includeHeader, nSurfaces, state, comment){
+J.jvxl.data.JvxlCoder.checkHaveXMLUtil();
+var data = new JU.SB();
+if ("TRAILERONLY".equals(msg)) {
+JU.XmlUtil.closeTag(data, "jvxlSurfaceSet");
+JU.XmlUtil.closeTag(data, "jvxl");
+return data.toString();
+}var vertexDataOnly = (meshData != null);
+var isHeaderOnly = ("HEADERONLY".equals(msg));
+if (includeHeader) {
+JU.XmlUtil.openDocument(data);
+JU.XmlUtil.openTagAttr(data, "jvxl", Clazz.newArray(-1, ["version", "2.4", "jmolVersion", jvxlData.version, "xmlns", "http://jmol.org/jvxl_schema", "xmlns:cml", "http://www.xml-cml.org/schema"]));
+JU.XmlUtil.appendCdata(data, "jvxlFileTitle", null, jvxlData.jvxlFileTitle == null ? "\n" : "\n" + jvxlData.jvxlFileTitle);
+if (jvxlData.moleculeXml != null) data.append(jvxlData.moleculeXml);
+var volumeDataXml = (vertexDataOnly ? null : jvxlData.jvxlVolumeDataXml);
+if (volumeDataXml == null) volumeDataXml = ( new J.jvxl.data.VolumeData()).setVolumetricXml();
+data.append(volumeDataXml);
+JU.XmlUtil.openTagAttr(data, "jvxlSurfaceSet", Clazz.newArray(-1, ["count", "" + (nSurfaces > 0 ? nSurfaces : 1)]));
+if (isHeaderOnly) return data.toString();
+}var sb;
+var type = (vertexDataOnly ? "pmesh" : jvxlData.jvxlPlane == null ? "isosurface" : "plane");
+if (jvxlData.jvxlColorData != null && jvxlData.jvxlColorData.length > 0) type = "mapped " + type;
+JU.XmlUtil.openTagAttr(data, "jvxlSurface", Clazz.newArray(-1, ["type", type]));
+data.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(jvxlData, vertexDataOnly));
+J.jvxl.data.JvxlCoder.jvxlAppendCommandState(data, comment, state);
+if (title != null || msg != null && msg.length > 0) {
+sb = new JU.SB();
+if (msg != null && msg.length > 0) sb.append(msg).append("\n");
+if (title != null) for (var i = 0; i < title.length; i++) sb.append(title[i]).appendC('\n');
+
+JU.XmlUtil.appendCdata(data, "jvxlSurfaceTitle", null, sb.toString());
+}sb = new JU.SB();
+JU.XmlUtil.openTagAttr(sb, "jvxlSurfaceData", (vertexDataOnly || jvxlData.jvxlPlane == null ? null : jvxlData.mapLattice == null ? Clazz.newArray(-1, ["plane", JU.Escape.eP4(jvxlData.jvxlPlane)]) : Clazz.newArray(-1, ["plane", JU.Escape.eP4(jvxlData.jvxlPlane), "maplattice", JU.Escape.eP(jvxlData.mapLattice)])));
+if (vertexDataOnly) {
+J.jvxl.data.JvxlCoder.appendXmlVertexOnlyData(sb, jvxlData, meshData, true);
+} else if (jvxlData.jvxlPlane == null) {
+if (jvxlData.jvxlEdgeData == null) return "";
+J.jvxl.data.JvxlCoder.appendXmlEdgeData(sb, jvxlData);
+J.jvxl.data.JvxlCoder.appendXmlColorData(sb, jvxlData.jvxlColorData, true, jvxlData.isJvxlPrecisionColor, jvxlData.valueMappedToRed, jvxlData.valueMappedToBlue);
+} else {
+J.jvxl.data.JvxlCoder.appendXmlColorData(sb, jvxlData.jvxlColorData, true, jvxlData.isJvxlPrecisionColor, jvxlData.valueMappedToRed, jvxlData.valueMappedToBlue);
+}J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(sb, "jvxlInvalidatedVertexData", jvxlData.jvxlExcluded[1], -1, null);
+if (jvxlData.excludedVertexCount > 0) {
+J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(sb, "jvxlExcludedVertexData", jvxlData.jvxlExcluded[0], jvxlData.excludedVertexCount, null);
+J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(sb, "jvxlExcludedPlaneData", jvxlData.jvxlExcluded[2], -1, null);
+}J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(sb, "jvxlExcludedTriangleData", jvxlData.jvxlExcluded[3], jvxlData.excludedTriangleCount, null);
+JU.XmlUtil.closeTag(sb, "jvxlSurfaceData");
+var len = sb.length();
+data.appendSB(sb);
+if (jvxlData.vContours != null && jvxlData.vContours.length > 0) {
+J.jvxl.data.JvxlCoder.jvxlEncodeContourData(jvxlData.vContours, data);
+}if (jvxlData.vertexColorMap != null) {
+if (jvxlData.baseColor == null) JU.XmlUtil.openTag(data, "jvxlVertexColorData");
+ else JU.XmlUtil.openTagAttr(data, "jvxlVertexColorData", Clazz.newArray(-1, ["baseColor", jvxlData.baseColor]));
+for (var entry, $entry = jvxlData.vertexColorMap.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(data, "jvxlColorMap", entry.getValue(), -1, Clazz.newArray(-1, ["color", entry.getKey()]));
+
+jvxlData.vertexColorMap = null;
+JU.XmlUtil.closeTag(data, "jvxlVertexColorData");
+}JU.XmlUtil.closeTag(data, "jvxlSurface");
+if (includeHeader) {
+JU.XmlUtil.closeTag(data, "jvxlSurfaceSet");
+JU.XmlUtil.closeTag(data, "jvxl");
+}return J.jvxl.data.JvxlCoder.jvxlSetCompressionRatio(data, jvxlData, len);
+}, "J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~A,~S,~B,~N,~S,~S");
+c$.checkHaveXMLUtil = Clazz.defineMethod(c$, "checkHaveXMLUtil",
+function(){
+if (!J.jvxl.data.JvxlCoder.haveXMLUtil) {
+if (JV.Viewer.isJS) J.api.Interface.getInterface("JU.XmlUtil", null, "show");
+J.jvxl.data.JvxlCoder.haveXMLUtil = true;
+}});
+c$.appendEncodedBitSetTag = Clazz.defineMethod(c$, "appendEncodedBitSetTag",
+function(sb, name, bs, count, attribs){
+if (count < 0) count = JU.BSUtil.cardinalityOf(bs);
+if (count == 0) return;
+var sb1 = new JU.SB();
+sb1.append("\n ");
+J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(bs, -1, sb1);
+JU.XmlUtil.appendTagObj(sb, name, Clazz.newArray(-1, [attribs, "bsEncoding", "base90+35", "count", "" + count, "len", "" + bs.length()]), J.jvxl.data.JvxlCoder.jvxlCompressString(sb1.toString(), true));
+}, "JU.SB,~S,JU.BS,~N,~A");
+c$.jvxlSetCompressionRatio = Clazz.defineMethod(c$, "jvxlSetCompressionRatio",
+function(data, jvxlData, len){
+var s = data.toString();
+var r = Clazz.floatToInt(jvxlData.nBytes > 0 ? (jvxlData.nBytes) / len : ((jvxlData.nPointsX * jvxlData.nPointsY * jvxlData.nPointsZ * 13)) / len);
+return JU.PT.rep(s, "\"not calculated\"", (r > 0 ? "\"" + r + ":1\"" : "\"?\""));
+}, "JU.SB,J.jvxl.data.JvxlData,~N");
+c$.appendXmlEdgeData = Clazz.defineMethod(c$, "appendXmlEdgeData",
+function(sb, jvxlData){
+JU.XmlUtil.appendTagObj(sb, "jvxlEdgeData", Clazz.newArray(-1, ["count", "" + (jvxlData.jvxlEdgeData.length - 1), "encoding", "base90f1", "bsEncoding", "base90+35c", "isXLowToHigh", "" + jvxlData.isXLowToHigh, "data", J.jvxl.data.JvxlCoder.jvxlCompressString(jvxlData.jvxlEdgeData, true)]), "\n" + J.jvxl.data.JvxlCoder.jvxlCompressString(jvxlData.jvxlSurfaceData, true));
+}, "JU.SB,J.jvxl.data.JvxlData");
+c$.jvxlAppendCommandState = Clazz.defineMethod(c$, "jvxlAppendCommandState",
+function(data, cmd, state){
+if (cmd != null) JU.XmlUtil.appendCdata(data, "jvxlIsosurfaceCommand", null, "\n" + (cmd.indexOf("#") < 0 ? cmd : cmd.substring(0, cmd.indexOf("#"))) + "\n");
+if (state != null) {
+if (state.indexOf("** XML ** ") >= 0) {
+state = JU.PT.split(state, "** XML **")[1].trim();
+JU.XmlUtil.appendTag(data, "jvxlIsosurfaceState", "\n" + state + "\n");
+} else {
+JU.XmlUtil.appendCdata(data, "jvxlIsosurfaceState", null, "\n" + state);
+}}}, "JU.SB,~S,~S");
+c$.appendXmlColorData = Clazz.defineMethod(c$, "appendXmlColorData",
+function(sb, data, isEncoded, isPrecisionColor, value1, value2){
+var n;
+if (data == null || (n = data.length - 1) < 0) return;
+if (isPrecisionColor) n /= 2;
+JU.XmlUtil.appendTagObj(sb, "jvxlColorData", Clazz.newArray(-1, ["count", "" + n, "encoding", (isEncoded ? "base90f" + (isPrecisionColor ? "2" : "1") : "none"), "min", "" + value1, "max", "" + value2, "data", J.jvxl.data.JvxlCoder.jvxlCompressString(data, true)]), null);
+}, "JU.SB,~S,~B,~B,~N,~N");
+c$.jvxlGetInfo = Clazz.defineMethod(c$, "jvxlGetInfo",
+function(jvxlData){
+return J.jvxl.data.JvxlCoder.jvxlGetInfoData(jvxlData, jvxlData.vertexDataOnly);
+}, "J.jvxl.data.JvxlData");
+c$.jvxlGetInfoData = Clazz.defineMethod(c$, "jvxlGetInfoData",
+function(jvxlData, vertexDataOnly){
+if (jvxlData.jvxlSurfaceData == null) return "";
+J.jvxl.data.JvxlCoder.checkHaveXMLUtil();
+var attribs = new JU.Lst();
+var nSurfaceInts = jvxlData.nSurfaceInts;
+var bytesUncompressedEdgeData = (vertexDataOnly ? 0 : jvxlData.jvxlEdgeData.length - 1);
+var nColorData = (jvxlData.jvxlColorData == null ? -1 : (jvxlData.jvxlColorData.length - 1));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n isModelConnected", "" + jvxlData.isModelConnected);
+if (!vertexDataOnly) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n cutoff", (jvxlData.cutoffRange == null ? "" + jvxlData.cutoff : jvxlData.cutoffRange[0] + " " + jvxlData.cutoffRange[1]));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n isCutoffAbsolute", "" + jvxlData.isCutoffAbsolute);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n pointsPerAngstrom", "" + jvxlData.pointsPerAngstrom);
+var n = jvxlData.jvxlSurfaceData.length + bytesUncompressedEdgeData + nColorData + 1;
+if (n > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nBytesData", "" + n);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n isXLowToHigh", "" + jvxlData.isXLowToHigh);
+if (jvxlData.jvxlPlane == null) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nSurfaceInts", "" + nSurfaceInts);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nBytesUncompressedEdgeData", "" + bytesUncompressedEdgeData);
+}if (nColorData > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nBytesUncompressedColorData", "" + nColorData);
+}jvxlData.excludedVertexCount = JU.BSUtil.cardinalityOf(jvxlData.jvxlExcluded[0]);
+jvxlData.excludedTriangleCount = JU.BSUtil.cardinalityOf(jvxlData.jvxlExcluded[3]);
+if (jvxlData.excludedVertexCount > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nExcludedVertexes", "" + jvxlData.excludedVertexCount);
+if (jvxlData.excludedTriangleCount > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nExcludedTriangles", "" + jvxlData.excludedTriangleCount);
+var n = JU.BSUtil.cardinalityOf(jvxlData.jvxlExcluded[1]);
+if (n > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nInvalidatedVertexes", "" + n);
+if (jvxlData.slabInfo != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n slabInfo", jvxlData.slabInfo);
+if (jvxlData.isJvxlPrecisionColor) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n precisionColor", "true");
+if (jvxlData.colorDensity) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorDensity", "true");
+if (!Float.isNaN(jvxlData.pointSize)) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n pointSize", "" + jvxlData.pointSize);
+ else if (jvxlData.diameter != 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n diameter", "" + jvxlData.diameter);
+if (!jvxlData.allowVolumeRender) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n allowVolumeRender", "false");
+if (jvxlData.jvxlPlane == null || vertexDataOnly) {
+if (jvxlData.fixedLattice != null && !vertexDataOnly) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n fixedLattice", "" + jvxlData.fixedLattice);
+if (jvxlData.isContoured) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n contoured", "true");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorMapped", "true");
+} else if (jvxlData.isBicolorMap) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n bicolorMap", "true");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorNegative", JU.C.getHexCode(jvxlData.minColorIndex));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorPositive", JU.C.getHexCode(jvxlData.maxColorIndex));
+} else if (nColorData > 0) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorMapped", "true");
+}if (jvxlData.vContours != null && jvxlData.vContours.length > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nContourData", "" + jvxlData.vContours.length);
+} else {
+if (jvxlData.mapLattice != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n mapLattice", "" + jvxlData.mapLattice);
+if (jvxlData.scale3d != 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n scale3d", "" + jvxlData.scale3d);
+if (nColorData > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorMapped", "true");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n plane", JU.Escape.eP4(jvxlData.jvxlPlane));
+}if (jvxlData.color != null && jvxlData.color.indexOf("null") < 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n color", jvxlData.color);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n translucency", "" + jvxlData.translucency);
+if (jvxlData.meshColor != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n meshColor", jvxlData.meshColor);
+if (jvxlData.colorScheme != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n colorScheme", jvxlData.colorScheme);
+if (jvxlData.rendering != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n rendering", jvxlData.rendering);
+if (jvxlData.thisSet != null) {
+var s = J.jvxl.data.JvxlCoder.subsetString(jvxlData.thisSet);
+if (s.startsWith("[")) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n subset", s);
+ else J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n set", s);
+}if (jvxlData.slabValue != -2147483648) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n slabValue", "" + jvxlData.slabValue);
+if (jvxlData.isSlabbable) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n slabbable", "true");
+if (jvxlData.nVertexColors > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nVertexColors", "" + jvxlData.nVertexColors);
+var min = (jvxlData.mappedDataMin == 3.4028235E38 ? 0 : jvxlData.mappedDataMin);
+var blue = (jvxlData.isColorReversed ? jvxlData.valueMappedToRed : jvxlData.valueMappedToBlue);
+var red = (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue : jvxlData.valueMappedToRed);
+if (jvxlData.jvxlColorData != null && jvxlData.jvxlColorData.length > 0 && !jvxlData.isBicolorMap) {
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n dataMinimum", "" + min);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n dataMaximum", "" + jvxlData.mappedDataMax);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n valueMappedToRed", "" + red);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n valueMappedToBlue", "" + blue);
+}if (jvxlData.isContoured) {
+if (jvxlData.contourValues == null || jvxlData.contourColixes == null) {
+if (jvxlData.vContours == null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nContours", "" + Math.abs(jvxlData.nContours));
+} else {
+if (jvxlData.jvxlPlane != null) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n contoured", "true");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n nContours", "" + jvxlData.contourValues.length);
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n contourValues", JU.Escape.eAF(jvxlData.contourValuesUsed == null ? jvxlData.contourValues : jvxlData.contourValuesUsed));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n contourColors", jvxlData.contourColors);
+}if (jvxlData.thisContour > 0) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n thisContour", "" + jvxlData.thisContour);
+}if (jvxlData.insideOut) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n insideOut", "true");
+if (jvxlData.vertexDataOnly) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n note", "vertex/face data only");
+ else if (jvxlData.isXLowToHigh) J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n note", "progressive JVXL+ -- X values read from low(0) to high(" + (jvxlData.nPointsX - 1) + ")");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n xyzMin", JU.Escape.eP(jvxlData.boundingBox[0]));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n xyzMax", JU.Escape.eP(jvxlData.boundingBox[1]));
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n approximateCompressionRatio", "not calculated");
+J.jvxl.data.JvxlCoder.addAttrib(attribs, "\n jmolVersion", jvxlData.version);
+var info = new JU.SB();
+JU.XmlUtil.openTagAttr(info, "jvxlSurfaceInfo", attribs.toArray( new Array(attribs.size())));
+JU.XmlUtil.closeTag(info, "jvxlSurfaceInfo");
+return info.toString();
+}, "J.jvxl.data.JvxlData,~B");
+c$.subsetString = Clazz.defineMethod(c$, "subsetString",
+function(bs){
+var n = bs.cardinality();
+if (n > 1) {
+var a = "[ ";
+for (var ia = bs.nextSetBit(0); ia >= 0; ia = bs.nextSetBit(ia)) a += (++ia) + " ";
+
+return a + "]";
+}return "" + (bs.nextSetBit(0) + 1);
+}, "JU.BS");
+c$.addAttrib = Clazz.defineMethod(c$, "addAttrib",
+function(attribs, name, value){
+attribs.addLast( Clazz.newArray(-1, [name, value]));
+}, "JU.Lst,~S,~S");
+c$.jvxlEncodeContourData = Clazz.defineMethod(c$, "jvxlEncodeContourData",
+function(contours, sb){
+JU.XmlUtil.openTagAttr(sb, "jvxlContourData", Clazz.newArray(-1, ["count", "" + contours.length]));
+for (var i = 0; i < contours.length; i++) {
+if (contours[i].size() < 6) {
+continue;
+}var nPolygons = (contours[i].get(0)).intValue();
+var sb1 = new JU.SB();
+sb1.append("\n");
+var bs = contours[i].get(1);
+J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(bs, nPolygons, sb1);
+JU.XmlUtil.appendTagObj(sb, "jvxlContour", Clazz.newArray(-1, ["index", "" + i, "value", "" + contours[i].get(2), "color", JU.Escape.escapeColor((contours[i].get(4))[0]), "count", "" + bs.length(), "encoding", "base90iff1", "bsEncoding", "base90+35c", "data", J.jvxl.data.JvxlCoder.jvxlCompressString(contours[i].get(5).toString(), true)]), J.jvxl.data.JvxlCoder.jvxlCompressString(sb1.toString(), true));
+}
+JU.XmlUtil.closeTag(sb, "jvxlContourData");
+}, "~A,JU.SB");
+c$.set3dContourVector = Clazz.defineMethod(c$, "set3dContourVector",
+function(v, polygonIndexes, vertices){
+if (v.size() < 6) return;
+var fData = v.get(5);
+var bs = v.get(1);
+var pt = 0;
+var nBuf = fData.length();
+var type = 0;
+var c1 = ' ';
+var c2 = ' ';
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+var vertexIndexes = polygonIndexes[i];
+while (pt < nBuf && !JU.PT.isDigit(c1 = fData.charAt(pt++))) {
+}
+type = c1.charCodeAt(0) - 48;
+while (pt < nBuf && JU.PT.isWhitespace(c1 = fData.charAt(pt++))) {
+}
+while (pt < nBuf && JU.PT.isWhitespace(c2 = fData.charAt(pt++))) {
+}
+var f1 = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(c1.charCodeAt(0), 35, 90, 0);
+var f2 = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(c2.charCodeAt(0), 35, 90, 0);
+var i1;
+var i2;
+var i3;
+var i4;
+if ((type & 1) == 0) {
+i1 = vertexIndexes[1];
+i2 = i3 = vertexIndexes[2];
+i4 = vertexIndexes[0];
+} else {
+i1 = vertexIndexes[0];
+i2 = vertexIndexes[1];
+if ((type & 2) != 0) {
+i3 = i2;
+i4 = vertexIndexes[2];
+} else {
+i3 = vertexIndexes[2];
+i4 = i1;
+}}v.addLast(J.jvxl.data.JvxlCoder.getContourPoint(vertices, i1, i2, f1));
+v.addLast(J.jvxl.data.JvxlCoder.getContourPoint(vertices, i3, i4, f2));
+}
+}, "JU.Lst,~A,~A");
+c$.getContourPoint = Clazz.defineMethod(c$, "getContourPoint",
+function(vertices, i, j, f){
+var pt = new JU.P3();
+pt.sub2(vertices[j], vertices[i]);
+pt.scaleAdd2(f, pt, vertices[i]);
+return pt;
+}, "~A,~N,~N,~N");
+c$.appendContourTriangleIntersection = Clazz.defineMethod(c$, "appendContourTriangleIntersection",
+function(type, f1, f2, fData){
+fData.appendI(type);
+fData.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(f1));
+fData.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(f2));
+}, "~N,~N,~N,JU.SB");
+c$.jvxlCreateColorData = Clazz.defineMethod(c$, "jvxlCreateColorData",
+function(jvxlData, vertexValues){
+if (vertexValues == null) {
+jvxlData.jvxlColorData = "";
+return;
+}var writePrecisionColor = jvxlData.isJvxlPrecisionColor;
+var doTruncate = jvxlData.isTruncated;
+var colorFractionBase = jvxlData.colorFractionBase;
+var colorFractionRange = jvxlData.colorFractionRange;
+var valueBlue = jvxlData.valueMappedToBlue;
+var valueRed = jvxlData.valueMappedToRed;
+var vertexCount = (jvxlData.saveVertexCount > 0 ? jvxlData.saveVertexCount : jvxlData.vertexCount);
+if (vertexCount > vertexValues.length) System.out.println("JVXLCODER ERROR");
+var isPrecisionColor = jvxlData.isJvxlPrecisionColor;
+var min = (isPrecisionColor ? jvxlData.mappedDataMin : jvxlData.valueMappedToRed);
+var max = (isPrecisionColor ? jvxlData.mappedDataMax : jvxlData.valueMappedToBlue);
+if (vertexValues.length < vertexCount) System.out.println("JVXLCOLOR OHOHO");
+jvxlData.jvxlColorData = J.jvxl.data.JvxlCoder.jvxlEncodeColorData(vertexValues, min, max, colorFractionBase, colorFractionRange, jvxlData.isTruncated, isPrecisionColor);
+}, "J.jvxl.data.JvxlData,~A");
+c$.jvxlEncodeColorData = Clazz.defineMethod(c$, "jvxlEncodeColorData",
+function(vertexValues, min, max, colorFractionBase, colorFractionRange, doTruncate, isPrecisionColor){
+var list1 = new JU.SB();
+var list2 = new JU.SB();
+for (var i = 0, n = vertexValues.length; i < n; i++) {
+var value = vertexValues[i];
+if (Float.isNaN(value)) value = min;
+if (doTruncate) value = (value > 0 ? 0.999 : -0.999);
+if (isPrecisionColor) J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(value, min, max, colorFractionBase, colorFractionRange, list1, list2);
+ else list1.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(value, min, max, colorFractionBase, colorFractionRange));
+}
+return list1.appendSB(list2).appendC('\n').toString();
+}, "~A,~N,~N,~N,~N,~B,~B");
+c$.appendXmlVertexOnlyData = Clazz.defineMethod(c$, "appendXmlVertexOnlyData",
+function(sb, jvxlData, meshData, escapeXml){
+var vertexIdNew = Clazz.newIntArray (meshData.vc, 0);
+if (J.jvxl.data.JvxlCoder.appendXmlTriangleData(sb, meshData.pis, meshData.pc, meshData.bsSlabDisplay, vertexIdNew, escapeXml)) J.jvxl.data.JvxlCoder.appendXmlVertexData(sb, jvxlData, vertexIdNew, meshData.vs, meshData.vvs, meshData.vc, meshData.polygonColorData, meshData.pc, meshData.bsSlabDisplay, jvxlData.vertexColors, jvxlData.jvxlColorData.length > 0, escapeXml);
+}, "JU.SB,J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~B");
+c$.appendXmlTriangleData = Clazz.defineMethod(c$, "appendXmlTriangleData",
+function(sb, triangles, nData, bsSlabDisplay, vertexIdNew, escapeXml){
+var list1 = new JU.SB();
+var list2 = new JU.SB();
+var ilast = 1;
+var p = 0;
+var inew = 0;
+var addPlus = false;
+var nTri = 0;
+var removeSlabbed = (bsSlabDisplay != null);
+for (var i = 0; i < nData; ) {
+if (triangles[i] == null || (removeSlabbed && !bsSlabDisplay.get(i))) {
+i++;
+continue;
+}var idata = triangles[i][p];
+if (vertexIdNew[idata] > 0) {
+idata = vertexIdNew[idata];
+} else {
+idata = vertexIdNew[idata] = ++inew;
+}var diff = idata - ilast;
+ilast = idata;
+if (diff == 0) {
+list1.appendC('!');
+addPlus = false;
+} else if (diff > 32) {
+if (addPlus) list1.appendC('+');
+list1.appendI(diff);
+addPlus = true;
+} else if (diff < -32) {
+list1.appendI(diff);
+addPlus = true;
+} else {
+list1.appendC(String.fromCharCode(92 + diff));
+addPlus = false;
+}if (++p % 3 == 0) {
+list2.appendI(triangles[i][3]);
+p = 0;
+i++;
+nTri++;
+}}
+if (list1.length() == 0) return true;
+JU.XmlUtil.appendTagObj(sb, "jvxlTriangleData", Clazz.newArray(-1, ["count", "" + nTri, "encoding", "jvxltdiff", "data", J.jvxl.data.JvxlCoder.jvxlCompressString(list1.toString(), escapeXml)]), null);
+JU.XmlUtil.appendTagObj(sb, "jvxlTriangleEdgeData", Clazz.newArray(-1, ["count", "" + nTri, "encoding", "jvxlsc", "data", J.jvxl.data.JvxlCoder.jvxlCompressString(list2.toString(), escapeXml)]), null);
+return true;
+}, "JU.SB,~A,~N,JU.BS,~A,~B");
+c$.appendXmlVertexData = Clazz.defineMethod(c$, "appendXmlVertexData",
+function(sb, jvxlData, vertexIdNew, vertices, vertexValues, vertexCount, polygonColorData, polygonCount, bsSlabDisplay, vertexColors, addColorData, escapeXml){
+var colorFractionBase = jvxlData.colorFractionBase;
+var colorFractionRange = jvxlData.colorFractionRange;
+var p;
+var min = jvxlData.boundingBox[0];
+var max = jvxlData.boundingBox[1];
+var list1 = new JU.SB();
+var list2 = new JU.SB();
+var vertexIdOld = null;
+var removeSlabbed = (bsSlabDisplay != null);
+if (polygonCount > 0) {
+if (removeSlabbed) polygonCount = bsSlabDisplay.cardinality();
+removeSlabbed = false;
+vertexIdOld = Clazz.newIntArray (vertexCount, 0);
+for (var i = 0; i < vertexCount; i++) if (vertexIdNew[i] > 0) vertexIdOld[vertexIdNew[i] - 1] = i;
+
+}var n = 0;
+for (var i = 0; i < vertexCount; i++) if (!removeSlabbed || bsSlabDisplay.get(i)) {
+n++;
+p = vertices[(polygonCount == 0 ? i : vertexIdOld[i])];
+J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(p.x, min.x, max.x, colorFractionBase, colorFractionRange, list1, list2);
+J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(p.y, min.y, max.y, colorFractionBase, colorFractionRange, list1, list2);
+J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(p.z, min.z, max.z, colorFractionBase, colorFractionRange, list1, list2);
+}
+list1.appendSB(list2);
+JU.XmlUtil.appendTagObj(sb, "jvxlVertexData", Clazz.newArray(-1, ["count", "" + n, "min", JU.Escape.eP(min), "max", JU.Escape.eP(max), "encoding", "base90xyz2", "data", J.jvxl.data.JvxlCoder.jvxlCompressString(list1.toString(), escapeXml)]), null);
+if (polygonColorData != null) JU.XmlUtil.appendTagObj(sb, "jvxlPolygonColorData", Clazz.newArray(-1, ["encoding", "jvxlnc", "count", "" + polygonCount]), "\n" + polygonColorData);
+if (!addColorData) return;
+list1 = new JU.SB();
+list2 = new JU.SB();
+if (vertexColors == null) {
+for (var i = 0; i < vertexCount; i++) if (!removeSlabbed || bsSlabDisplay.get(i)) {
+var value = vertexValues[polygonCount == 0 ? i : vertexIdOld[i]];
+J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(value, jvxlData.mappedDataMin, jvxlData.mappedDataMax, colorFractionBase, colorFractionRange, list1, list2);
+}
+} else {
+var lastColor = 0;
+list1.appendI(n).append(" ");
+for (var i = 0; i < vertexCount; i++) if (!removeSlabbed || bsSlabDisplay.get(i)) {
+var c = vertexColors[polygonCount == 0 ? i : vertexIdOld[i]];
+if (c == lastColor) c = 0;
+ else lastColor = c;
+list1.appendI(c);
+list1.append(" ");
+}
+}J.jvxl.data.JvxlCoder.appendXmlColorData(sb, list1.appendSB(list2).append("\n").toString(), (vertexColors == null), true, jvxlData.valueMappedToRed, jvxlData.valueMappedToBlue);
+}, "JU.SB,J.jvxl.data.JvxlData,~A,~A,~A,~N,~S,~N,JU.BS,~A,~B,~B");
+c$.jvxlFractionAsCharacter = Clazz.defineMethod(c$, "jvxlFractionAsCharacter",
+function(fraction){
+return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(fraction, 35, 90);
+}, "~N");
+c$.jvxlFractionAsCharacterRange = Clazz.defineMethod(c$, "jvxlFractionAsCharacterRange",
+function(fraction, base, range){
+if (fraction > 0.9999) fraction = 0.9999;
+ else if (Float.isNaN(fraction)) fraction = 1.0001;
+var ich = Clazz.doubleToInt(Math.floor(fraction * range + base));
+if (ich < base) return String.fromCharCode(base);
+if (ich == 92) return '!';
+return String.fromCharCode(ich);
+}, "~N,~N,~N");
+c$.jvxlAppendCharacter2 = Clazz.defineMethod(c$, "jvxlAppendCharacter2",
+function(value, min, max, base, range, list1, list2){
+var fraction = (min == max ? value : (value - min) / (max - min));
+var ch1 = J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(fraction, base, range);
+list1.appendC(ch1);
+fraction -= J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(ch1.charCodeAt(0), base, range, 0);
+list2.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(fraction * range, base, range));
+}, "~N,~N,~N,~N,~N,JU.SB,JU.SB");
+c$.jvxlFractionFromCharacter = Clazz.defineMethod(c$, "jvxlFractionFromCharacter",
+function(ich, base, range, fracOffset){
+if (ich == base + range) return NaN;
+if (ich < base) ich = 92;
+var fraction = (ich - base + fracOffset) / range;
+if (fraction < 0) return 0;
+if (fraction > 1) return 0.999999;
+return fraction;
+}, "~N,~N,~N,~N");
+c$.jvxlFractionFromCharacter2 = Clazz.defineMethod(c$, "jvxlFractionFromCharacter2",
+function(ich1, ich2, base, range){
+var fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(ich1, base, range, 0);
+var remains = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(ich2, base, range, 0.5);
+return fraction + remains / range;
+}, "~N,~N,~N,~N");
+c$.jvxlValueAsCharacter = Clazz.defineMethod(c$, "jvxlValueAsCharacter",
+function(value, min, max, base, range){
+var fraction = (min == max ? value : (value - min) / (max - min));
+return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(fraction, base, range);
+}, "~N,~N,~N,~N,~N");
+c$.jvxlValueFromCharacter2 = Clazz.defineMethod(c$, "jvxlValueFromCharacter2",
+function(ich, ich2, min, max, base, range){
+var fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(ich, ich2, base, range);
+return (max == min ? fraction : min + fraction * (max - min));
+}, "~N,~N,~N,~N,~N,~N");
+c$.jvxlEncodeBitSet0 = Clazz.defineMethod(c$, "jvxlEncodeBitSet0",
+function(bs, nPoints, sb){
+var dataCount = 0;
+var prevCount = -1;
+var nPrev = 0;
+if (nPoints < 0) nPoints = bs.length();
+var n = 0;
+var isset = false;
+var lastPoint = nPoints - 1;
+for (var i = 0; i < nPoints; ++i) {
+if (isset == bs.get(i)) {
+dataCount++;
+} else {
+if (dataCount == prevCount && i != lastPoint) {
+nPrev++;
+} else {
+if (nPrev > 0) {
+sb.appendC(' ').appendI(-nPrev);
+nPrev = 0;
+n++;
+}sb.appendC(' ').appendI(dataCount);
+n++;
+prevCount = dataCount;
+}dataCount = 1;
+isset = !isset;
+}}
+sb.appendC(' ').appendI(dataCount).appendC('\n');
+return n;
+}, "JU.BS,~N,JU.SB");
+c$.jvxlEncodeBitSet = Clazz.defineMethod(c$, "jvxlEncodeBitSet",
+function(bs){
+var sb = new JU.SB();
+J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(bs, -1, sb);
+return sb.toString();
+}, "JU.BS");
+c$.jvxlEncodeBitSetBuffer = Clazz.defineMethod(c$, "jvxlEncodeBitSetBuffer",
+function(bs, nPoints, sb){
+var dataCount = 0;
+var n = 0;
+var isset = false;
+if (nPoints < 0) nPoints = bs.length();
+if (nPoints == 0) return 0;
+sb.append("-");
+for (var i = 0; i < nPoints; ++i) {
+if (isset == bs.get(i)) {
+dataCount++;
+} else {
+J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(sb, dataCount, 35, 90);
+n++;
+dataCount = 1;
+isset = !isset;
+}}
+J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(sb, dataCount, 35, 90);
+sb.appendC('\n');
+return n;
+}, "JU.BS,~N,JU.SB");
+c$.jvxlAppendEncodedNumber = Clazz.defineMethod(c$, "jvxlAppendEncodedNumber",
+function(sb, n, base, range){
+var isInRange = (n < range);
+if (n == 0) sb.appendC(String.fromCharCode(base));
+ else if (!isInRange) sb.appendC(String.fromCharCode(base + range));
+while (n > 0) {
+var n1 = Clazz.doubleToInt(n / range);
+var x = base + n - n1 * range;
+if (x == 92) x = 33;
+sb.appendC(String.fromCharCode(x));
+n = n1;
+}
+if (!isInRange) sb.append(" ");
+}, "JU.SB,~N,~N,~N");
+c$.jvxlDecodeBitSetRange = Clazz.defineMethod(c$, "jvxlDecodeBitSetRange",
+function(data, base, range){
+var bs = new JU.BS();
+var dataCount = 0;
+var ptr = 0;
+var isset = false;
+var next = Clazz.newIntArray (1, 0);
+while ((dataCount = J.jvxl.data.JvxlCoder.jvxlParseEncodedInt(data, base, range, next)) != -2147483648) {
+if (isset) bs.setBits(ptr, ptr + dataCount);
+ptr += dataCount;
+isset = !isset;
+}
+return bs;
+}, "~S,~N,~N");
+c$.jvxlParseEncodedInt = Clazz.defineMethod(c$, "jvxlParseEncodedInt",
+function(str, offset, base, next){
+var digitSeen = false;
+var value = 0;
+var ich = next[0];
+var ichMax = str.length;
+if (ich < 0) return -2147483648;
+while (ich < ichMax && JU.PT.isWhitespace(str.charAt(ich))) ++ich;
+
+if (ich >= ichMax) return -2147483648;
+var factor = 1;
+var isLong = ((str.charAt(ich)).charCodeAt(0) == (offset + base));
+if (isLong) ich++;
+while (ich < ichMax && !JU.PT.isWhitespace(str.charAt(ich))) {
+var i = (str.charAt(ich)).charCodeAt(0);
+if (i < offset) i = 92;
+value += (i - offset) * factor;
+digitSeen = true;
+++ich;
+if (!isLong) break;
+factor *= base;
+}
+if (!digitSeen) value = -2147483648;
+next[0] = ich;
+return value;
+}, "~S,~N,~N,~A");
+c$.jvxlDecodeBitSet = Clazz.defineMethod(c$, "jvxlDecodeBitSet",
+function(data){
+if (data.startsWith("-")) return J.jvxl.data.JvxlCoder.jvxlDecodeBitSetRange(J.jvxl.data.JvxlCoder.jvxlDecompressString(data.substring(1)), 35, 90);
+var bs = new JU.BS();
+var dataCount = 0;
+var lastCount = 0;
+var nPrev = 0;
+var ptr = 0;
+var isset = false;
+var next = Clazz.newIntArray (1, 0);
+while (true) {
+dataCount = (nPrev++ < 0 ? dataCount : JU.PT.parseIntNext(data, next));
+if (dataCount == -2147483648) break;
+if (dataCount < 0) {
+nPrev = dataCount;
+dataCount = lastCount;
+continue;
+}if (isset) bs.setBits(ptr, ptr + dataCount);
+ptr += dataCount;
+lastCount = dataCount;
+isset = !isset;
+}
+return bs;
+}, "~S");
+c$.jvxlCompressString = Clazz.defineMethod(c$, "jvxlCompressString",
+function(data, escapeXml){
+if (data.indexOf("~") >= 0) return data;
+var dataOut = new JU.SB();
+var chLast = '\u0000';
+var escaped = false;
+var lastEscaped = false;
+var nLast = 0;
+var n = data.length;
+for (var i = 0; i <= n; i++) {
+var ch = (i == n ? '\0' : data.charAt(i));
+switch ((ch).charCodeAt(0)) {
+case 10:
+case 13:
+continue;
+case 38:
+case 60:
+escaped = escapeXml;
+break;
+default:
+escaped = false;
+}
+if (ch == chLast) {
+++nLast;
+ch = '\0';
+} else if (nLast > 0 || lastEscaped) {
+if (nLast < 4 && !lastEscaped || chLast == ' ' || chLast == '\t') {
+while (--nLast >= 0) dataOut.appendC(chLast);
+
+} else {
+if (lastEscaped) lastEscaped = false;
+ else dataOut.appendC('~');
+dataOut.appendI(nLast);
+dataOut.appendC(' ');
+}nLast = 0;
+}if (ch != '\0') {
+if (escaped) {
+lastEscaped = true;
+escaped = false;
+dataOut.appendC('~');
+chLast = ch;
+ch = String.fromCharCode(ch.charCodeAt(0)-1);
+} else {
+chLast = ch;
+}dataOut.appendC(ch);
+}}
+return dataOut.toString();
+}, "~S,~B");
+c$.jvxlDecompressString = Clazz.defineMethod(c$, "jvxlDecompressString",
+function(data){
+if (data.indexOf("~") < 0) return data;
+var dataOut = new JU.SB();
+var chLast = '\u0000';
+var next = Clazz.newIntArray (1, 0);
+for (var i = 0; i < data.length; i++) {
+var ch = data.charAt(i);
+if (ch == '~') {
+next[0] = ++i;
+switch ((ch = data.charAt(i)).charCodeAt(0)) {
+case 59:
+case 37:
+next[0]++;
+dataOut.appendC(chLast = (ch = String.fromCharCode(ch.charCodeAt(0)+1)));
+case 49:
+case 50:
+case 51:
+case 52:
+case 53:
+case 54:
+case 55:
+case 56:
+case 57:
+var nChar = JU.PT.parseIntNext(data, next);
+for (var c = 0; c < nChar; c++) dataOut.appendC(chLast);
+
+i = next[0];
+continue;
+case 126:
+--i;
+break;
+default:
+JU.Logger.error("Error uncompressing string " + data.substring(0, i) + "?");
+}
+}dataOut.appendC(ch);
+chLast = ch;
+}
+return dataOut.toString();
+}, "~S");
+c$.jvxlCreateHeaderWithoutTitleOrAtoms = Clazz.defineMethod(c$, "jvxlCreateHeaderWithoutTitleOrAtoms",
+function(v, bs){
+J.jvxl.data.JvxlCoder.jvxlCreateHeader(v, bs);
+}, "J.jvxl.data.VolumeData,JU.SB");
+c$.jvxlCreateHeader = Clazz.defineMethod(c$, "jvxlCreateHeader",
+function(v, sb){
+v.setVolumetricXml();
+if (sb.length() == 0) sb.append("Line 1\nLine 2\n");
+}, "J.jvxl.data.VolumeData,JU.SB");
+c$.haveXMLUtil = false;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlData.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlData.js
new file mode 100755
index 000000000000..df2ab2f7e06d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/JvxlData.js
@@ -0,0 +1,162 @@
+Clazz.declarePackage("J.jvxl.data");
+Clazz.load(null, "J.jvxl.data.JvxlData", ["JU.SB", "J.jvxl.data.JvxlCoder"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.msg = "";
+this.wasJvxl = false;
+this.wasCubic = false;
+this.jvxlFileSource = null;
+this.jvxlFileTitle = null;
+this.jvxlFileMessage = null;
+this.jvxlSurfaceData = null;
+this.jvxlEdgeData = null;
+this.jvxlColorData = null;
+this.jvxlVolumeDataXml = null;
+this.jvxlExcluded = null;
+this.jvxlPlane = null;
+this.isJvxlPrecisionColor = false;
+this.jvxlDataIsColorMapped = false;
+this.jvxlDataIs2dContour = false;
+this.jvxlDataIsColorDensity = false;
+this.isColorReversed = false;
+this.thisSet = null;
+this.edgeFractionBase = 35;
+this.edgeFractionRange = 90;
+this.colorFractionBase = 35;
+this.colorFractionRange = 90;
+this.isValid = true;
+this.insideOut = false;
+this.isXLowToHigh = false;
+this.isContoured = false;
+this.isBicolorMap = false;
+this.isTruncated = false;
+this.isCutoffAbsolute = false;
+this.isModelConnected = false;
+this.vertexDataOnly = false;
+this.mappedDataMin = 0;
+this.mappedDataMax = 0;
+this.valueMappedToRed = 0;
+this.valueMappedToBlue = 0;
+this.cutoff = 0;
+this.cutoffRange = null;
+this.pointsPerAngstrom = 0;
+this.nPointsX = 0;
+this.nPointsY = 0;
+this.nPointsZ = 0;
+this.nBytes = 0;
+this.nContours = 0;
+this.nEdges = 0;
+this.nSurfaceInts = 0;
+this.vertexCount = 0;
+this.vContours = null;
+this.contourColixes = null;
+this.contourColors = null;
+this.contourValues = null;
+this.contourValuesUsed = null;
+this.thisContour = -1;
+this.scale3d = 0;
+this.minColorIndex = -1;
+this.maxColorIndex = 0;
+this.title = null;
+this.version = null;
+this.boundingBox = null;
+this.excludedTriangleCount = 0;
+this.excludedVertexCount = 0;
+this.colorDensity = false;
+this.pointSize = 0;
+this.moleculeXml = null;
+this.dataMin = 0;
+this.dataMax = 0;
+this.saveVertexCount = 0;
+this.vertexColorMap = null;
+this.nVertexColors = 0;
+this.vertexColors = null;
+this.color = null;
+this.meshColor = null;
+this.translucency = 0;
+this.colorScheme = null;
+this.rendering = null;
+this.slabValue = -2147483648;
+this.isSlabbable = false;
+this.diameter = 0;
+this.slabInfo = null;
+this.allowVolumeRender = false;
+this.voxelVolume = 0;
+this.mapLattice = null;
+this.fixedLattice = null;
+this.baseColor = null;
+this.integration = NaN;
+this.sbOut = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.data, "JvxlData", null);
+Clazz.prepareFields (c$, function(){
+this.jvxlExcluded = new Array(4);
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.defineMethod(c$, "clear",
+function(){
+this.allowVolumeRender = true;
+this.jvxlSurfaceData = "";
+this.jvxlEdgeData = "";
+this.jvxlColorData = "";
+this.jvxlVolumeDataXml = "";
+this.color = null;
+this.colorScheme = null;
+this.colorDensity = false;
+this.pointSize = NaN;
+this.contourValues = null;
+this.contourValuesUsed = null;
+this.contourColixes = null;
+this.contourColors = null;
+this.integration = NaN;
+this.isSlabbable = false;
+this.isValid = true;
+this.mapLattice = null;
+this.meshColor = null;
+this.msg = "";
+this.nPointsX = 0;
+this.nVertexColors = 0;
+this.fixedLattice = null;
+this.slabInfo = null;
+this.slabValue = -2147483648;
+this.thisSet = null;
+this.rendering = null;
+this.thisContour = -1;
+this.translucency = 0;
+this.vContours = null;
+this.vertexColorMap = null;
+this.vertexColors = null;
+this.voxelVolume = 0;
+});
+Clazz.defineMethod(c$, "setSurfaceInfo",
+function(thePlane, mapLattice, nSurfaceInts, surfaceData){
+this.jvxlSurfaceData = surfaceData;
+this.jvxlPlane = thePlane;
+this.mapLattice = mapLattice;
+this.nSurfaceInts = nSurfaceInts;
+}, "JU.P4,JU.P3,~N,~S");
+Clazz.defineMethod(c$, "setSurfaceInfoFromBitSet",
+function(bs, thePlane){
+this.setSurfaceInfoFromBitSetPts(bs, thePlane, null);
+}, "JU.BS,JU.P4");
+Clazz.defineMethod(c$, "setSurfaceInfoFromBitSetPts",
+function(bs, thePlane, mapLattice){
+var sb = new JU.SB();
+var nSurfaceInts = (thePlane != null ? 0 : J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(bs, this.nPointsX * this.nPointsY * this.nPointsZ, sb));
+this.setSurfaceInfo(thePlane, mapLattice, nSurfaceInts, sb.toString());
+}, "JU.BS,JU.P4,JU.P3");
+Clazz.defineMethod(c$, "jvxlUpdateInfo",
+function(title, nBytes){
+this.title = title;
+this.nBytes = nBytes;
+}, "~A,~N");
+c$.updateSurfaceData = Clazz.defineMethod(c$, "updateSurfaceData",
+function(edgeData, vertexValues, vertexCount, vertexIncrement, isNaN){
+if (edgeData.length == 0) return "";
+var chars = edgeData.toCharArray();
+for (var i = 0, ipt = 0; i < vertexCount; i += vertexIncrement, ipt++) if (Float.isNaN(vertexValues[i])) chars[ipt] = isNaN;
+
+return String.copyValueOf(chars);
+}, "~S,~A,~N,~N,~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/MeshData.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/MeshData.js
new file mode 100755
index 000000000000..9bf984722d96
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/MeshData.js
@@ -0,0 +1,206 @@
+Clazz.declarePackage("J.jvxl.data");
+Clazz.load(["JU.MeshSurface"], "J.jvxl.data.MeshData", ["java.util.Arrays", "JU.AU", "$.BS", "$.V3", "JU.BSUtil"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.setsSuccessful = false;
+this.vertexIncrement = 1;
+this.polygonColorData = null;
+if (!Clazz.isClassDefined("J.jvxl.data.MeshData.SSet")) {
+J.jvxl.data.MeshData.$MeshData$SSet$ ();
+}
+if (!Clazz.isClassDefined("J.jvxl.data.MeshData.SortSet")) {
+J.jvxl.data.MeshData.$MeshData$SortSet$ ();
+}
+Clazz.instantialize(this, arguments);}, J.jvxl.data, "MeshData", JU.MeshSurface);
+Clazz.defineMethod(c$, "addVertexCopy",
+function(vertex, value, assocVertex, asCopy){
+if (assocVertex < 0) this.vertexIncrement = -assocVertex;
+return this.addVCVal(vertex, value, asCopy);
+}, "JU.T3,~N,~N,~B");
+Clazz.defineMethod(c$, "getSurfaceSet",
+function(){
+return (this.surfaceSet == null ? this.getSurfaceSetForLevel(0) : this.surfaceSet);
+});
+Clazz.defineMethod(c$, "getSurfaceSetForLevel",
+function(level){
+if (level == 0) {
+this.surfaceSet = new Array(100);
+this.nSets = 0;
+}this.setsSuccessful = true;
+for (var i = 0; i < this.pc; i++) if (this.pis[i] != null) {
+if (this.bsSlabDisplay != null && !this.bsSlabDisplay.get(i)) continue;
+var p = this.pis[i];
+var pt0 = this.findSet(p[0]);
+var pt1 = this.findSet(p[1]);
+var pt2 = this.findSet(p[2]);
+if (pt0 < 0 && pt1 < 0 && pt2 < 0) {
+this.createSet(p[0], p[1], p[2]);
+continue;
+}if (pt0 == pt1 && pt1 == pt2) continue;
+if (pt0 >= 0) {
+this.surfaceSet[pt0].set(p[1]);
+this.surfaceSet[pt0].set(p[2]);
+if (pt1 >= 0 && pt1 != pt0) this.mergeSets(pt0, pt1);
+if (pt2 >= 0 && pt2 != pt0 && pt2 != pt1) this.mergeSets(pt0, pt2);
+continue;
+}if (pt1 >= 0) {
+this.surfaceSet[pt1].set(p[0]);
+this.surfaceSet[pt1].set(p[2]);
+if (pt2 >= 0 && pt2 != pt1) this.mergeSets(pt1, pt2);
+continue;
+}this.surfaceSet[pt2].set(p[0]);
+this.surfaceSet[pt2].set(p[1]);
+}
+var n = 0;
+for (var i = 0; i < this.nSets; i++) if (this.surfaceSet[i] != null) n++;
+
+var temp = new Array(this.surfaceSet.length);
+n = 0;
+for (var i = 0; i < this.nSets; i++) if (this.surfaceSet[i] != null) temp[n++] = this.surfaceSet[i];
+
+this.nSets = n;
+this.surfaceSet = temp;
+if (!this.setsSuccessful && level < 2) this.getSurfaceSetForLevel(level + 1);
+if (level == 0) {
+var sets = new Array(this.nSets);
+for (var i = 0; i < this.nSets; i++) sets[i] = Clazz.innerTypeInstance(J.jvxl.data.MeshData.SSet, this, null, this.surfaceSet[i]);
+
+java.util.Arrays.sort(sets, Clazz.innerTypeInstance(J.jvxl.data.MeshData.SortSet, this, null));
+for (var i = 0; i < this.nSets; i++) this.surfaceSet[i] = sets[i].bs;
+
+this.setVertexSets(false);
+}return this.surfaceSet;
+}, "~N");
+Clazz.defineMethod(c$, "setVertexSets",
+function(onlyIfNull){
+if (this.surfaceSet == null) return;
+var nNull = 0;
+for (var i = 0; i < this.nSets; i++) {
+if (this.surfaceSet[i] != null && this.surfaceSet[i].nextSetBit(0) < 0) this.surfaceSet[i] = null;
+if (this.surfaceSet[i] == null) nNull++;
+}
+if (nNull > 0) {
+var bsNew = new Array(this.nSets - nNull);
+for (var i = 0, n = 0; i < this.nSets; i++) if (this.surfaceSet[i] != null) bsNew[n++] = this.surfaceSet[i];
+
+this.surfaceSet = bsNew;
+this.nSets -= nNull;
+} else if (onlyIfNull) {
+return;
+}this.vertexSets = Clazz.newIntArray (this.vc, 0);
+for (var i = 0; i < this.nSets; i++) for (var j = this.surfaceSet[i].nextSetBit(0); j >= 0; j = this.surfaceSet[i].nextSetBit(j + 1)) this.vertexSets[j] = i;
+
+
+}, "~B");
+Clazz.defineMethod(c$, "findSet",
+function(vertex){
+for (var i = 0; i < this.nSets; i++) if (this.surfaceSet[i] != null && this.surfaceSet[i].get(vertex)) return i;
+
+return -1;
+}, "~N");
+Clazz.defineMethod(c$, "createSet",
+function(v1, v2, v3){
+var i;
+for (i = 0; i < this.nSets; i++) if (this.surfaceSet[i] == null) break;
+
+if (i == this.surfaceSet.length) this.surfaceSet = JU.AU.ensureLength(this.surfaceSet, this.surfaceSet.length + 100);
+this.surfaceSet[i] = new JU.BS();
+this.surfaceSet[i].set(v1);
+this.surfaceSet[i].set(v2);
+this.surfaceSet[i].set(v3);
+if (i == this.nSets) this.nSets++;
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "mergeSets",
+function(a, b){
+this.surfaceSet[a].or(this.surfaceSet[b]);
+this.surfaceSet[b] = null;
+}, "~N,~N");
+Clazz.defineMethod(c$, "invalidateSurfaceSet",
+function(i){
+for (var j = this.surfaceSet[i].nextSetBit(0); j >= 0; j = this.surfaceSet[i].nextSetBit(j + 1)) this.vvs[j] = NaN;
+
+this.surfaceSet[i] = null;
+}, "~N");
+c$.checkCutoff = Clazz.defineMethod(c$, "checkCutoff",
+function(iA, iB, iC, vertexValues){
+if (iA < 0 || iB < 0 || iC < 0) return false;
+var val1 = vertexValues[iA];
+var val2 = vertexValues[iB];
+var val3 = vertexValues[iC];
+return (val1 >= 0 && val2 >= 0 && val3 >= 0 || val1 <= 0 && val2 <= 0 && val3 <= 0);
+}, "~N,~N,~N,~A");
+c$.calculateVolumeOrArea = Clazz.defineMethod(c$, "calculateVolumeOrArea",
+function(m, thisSet, isArea, getSets){
+if (getSets || m.nSets <= 0) m.getSurfaceSet();
+var justOne = (thisSet != null && thisSet.cardinality() == 1);
+var n = (justOne || m.nSets <= 0 ? 1 : m.nSets);
+var v = Clazz.newDoubleArray (n, 0);
+var vAB = new JU.V3();
+var vAC = new JU.V3();
+var vTemp = new JU.V3();
+for (var i = m.pc; --i >= 0; ) {
+if (m.setABC(i) == null) continue;
+var iSet = (m.nSets <= 0 ? 0 : m.vertexSets[m.iA]);
+if (thisSet != null && !thisSet.get(iSet)) continue;
+if (isArea) {
+vAB.sub2(m.vs[m.iB], m.vs[m.iA]);
+vAC.sub2(m.vs[m.iC], m.vs[m.iA]);
+vTemp.cross(vAB, vAC);
+v[justOne ? 0 : iSet] += vTemp.length();
+} else {
+vAB.setT(m.vs[m.iB]);
+vAC.setT(m.vs[m.iC]);
+vTemp.cross(vAB, vAC);
+vAC.setT(m.vs[m.iA]);
+v[justOne ? 0 : iSet] += vAC.dot(vTemp);
+}}
+var factor = (isArea ? 2 : 6);
+for (var i = 0; i < n; i++) v[i] /= factor;
+
+if (justOne) return Float.$valueOf(v[0]);
+if (thisSet != null) {
+thisSet.and(JU.BSUtil.newBitSet2(0, v.length));
+var v1 = Clazz.newDoubleArray (thisSet.cardinality(), 0);
+for (var pt = 0, i = thisSet.nextSetBit(0); i >= 0; i = thisSet.nextSetBit(i + 1)) {
+v1[pt++] = v[i];
+}
+v = v1;
+}return v;
+}, "J.jvxl.data.MeshData,JU.BS,~B,~B");
+Clazz.defineMethod(c$, "updateInvalidatedVertices",
+function(bs){
+bs.clearAll();
+for (var i = 0; i < this.vc; i += this.vertexIncrement) if (Float.isNaN(this.vvs[i])) bs.set(i);
+
+}, "JU.BS");
+Clazz.defineMethod(c$, "invalidateVertices",
+function(bsInvalid){
+for (var i = bsInvalid.nextSetBit(0); i >= 0; i = bsInvalid.nextSetBit(i + 1)) this.vvs[i] = NaN;
+
+}, "JU.BS");
+c$.$MeshData$SSet$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.bs = null;
+this.n = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.data.MeshData, "SSet", null);
+Clazz.makeConstructor(c$,
+function(bs){
+this.bs = bs;
+this.n = bs.cardinality();
+}, "JU.BS");
+/*eoif4*/})();
+};
+c$.$MeshData$SortSet$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+Clazz.instantialize(this, arguments);}, J.jvxl.data.MeshData, "SortSet", null, java.util.Comparator);
+Clazz.overrideMethod(c$, "compare",
+function(o1, o2){
+return (o1.n > o2.n ? -1 : o1.n < o2.n ? 1 : 0);
+}, "J.jvxl.data.MeshData.SSet,J.jvxl.data.MeshData.SSet");
+/*eoif4*/})();
+};
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/VolumeData.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/VolumeData.js
new file mode 100755
index 000000000000..d2e049ddd658
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/data/VolumeData.js
@@ -0,0 +1,384 @@
+Clazz.declarePackage("J.jvxl.data");
+Clazz.load(["JU.M3", "$.P3", "$.V3"], "J.jvxl.data.VolumeData", ["java.util.Hashtable", "JU.SB", "JU.Escape", "$.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.sr = null;
+this.doIterate = true;
+this.volumetricOrigin = null;
+this.origin = null;
+this.volumetricVectors = null;
+this.voxelCounts = null;
+this.nPoints = 0;
+this.voxelData = null;
+this.voxelMap = null;
+this.volumetricVectorLengths = null;
+this.maxVectorLength = 0;
+this.minToPlaneDistance = 0;
+this.yzCount = 0;
+this.unitVolumetricVectors = null;
+this.volumetricMatrix = null;
+this.inverseMatrix = null;
+this.thePlane = null;
+this.thePlaneNormalMag = 0;
+this.ptXyzTemp = null;
+this.xmlData = null;
+this.mappingPlane = null;
+this.mappingPlaneNormalMag = 0;
+this.minGrid = 0;
+this.maxGrid = 0;
+this.voxelVolume = 0;
+this.oabc = null;
+this.isPeriodic = false;
+this.isSquared = false;
+this.edgeVector = null;
+this.ptTemp = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.data, "VolumeData", null);
+Clazz.prepareFields (c$, function(){
+this.volumetricOrigin = new JU.P3();
+this.origin = Clazz.newFloatArray (3, 0);
+this.volumetricVectors = new Array(3);
+this.voxelCounts = Clazz.newIntArray (3, 0);
+this.volumetricVectorLengths = Clazz.newFloatArray (3, 0);
+this.unitVolumetricVectors = new Array(3);
+this.volumetricMatrix = new JU.M3();
+this.inverseMatrix = new JU.M3();
+this.ptXyzTemp = new JU.P3();
+this.edgeVector = new JU.V3();
+this.ptTemp = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+this.volumetricVectors[0] = new JU.V3();
+this.volumetricVectors[1] = new JU.V3();
+this.volumetricVectors[2] = new JU.V3();
+this.unitVolumetricVectors[0] = new JU.V3();
+this.unitVolumetricVectors[1] = new JU.V3();
+this.unitVolumetricVectors[2] = new JU.V3();
+});
+Clazz.defineMethod(c$, "getVoxelData",
+function(){
+return this.voxelData;
+});
+Clazz.defineMethod(c$, "setVoxelDataAsArray",
+function(voxelData){
+this.voxelData = voxelData;
+if (voxelData != null) this.sr = null;
+}, "~A");
+Clazz.defineMethod(c$, "hasPlane",
+function(){
+return (this.thePlane != null);
+});
+Clazz.defineMethod(c$, "setMappingPlane",
+function(plane){
+this.mappingPlane = plane;
+if (plane == null) return;
+this.mappingPlaneNormalMag = Math.sqrt(plane.x * plane.x + plane.y * plane.y + plane.z * plane.z);
+}, "JU.P4");
+Clazz.defineMethod(c$, "distanceToMappingPlane",
+function(pt){
+return (this.mappingPlane.x * pt.x + this.mappingPlane.y * pt.y + this.mappingPlane.z * pt.z + this.mappingPlane.w) / this.mappingPlaneNormalMag;
+}, "JU.T3");
+Clazz.defineMethod(c$, "setVolumetricOrigin",
+function(x, y, z){
+this.volumetricOrigin.set(x, y, z);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "getOriginFloat",
+function(){
+return this.origin;
+});
+Clazz.defineMethod(c$, "getYzCount",
+function(){
+this.minGrid = this.volumetricVectors[0].length();
+this.minGrid = Math.min(this.minGrid, this.volumetricVectors[1].length());
+this.minGrid = Math.min(this.minGrid, this.volumetricVectors[2].length());
+this.maxGrid = this.volumetricVectors[0].length();
+this.maxGrid = Math.max(this.maxGrid, this.volumetricVectors[1].length());
+this.maxGrid = Math.max(this.maxGrid, this.volumetricVectors[2].length());
+this.nPoints = this.voxelCounts[0] * this.voxelCounts[1] * this.voxelCounts[2];
+return this.yzCount = this.voxelCounts[1] * this.voxelCounts[2];
+});
+Clazz.defineMethod(c$, "getVolumetricVectorLengths",
+function(){
+return this.volumetricVectorLengths;
+});
+Clazz.defineMethod(c$, "setVolumetricVector",
+function(i, x, y, z){
+this.volumetricVectors[i].x = x;
+this.volumetricVectors[i].y = y;
+this.volumetricVectors[i].z = z;
+this.setUnitVectors();
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "getVoxelCounts",
+function(){
+return this.voxelCounts;
+});
+Clazz.defineMethod(c$, "setVoxelCounts",
+function(nPointsX, nPointsY, nPointsZ){
+this.voxelCounts[0] = nPointsX;
+this.voxelCounts[1] = nPointsY;
+this.voxelCounts[2] = nPointsZ;
+return nPointsX * nPointsY * nPointsZ;
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "getVoxelDataAt",
+function(pt){
+var ix = Clazz.doubleToInt(pt / this.yzCount);
+pt -= ix * this.yzCount;
+var iy = Clazz.doubleToInt(pt / this.voxelCounts[2]);
+var iz = pt - iy * this.voxelCounts[2];
+return this.voxelData[ix][iy][iz];
+}, "~N");
+Clazz.defineMethod(c$, "getPointIndex",
+function(x, y, z){
+return x * this.yzCount + y * this.voxelCounts[2] + z;
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "getPoint",
+function(ipt, pt){
+var ix = Clazz.doubleToInt(ipt / this.yzCount);
+ipt -= ix * this.yzCount;
+var iy = Clazz.doubleToInt(ipt / this.voxelCounts[2]);
+var iz = ipt - iy * this.voxelCounts[2];
+this.voxelPtToXYZ(ix, iy, iz, pt);
+}, "~N,JU.P3");
+Clazz.defineMethod(c$, "setVoxelData",
+function(pt, value){
+var ix = Clazz.doubleToInt(pt / this.yzCount);
+pt -= ix * this.yzCount;
+var iy = Clazz.doubleToInt(pt / this.voxelCounts[2]);
+var iz = pt - iy * this.voxelCounts[2];
+this.voxelData[ix][iy][iz] = value;
+}, "~N,~N");
+Clazz.defineMethod(c$, "setVoxelMap",
+function(){
+this.voxelMap = new java.util.Hashtable();
+this.getYzCount();
+});
+Clazz.defineMethod(c$, "setMatrix",
+function(){
+for (var i = 0; i < 3; i++) this.volumetricMatrix.setColumnV(i, this.volumetricVectors[i]);
+
+try {
+this.inverseMatrix.invertM(this.volumetricMatrix);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? ");
+return false;
+} else {
+throw e;
+}
+}
+return true;
+});
+Clazz.defineMethod(c$, "transform",
+function(v1, v2){
+this.volumetricMatrix.rotate2(v1, v2);
+}, "JU.V3,JU.V3");
+Clazz.defineMethod(c$, "setPlaneParameters",
+function(plane){
+this.thePlane = plane;
+this.thePlaneNormalMag = Math.sqrt(plane.x * plane.x + plane.y * plane.y + plane.z * plane.z);
+}, "JU.P4");
+Clazz.defineMethod(c$, "calcVoxelPlaneDistance",
+function(x, y, z){
+this.voxelPtToXYZ(x, y, z, this.ptXyzTemp);
+return this.distancePointToPlane(this.ptXyzTemp);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "getToPlaneParameter",
+function(){
+return (Math.sqrt(this.thePlane.x * this.thePlane.x + this.thePlane.y * this.thePlane.y + this.thePlane.z * this.thePlane.z) * this.minToPlaneDistance);
+});
+Clazz.defineMethod(c$, "isNearPlane",
+function(x, y, z, toPlaneParameter){
+this.voxelPtToXYZ(x, y, z, this.ptXyzTemp);
+return ((this.thePlane.x * this.ptXyzTemp.x + this.thePlane.y * this.ptXyzTemp.y + this.thePlane.z * this.ptXyzTemp.z + this.thePlane.w) < toPlaneParameter);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "distancePointToPlane",
+function(pt){
+return (this.thePlane.x * pt.x + this.thePlane.y * pt.y + this.thePlane.z * pt.z + this.thePlane.w) / this.thePlaneNormalMag;
+}, "JU.T3");
+Clazz.defineMethod(c$, "voxelPtToXYZ",
+function(x, y, z, pt){
+pt.scaleAdd2(x, this.volumetricVectors[0], this.volumetricOrigin);
+pt.scaleAdd2(y, this.volumetricVectors[1], pt);
+pt.scaleAdd2(z, this.volumetricVectors[2], pt);
+}, "~N,~N,~N,JU.T3");
+Clazz.defineMethod(c$, "setUnitVectors",
+function(){
+this.maxVectorLength = 0;
+this.voxelVolume = 1;
+for (var i = 0; i < 3; i++) {
+var d = this.volumetricVectorLengths[i] = this.volumetricVectors[i].length();
+if (d == 0) return false;
+if (d > this.maxVectorLength) this.maxVectorLength = d;
+this.voxelVolume *= d;
+this.unitVolumetricVectors[i].setT(this.volumetricVectors[i]);
+this.unitVolumetricVectors[i].normalize();
+}
+this.minToPlaneDistance = this.maxVectorLength * 2;
+this.origin[0] = this.volumetricOrigin.x;
+this.origin[1] = this.volumetricOrigin.y;
+this.origin[2] = this.volumetricOrigin.z;
+this.oabc = new Array(4);
+this.oabc[0] = JU.V3.newV(this.volumetricOrigin);
+for (var i = 0; i < 3; i++) {
+var v = this.oabc[i + 1] = new JU.V3();
+v.scaleAdd2(this.voxelCounts[i] - 1, this.volumetricVectors[i], v);
+}
+return this.setMatrix();
+});
+Clazz.defineMethod(c$, "xyzToVoxelPt",
+function(x, y, z, pt3i){
+this.ptXyzTemp.set(x, y, z);
+this.ptXyzTemp.sub(this.volumetricOrigin);
+this.inverseMatrix.rotate(this.ptXyzTemp);
+pt3i.set(Math.round(this.ptXyzTemp.x), Math.round(this.ptXyzTemp.y), Math.round(this.ptXyzTemp.z));
+}, "~N,~N,~N,JU.T3i");
+Clazz.defineMethod(c$, "lookupInterpolatedVoxelValue",
+function(point, getSource){
+if (this.mappingPlane != null) return this.distanceToMappingPlane(point);
+if (this.sr != null) {
+var v = this.sr.getValueAtPoint(point, getSource);
+return (this.isSquared ? v * v : v);
+}this.ptXyzTemp.sub2(point, this.volumetricOrigin);
+this.inverseMatrix.rotate(this.ptXyzTemp);
+var iMax;
+var xLower = this.indexLower(this.ptXyzTemp.x, iMax = this.voxelCounts[0] - 1);
+var xUpper = this.indexUpper(this.ptXyzTemp.x, xLower, iMax);
+var yLower = this.indexLower(this.ptXyzTemp.y, iMax = this.voxelCounts[1] - 1);
+var yUpper = this.indexUpper(this.ptXyzTemp.y, yLower, iMax);
+var zLower = this.indexLower(this.ptXyzTemp.z, iMax = this.voxelCounts[2] - 1);
+var zUpper = this.indexUpper(this.ptXyzTemp.z, zLower, iMax);
+var v1 = J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x - xLower), this.mantissa(this.ptXyzTemp.y - yLower), this.getVoxelValue(xLower, yLower, zLower), this.getVoxelValue(xUpper, yLower, zLower), this.getVoxelValue(xLower, yUpper, zLower), this.getVoxelValue(xUpper, yUpper, zLower));
+var v2 = J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x - xLower), this.mantissa(this.ptXyzTemp.y - yLower), this.getVoxelValue(xLower, yLower, zUpper), this.getVoxelValue(xUpper, yLower, zUpper), this.getVoxelValue(xLower, yUpper, zUpper), this.getVoxelValue(xUpper, yUpper, zUpper));
+return v1 + this.mantissa(this.ptXyzTemp.z - zLower) * (v2 - v1);
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "mantissa",
+function(f){
+return (this.isPeriodic ? f - Math.floor(f) : f);
+}, "~N");
+Clazz.defineMethod(c$, "getVoxelValue",
+function(x, y, z){
+if (this.voxelMap == null) return this.voxelData[x][y][z];
+var f = this.voxelMap.get(Integer.$valueOf(this.getPointIndex(x, y, z)));
+return (f == null ? NaN : f.floatValue());
+}, "~N,~N,~N");
+c$.getFractional2DValue = Clazz.defineMethod(c$, "getFractional2DValue",
+function(fx, fy, x11, x12, x21, x22){
+var v1 = x11 + fx * (x12 - x11);
+var v2 = x21 + fx * (x22 - x21);
+return v1 + fy * (v2 - v1);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "indexLower",
+function(x, xMax){
+if (this.isPeriodic && xMax > 0) {
+while (x < 0) x += xMax;
+
+while (x >= xMax) x -= xMax;
+
+return Clazz.doubleToInt(Math.floor(x));
+}if (x < 0) return 0;
+var floor = Clazz.doubleToInt(Math.floor(x));
+return (floor > xMax ? xMax : floor);
+}, "~N,~N");
+Clazz.defineMethod(c$, "indexUpper",
+function(x, xLower, xMax){
+return (!this.isPeriodic && x < 0 || xLower == xMax ? xLower : xLower + 1);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "offsetCenter",
+function(center){
+var pt = new JU.P3();
+pt.scaleAdd2((this.voxelCounts[0] - 1) / 2, this.volumetricVectors[0], pt);
+pt.scaleAdd2((this.voxelCounts[1] - 1) / 2, this.volumetricVectors[1], pt);
+pt.scaleAdd2((this.voxelCounts[2] - 1) / 2, this.volumetricVectors[2], pt);
+this.volumetricOrigin.sub2(center, pt);
+}, "JU.P3");
+Clazz.defineMethod(c$, "setDataDistanceToPlane",
+function(plane){
+this.setPlaneParameters(plane);
+var nx = this.voxelCounts[0];
+var ny = this.voxelCounts[1];
+var nz = this.voxelCounts[2];
+this.voxelData = Clazz.newFloatArray (nx, ny, nz, 0);
+for (var x = 0; x < nx; x++) for (var y = 0; y < ny; y++) for (var z = 0; z < nz; z++) this.voxelData[x][y][z] = this.calcVoxelPlaneDistance(x, y, z);
+
+
+
+}, "JU.P4");
+Clazz.defineMethod(c$, "filterData",
+function(isSquared, invertCutoff){
+var doInvert = (!Float.isNaN(invertCutoff));
+if (this.sr != null) {
+this.isSquared = isSquared;
+return;
+}var nx = this.voxelCounts[0];
+var ny = this.voxelCounts[1];
+var nz = this.voxelCounts[2];
+if (isSquared) for (var x = 0; x < nx; x++) for (var y = 0; y < ny; y++) for (var z = 0; z < nz; z++) this.voxelData[x][y][z] *= this.voxelData[x][y][z];
+
+
+
+if (doInvert) for (var x = 0; x < nx; x++) for (var y = 0; y < ny; y++) for (var z = 0; z < nz; z++) this.voxelData[x][y][z] = invertCutoff - this.voxelData[x][y][z];
+
+
+
+}, "~B,~N");
+Clazz.defineMethod(c$, "capData",
+function(plane, cutoff){
+if (this.voxelData == null) return;
+var nx = this.voxelCounts[0];
+var ny = this.voxelCounts[1];
+var nz = this.voxelCounts[2];
+var normal = JU.V3.new3(plane.x, plane.y, plane.z);
+normal.normalize();
+var f = 1;
+for (var x = 0; x < nx; x++) for (var y = 0; y < ny; y++) for (var z = 0; z < nz; z++) {
+var value = this.voxelData[x][y][z] - cutoff;
+this.voxelPtToXYZ(x, y, z, this.ptXyzTemp);
+var d = (this.ptXyzTemp.x * normal.x + this.ptXyzTemp.y * normal.y + this.ptXyzTemp.z * normal.z + plane.w - cutoff) / f;
+if (d >= 0 || d > value) this.voxelData[x][y][z] = d;
+}
+
+
+}, "JU.P4,~N");
+Clazz.defineMethod(c$, "setVolumetricXml",
+function(){
+var sb = new JU.SB();
+if (this.voxelCounts[0] == 0) {
+sb.append("\n");
+} else {
+sb.append("\n");
+for (var i = 0; i < 3; i++) sb.append(" \n");
+return this.xmlData = sb.toString();
+});
+Clazz.defineMethod(c$, "setVoxelMapValue",
+function(x, y, z, v){
+if (this.voxelMap == null) return;
+this.voxelMap.put(Integer.$valueOf(this.getPointIndex(x, y, z)), Float.$valueOf(v));
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "calculateFractionalPoint",
+function(cutoff, pointA, pointB, valueA, valueB, pt){
+var d = (valueB - valueA);
+var fraction = (cutoff - valueA) / d;
+this.edgeVector.sub2(pointB, pointA);
+pt.scaleAdd2(fraction, this.edgeVector, pointA);
+if (this.sr == null || !this.doIterate || valueB == valueA || fraction < 0.01 || fraction > 0.99 || (this.edgeVector.length()) < 0.01) return cutoff;
+var n = 0;
+this.ptTemp.setT(pt);
+var v = this.lookupInterpolatedVoxelValue(this.ptTemp, false);
+var v0 = NaN;
+while (++n < 10) {
+var fnew = (v - valueA) / d;
+if (fnew < 0 || fnew > 1) break;
+var diff = (cutoff - v) / d / 2;
+fraction += diff;
+if (fraction < 0 || fraction > 1) break;
+pt.setT(this.ptTemp);
+v0 = v;
+if (Math.abs(diff) < 0.005) break;
+this.ptTemp.scaleAdd2(diff, this.edgeVector, pt);
+v = this.lookupInterpolatedVoxelValue(this.ptTemp, false);
+}
+return v0;
+}, "~N,JU.P3,JU.P3,~N,~N,JU.P3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ApbsReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ApbsReader.js
new file mode 100755
index 000000000000..1cab0763172b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ApbsReader.js
@@ -0,0 +1,37 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.ApbsReader", ["JU.PT", "$.SB"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "ApbsReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.ApbsReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.isAngstroms = true;
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = JU.SB.newS(this.skipComments(false));
+while (this.line != null && this.line.length == 0) this.rd();
+
+this.jvxlFileHeaderBuffer.append("APBS OpenDx DATA ").append(this.line).append("\n");
+this.jvxlFileHeaderBuffer.append("see http://apbs.sourceforge.net\n");
+var atomLine = this.rd();
+var tokens = JU.PT.getTokens(atomLine);
+if (tokens.length >= 4) {
+this.volumetricOrigin.set(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+}J.jvxl.readers.VolumeFileReader.checkAtomLine(this.isXLowToHigh, this.isAngstroms, tokens[0], atomLine, this.jvxlFileHeaderBuffer);
+this.readVoxelVector(0);
+this.readVoxelVector(1);
+this.readVoxelVector(2);
+this.rd();
+tokens = this.getTokens();
+for (var i = 0; i < 3; i++) this.voxelCounts[i] = this.parseIntStr(tokens[i + 5]);
+
+this.rd();
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomDataReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomDataReader.js
new file mode 100755
index 000000000000..3190055ceae3
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomDataReader.js
@@ -0,0 +1,378 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeDataReader", "JU.BS", "$.P3", "$.P3i", "J.atomdata.AtomData"], "J.jvxl.readers.AtomDataReader", ["java.util.Date", "JU.AU", "$.SB", "$.V3", "J.atomdata.RadiusData", "J.c.VDW", "J.jvxl.data.JvxlCoder", "JU.BSUtil", "$.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.maxDistance = 0;
+this.contactPair = null;
+this.fileName = null;
+this.fileDotModel = null;
+this.modelIndex = 0;
+this.atomData = null;
+this.atomXyzTruncated = null;
+this.atomRadius = null;
+this.atomProp = null;
+this.atomNo = null;
+this.atomIndex = null;
+this.myIndex = null;
+this.ac = 0;
+this.myAtomCount = 0;
+this.nearbyAtomCount = 0;
+this.firstNearbyAtom = 0;
+this.bsMySelected = null;
+this.bsMyIgnored = null;
+this.bsNearby = null;
+this.doAddHydrogens = false;
+this.havePlane = false;
+this.doUseIterator = false;
+this.theProperty = 0;
+this.haveOneProperty = false;
+this.minPtsPerAng = 0;
+this.sr = 0;
+this.rs = null;
+this.rs2 = null;
+this.maxRS = 0;
+this.thisPlane = null;
+this.thisAtomSet = null;
+this.thisX = 0;
+this.margin = 0;
+this.vl0 = 0;
+this.vl1 = 0;
+this.vl2 = 0;
+this.bsSurfaceVoxels = null;
+this.validSpheres = null;
+this.noFaceSpheres = null;
+this.voxelSource = null;
+this.ptY0 = null;
+this.ptZ0 = null;
+this.pt0 = null;
+this.pt1 = null;
+this.ptV = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "AtomDataReader", J.jvxl.readers.VolumeDataReader);
+Clazz.prepareFields (c$, function(){
+this.atomData = new J.atomdata.AtomData();
+this.bsMySelected = new JU.BS();
+this.bsMyIgnored = new JU.BS();
+this.ptY0 = new JU.P3();
+this.ptZ0 = new JU.P3();
+this.pt0 = new JU.P3i();
+this.pt1 = new JU.P3i();
+this.ptV = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.AtomDataReader, []);
+});
+Clazz.defineMethod(c$, "initADR",
+function(sg){
+this.initVDR(sg);
+this.precalculateVoxelData = true;
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+}, "~B");
+Clazz.defineMethod(c$, "setup2",
+function(){
+this.contactPair = this.params.contactPair;
+this.doAddHydrogens = (this.sg.atomDataServer != null && this.params.addHydrogens);
+this.modelIndex = this.params.modelIndex;
+if (this.params.bsIgnore != null) this.bsMyIgnored = this.params.bsIgnore;
+if (this.params.volumeData != null) {
+this.setVolumeDataV(this.params.volumeData);
+this.setBBox(this.volumeData.volumetricOrigin, 0);
+this.ptV.setT(this.volumeData.volumetricOrigin);
+for (var i = 0; i < 3; i++) this.ptV.scaleAdd2(this.volumeData.voxelCounts[i] - 1, this.volumeData.volumetricVectors[i], this.ptV);
+
+this.setBBox(this.ptV, 0);
+}this.havePlane = (this.params.thePlane != null);
+if (this.havePlane) this.volumeData.setPlaneParameters(this.params.thePlane);
+});
+Clazz.defineMethod(c$, "markPlaneVoxels",
+function(p, r){
+for (var i = 0, pt = this.thisX * this.yzCount, pt1 = pt + this.yzCount; pt < pt1; pt++, i++) {
+this.volumeData.getPoint(pt, this.ptV);
+this.thisPlane[i] = this.ptV.distance(p) - r;
+}
+}, "JU.P3,~N");
+Clazz.defineMethod(c$, "setVolumeForPlane",
+function(){
+if (this.useOriginStepsPoints) {
+this.xyzMin = JU.P3.newP(this.params.origin);
+this.xyzMax = JU.P3.newP(this.params.origin);
+this.xyzMax.add3((this.params.points.x - 1) * this.params.steps.x, (this.params.points.y - 1) * this.params.steps.y, (this.params.points.z - 1) * this.params.steps.z);
+} else if (this.params.boundingBox == null) {
+this.getAtoms(this.params.bsSelected, false, true, false, false, false, false, this.params.mep_marginAngstroms, this.params.modelInvRotation);
+if (this.xyzMin == null) {
+this.xyzMin = JU.P3.new3(-10, -10, -10);
+this.xyzMax = JU.P3.new3(10, 10, 10);
+}} else {
+this.xyzMin = JU.P3.newP(this.params.boundingBox[0]);
+this.xyzMax = JU.P3.newP(this.params.boundingBox[1]);
+}this.setRanges(this.params.plane_ptsPerAngstrom, this.params.plane_gridMax, 0);
+});
+Clazz.defineMethod(c$, "getAtoms",
+function(bsSelected, doAddHydrogens, getRadii, getMolecules, getAllModels, addNearbyAtoms, getAtomMinMax, marginAtoms, modelInvRotation){
+if (addNearbyAtoms) getRadii = true;
+if (getRadii) {
+if (this.params.atomRadiusData == null) this.params.atomRadiusData = new J.atomdata.RadiusData(null, 1, J.atomdata.RadiusData.EnumType.FACTOR, J.c.VDW.AUTO);
+this.atomData.radiusData = this.params.atomRadiusData;
+this.atomData.radiusData.valueExtended = this.params.solventExtendedAtomRadius;
+if (doAddHydrogens) this.atomData.radiusData.vdwType = J.c.VDW.NOJMOL;
+}this.atomData.modelIndex = this.modelIndex;
+this.atomData.bsSelected = bsSelected;
+this.atomData.bsIgnored = this.bsMyIgnored;
+this.sg.fillAtomData(this.atomData, 1 | (getAllModels ? 16 : 0) | (getMolecules ? 4 : 0) | (getRadii ? 2 : 0));
+if (this.doUseIterator) this.atomData.bsSelected = null;
+this.ac = this.atomData.ac;
+this.modelIndex = this.atomData.firstModelIndex;
+if (modelInvRotation != null) this.atomData.transformXYZ(modelInvRotation, bsSelected);
+var needRadius = false;
+for (var i = 0; i < this.ac; i++) {
+if ((bsSelected == null || bsSelected.get(i)) && (!this.bsMyIgnored.get(i))) {
+if (this.havePlane && Math.abs(this.volumeData.distancePointToPlane(this.atomData.xyz[i])) > 2 * (this.atomData.atomRadius[i] = this.getWorkingRadius(i, marginAtoms))) continue;
+this.bsMySelected.set(i);
+needRadius = !this.havePlane;
+}if (getRadii && (addNearbyAtoms || needRadius)) this.atomData.atomRadius[i] = this.getWorkingRadius(i, marginAtoms);
+}
+var rH = (getRadii && doAddHydrogens ? this.getWorkingRadius(-1, marginAtoms) : 0);
+this.myAtomCount = JU.BSUtil.cardinalityOf(this.bsMySelected);
+var atomSet = JU.BSUtil.copy(this.bsMySelected);
+var nH = 0;
+this.atomProp = null;
+this.theProperty = 3.4028235E38;
+this.haveOneProperty = false;
+var props = this.params.theProperty;
+if (this.myAtomCount > 0) {
+var hAtoms = null;
+if (doAddHydrogens) {
+this.atomData.bsSelected = atomSet;
+this.sg.atomDataServer.fillAtomData(this.atomData, 8);
+hAtoms = new Array(nH = this.atomData.hydrogenAtomCount);
+for (var i = 0; i < this.atomData.hAtoms.length; i++) if (this.atomData.hAtoms[i] != null) for (var j = this.atomData.hAtoms[i].length; --j >= 0; ) hAtoms[--nH] = this.atomData.hAtoms[i][j];
+
+
+nH = hAtoms.length;
+JU.Logger.info(nH + " attached hydrogens added");
+}var n = nH + this.myAtomCount;
+if (getRadii) this.atomRadius = Clazz.newFloatArray (n, 0);
+this.atomXyzTruncated = new Array(n);
+if (this.params.theProperty != null) this.atomProp = Clazz.newFloatArray (n, 0);
+this.atomNo = Clazz.newIntArray (n, 0);
+this.atomIndex = Clazz.newIntArray (n, 0);
+this.myIndex = Clazz.newIntArray (this.ac, 0);
+for (var i = 0; i < nH; i++) {
+if (getRadii) this.atomRadius[i] = rH;
+this.atomXyzTruncated[i] = hAtoms[i];
+this.atomNo[i] = -1;
+if (this.atomProp != null) this.addAtomProp(i, NaN);
+}
+this.myAtomCount = nH;
+for (var i = atomSet.nextSetBit(0); i >= 0; i = atomSet.nextSetBit(i + 1)) {
+if (this.atomProp != null) this.addAtomProp(this.myAtomCount, (props != null && i < props.length ? props[i] : NaN));
+this.atomXyzTruncated[this.myAtomCount] = this.atomData.xyz[i];
+this.atomNo[this.myAtomCount] = this.atomData.atomicNumber[i];
+this.atomIndex[this.myAtomCount] = i;
+this.myIndex[i] = this.myAtomCount;
+if (getRadii) this.atomRadius[this.myAtomCount] = this.atomData.atomRadius[i];
+this.myAtomCount++;
+}
+}this.firstNearbyAtom = this.myAtomCount;
+if (!this.isQuiet) JU.Logger.info(this.myAtomCount + " atoms will be used in the surface calculation");
+if (this.myAtomCount == 0) {
+this.setBBox(JU.P3.new3(10, 10, 10), 0);
+this.setBBox(JU.P3.new3(-10, -10, -10), 0);
+}for (var i = 0; i < this.myAtomCount; i++) this.setBBox(this.atomXyzTruncated[i], getRadii ? this.atomRadius[i] + 0.5 : 0);
+
+if (!Float.isNaN(this.params.scale)) {
+var v = JU.V3.newVsub(this.xyzMax, this.xyzMin);
+v.scale(0.5);
+this.xyzMin.add(v);
+v.scale(this.params.scale);
+this.xyzMax.add2(this.xyzMin, v);
+this.xyzMin.sub(v);
+}if (!addNearbyAtoms || this.myAtomCount == 0) return;
+var pt = new JU.P3();
+this.bsNearby = new JU.BS();
+for (var i = 0; i < this.ac; i++) {
+if (atomSet.get(i) || this.bsMyIgnored.get(i)) continue;
+var rA = this.atomData.atomRadius[i];
+if (this.params.thePlane != null && Math.abs(this.volumeData.distancePointToPlane(this.atomData.xyz[i])) > 2 * rA) continue;
+if (this.params.theProperty != null) rA += this.maxDistance;
+pt = this.atomData.xyz[i];
+if (pt.x + rA > this.xyzMin.x && pt.x - rA < this.xyzMax.x && pt.y + rA > this.xyzMin.y && pt.y - rA < this.xyzMax.y && pt.z + rA > this.xyzMin.z && pt.z - rA < this.xyzMax.z) {
+this.bsNearby.set(i);
+this.nearbyAtomCount++;
+}}
+var nAtoms = this.myAtomCount;
+if (this.nearbyAtomCount != 0) {
+nAtoms += this.nearbyAtomCount;
+this.atomRadius = JU.AU.arrayCopyF(this.atomRadius, nAtoms);
+this.atomXyzTruncated = JU.AU.arrayCopyObject(this.atomXyzTruncated, nAtoms);
+if (this.atomIndex != null) this.atomIndex = JU.AU.arrayCopyI(this.atomIndex, nAtoms);
+if (props != null) this.atomProp = JU.AU.arrayCopyF(this.atomProp, nAtoms);
+for (var i = this.bsNearby.nextSetBit(0); i >= 0; i = this.bsNearby.nextSetBit(i + 1)) {
+if (props != null) this.addAtomProp(this.myAtomCount, props[i]);
+this.myIndex[i] = this.myAtomCount;
+this.atomIndex[this.myAtomCount] = i;
+this.atomXyzTruncated[this.myAtomCount] = this.atomData.xyz[i];
+this.atomRadius[this.myAtomCount++] = this.atomData.atomRadius[i];
+}
+}if (getRadii) this.setRadii();
+this.haveOneProperty = (!Float.isNaN(this.theProperty));
+}, "JU.BS,~B,~B,~B,~B,~B,~B,~N,JU.M4");
+Clazz.defineMethod(c$, "setRadii",
+function(){
+if (this.rs != null) return;
+this.maxRS = 0;
+this.rs = Clazz.newFloatArray (this.myAtomCount, 0);
+this.rs2 = Clazz.newFloatArray (this.myAtomCount, 0);
+for (var i = 0; i < this.myAtomCount; i++) {
+var r = this.rs[i] = this.atomRadius[i] + this.sr;
+if (r > this.maxRS) this.maxRS = r;
+this.rs2[i] = this.rs[i] * this.rs[i];
+}
+});
+Clazz.defineMethod(c$, "addAtomProp",
+function(i, f){
+this.atomProp[i] = f;
+if (!Float.isNaN(this.theProperty)) if (f != this.theProperty) this.theProperty = (this.theProperty == 3.4028235E38 ? f : NaN);
+}, "~N,~N");
+Clazz.defineMethod(c$, "getWorkingRadius",
+function(i, marginAtoms){
+var r = (i < 0 ? this.atomData.hAtomRadius : this.atomData.atomRadius[i]);
+return (Float.isNaN(marginAtoms) ? Math.max(r, 0.1) : r + marginAtoms);
+}, "~N,~N");
+Clazz.defineMethod(c$, "setHeader",
+function(calcType, line2){
+this.jvxlFileHeaderBuffer = new JU.SB();
+if (this.atomData.programInfo != null) this.jvxlFileHeaderBuffer.append("#created by ").append(this.atomData.programInfo).append(" on ").append("" + new java.util.Date()).append("\n");
+this.jvxlFileHeaderBuffer.append(calcType).append("\n").append(line2).append("\n");
+}, "~S,~S");
+Clazz.defineMethod(c$, "setRanges",
+function(ptsPerAngstrom, maxGrid, minPtsPerAng){
+if (this.xyzMin == null) return;
+this.ptsPerAngstrom = ptsPerAngstrom;
+this.maxGrid = maxGrid;
+this.minPtsPerAng = minPtsPerAng;
+this.setVolumeData();
+J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData, this.jvxlFileHeaderBuffer);
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "setVolumeData",
+function(){
+this.setVolumeDataADR();
+});
+Clazz.defineMethod(c$, "setVolumeDataADR",
+function(){
+if (!this.setVolumeDataParams()) {
+this.setVoxelRange(0, this.xyzMin.x, this.xyzMax.x, this.ptsPerAngstrom, this.maxGrid, this.minPtsPerAng);
+this.setVoxelRange(1, this.xyzMin.y, this.xyzMax.y, this.ptsPerAngstrom, this.maxGrid, this.minPtsPerAng);
+this.setVoxelRange(2, this.xyzMin.z, this.xyzMax.z, this.ptsPerAngstrom, this.maxGrid, this.minPtsPerAng);
+}});
+Clazz.defineMethod(c$, "setVertexSource",
+function(){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+if (this.params.vertexSource != null) {
+this.params.vertexSource = JU.AU.arrayCopyI(this.params.vertexSource, this.meshData.vc);
+for (var i = 0; i < this.meshData.vc; i++) this.params.vertexSource[i] = Math.abs(this.params.vertexSource[i]) - 1;
+
+}});
+Clazz.defineMethod(c$, "resetPlane",
+function(value){
+for (var i = 0; i < this.yzCount; i++) this.thisPlane[i] = value;
+
+}, "~N");
+Clazz.defineMethod(c$, "resetVoxelData",
+function(value){
+for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) this.voxelData[x][y][z] = value;
+
+
+
+}, "~N");
+Clazz.defineMethod(c$, "getVoxel",
+function(i, j, k, ipt){
+return (this.isProgressive ? this.thisPlane[ipt % this.yzCount] : this.voxelData[i][j][k]);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "unsetVoxelData",
+function(){
+this.unsetVoxelData2();
+});
+Clazz.defineMethod(c$, "unsetVoxelData2",
+function(){
+if (this.isProgressive) for (var i = 0; i < this.yzCount; i++) {
+if (this.thisPlane[i] == 3.4028235E38) this.thisPlane[i] = NaN;
+}
+ else for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) if (this.voxelData[x][y][z] == 3.4028235E38) this.voxelData[x][y][z] = NaN;
+
+
+
+});
+Clazz.defineMethod(c$, "setGridLimitsForAtom",
+function(ptA, rA, pt0, pt1){
+rA += this.margin;
+this.volumeData.xyzToVoxelPt(ptA.x, ptA.y, ptA.z, pt0);
+var x = Clazz.doubleToInt(Math.floor(rA / this.volumeData.volumetricVectorLengths[0]));
+var y = Clazz.doubleToInt(Math.floor(rA / this.volumeData.volumetricVectorLengths[1]));
+var z = Clazz.doubleToInt(Math.floor(rA / this.volumeData.volumetricVectorLengths[2]));
+pt1.set(pt0.x + x, pt0.y + y, pt0.z + z);
+pt0.set(pt0.x - x, pt0.y - y, pt0.z - z);
+pt0.x = Math.max(pt0.x - 1, 0);
+pt0.y = Math.max(pt0.y - 1, 0);
+pt0.z = Math.max(pt0.z - 1, 0);
+pt1.x = Math.min(pt1.x + 1, this.nPointsX);
+pt1.y = Math.min(pt1.y + 1, this.nPointsY);
+pt1.z = Math.min(pt1.z + 1, this.nPointsZ);
+}, "JU.P3,~N,JU.P3i,JU.P3i");
+Clazz.defineMethod(c$, "getAtomMinMax",
+function(bs, bsAtomMinMax){
+for (var i = 0; i < this.nPointsX; i++) bsAtomMinMax[i] = new JU.BS();
+
+for (var iAtom = this.myAtomCount; --iAtom >= 0; ) {
+if (bs != null && !bs.get(iAtom)) continue;
+this.setGridLimitsForAtom(this.atomXyzTruncated[iAtom], this.atomRadius[iAtom], this.pt0, this.pt1);
+for (var i = this.pt0.x; i < this.pt1.x; i++) bsAtomMinMax[i].set(iAtom);
+
+}
+}, "JU.BS,~A");
+Clazz.defineMethod(c$, "markSphereVoxels",
+function(r0, distance){
+var isWithin = (distance != 3.4028235E38 && this.point != null);
+var v0 = this.volumetricVectors[0];
+var v1 = this.volumetricVectors[1];
+var v2 = this.volumetricVectors[2];
+for (var iAtom = this.thisAtomSet.nextSetBit(0); iAtom >= 0; iAtom = this.thisAtomSet.nextSetBit(iAtom + 1)) {
+if (!this.havePlane && this.validSpheres != null && !this.validSpheres.get(iAtom)) continue;
+var isSurface = (this.noFaceSpheres != null && this.noFaceSpheres.get(iAtom));
+var isNearby = (iAtom >= this.firstNearbyAtom);
+var ptA = this.atomXyzTruncated[iAtom];
+var rA = this.atomRadius[iAtom];
+if (isWithin && ptA.distance(this.point) > distance + rA + 0.5) continue;
+var rA0 = rA + r0;
+this.setGridLimitsForAtom(ptA, rA0, this.pt0, this.pt1);
+if (this.isProgressive) {
+this.pt0.x = this.thisX;
+this.pt1.x = this.thisX + 1;
+}this.volumeData.voxelPtToXYZ(this.pt0.x, this.pt0.y, this.pt0.z, this.ptV);
+for (var i = this.pt0.x; i < this.pt1.x; i++, this.ptV.add2(v0, this.ptY0)) {
+this.ptY0.setT(this.ptV);
+for (var j = this.pt0.y; j < this.pt1.y; j++, this.ptV.add2(v1, this.ptZ0)) {
+this.ptZ0.setT(this.ptV);
+for (var k = this.pt0.z; k < this.pt1.z; k++, this.ptV.add(v2)) {
+var value = this.ptV.distance(ptA) - rA;
+var ipt = this.volumeData.getPointIndex(i, j, k);
+if ((r0 == 0 || value <= rA0) && value < this.getVoxel(i, j, k, ipt)) {
+if (isNearby || isWithin && this.ptV.distance(this.point) > distance) value = NaN;
+this.setVoxel(i, j, k, ipt, value);
+if (!Float.isNaN(value)) {
+if (this.voxelSource != null) this.voxelSource[ipt] = iAtom + 1;
+if (value < 0 && isSurface) this.bsSurfaceVoxels.set(ipt);
+}}}
+}
+}
+}
+}, "~N,~N");
+Clazz.defineMethod(c$, "setVoxel",
+function(i, j, k, ipt, value){
+if (this.isProgressive) this.thisPlane[ipt % this.yzCount] = value;
+ else this.voxelData[i][j][k] = value;
+}, "~N,~N,~N,~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomPropertyMapper.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomPropertyMapper.js
new file mode 100755
index 000000000000..63a709f5f439
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/AtomPropertyMapper.js
@@ -0,0 +1,118 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.AtomPropertyMapper", ["J.api.Interface", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.mepCalc = null;
+this.mepType = null;
+this.calcType = 0;
+this.doSmoothProperty = false;
+this.iter = null;
+this.smoothingPower = 0;
+this.iAtomSurface = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "AtomPropertyMapper", J.jvxl.readers.AtomDataReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.AtomPropertyMapper, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+this.mepType = sg.getReaderData();
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+this.haveSurfaceAtoms = true;
+this.volumeData.sr = this;
+this.volumeData.doIterate = false;
+this.point = this.params.point;
+this.doSmoothProperty = this.params.propertySmoothing;
+this.doUseIterator = true;
+if (this.doSmoothProperty) {
+this.smoothingPower = this.params.propertySmoothingPower;
+if (this.smoothingPower < 0) this.smoothingPower = 0;
+ else if (this.smoothingPower > 10) this.smoothingPower = 10;
+if (this.smoothingPower == 0) this.doSmoothProperty = false;
+this.smoothingPower = (this.smoothingPower - 11) / 2;
+}this.maxDistance = this.params.propertyDistanceMax;
+if (this.mepType != null) {
+this.doSmoothProperty = true;
+if (this.params.mep_calcType >= 0) this.calcType = this.params.mep_calcType;
+this.mepCalc = J.api.Interface.getOption("quantum." + this.mepType + "Calculation", this.sg.atomDataServer, "file");
+}if (!this.doSmoothProperty && this.maxDistance == 2147483647) this.maxDistance = 5;
+this.getAtoms(this.params.bsSelected, this.doAddHydrogens, true, false, false, true, false, NaN, null);
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+if (!this.doSmoothProperty && this.meshData.vertexSource != null) {
+this.hasColorData = true;
+for (var i = this.meshData.vc; --i >= 0; ) {
+var iAtom = this.meshData.vertexSource[i];
+if (iAtom >= 0) {
+this.meshData.vvs[i] = this.params.theProperty[iAtom];
+} else {
+this.hasColorData = false;
+break;
+}}
+}this.setHeader("property", this.params.calculationType);
+this.setRanges(this.params.solvent_ptsPerAngstrom, this.params.solvent_gridMax, 0);
+this.params.cutoff = 0;
+}, "~B");
+Clazz.overrideMethod(c$, "setVolumeData",
+function(){
+if (this.params.thePlane != null) this.setVolumeDataADR();
+});
+Clazz.overrideMethod(c$, "initializeMapping",
+function(){
+if (this.params.showTiming) JU.Logger.startTimer("property mapping");
+if (this.bsNearby != null) this.bsMySelected.or(this.bsNearby);
+this.iter = this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected, false, false, false);
+});
+Clazz.overrideMethod(c$, "finalizeMapping",
+function(){
+this.iter.release();
+this.iter = null;
+if (this.params.showTiming) JU.Logger.checkTimer("property mapping", false);
+});
+Clazz.overrideMethod(c$, "generateCube",
+function(){
+});
+Clazz.overrideMethod(c$, "getSurfaceAtomIndex",
+function(){
+return this.iAtomSurface;
+});
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+if (this.haveOneProperty && !getSource) return this.theProperty;
+var dmin = 3.4028235E38;
+var dminNearby = 3.4028235E38;
+var value = (this.doSmoothProperty ? 0 : NaN);
+var vdiv = 0;
+this.sg.atomDataServer.setIteratorForPoint(this.iter, this.modelIndex, pt, this.maxDistance);
+this.iAtomSurface = -1;
+while (this.iter.hasNext()) {
+var ia = this.iter.next();
+var myAtom = this.myIndex[ia];
+var isNearby = (myAtom >= this.firstNearbyAtom);
+var ptA = this.atomXyzTruncated[myAtom];
+var p = this.atomProp[myAtom];
+if (Float.isNaN(p)) continue;
+var d2 = pt.distanceSquared(ptA);
+if (isNearby) {
+if (d2 < dminNearby) {
+dminNearby = d2;
+if (!this.doSmoothProperty && dminNearby < dmin) {
+dmin = d2;
+value = NaN;
+}}} else if (d2 < dmin) {
+dmin = d2;
+this.iAtomSurface = ia;
+if (!this.doSmoothProperty) value = p;
+}if (this.mepCalc != null) {
+value += this.mepCalc.valueFor(p, d2, this.calcType);
+} else if (this.doSmoothProperty) {
+d2 = Math.pow(d2, this.smoothingPower);
+vdiv += d2;
+value += d2 * p;
+}}
+return (this.mepCalc != null ? value : this.doSmoothProperty ? (vdiv == 0 || dminNearby < dmin ? NaN : value / vdiv) : value);
+}, "JU.T3,~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/BCifDensityReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/BCifDensityReader.js
new file mode 100755
index 000000000000..0977489e3a9e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/BCifDensityReader.js
@@ -0,0 +1,201 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.MapFileReader"], "J.jvxl.readers.BCifDensityReader", ["java.io.BufferedInputStream", "$.ByteArrayInputStream", "JU.AU", "$.BC", "$.MessagePackReader", "$.P3", "$.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.header = null;
+this.pt = 0;
+this.checkSum = 0;
+this.values = null;
+this.cifData = null;
+this.thisData = null;
+this.isDiff = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "BCifDensityReader", J.jvxl.readers.MapFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.BCifDensityReader, []);
+});
+Clazz.defineMethod(c$, "getCifData",
+function(fileName, data){
+this.binarydoc = this.newBinaryDocument();
+if (JU.AU.isAB(data)) this.binarydoc.setStream( new java.io.BufferedInputStream( new java.io.ByteArrayInputStream(data)), true);
+ else this.setStream(fileName, true);
+this.nSurfaces = 1;
+}, "~S,~O");
+Clazz.defineMethod(c$, "readCifP3",
+function(key, p3){
+if (p3 == null) p3 = new JU.P3();
+var x = this.getCifFloat(key + "[0]");
+if (Float.isNaN(x)) {
+p3.x = NaN;
+} else {
+p3.x = x;
+p3.y = this.getCifFloat(key + "[1]");
+p3.z = this.getCifFloat(key + "[2]");
+}return p3;
+}, "~S,JU.P3");
+Clazz.defineMethod(c$, "getCifMap",
+function(type){
+if (this.cifData == null) try {
+this.cifData = ( new JU.MessagePackReader(this.binarydoc, true)).readMap();
+System.out.println("BCifDensityReader BCIF encoder " + this.cifData.get("encoder") + " BCIF version " + this.cifData.get("version"));
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println("BCifDensityReader error " + e);
+} else {
+throw e;
+}
+}
+var dataBlocks = this.cifData.get("dataBlocks");
+for (var i = dataBlocks.length; --i >= 0; ) {
+var map = dataBlocks[i];
+this.header = map.get("header").toString();
+if ("EM".equals(this.header) || type.equalsIgnoreCase(this.header)) {
+var categories = map.get("categories");
+for (var j = categories.length; --j >= 0; ) {
+var cat = categories[j];
+var catName = cat.get("name");
+var columns = cat.get("columns");
+for (var k = columns.length; --k >= 0; ) {
+var col = columns[k];
+map.put(catName + "_" + col.get("name"), col.get("data"));
+}
+}
+map.remove("categories");
+return this.thisData = map;
+}}
+return null;
+}, "~S");
+Clazz.defineMethod(c$, "getCifFloat",
+function(key){
+var map = this.thisData.get(key);
+var data = map.get("data");
+var encoding = (((map.get("encoding"))[0]).get("type")).intValue();
+var f = NaN;
+try {
+switch (encoding) {
+case 3:
+f = JU.BC.bytesToInt(data, 0, false);
+break;
+case 33:
+f = JU.BC.bytesToDoubleToFloat(data, 0, false);
+break;
+default:
+System.out.println("BCifDensityReader: Number encoding not recognized: " + encoding);
+break;
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+}
+return f;
+}, "~S");
+Clazz.defineMethod(c$, "readCifFloats",
+function(key, values){
+var map = this.thisData.get(key);
+var data = map.get("data");
+var encoding = (map.get("encoding"))[0];
+var min = (encoding.get("min")).floatValue();
+var max = (encoding.get("max")).floatValue();
+var numSteps = (encoding.get("numSteps")).intValue();
+var kind = encoding.get("kind");
+if ("IntervalQuantization".equals(kind)) {
+var delta = (max - min) / (numSteps - 1);
+for (var i = data.length; --i >= 0; ) {
+values[i] = min + delta * ((data[i] + 256) % 256);
+}
+} else {
+System.out.println("BCifDensityReader: value encoding type? " + kind);
+}return values;
+}, "~S,~A");
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.allowSigma = true;
+this.init2MFR(sg, br);
+var o2 = sg.getReaderData();
+var fileName = o2[0];
+var data = o2[1];
+this.isDiff = (fileName != null && fileName.indexOf("&diff=1") >= 0 || (typeof(data)=='string') && (data).indexOf("#diff=1") >= 0);
+this.getCifData(fileName, data);
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.getCifMap(this.isDiff ? "FO-FC" : "2FO-FC");
+this.readCifP3("_volume_data_3d_info_axis_order", this.p3);
+var axis_order = this.readCifP3("_volume_data_3d_info_axis_order", null);
+var fracOrigin = this.readCifP3("_volume_data_3d_info_origin", null);
+var fracDimensions = this.readCifP3("_volume_data_3d_info_dimensions", null);
+var sampleCounts = this.readCifP3("_volume_data_3d_info_sample_count", this.p3);
+this.mapc = Clazz.floatToInt(axis_order.x) + 1;
+this.mapr = Clazz.floatToInt(axis_order.y) + 1;
+this.maps = Clazz.floatToInt(axis_order.z) + 1;
+var crs2abc = Clazz.newIntArray (3, 0);
+crs2abc[this.mapc - 1] = 0;
+crs2abc[this.mapr - 1] = 1;
+crs2abc[this.maps - 1] = 2;
+this.n0 = Clazz.floatToInt(sampleCounts.x);
+this.n1 = Clazz.floatToInt(sampleCounts.y);
+this.n2 = Clazz.floatToInt(sampleCounts.z);
+this.na = Clazz.floatToInt(this.getXYZ(sampleCounts, crs2abc[0]));
+this.nb = Clazz.floatToInt(this.getXYZ(sampleCounts, crs2abc[1]));
+this.nc = Clazz.floatToInt(this.getXYZ(sampleCounts, crs2abc[2]));
+this.readCifP3("_volume_data_3d_info_spacegroup_cell_size", this.p3);
+this.a = this.p3.x;
+this.b = this.p3.y;
+this.c = this.p3.z;
+var fa = this.getXYZ(fracDimensions, crs2abc[0]);
+var fb = this.getXYZ(fracDimensions, crs2abc[1]);
+var fc = this.getXYZ(fracDimensions, crs2abc[2]);
+this.xyzStart[this.xIndex = 0] = this.getXYZ(fracOrigin, crs2abc[0]) * this.na / fa;
+this.xyzStart[this.yIndex = 1] = this.getXYZ(fracOrigin, crs2abc[1]) * this.nb / fb;
+this.xyzStart[this.zIndex = 2] = this.getXYZ(fracOrigin, crs2abc[2]) * this.nc / fc;
+this.a *= fa;
+this.b *= fb;
+this.c *= fc;
+this.readCifP3("_volume_data_3d_info_spacegroup_cell_angles", this.p3);
+this.alpha = this.p3.x;
+this.beta = this.p3.y;
+this.gamma = this.p3.z;
+this.values = this.readCifFloats("_volume_data_3d_values", Clazz.newFloatArray (this.na * this.nb * this.nc, 0));
+this.getVectorsAndOrigin();
+if (this.params.thePlane == null && (this.params.cutoffAutomatic || !Float.isNaN(this.params.sigma))) {
+var sigma = (this.params.sigma < 0 || Float.isNaN(this.params.sigma) ? 1 : this.params.sigma);
+this.dmean = this.getCifFloat("_volume_data_3d_info_mean_sampled");
+var rmsDeviation = this.getCifFloat("_volume_data_3d_info_sigma_sampled");
+this.params.cutoff = rmsDeviation * sigma + this.dmean;
+JU.Logger.info("Cutoff set to (mean + rmsDeviation*" + sigma + " = " + this.params.cutoff + ")\n");
+}this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("BCifDensity reader type=" + this.header + "\n");
+});
+Clazz.defineMethod(c$, "getXYZ",
+function(a, x){
+switch (Clazz.floatToInt(x)) {
+case 0:
+return a.x;
+case 1:
+return a.y;
+case 2:
+default:
+return a.z;
+}
+}, "JU.P3,~N");
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+var v = this.values[this.pt++];
+this.checkSum += v;
+return v;
+});
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+this.pt += nPoints;
+}, "~N");
+Clazz.defineMethod(c$, "closeReader",
+function(){
+if (this.readerClosed) return;
+System.out.println("CifDensityReader checkSum=" + this.checkSum);
+Clazz.superCall(this, J.jvxl.readers.BCifDensityReader, "closeReader", []);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CastepDensityReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CastepDensityReader.js
new file mode 100755
index 000000000000..3c59a6d2374d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CastepDensityReader.js
@@ -0,0 +1,87 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PeriodicVolumeFileReader"], "J.jvxl.readers.CastepDensityReader", ["JU.PT", "$.SB"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nFilePoints = 0;
+this.nSkip = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "CastepDensityReader", J.jvxl.readers.PeriodicVolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.CastepDensityReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+this.isProgressive = false;
+this.isAngstroms = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "gotoData",
+function(n, nPoints){
+this.nSkip = n;
+}, "~N,~N");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB();
+while (this.rd() != null && this.line.indexOf(".") < 0) {
+}
+for (var i = 0; i < 3; ++i) {
+var voxelVector = this.volumetricVectors[i];
+voxelVector.set(this.parseFloatStr(this.line), this.parseFloat(), this.parseFloat());
+this.rd();
+}
+this.nSurfaces = this.parseIntStr(this.rd());
+this.rd();
+this.voxelCounts[0] = (this.nPointsX = this.parseIntStr(this.line)) + 1;
+this.voxelCounts[1] = (this.nPointsY = this.parseInt()) + 1;
+this.voxelCounts[2] = (this.nPointsZ = this.parseInt()) + 1;
+this.nFilePoints = (this.nPointsX++) * (this.nPointsY++) * (this.nPointsZ++);
+this.volumetricOrigin.set(0, 0, 0);
+for (var i = 0; i < 3; i++) {
+this.volumetricVectors[i].scale(1 / (this.voxelCounts[i] - 1));
+if (this.isAnisotropic) this.setVectorAnisotropy(this.volumetricVectors[i]);
+}
+while (this.rd().trim().length > 0) {
+}
+});
+Clazz.overrideMethod(c$, "getPeriodicVoxels",
+function(){
+this.rd();
+var tokens = this.getTokens();
+if (this.nSkip > 0 && tokens.length < 3 + this.nSurfaces) {
+for (var j = 0; j < this.nSkip; j++) for (var i = 0; i < this.nFilePoints; i++) this.rd();
+
+
+this.nSkip = 0;
+}var dsf = this.downsampleFactor;
+if (dsf > 1) {
+for (var i = 0; i < this.nFilePoints; i++) {
+var x = this.parseIntStr(this.line) - 1;
+var y = this.parseInt() - 1;
+var z = this.parseInt() - 1;
+if (x % dsf == 0 && y % dsf == 0 && z % dsf == 0) {
+if (this.nSkip > 0) this.skipPoints(this.nSkip);
+this.voxelData[Clazz.doubleToInt(x / dsf)][Clazz.doubleToInt(y / dsf)][Clazz.doubleToInt(z / dsf)] = this.recordData(this.parseFloat());
+}this.rd();
+}
+} else {
+for (var i = 0; i < this.nFilePoints; i++) {
+var x = this.parseIntStr(this.line) - 1;
+var y = this.parseInt() - 1;
+var z = this.parseInt() - 1;
+if (this.nSkip > 0) this.skipPoints(this.nSkip);
+this.voxelData[x][y][z] = this.recordData(this.parseFloat());
+this.rd();
+}
+}});
+Clazz.defineMethod(c$, "skipPoints",
+function(n){
+var pt = this.next[0];
+for (var i = 0; i < n; i++) {
+while (pt < this.line.length && JU.PT.isWhitespace(this.line.charAt(pt++))) {
+}
+while (pt < this.line.length && !JU.PT.isWhitespace(this.line.charAt(pt++))) {
+}
+}
+this.next[0] = pt;
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CifDensityReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CifDensityReader.js
new file mode 100755
index 000000000000..8d98c7691e58
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CifDensityReader.js
@@ -0,0 +1,53 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.BCifDensityReader"], "J.jvxl.readers.CifDensityReader", ["JU.P3", "$.PT"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "CifDensityReader", J.jvxl.readers.BCifDensityReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.CifDensityReader, []);
+});
+Clazz.overrideMethod(c$, "getCifData",
+function(fileName, data){
+this.cifData = this.sg.atomDataServer.readCifData(fileName, data, "CIF");
+}, "~S,~O");
+Clazz.overrideMethod(c$, "readCifP3",
+function(key, p3){
+if (p3 == null) p3 = new JU.P3();
+var x = this.getCifFloat(key + "[0]");
+if (Float.isNaN(x)) {
+p3.x = NaN;
+} else {
+p3.x = x;
+p3.y = this.getCifFloat(key + "[1]");
+p3.z = this.getCifFloat(key + "[2]");
+}return p3;
+}, "~S,JU.P3");
+Clazz.overrideMethod(c$, "getCifMap",
+function(type){
+type = "data_" + type;
+var list = this.cifData.get("models");
+for (var i = 0; i < list.size(); i++) {
+var map = list.get(i);
+if (type.equalsIgnoreCase(map.get("name").toString())) return this.thisData = map;
+}
+return null;
+}, "~S");
+Clazz.overrideMethod(c$, "getCifFloat",
+function(key){
+var o = this.thisData.get(key);
+var x = NaN;
+if (o != null) {
+if ((typeof(o)=='string')) {
+x = JU.PT.parseFloat(o);
+} else if (Clazz.instanceOf(o, Number)) {
+x = (o).floatValue();
+}}return x;
+}, "~S");
+Clazz.overrideMethod(c$, "readCifFloats",
+function(key, values){
+var list = this.thisData.get(key);
+for (var i = 0, n = values.length; i < n; i++) values[i] = JU.PT.parseFloat(list.get(i));
+
+return values;
+}, "~S,~A");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CubeReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CubeReader.js
new file mode 100755
index 000000000000..cfad7070cc82
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/CubeReader.js
@@ -0,0 +1,37 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.CubeReader", ["JU.PT", "$.SB", "JU.Logger"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "CubeReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.CubeReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append(this.rd()).appendC('\n');
+this.jvxlFileHeaderBuffer.append(this.rd()).appendC('\n');
+var atomLine = this.rd();
+var tokens = JU.PT.getTokensAt(atomLine, 0);
+this.ac = this.parseIntStr(tokens[0]);
+this.negativeAtomCount = (this.ac < 0);
+if (this.negativeAtomCount) this.ac = -this.ac;
+this.volumetricOrigin.set(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+J.jvxl.readers.VolumeFileReader.checkAtomLine(this.isXLowToHigh, this.isAngstroms, tokens[0], atomLine, this.jvxlFileHeaderBuffer);
+if (!this.isAngstroms) this.volumetricOrigin.scale(0.5291772);
+for (var i = 0; i < 3; ++i) this.readVoxelVector(i);
+
+for (var i = 0; i < this.ac; ++i) this.jvxlFileHeaderBuffer.append(this.rd() + "\n");
+
+if (!this.negativeAtomCount) {
+this.nSurfaces = 1;
+} else {
+this.rd();
+JU.Logger.info("Reading extra CUBE information line: " + this.line);
+this.nSurfaces = this.parseIntStr(this.line);
+}});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/DelPhiBinaryReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/DelPhiBinaryReader.js
new file mode 100755
index 000000000000..acf6849c43ad
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/DelPhiBinaryReader.js
@@ -0,0 +1,79 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.DelPhiBinaryReader", ["JU.SB", "$.V3", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.data = null;
+this.pt = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "DelPhiBinaryReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.DelPhiBinaryReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+var fileName = (sg.getReaderData())[0];
+this.init2VFR(sg, br);
+this.binarydoc = this.newBinaryDocument();
+this.setStream(fileName, false);
+this.nSurfaces = 1;
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.allowSigma = false;
+this.isAngstroms = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var uplbl = this.readString();
+JU.Logger.info(uplbl);
+var nxttoplbl = this.readString();
+JU.Logger.info(nxttoplbl);
+this.data = this.readFloatArray();
+JU.Logger.info("DelPhi data length: " + this.data.length);
+var botlbl = this.readString();
+JU.Logger.info(botlbl);
+var scalemid = this.readFloatArray();
+var scale = scalemid[0];
+JU.Logger.info("DelPhi scale: " + scale);
+var dx = (scale == 1 ? 0.84375 : 1 / scale);
+this.volumetricVectors[0] = JU.V3.new3(0, 0, dx);
+this.volumetricVectors[1] = JU.V3.new3(0, dx, 0);
+this.volumetricVectors[2] = JU.V3.new3(dx, 0, 0);
+JU.Logger.info("DelPhi resolution (pts/angstrom) set to: " + dx);
+var nx = 65;
+this.voxelCounts[0] = this.voxelCounts[1] = this.voxelCounts[2] = nx;
+JU.Logger.info("DelPhi voxel counts: " + nx);
+dx *= Clazz.doubleToInt((nx - 1) / 2);
+this.volumetricOrigin.set(scalemid[1], scalemid[2], scalemid[3]);
+JU.Logger.info("DelPhi center " + this.volumetricOrigin);
+this.volumetricOrigin.x -= dx;
+this.volumetricOrigin.y -= dx;
+this.volumetricOrigin.z -= dx;
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("DelPhi DATA ").append(nxttoplbl.$replace('\n', ' ').trim()).append("\n\n");
+});
+Clazz.defineMethod(c$, "readString",
+function(){
+var n = this.binarydoc.readInt();
+var buf = Clazz.newByteArray (n, 0);
+this.binarydoc.readByteArray(buf, 0, n);
+this.binarydoc.readInt();
+return String.instantialize(buf);
+});
+Clazz.defineMethod(c$, "readFloatArray",
+function(){
+var n = this.binarydoc.readInt() >> 2;
+var a = Clazz.newFloatArray (n, 0);
+for (var i = 0; i < n; i++) a[i] = this.binarydoc.readFloat();
+
+this.binarydoc.readInt();
+return a;
+});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+this.nBytes += 4;
+return this.data[this.pt++];
+});
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+this.pt += nPoints;
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Dsn6BinaryReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Dsn6BinaryReader.js
new file mode 100755
index 000000000000..d2b1a92552e9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Dsn6BinaryReader.js
@@ -0,0 +1,125 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.MapFileReader"], "J.jvxl.readers.Dsn6BinaryReader", ["java.io.DataInputStream", "JU.Rdr", "$.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.byteFactor = 0;
+this.xyCount = 0;
+this.nBrickX = 0;
+this.nBrickY = 0;
+this.brickLayerVoxelCount = 0;
+this.brickLayerByteCount = 0;
+this.brickRowByteCount = 0;
+this.brickLayer = null;
+this.pt = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "Dsn6BinaryReader", J.jvxl.readers.MapFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.Dsn6BinaryReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, brNull){
+this.init2MFR(sg, this.br);
+this.binarydoc = this.newBinaryDocument();
+var o2 = sg.getReaderData();
+var fileName = o2[0];
+var data = o2[1];
+if (data == null) this.binarydoc.setStream(sg.atomDataServer.getBufferedInputStream(fileName), true);
+ else this.binarydoc.setStreamData( new java.io.DataInputStream(JU.Rdr.getBIS(data.getBytes())), true);
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var header = Clazz.newShortArray (19, 0);
+for (var i = 0; i < 19; i++) header[i] = this.binarydoc.readShort();
+
+if (header[18] != 100) {
+this.binarydoc.setStream(null, false);
+for (var i = 0; i < 19; i++) header[i] = this.binarydoc.swapBytesS(header[i]);
+
+}this.xyzStart[0] = header[0];
+this.xyzStart[1] = header[1];
+this.xyzStart[2] = header[2];
+this.n0 = header[3];
+this.n1 = header[4];
+this.n2 = header[5];
+this.na = header[6];
+this.nb = header[7];
+this.nc = header[8];
+this.a = header[9];
+this.b = header[10];
+this.c = header[11];
+this.alpha = header[12];
+this.beta = header[13];
+this.gamma = header[14];
+var header16 = header[15];
+var header17 = header[16];
+var scalingFactor = header[17];
+var header19 = header[18];
+this.maps = 3;
+this.mapr = 2;
+this.mapc = 1;
+this.dmin = (0 - header17) * header19 / header16;
+this.dmax = (255 - header17) * header19 / header16;
+this.drange = this.dmax - this.dmin;
+this.byteFactor = this.drange / 255;
+var dminError1 = (0 - header17 - 0.5) * header19 / (header16 - 0.5);
+var dminError2 = (0 - header17 + 0.5) * header19 / (header16 + 0.5);
+var dmaxError1 = (255 - header17 - 0.5) * header19 / (header16 - 0.5);
+var dmaxError2 = (255 - header17 + 0.5) * header19 / (header16 + 0.5);
+var dminError = Math.round((dminError2 - dminError1) / 0.002) * 0.001;
+var dmaxError = Math.round((dmaxError2 - dmaxError1) / 0.002) * 0.001;
+JU.Logger.info("DNS6 dmin,dmax = " + this.dmin + "+/-" + dminError + "," + this.dmax + "+/-" + dmaxError);
+this.a /= scalingFactor;
+this.b /= scalingFactor;
+this.c /= scalingFactor;
+this.alpha /= scalingFactor;
+this.beta /= scalingFactor;
+this.gamma /= scalingFactor;
+this.binarydoc.seek(0x200);
+this.getVectorsAndOrigin();
+this.setCutoffAutomatic();
+this.xyCount = this.n0 * this.n1;
+this.brickLayerVoxelCount = this.xyCount * 8;
+this.nBrickX = Clazz.doubleToInt((this.n0 + 7) / 8);
+this.nBrickY = Clazz.doubleToInt((this.n1 + 7) / 8);
+this.brickRowByteCount = this.nBrickX * 512;
+this.brickLayerByteCount = this.brickRowByteCount * this.nBrickY;
+this.brickLayer = Clazz.newByteArray (this.brickLayerByteCount, 0);
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("DNS6/O progressive brick data reader\n");
+this.jvxlFileHeaderBuffer.append("see http://www.uoxray.uoregon.edu/tnt/manual/node104.html\n");
+});
+Clazz.defineMethod(c$, "readBrickLayer",
+function(){
+this.binarydoc.readByteArray(this.brickLayer, 0, this.brickLayerByteCount);
+this.pt = 0;
+this.nBytes = this.binarydoc.getPosition();
+});
+Clazz.defineMethod(c$, "getBrickValue",
+function(pt){
+var x = pt % this.n0;
+var y = (Clazz.doubleToInt(pt / this.n0)) % this.n1;
+var z = Clazz.doubleToInt(pt / this.xyCount);
+var brickX = x % 8;
+var brickY = y % 8;
+var brickZ = z % 8;
+var bX = Clazz.doubleToInt(x / 8);
+var bY = Clazz.doubleToInt(y / 8);
+var bPt = bY * 512 * this.nBrickX + bX * 512 + brickZ * 64 + brickY * 8 + brickX;
+if (bPt % 2 == 0) bPt++;
+ else bPt--;
+var value = (this.brickLayer[bPt] + 256) % 256;
+return this.dmin + value * this.byteFactor;
+}, "~N");
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+if ((this.pt % this.brickLayerVoxelCount) == 0) this.readBrickLayer();
+return this.getBrickValue(this.pt++);
+});
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+for (var i = 0; i < nPoints; i++) this.binarydoc.readByte();
+
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/EfvetReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/EfvetReader.js
new file mode 100755
index 000000000000..d408ef41619b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/EfvetReader.js
@@ -0,0 +1,80 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PolygonFileReader"], "J.jvxl.readers.EfvetReader", ["JU.CU", "$.P3", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vertexMap = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "EfvetReader", J.jvxl.readers.PolygonFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.EfvetReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PFR(sg, br);
+this.jvxlFileHeaderBuffer.append("efvet file format\nvertices and triangles only\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+this.hasColorData = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "getSurfaceData",
+function(){
+this.getHeader();
+this.getVertices();
+this.getTriangles();
+JU.Logger.info("efvet file contains " + this.nVertices + " vertices and " + this.nTriangles + " triangles");
+});
+Clazz.defineMethod(c$, "getHeader",
+function(){
+this.skipTo(" 0 && this.line.indexOf(">") < 0) this.jvxlFileHeaderBuffer.append("# " + this.line + "\n");
+
+JU.Logger.info(this.jvxlFileHeaderBuffer.toString());
+});
+Clazz.defineMethod(c$, "getVertices",
+function(){
+var pt = new JU.P3();
+var value = 0;
+this.skipTo(" 0 && dataIndex < tokens.length) JU.Logger.info("property " + tokens[dataIndex]);
+ else JU.Logger.info(this.line);
+for (var i = 0; i < this.nVertices; i++) {
+this.skipTo("");
+pt.set(values[0], values[1], values[2]);
+this.skipTo(null, "property");
+for (var j = 0; j < dataIndex; j++) value = this.parseFloat();
+
+if (this.isAnisotropic) this.setVertexAnisotropy(pt);
+var v = this.vertexMap[i + 1] = this.addVC(pt, value, i, true);
+if (v >= 0 && this.jvxlData.vertexColors != null) {
+this.jvxlData.vertexColors[v] = JU.CU.colorTriadToFFRGB(values[6], values[7], values[8]);
+this.jvxlData.nVertexColors++;
+}}
+});
+Clazz.defineMethod(c$, "getTriangles",
+function(){
+this.skipTo("= 0 && b >= 0 && c >= 0) this.addTriangleCheck(a, b, c, 7, 0, false, 0);
+}
+});
+Clazz.defineMethod(c$, "getInt",
+function(){
+return this.vertexMap[this.parseInt()];
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyReader.js
new file mode 100755
index 000000000000..89cb8c795d9b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyReader.js
@@ -0,0 +1,99 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.IsoFxyReader", ["JU.SB", "J.jvxl.data.JvxlCoder"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.data = null;
+this.isPlanarMapping = false;
+this.func = null;
+this.values = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoFxyReader", J.jvxl.readers.AtomDataReader);
+Clazz.prepareFields (c$, function(){
+this.values = Clazz.newFloatArray (3, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoFxyReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initIFR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "initIFR",
+function(sg){
+this.initADR(sg);
+this.isXLowToHigh = true;
+this.precalculateVoxelData = false;
+this.params.fullyLit = true;
+this.isPlanarMapping = (this.params.thePlane != null || this.params.state == 3);
+this.volumeData.sr = (this.params.func == null ? null : this);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+if (this.params.functionInfo.size() > 5) this.data = this.params.functionInfo.get(5);
+this.setupType("functionXY");
+}, "~B");
+Clazz.defineMethod(c$, "setupType",
+function(type){
+this.func = this.params.func;
+var functionName = this.params.functionInfo.get(0);
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append(type).append("\n").append(functionName).append("\n");
+if (this.params.thePlane != null || this.data == null && !this.useOriginStepsPoints) this.setVolumeForPlane();
+ else if (this.data == null) this.setVolumeDataParams();
+ else this.setVolumeData();
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+}, "~S");
+Clazz.overrideMethod(c$, "setVolumeData",
+function(){
+if (this.data == null) {
+this.setVolumeDataADR();
+return;
+}this.volumetricOrigin.setT(this.params.functionInfo.get(1));
+for (var i = 0; i < 3; i++) {
+var info = this.params.functionInfo.get(i + 2);
+this.voxelCounts[i] = Math.abs(Clazz.floatToInt(info.x));
+this.volumetricVectors[i].set(info.y, info.z, info.w);
+}
+if (this.isAnisotropic) this.setVolumetricAnisotropy();
+});
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+if (this.volumeData.sr != null) return;
+this.readSurfaceDataVDR(isMapData);
+}, "~B");
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+var plane = this.getPlaneSR(x);
+this.setPlane(x, plane);
+return plane;
+}, "~N");
+Clazz.defineMethod(c$, "setPlane",
+function(x, plane){
+for (var y = 0, ptyz = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) plane[ptyz++] = this.getValue(x, y, z, 0);
+
+
+}, "~N,~A");
+Clazz.overrideMethod(c$, "getValue",
+function(x, y, z, pxyz){
+var value;
+if (this.data == null) {
+value = this.evaluateValue(x, y, z);
+} else {
+this.volumeData.voxelPtToXYZ(x, y, z, this.ptTemp);
+value = this.data[x][y];
+}return (this.isPlanarMapping ? value : value - this.ptTemp.z);
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+if (this.params.func == null) return 0;
+this.values[0] = pt.x;
+this.values[1] = pt.y;
+this.values[2] = pt.z;
+return this.sg.atomDataServer.evalFunctionFloat(this.func[0], this.func[1], this.values);
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "evaluateValue",
+function(x, y, z){
+this.volumeData.voxelPtToXYZ(x, y, z, this.ptTemp);
+return this.getValueAtPoint(this.ptTemp, false);
+}, "~N,~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyzReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyzReader.js
new file mode 100755
index 000000000000..2ea3123f1920
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoFxyzReader.js
@@ -0,0 +1,20 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.IsoFxyReader"], "J.jvxl.readers.IsoFxyzReader", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.$data = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoFxyzReader", J.jvxl.readers.IsoFxyReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoFxyzReader, []);
+});
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+if (this.params.functionInfo.size() > 5) this.$data = this.params.functionInfo.get(5);
+this.setupType("functionXYZ");
+}, "~B");
+Clazz.overrideMethod(c$, "getValue",
+function(x, y, z, xyz){
+return (this.$data == null ? this.evaluateValue(x, y, z) : this.$data[x][y][z]);
+}, "~N,~N,~N,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectAtomReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectAtomReader.js
new file mode 100755
index 000000000000..9926c80237e4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectAtomReader.js
@@ -0,0 +1,136 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader", "JU.BS"], "J.jvxl.readers.IsoIntersectAtomReader", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.myBsA = null;
+this.myBsB = null;
+this.bsAtomMinMax = null;
+this.func = null;
+this.funcType = 0;
+this.thisPlaneB = null;
+this.values = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoIntersectAtomReader", J.jvxl.readers.AtomDataReader);
+Clazz.prepareFields (c$, function(){
+this.myBsA = new JU.BS();
+this.myBsB = new JU.BS();
+this.bsAtomMinMax = new Array(2);
+this.values = Clazz.newFloatArray (2, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoIntersectAtomReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.setup(isMapData);
+if (isMapData) return false;
+this.initializeVolumetricData();
+this.volumeData.setUnitVectors();
+this.thisPlaneB = Clazz.newFloatArray (this.volumeData.getYzCount(), 0);
+this.voxelSource = Clazz.newIntArray (this.volumeData.nPoints, 0);
+this.vl0 = this.volumeData.volumetricVectorLengths[0];
+this.vl1 = this.volumeData.volumetricVectorLengths[1];
+this.vl2 = this.volumeData.volumetricVectorLengths[2];
+this.getAtomMinMax(this.myBsA, this.bsAtomMinMax[0] = new Array(this.nPointsX));
+this.getAtomMinMax(this.myBsB, this.bsAtomMinMax[1] = new Array(this.nPointsX));
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+this.params.fullyLit = true;
+this.point = this.params.point;
+if ((typeof(this.params.func)=='string')) {
+this.funcType = (this.params.func.equals("a-b") ? 2 : this.params.func.equals("a+b") ? 1 : 3);
+} else if (this.params.func == null || this.sg.atomDataServer == null) {
+this.funcType = 2;
+} else {
+this.func = this.params.func;
+}if (this.contactPair == null) {
+var bsA = this.params.intersection[0];
+var bsB = this.params.intersection[1];
+var bsSelected = new JU.BS();
+bsSelected.or(bsA);
+bsSelected.or(bsB);
+this.doUseIterator = true;
+this.getAtoms(bsSelected, this.doAddHydrogens, true, true, false, false, false, NaN, null);
+for (var i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) this.myBsA.set(this.myIndex[i]);
+
+for (var i = bsB.nextSetBit(0); i >= 0; i = bsB.nextSetBit(i + 1)) this.myBsB.set(this.myIndex[i]);
+
+this.setHeader("VDW intersection surface", this.params.calculationType);
+this.setRanges(this.params.solvent_ptsPerAngstrom, this.params.solvent_gridMax, 0);
+this.margin = 5;
+} else {
+this.setVolumeData();
+}this.isProgressive = this.isXLowToHigh = true;
+}, "~B");
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+if (this.yzCount == 0) {
+this.initPlanes();
+}this.thisX = x;
+this.thisPlane = this.yzPlanes[x % 2];
+if (this.contactPair == null) {
+this.thisAtomSet = this.bsAtomMinMax[0][x];
+this.resetPlane(3.4028235E38);
+this.markSphereVoxels(0, this.params.distance);
+this.thisPlane = this.thisPlaneB;
+this.thisAtomSet = this.bsAtomMinMax[1][x];
+this.resetPlane(3.4028235E38);
+this.markSphereVoxels(0, this.params.distance);
+} else {
+this.markPlaneVoxels(this.contactPair.myAtoms[0], this.contactPair.radii[0]);
+this.thisPlane = this.thisPlaneB;
+this.markPlaneVoxels(this.contactPair.myAtoms[1], this.contactPair.radii[1]);
+}this.thisPlane = this.yzPlanes[x % 2];
+if (!this.setVoxels()) this.resetPlane(0);
+if (this.contactPair == null) this.unsetVoxelData();
+return this.thisPlane;
+}, "~N");
+Clazz.defineMethod(c$, "setVoxels",
+function(){
+for (var i = 0; i < this.yzCount; i++) {
+var va = this.thisPlane[i];
+var vb = this.thisPlaneB[i];
+var v = this.getValueAB(va, vb);
+if (Float.isNaN(v)) return false;
+this.thisPlane[i] = v;
+}
+return true;
+});
+Clazz.defineMethod(c$, "getValueAB",
+function(va, vb){
+if (va == 3.4028235E38 || vb == 3.4028235E38 || Float.isNaN(va) || Float.isNaN(vb)) return 3.4028235E38;
+switch (this.funcType) {
+case 1:
+return (va + vb);
+case 2:
+case 4:
+return (va - vb);
+case 3:
+return (va > vb ? va : vb);
+default:
+this.values[0] = va;
+this.values[1] = vb;
+return this.sg.atomDataServer.evalFunctionFloat(this.func[0], this.func[1], this.values);
+}
+}, "~N,~N");
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+return this.getValueAB(this.getValueAtPoint2(pt, this.myBsA), this.getValueAtPoint2(pt, this.myBsB));
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "getValueAtPoint2",
+function(pt, bs){
+var value = 3.4028235E38;
+for (var iAtom = bs.nextSetBit(0); iAtom >= 0; iAtom = bs.nextSetBit(iAtom + 1)) {
+var r = pt.distance(this.atomXyzTruncated[iAtom]) - this.atomRadius[iAtom];
+if (r < value) value = r;
+}
+return (value == 3.4028235E38 ? NaN : value);
+}, "JU.T3,JU.BS");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectGridReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectGridReader.js
new file mode 100755
index 000000000000..8d6cbc8bcbe9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectGridReader.js
@@ -0,0 +1,41 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.IsoIntersectGridReader", ["JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.readers = null;
+this.factors = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoIntersectGridReader", J.jvxl.readers.VolumeFileReader);
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initSR(sg);
+var data = sg.getReaderData();
+this.readers = data[0];
+this.factors = data[1];
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "readVolumeParameters",
+function(isMapData){
+for (var i = this.readers.length; --i >= 0; ) if (!this.readers[i].readVolumeParameters(isMapData)) return false;
+
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "getNextVoxelValue",
+function(){
+var f = 0;
+for (var i = this.readers.length; --i >= 0; ) f += this.factors[i] * this.readers[i].getNextVoxelValue();
+
+return f;
+});
+Clazz.overrideMethod(c$, "closeReader",
+function(){
+if (this.readerClosed) return;
+this.readerClosed = true;
+for (var i = this.readers.length; --i >= 0; ) this.readers[i].closeReaderSFR();
+
+if (this.nData == 0 || this.dataMax == -3.4028235E38) return;
+this.dataMean /= this.nData;
+JU.Logger.info("IsoIntersectFileReader closing file: " + this.nData + " points read \ndata min/max/mean = " + this.dataMin + "/" + this.dataMax + "/" + this.dataMean);
+});
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectReader.js
new file mode 100755
index 000000000000..ccbfc6ab0ef4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoIntersectReader.js
@@ -0,0 +1,136 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader", "JU.BS"], "J.jvxl.readers.IsoIntersectReader", null, function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.myBsA = null;
+this.myBsB = null;
+this.bsAtomMinMax = null;
+this.func = null;
+this.funcType = 0;
+this.thisPlaneB = null;
+this.values = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoIntersectReader", J.jvxl.readers.AtomDataReader);
+Clazz.prepareFields (c$, function(){
+this.myBsA = new JU.BS();
+this.myBsB = new JU.BS();
+this.bsAtomMinMax = new Array(2);
+this.values = Clazz.newFloatArray (2, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoIntersectReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.setup(isMapData);
+if (isMapData) return false;
+this.initializeVolumetricData();
+this.volumeData.setUnitVectors();
+this.thisPlaneB = Clazz.newFloatArray (this.volumeData.getYzCount(), 0);
+this.voxelSource = Clazz.newIntArray (this.volumeData.nPoints, 0);
+this.vl0 = this.volumeData.volumetricVectorLengths[0];
+this.vl1 = this.volumeData.volumetricVectorLengths[1];
+this.vl2 = this.volumeData.volumetricVectorLengths[2];
+this.getAtomMinMax(this.myBsA, this.bsAtomMinMax[0] = new Array(this.nPointsX));
+this.getAtomMinMax(this.myBsB, this.bsAtomMinMax[1] = new Array(this.nPointsX));
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+this.params.fullyLit = true;
+this.point = this.params.point;
+if ((typeof(this.params.func)=='string')) {
+this.funcType = (this.params.func.equals("a-b") ? 2 : this.params.func.equals("a+b") ? 1 : 3);
+} else if (this.params.func == null || this.sg.atomDataServer == null) {
+this.funcType = 2;
+} else {
+this.func = this.params.func;
+}if (this.contactPair == null) {
+var bsA = this.params.intersection[0];
+var bsB = this.params.intersection[1];
+var bsSelected = new JU.BS();
+bsSelected.or(bsA);
+bsSelected.or(bsB);
+this.doUseIterator = true;
+this.getAtoms(bsSelected, this.doAddHydrogens, true, true, false, false, false, NaN, null);
+for (var i = bsA.nextSetBit(0); i >= 0; i = bsA.nextSetBit(i + 1)) this.myBsA.set(this.myIndex[i]);
+
+for (var i = bsB.nextSetBit(0); i >= 0; i = bsB.nextSetBit(i + 1)) this.myBsB.set(this.myIndex[i]);
+
+this.setHeader("VDW intersection surface", this.params.calculationType);
+this.setRanges(this.params.solvent_ptsPerAngstrom, this.params.solvent_gridMax, 0);
+this.margin = 5;
+} else {
+this.setVolumeData();
+}this.isProgressive = this.isXLowToHigh = true;
+}, "~B");
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+if (this.yzCount == 0) {
+this.initPlanes();
+}this.thisX = x;
+this.thisPlane = this.yzPlanes[x % 2];
+if (this.contactPair == null) {
+this.thisAtomSet = this.bsAtomMinMax[0][x];
+this.resetPlane(3.4028235E38);
+this.markSphereVoxels(0, this.params.distance);
+this.thisPlane = this.thisPlaneB;
+this.thisAtomSet = this.bsAtomMinMax[1][x];
+this.resetPlane(3.4028235E38);
+this.markSphereVoxels(0, this.params.distance);
+} else {
+this.markPlaneVoxels(this.contactPair.myAtoms[0], this.contactPair.radii[0]);
+this.thisPlane = this.thisPlaneB;
+this.markPlaneVoxels(this.contactPair.myAtoms[1], this.contactPair.radii[1]);
+}this.thisPlane = this.yzPlanes[x % 2];
+if (!this.setVoxels()) this.resetPlane(0);
+if (this.contactPair == null) this.unsetVoxelData();
+return this.thisPlane;
+}, "~N");
+Clazz.defineMethod(c$, "setVoxels",
+function(){
+for (var i = 0; i < this.yzCount; i++) {
+var va = this.thisPlane[i];
+var vb = this.thisPlaneB[i];
+var v = this.getValueAB(va, vb);
+if (Float.isNaN(v)) return false;
+this.thisPlane[i] = v;
+}
+return true;
+});
+Clazz.defineMethod(c$, "getValueAB",
+function(va, vb){
+if (va == 3.4028235E38 || vb == 3.4028235E38 || Float.isNaN(va) || Float.isNaN(vb)) return 3.4028235E38;
+switch (this.funcType) {
+case 1:
+return (va + vb);
+case 2:
+case 4:
+return (va - vb);
+case 3:
+return (va > vb ? va : vb);
+default:
+this.values[0] = va;
+this.values[1] = vb;
+return this.sg.atomDataServer.evalFunctionFloat(this.func[0], this.func[1], this.values);
+}
+}, "~N,~N");
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+return this.getValueAB(this.getValueAtPoint2(pt, this.myBsA), this.getValueAtPoint2(pt, this.myBsB));
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "getValueAtPoint2",
+function(pt, bs){
+var value = 3.4028235E38;
+for (var iAtom = bs.nextSetBit(0); iAtom >= 0; iAtom = bs.nextSetBit(iAtom + 1)) {
+var r = pt.distance(this.atomXyzTruncated[iAtom]) - this.atomRadius[iAtom];
+if (r < value) value = r;
+}
+return (value == 3.4028235E38 ? NaN : value);
+}, "JU.T3,JU.BS");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMOReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMOReader.js
new file mode 100755
index 000000000000..44483970e71d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMOReader.js
@@ -0,0 +1,248 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.IsoMOReader", ["java.util.Random", "JU.AU", "$.Measure", "$.P3", "$.PT", "$.V3", "J.api.Interface", "J.quantum.QS", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.random = null;
+this.points = null;
+this.vTemp = null;
+this.q = null;
+this.mos = null;
+this.isNci = false;
+this.coef = null;
+this.dfCoefMaps = null;
+this.linearCombination = null;
+this.coefs = null;
+this.isElectronDensityCalc = false;
+this.mo = null;
+this.vDist = null;
+this.qSetupDone = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoMOReader", J.jvxl.readers.AtomDataReader);
+Clazz.prepareFields (c$, function(){
+this.vDist = Clazz.newFloatArray (3, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoMOReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+this.isNci = (this.params.qmOrbitalType == 3);
+if (this.isNci) {
+this.isXLowToHigh = this.hasColorData = true;
+this.precalculateVoxelData = false;
+this.params.insideOut = !this.params.insideOut;
+}}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.mos = this.params.moData.get("mos");
+this.linearCombination = this.params.qm_moLinearCombination;
+this.mo = (this.mos != null && this.linearCombination == null ? this.mos.get(this.params.qm_moNumber - 1) : null);
+var haveVolumeData = this.params.moData.containsKey("haveVolumeData");
+if (haveVolumeData && this.mo != null) this.params.volumeData = this.mo.get("volumeData");
+this.setup2();
+this.doAddHydrogens = false;
+this.getAtoms(this.params.bsSelected, this.doAddHydrogens, !this.isNci, this.isNci, this.isNci, false, false, this.params.qm_marginAngstroms, (this.isNci ? null : this.params.modelInvRotation));
+var className;
+if (this.isNci) {
+className = "quantum.NciCalculation";
+this.setHeader("NCI (promolecular)", "see NCIPLOT: A Program for Plotting Noncovalent Interaction Regions, Julia Contreras-Garcia, et al., J. of Chemical Theory and Computation, 2011, 7, 625-632");
+} else {
+className = "quantum.MOCalculation";
+this.setHeader("MO", "calculation type: " + this.params.moData.get("calculationType"));
+}this.setRanges(this.params.qm_ptsPerAngstrom, this.params.qm_gridMax, 0);
+if (haveVolumeData) {
+for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, this.mo);
+
+} else {
+this.q = J.api.Interface.getOption(className, this.sg.atomDataServer, "file");
+if (this.isNci) {
+this.qpc = this.q;
+} else {
+if (this.linearCombination == null) {
+for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, this.mo);
+
+this.coef = this.mo.get("coefficients");
+this.dfCoefMaps = this.mo.get("dfCoefMaps");
+} else {
+this.coefs = JU.AU.newFloat2(this.mos.size());
+for (var i = 1; i < this.linearCombination.length; i += 2) {
+var j = Clazz.floatToInt(this.linearCombination[i]);
+if (j > this.mos.size() || j < 1) return;
+this.coefs[j - 1] = this.mos.get(j - 1).get("coefficients");
+}
+for (var i = this.params.title.length; --i >= 0; ) this.fixTitleLine(i, null);
+
+}}this.isElectronDensityCalc = (this.coef == null && this.linearCombination == null && !this.isNci);
+}this.volumeData.sr = null;
+if (isMapData && !this.isElectronDensityCalc && !haveVolumeData) {
+this.volumeData.doIterate = false;
+this.volumeData.setVoxelDataAsArray(this.voxelData = Clazz.newFloatArray (1, 1, 1, 0));
+this.volumeData.sr = this;
+this.points = new Array(1);
+this.points[0] = new JU.P3();
+if (!this.setupCalculation()) this.q = null;
+} else if (this.params.psi_monteCarloCount > 0) {
+this.vertexDataOnly = true;
+this.random = new java.util.Random(this.params.randomSeed);
+}}, "~B");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.setup(isMapData);
+if (this.volumeData.sr == null) this.initializeVolumetricData();
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "fixTitleLine",
+function(iLine, mo){
+if (this.params.title == null) return;
+var line = this.params.title[iLine];
+if (line.indexOf(" MO ") >= 0) {
+var nboType = this.params.moData.get("nboType");
+if (nboType != null) line = JU.PT.rep(line, " MO ", " " + nboType + " ");
+}if (line.indexOf("%M") >= 0) line = this.params.title[iLine] = JU.PT.formatStringS(line, "M", this.atomData.modelName);
+if (line.indexOf("%F") >= 0) line = this.params.title[iLine] = JU.PT.formatStringS(line, "F", JU.PT.rep(this.params.fileName, "DROP_", ""));
+var pt = line.indexOf("%");
+if (line.length == 0 || pt < 0) return;
+var rep = 0;
+if (line.indexOf("%I") >= 0) line = JU.PT.formatStringS(line, "I", this.params.qm_moLinearCombination == null ? "" + this.params.qm_moNumber : J.quantum.QS.getMOString(this.params.qm_moLinearCombination));
+if (line.indexOf("%N") >= 0) line = JU.PT.formatStringS(line, "N", "" + this.params.qmOrbitalCount);
+var energy = null;
+if (mo == null) {
+for (var i = 0; i < this.linearCombination.length; i += 2) if (this.linearCombination[i] != 0) {
+mo = this.mos.get(Clazz.floatToInt(this.linearCombination[i + 1]) - 1);
+var e = mo.get("energy");
+if (energy == null) {
+if (e == null) break;
+energy = e;
+} else if (!energy.equals(e)) {
+energy = null;
+break;
+}}
+} else {
+if (mo.containsKey("energy")) energy = mo.get("energy");
+}if (line.indexOf("%E") >= 0) {
+line = JU.PT.formatStringS(line, "E", energy != null && ++rep != 0 ? "" + energy : "");
+} else if (energy != null) {
+var s = JU.PT.formatStringF(line, "E", energy.floatValue());
+if (s !== line) {
+line = s;
+rep++;
+}}if (line.indexOf("%U") >= 0) line = JU.PT.formatStringS(line, "U", energy != null && this.params.moData.containsKey("energyUnits") && ++rep != 0 ? this.params.moData.get("energyUnits") : "");
+if (line.indexOf("%S") >= 0) line = JU.PT.formatStringS(line, "S", mo != null && mo.containsKey("symmetry") && ++rep != 0 ? "" + mo.get("symmetry") : "");
+if (line.indexOf("%O") >= 0) {
+var obj = (mo == null ? null : mo.get("occupancy"));
+var o = (obj == null ? 0 : obj.floatValue());
+line = JU.PT.formatStringS(line, "O", obj != null && this.params.qm_moLinearCombination == null && ++rep != 0 ? (o == Clazz.floatToInt(o) ? "" + Clazz.floatToInt(o) : JU.PT.formatF(o, 0, 4, false, false)) : "");
+}if (line.indexOf("%T") >= 0) line = JU.PT.formatStringS(line, "T", mo != null && mo.containsKey("type") ? (this.params.qm_moLinearCombination == null && ++rep != 0 ? "" + mo.get("type") : "") + ((this.params.isSquared || this.params.isSquaredLinear) && ++rep != 0 ? " ^2" : "") : "");
+if (line.equals("string")) {
+this.params.title[iLine] = "";
+return;
+}var isOptional = (line.indexOf("?") == 0);
+this.params.title[iLine] = (!isOptional ? line : rep > 0 && !line.trim().endsWith("=") ? line.substring(1) : "");
+}, "~N,java.util.Map");
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+if (this.volumeData.sr != null) return;
+if (this.params.psi_monteCarloCount <= 0) {
+this.readSurfaceDataVDR(isMapData);
+return;
+}if (this.points != null) return;
+this.points = new Array(1000);
+for (var j = 0; j < 1000; j++) this.points[j] = new JU.P3();
+
+if (this.params.thePlane != null) this.vTemp = new JU.V3();
+for (var i = 0; i < 3; i++) this.vDist[i] = this.volumeData.volumetricVectorLengths[i] * this.volumeData.voxelCounts[i];
+
+this.volumeData.setVoxelDataAsArray(this.voxelData = Clazz.newFloatArray (1000, 1, 1, 0));
+this.getValues();
+var value;
+var f = 0;
+for (var j = 0; j < 1000; j++) if ((value = Math.abs(this.voxelData[j][0][0])) > f) f = value;
+
+if (f < 0.0001) return;
+for (var i = 0; i < this.params.psi_monteCarloCount; ) {
+this.getValues();
+for (var j = 0; j < 1000; j++) {
+value = this.voxelData[j][0][0];
+var absValue = Math.abs(value);
+if (absValue <= this.getRnd(f)) continue;
+this.addVC(this.points[j], value, 0, false);
+if (++i == this.params.psi_monteCarloCount) break;
+}
+}
+}, "~B");
+Clazz.overrideMethod(c$, "postProcessVertices",
+function(){
+});
+Clazz.defineMethod(c$, "getValues",
+function(){
+for (var j = 0; j < 1000; j++) {
+this.voxelData[j][0][0] = 0;
+this.points[j].set(this.volumeData.volumetricOrigin.x + this.getRnd(this.vDist[0]), this.volumeData.volumetricOrigin.y + this.getRnd(this.vDist[1]), this.volumeData.volumetricOrigin.z + this.getRnd(this.vDist[2]));
+if (this.params.thePlane != null) JU.Measure.getPlaneProjection(this.points[j], this.params.thePlane, this.points[j], this.vTemp);
+}
+this.createOrbital();
+});
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+return (this.q == null ? 0 : this.q.processPt(pt));
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "getRnd",
+function(f){
+return this.random.nextFloat() * f;
+}, "~N");
+Clazz.overrideMethod(c$, "generateCube",
+function(){
+if (this.params.volumeData != null) return;
+this.newVoxelDataCube();
+this.createOrbital();
+});
+Clazz.defineMethod(c$, "createOrbital",
+function(){
+var isMonteCarlo = (this.params.psi_monteCarloCount > 0);
+if (this.isElectronDensityCalc) {
+if (this.mos == null || isMonteCarlo) return;
+System.out.println("createOrbital " + this.params.qm_moNumber);
+for (var i = this.params.qm_moNumber; --i >= 0; ) {
+JU.Logger.info(" generating isosurface data for MO " + (i + 1));
+var mo = this.mos.get(i);
+this.coef = mo.get("coefficients");
+this.dfCoefMaps = mo.get("dfCoefMaps");
+if (!this.setupCalculation()) return;
+this.q.createCube();
+}
+} else {
+if (!isMonteCarlo) JU.Logger.info("generating isosurface data for MO using cutoff " + this.params.cutoff);
+if (!this.setupCalculation()) return;
+this.q.createCube();
+this.jvxlData.integration = this.q.getIntegration();
+if (this.mo != null) this.mo.put("integration", Float.$valueOf(this.jvxlData.integration));
+}});
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+if (!this.qSetupDone) this.setupCalculation();
+return this.getPlaneSR(x);
+}, "~N");
+Clazz.defineMethod(c$, "setupCalculation",
+function(){
+this.qSetupDone = true;
+switch (this.params.qmOrbitalType) {
+case 5:
+break;
+case 2:
+case 1:
+return (this.q).setupCalculation(this.params.moData, this.params.qmOrbitalType == 2, this.volumeData, this.bsMySelected, this.atomData.xyz, this.atomData.atoms, this.atomData.firstAtomIndex, this.dfCoefMaps, this.coef, this.linearCombination, this.params.isSquaredLinear, this.coefs, this.points);
+case 3:
+return (this.q).setupCalculation(this.volumeData, this.bsMySelected, this.params.bsSolvent, this.atomData.bsMolecules, this.atomData.atoms, this.atomData.firstAtomIndex, true, this.points, this.params.parameters, this.params.testFlags);
+}
+return false;
+});
+Clazz.overrideMethod(c$, "getSurfacePointAndFraction",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+var zero = this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+if (this.q != null && !Float.isNaN(zero)) {
+zero = this.q.processPt(ptReturn);
+if (this.params.isSquared) zero *= zero;
+}return zero;
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMepReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMepReader.js
new file mode 100755
index 000000000000..4a252e7ca47f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMepReader.js
@@ -0,0 +1,34 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.IsoMepReader", ["J.api.Interface"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.type = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoMepReader", J.jvxl.readers.AtomDataReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoMepReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initIMR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "initIMR",
+function(sg){
+this.initADR(sg);
+this.type = "Mep";
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+this.doAddHydrogens = false;
+this.getAtoms(this.params.bsSelected, this.doAddHydrogens, true, false, false, false, false, this.params.mep_marginAngstroms, null);
+this.setHeader("MEP", "");
+this.setRanges(this.params.mep_ptsPerAngstrom, this.params.mep_gridMax, 0);
+}, "~B");
+Clazz.overrideMethod(c$, "generateCube",
+function(){
+this.newVoxelDataCube();
+var m = J.api.Interface.getOption("quantum." + this.type + "Calculation", this.sg.atomDataServer, "file");
+m.calculate(this.volumeData, this.bsMySelected, this.atomData.xyz, this.atomData.atoms, this.params.theProperty, this.params.mep_calcType);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMlpReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMlpReader.js
new file mode 100755
index 000000000000..7dea26bb4df0
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoMlpReader.js
@@ -0,0 +1,14 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.IsoMepReader"], "J.jvxl.readers.IsoMlpReader", null, function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "IsoMlpReader", J.jvxl.readers.IsoMepReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoMlpReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initIMR(sg);
+this.type = "Mlp";
+}, "J.jvxl.readers.SurfaceGenerator");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoPlaneReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoPlaneReader.js
new file mode 100755
index 000000000000..2634aecb144d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoPlaneReader.js
@@ -0,0 +1,21 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.AtomDataReader"], "J.jvxl.readers.IsoPlaneReader", null, function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "IsoPlaneReader", J.jvxl.readers.AtomDataReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoPlaneReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+this.precalculateVoxelData = false;
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+this.setHeader("PLANE", this.params.thePlane.toString());
+this.params.cutoff = 0;
+this.setVolumeForPlane();
+}, "~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoShapeReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoShapeReader.js
new file mode 100755
index 000000000000..f1472bb32e3c
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoShapeReader.js
@@ -0,0 +1,375 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeDataReader", "JU.P3"], "J.jvxl.readers.IsoShapeReader", ["java.util.Random", "JU.Measure", "$.SB", "$.V3", "J.jvxl.data.JvxlCoder", "JU.Logger", "$.MeshSurface"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.psi_n = 2;
+this.psi_l = 1;
+this.psi_m = 1;
+this.psi_Znuc = 1;
+this.sphere_radiusAngstroms = 0;
+this.monteCarloCount = 0;
+this.random = null;
+this.allowNegative = true;
+this.rfactor = null;
+this.pfactor = null;
+this.radius = 0;
+this.ptPsi = null;
+this.psi_normalization = 0;
+this.aoMax = 0;
+this.aoMax2 = 0;
+this.angMax2 = 0;
+this.planeU = null;
+this.planeV = null;
+this.planeCenter = null;
+this.planeRadius = 0;
+this.rnl = 0;
+this.surfaceDone = false;
+this.nTries = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoShapeReader", J.jvxl.readers.VolumeDataReader);
+Clazz.prepareFields (c$, function(){
+this.rfactor = Clazz.newDoubleArray (10, 0);
+this.pfactor = Clazz.newDoubleArray (10, 0);
+this.ptPsi = new JU.P3();
+this.psi_normalization = 1 / (2 * Math.sqrt(3.141592653589793));
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoShapeReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initVDR(sg);
+var o = sg.getReaderData();
+if (Clazz.instanceOf(o, Float)) {
+this.sphere_radiusAngstroms = (o).floatValue();
+} else {
+this.sphere_radiusAngstroms = 0;
+var data = o;
+this.psi_n = Clazz.floatToInt(data[0]);
+this.psi_l = Clazz.floatToInt(data[1]);
+this.psi_m = Clazz.floatToInt(data[2]);
+this.psi_Znuc = data[3];
+this.monteCarloCount = Clazz.floatToInt(data[4]);
+}}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.volumeData.sr = this;
+this.precalculateVoxelData = false;
+this.isQuiet = true;
+if (Float.isNaN(this.center.x)) this.center.set(0, 0, 0);
+var type = "sphere";
+switch (this.dataType) {
+case 1294:
+this.calcFactors(this.psi_n, this.psi_l, this.psi_m);
+this.autoScaleOrbital();
+this.ptsPerAngstrom = 5;
+this.maxGrid = 40;
+type = "hydrogen-like orbital";
+if (this.monteCarloCount > 0) {
+this.vertexDataOnly = true;
+this.random = new java.util.Random(this.params.randomSeed);
+} else {
+this.isQuiet = false;
+}break;
+case 70:
+case 71:
+type = "lp";
+this.vertexDataOnly = true;
+this.radius = 0;
+this.ptsPerAngstrom = 1;
+this.maxGrid = 1;
+break;
+case 68:
+this.allowNegative = false;
+this.calcFactors(this.psi_n, this.psi_l, this.psi_m);
+this.psi_normalization = 1;
+this.radius = 1.1 * this.eccentricityRatio * this.eccentricityScale;
+if (this.eccentricityScale > 0 && this.eccentricityScale < 1) this.radius /= this.eccentricityScale;
+this.ptsPerAngstrom = 10;
+this.maxGrid = 21;
+type = "lobe";
+break;
+case 67:
+type = "ellipsoid(thermal)";
+this.radius = 3.0 * this.sphere_radiusAngstroms;
+this.ptsPerAngstrom = 10;
+this.maxGrid = 22;
+break;
+case 74:
+if (!isMapData && this.monteCarloCount == 0) break;
+type = "geodesic";
+case 66:
+if (type.equals("sphere")) type = "ellipsoid";
+case 65:
+default:
+this.radius = 1.2 * this.sphere_radiusAngstroms * this.eccentricityScale;
+this.ptsPerAngstrom = 10;
+this.maxGrid = 22;
+break;
+}
+if (this.monteCarloCount == 0) this.setVolumeData();
+this.setHeader(type + "\n");
+}, "~B");
+Clazz.overrideMethod(c$, "setVolumeData",
+function(){
+this.setVoxelRange(0, -this.radius, this.radius, this.ptsPerAngstrom, this.maxGrid, 0);
+this.setVoxelRange(1, -this.radius, this.radius, this.ptsPerAngstrom, this.maxGrid, 0);
+if (this.allowNegative) this.setVoxelRange(2, -this.radius, this.radius, this.ptsPerAngstrom, this.maxGrid, 0);
+ else this.setVoxelRange(2, 0, this.radius / this.eccentricityRatio, this.ptsPerAngstrom, this.maxGrid, 0);
+});
+Clazz.overrideMethod(c$, "getValue",
+function(x, y, z, ptyz){
+this.volumeData.voxelPtToXYZ(x, y, z, this.ptPsi);
+return this.getValueAtPoint(this.ptPsi, false);
+}, "~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+this.ptTemp.sub2(pt, this.center);
+if (this.isEccentric) this.eccentricityMatrixInverse.rotate(this.ptTemp);
+if (this.isAnisotropic) {
+this.ptTemp.x /= this.anisotropy[0];
+this.ptTemp.y /= this.anisotropy[1];
+this.ptTemp.z /= this.anisotropy[2];
+}if (this.sphere_radiusAngstroms > 0) {
+if (this.params.anisoB != null) {
+return this.sphere_radiusAngstroms - Math.sqrt(this.ptTemp.x * this.ptTemp.x + this.ptTemp.y * this.ptTemp.y + this.ptTemp.z * this.ptTemp.z) / (Math.sqrt(this.params.anisoB[0] * this.ptTemp.x * this.ptTemp.x + this.params.anisoB[1] * this.ptTemp.y * this.ptTemp.y + this.params.anisoB[2] * this.ptTemp.z * this.ptTemp.z + this.params.anisoB[3] * this.ptTemp.x * this.ptTemp.y + this.params.anisoB[4] * this.ptTemp.x * this.ptTemp.z + this.params.anisoB[5] * this.ptTemp.y * this.ptTemp.z));
+}return this.sphere_radiusAngstroms - Math.sqrt(this.ptTemp.x * this.ptTemp.x + this.ptTemp.y * this.ptTemp.y + this.ptTemp.z * this.ptTemp.z);
+}var value = this.hydrogenAtomPsi(this.ptTemp);
+if (Math.abs(value) < 1.0E-7) value = 0;
+return (this.allowNegative || value >= 0 ? value : 0);
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "setHeader",
+function(line1){
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append(line1);
+if (this.sphere_radiusAngstroms > 0) {
+this.jvxlFileHeaderBuffer.append(" rad=").appendF(this.sphere_radiusAngstroms);
+} else {
+this.jvxlFileHeaderBuffer.append(" n=").appendI(this.psi_n).append(", l=").appendI(this.psi_l).append(", m=").appendI(this.psi_m).append(" Znuc=").appendF(this.psi_Znuc).append(" res=").appendF(this.ptsPerAngstrom).append(" rad=").appendF(this.radius);
+}this.jvxlFileHeaderBuffer.append(this.isAnisotropic ? " anisotropy=(" + this.anisotropy[0] + "," + this.anisotropy[1] + "," + this.anisotropy[2] + ")\n" : "\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+}, "~S");
+Clazz.defineMethod(c$, "calcFactors",
+function(n, el, m){
+var abm = Math.abs(m);
+var NnlLnl = Math.pow(2 * this.psi_Znuc / n / 0.52918, 1.5) * Math.sqrt(J.jvxl.readers.IsoShapeReader.fact[n - el - 1] * J.jvxl.readers.IsoShapeReader.fact[n + el] / 2 / n);
+var Plm = Math.pow(2, -el) * J.jvxl.readers.IsoShapeReader.fact[el] * J.jvxl.readers.IsoShapeReader.fact[el + abm] * Math.sqrt((2 * el + 1) * J.jvxl.readers.IsoShapeReader.fact[el - abm] / 2 / J.jvxl.readers.IsoShapeReader.fact[el + abm]);
+for (var p = 0; p <= n - el - 1; p++) this.rfactor[p] = NnlLnl / J.jvxl.readers.IsoShapeReader.fact[p] / J.jvxl.readers.IsoShapeReader.fact[n - el - p - 1] / J.jvxl.readers.IsoShapeReader.fact[2 * el + p + 1];
+
+for (var p = abm; p <= el; p++) this.pfactor[p] = Math.pow(-1, el - p) * Plm / J.jvxl.readers.IsoShapeReader.fact[p] / J.jvxl.readers.IsoShapeReader.fact[el + abm - p] / J.jvxl.readers.IsoShapeReader.fact[el - p] / J.jvxl.readers.IsoShapeReader.fact[p - abm];
+
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "autoScaleOrbital",
+function(){
+this.aoMax = 0;
+var rmax = 0;
+this.aoMax2 = 0;
+var rmax2 = 0;
+var d;
+if (this.params.distance == 0) {
+for (var ir = 0; ir < 1000; ir++) {
+var r = ir / 10;
+d = Math.abs(this.radialPart(r));
+if (JU.Logger.debugging) JU.Logger.debug("R\t" + r + "\t" + d);
+if (d >= this.aoMax) {
+rmax = r;
+this.aoMax = d;
+}d *= d * r * r;
+if (d >= this.aoMax2) {
+rmax2 = r;
+this.aoMax2 = d;
+}}
+} else {
+this.aoMax = Math.abs(this.radialPart(this.params.distance));
+this.aoMax2 = this.aoMax * this.aoMax * this.params.distance * this.params.distance;
+rmax = rmax2 = this.params.distance;
+}JU.Logger.info("Atomic Orbital radial max = " + this.aoMax + " at " + rmax);
+JU.Logger.info("Atomic Orbital r2R2 max = " + this.aoMax2 + " at " + rmax2);
+if (this.monteCarloCount >= 0) {
+this.angMax2 = 0;
+for (var ang = 0; ang < 180; ang += 1) {
+var th = ang / (6.283185307179586);
+d = Math.abs(this.angularPart(th, 0, 0));
+if (JU.Logger.debugging) JU.Logger.debug("A\t" + ang + "\t" + d);
+if (d > this.angMax2) {
+this.angMax2 = d;
+}}
+this.angMax2 *= this.angMax2;
+if (this.psi_m != 0) {
+this.angMax2 *= 2;
+}JU.Logger.info("Atomic Orbital phi^2theta^2 max = " + this.angMax2);
+}var min;
+if (this.params.cutoff == 0) {
+min = (this.monteCarloCount > 0 ? this.aoMax * 0.01 : 0.01);
+} else if (this.monteCarloCount > 0) {
+this.aoMax = Math.abs(this.params.cutoff);
+min = this.aoMax * 0.01;
+} else {
+min = Math.abs(this.params.cutoff / 2);
+if (this.params.isSquared) min = Math.sqrt(min / 2);
+}var r0 = 0;
+for (var ir = 1000; --ir >= 0; ir -= 1) {
+var r = ir / 10;
+d = Math.abs(this.radialPart(r));
+if (d >= min) {
+r0 = r;
+break;
+}}
+this.radius = r0 + (this.monteCarloCount == 0 ? 1 : 0);
+if (this.isAnisotropic) {
+var aMax = 0;
+for (var i = 3; --i >= 0; ) if (this.anisotropy[i] > aMax) aMax = this.anisotropy[i];
+
+this.radius *= aMax;
+}JU.Logger.info("Atomic Orbital radial extent set to " + this.radius + " for cutoff " + this.params.cutoff);
+if (this.params.thePlane != null && this.monteCarloCount > 0) {
+this.planeCenter = new JU.P3();
+this.planeU = new JU.V3();
+JU.Measure.getPlaneProjection(this.center, this.params.thePlane, this.planeCenter, this.planeU);
+this.planeU.set(this.params.thePlane.x, this.params.thePlane.y, this.params.thePlane.z);
+this.planeU.normalize();
+this.planeV = JU.V3.new3(1, 0, 0);
+if (Math.abs(this.planeU.dot(this.planeV)) > 0.5) this.planeV.set(0, 1, 0);
+this.planeV.cross(this.planeU, this.planeV);
+this.planeU.cross(this.planeU, this.planeV);
+this.aoMax2 = 0;
+d = this.center.distance(this.planeCenter);
+if (d < this.radius) {
+this.planeRadius = Math.sqrt(this.radius * this.radius - d * d);
+var ir = Clazz.floatToInt(this.planeRadius * 10);
+for (var ix = -ir; ix <= ir; ix++) for (var iy = -ir; iy <= ir; iy++) {
+this.ptPsi.setT(this.planeU);
+this.ptPsi.scale(ix / 10);
+this.ptPsi.scaleAdd2(iy / 10, this.planeV, this.ptPsi);
+d = this.hydrogenAtomPsi(this.ptPsi);
+d = Math.abs(this.hydrogenAtomPsi(this.ptPsi));
+if (d > this.aoMax2) this.aoMax2 = d;
+}
+
+if (this.aoMax2 < 0.001) this.aoMax2 = 0;
+ else this.aoMax2 *= this.aoMax2;
+}}});
+Clazz.defineMethod(c$, "radialPart",
+function(r){
+var rho = 2 * this.psi_Znuc * r / this.psi_n / 0.52918;
+var sum = 0;
+for (var p = 0; p <= this.psi_n - this.psi_l - 1; p++) sum += Math.pow(-rho, p) * this.rfactor[p];
+
+return Math.exp(-rho / 2) * Math.pow(rho, this.psi_l) * sum;
+}, "~N");
+Clazz.defineMethod(c$, "hydrogenAtomPsi",
+function(pt){
+var x2y2 = pt.x * pt.x + pt.y * pt.y;
+this.rnl = this.radialPart(Math.sqrt(x2y2 + pt.z * pt.z));
+var ph = Math.atan2(pt.y, pt.x);
+var th = Math.atan2(Math.sqrt(x2y2), pt.z);
+var theta_lm_phi_m = this.angularPart(th, ph, this.psi_m);
+return this.rnl * theta_lm_phi_m;
+}, "JU.P3");
+Clazz.defineMethod(c$, "angularPart",
+function(th, ph, m){
+var cth = Math.cos(th);
+var sth = Math.sin(th);
+var isS = (m == 0 && this.psi_l == 0);
+var abm = Math.abs(m);
+var sum = 0;
+if (isS) sum = this.pfactor[0];
+ else for (var p = abm; p <= this.psi_l; p++) sum += (p == abm ? 1 : Math.pow(1 + cth, p - abm)) * (p == this.psi_l ? 1 : Math.pow(1 - cth, this.psi_l - p)) * this.pfactor[p];
+
+var theta_lm = (abm == 0 ? sum : Math.abs(Math.pow(sth, abm)) * sum);
+var phi_m;
+if (m == 0) phi_m = 1;
+ else if (m > 0) phi_m = Math.cos(m * ph) * 1.414214;
+ else phi_m = Math.sin(m * ph) * 1.414214;
+return (Math.abs(phi_m) < 0.0000000001 ? 0 : theta_lm * phi_m * this.psi_normalization);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "createMonteCarloOrbital",
+function(){
+if (this.surfaceDone || this.aoMax2 == 0 || this.params.distance > this.radius) return;
+var isS = (this.psi_m == 0 && this.psi_l == 0);
+this.surfaceDone = true;
+var value;
+var rave = 0;
+this.nTries = 0;
+for (var i = 0; i < this.monteCarloCount; this.nTries++) {
+if (this.params.thePlane == null) {
+var r;
+if (this.params.distance == 0) {
+r = this.random.nextDouble() * this.radius;
+var rp = r * this.radialPart(r);
+if (rp * rp <= this.aoMax2 * this.random.nextDouble()) continue;
+} else {
+r = this.params.distance;
+}var u = this.random.nextDouble();
+var v = this.random.nextDouble();
+var theta = 2 * 3.141592653589793 * u;
+var cosPhi = 2 * v - 1;
+if (!isS) {
+var phi = Math.acos(cosPhi);
+var ap = this.angularPart(phi, theta, this.psi_m);
+if (ap * ap <= this.angMax2 * this.random.nextDouble()) continue;
+}var sinPhi = Math.sin(Math.acos(cosPhi));
+var x = r * Math.cos(theta) * sinPhi;
+var y = r * Math.sin(theta) * sinPhi;
+var z = r * cosPhi;
+this.ptPsi.set(x, y, z);
+this.ptPsi.add(this.center);
+value = this.getValueAtPoint(this.ptPsi, false);
+} else {
+this.ptPsi.setT(this.planeU);
+this.ptPsi.scale(this.random.nextFloat() * this.planeRadius * 2 - this.planeRadius);
+this.ptPsi.scaleAdd2(this.random.nextFloat() * this.planeRadius * 2 - this.planeRadius, this.planeV, this.ptPsi);
+this.ptPsi.add(this.planeCenter);
+value = this.getValueAtPoint(this.ptPsi, false);
+if (value * value <= this.aoMax2 * this.random.nextFloat()) continue;
+}rave += this.ptPsi.distance(this.center);
+this.addVC(this.ptPsi, value, 0, true);
+i++;
+}
+if (this.params.distance == 0) JU.Logger.info("Atomic Orbital mean radius = " + rave / this.monteCarloCount + " for " + this.monteCarloCount + " points (" + this.nTries + " tries)");
+});
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+switch (this.params.dataType) {
+case 1294:
+if (this.monteCarloCount <= 0) break;
+this.createMonteCarloOrbital();
+return;
+case 70:
+case 71:
+this.ptPsi.set(0, 0, this.eccentricityScale / 2);
+this.eccentricityMatrixInverse.rotate(this.ptPsi);
+this.ptPsi.add(this.center);
+this.addVC(this.center, 0, 0, true);
+this.addVC(this.ptPsi, 0, 0, true);
+this.addTriangleCheck(0, 0, 0, 0, 0, false, 0);
+return;
+case 74:
+if (!isMapData) {
+this.createGeodesic();
+return;
+}}
+this.readSurfaceDataVDR(isMapData);
+}, "~B");
+Clazz.defineMethod(c$, "createGeodesic",
+function(){
+var ms = JU.MeshSurface.getSphereData(4);
+var pts = ms.altVertices;
+for (var i = 0; i < pts.length; i++) {
+var pt = JU.P3.newP(pts[i]);
+pt.scale(this.params.distance);
+pt.add(this.center);
+this.addVC(pt, 0, i, false);
+}
+var faces = ms.pis;
+for (var i = 0; i < faces.length; i++) {
+var face = faces[i];
+this.addTriangleCheck(face[0], face[1], face[2], 7, 7, false, 0);
+}
+});
+c$.fact = Clazz.newFloatArray (20, 0);
+{
+J.jvxl.readers.IsoShapeReader.fact[0] = 1;
+for (var i = 1; i < 20; i++) J.jvxl.readers.IsoShapeReader.fact[i] = J.jvxl.readers.IsoShapeReader.fact[i - 1] * i;
+
+}});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoSolventReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoSolventReader.js
new file mode 100755
index 000000000000..0cafd9467172
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/IsoSolventReader.js
@@ -0,0 +1,633 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["JU.P3", "J.jvxl.readers.AtomDataReader", "JU.P4", "$.V3"], "J.jvxl.readers.IsoSolventReader", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.Measure", "J.jvxl.data.MeshData", "JU.BSUtil", "$.Logger", "$.MeshSurface", "$.TempArray"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.cavityRadius = 0;
+this.envelopeRadius = 0;
+this.dots = null;
+this.doCalculateTroughs = false;
+this.isCavity = false;
+this.isPocket = false;
+this.iter = null;
+this.bsSurfacePoints = null;
+this.bsSurfaceDone = null;
+this.bsLocale = null;
+this.htEdges = null;
+this.vEdges = null;
+this.vFaces = null;
+this.ptS1 = null;
+this.ptS2 = null;
+this.vTemp = null;
+this.plane = null;
+this.ptTemp2 = null;
+this.vTemp2 = null;
+this.p = null;
+this.bsAtomMinMax = null;
+this.isSurfacePoint = false;
+this.iAtomSurface = 0;
+this.nTest = 0;
+if (!Clazz.isClassDefined("J.jvxl.readers.IsoSolventReader.Edge")) {
+J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$ ();
+}
+if (!Clazz.isClassDefined("J.jvxl.readers.IsoSolventReader.Face")) {
+J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$ ();
+}
+this.rAS = 0;
+this.rBS = 0;
+this.rAS2 = 0;
+this.rBS2 = 0;
+this.dAB = 0;
+this.dAB2 = 0;
+this.ecosASB2 = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "IsoSolventReader", J.jvxl.readers.AtomDataReader);
+Clazz.prepareFields (c$, function(){
+this.ptS1 = new JU.P3();
+this.ptS2 = new JU.P3();
+this.vTemp = new JU.V3();
+this.plane = new JU.P4();
+this.ptTemp2 = new JU.P3();
+this.vTemp2 = new JU.V3();
+this.p = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.IsoSolventReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initADR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.setup(isMapData);
+this.initializeVolumetricData();
+this.volumeData.setUnitVectors();
+this.vl0 = this.volumeData.volumetricVectorLengths[0];
+this.vl1 = this.volumeData.volumetricVectorLengths[1];
+this.vl2 = this.volumeData.volumetricVectorLengths[2];
+if (this.isProgressive) {
+this.volumeData.getYzCount();
+this.bsAtomMinMax = new Array(this.nPointsX);
+this.getAtomMinMax(null, this.bsAtomMinMax);
+this.voxelSource = Clazz.newIntArray (this.volumeData.nPoints, 0);
+}return true;
+}, "~B");
+Clazz.overrideMethod(c$, "setup",
+function(isMapData){
+this.setup2();
+if (this.contactPair == null) {
+this.cavityRadius = this.params.cavityRadius;
+this.envelopeRadius = this.params.envelopeRadius;
+this.sr = this.params.solventRadius;
+this.point = this.params.point;
+this.isCavity = (this.params.isCavity && this.meshDataServer != null);
+this.isPocket = (this.params.pocket != null && this.meshDataServer != null);
+this.doCalculateTroughs = (!isMapData && this.sg.atomDataServer != null && !this.isCavity && this.sr > 0 && (this.dataType == 1195 || this.dataType == 1203));
+this.doUseIterator = this.doCalculateTroughs;
+this.getAtoms(this.params.bsSelected, this.doAddHydrogens, true, false, false, true, false, NaN, null);
+if (this.isCavity || this.isPocket) this.dots = this.meshDataServer.calculateGeodesicSurface(this.bsMySelected, this.envelopeRadius);
+this.setHeader("solvent/molecular surface", this.params.calculationType);
+if (this.havePlane || !isMapData) {
+var r = Math.max(this.params.solventExtendedAtomRadius, this.params.solventRadius);
+var minPtsPerAng = (r >= 1 ? 1.5 / r : 0);
+if (minPtsPerAng > 0) System.out.println("IsoSolventReader.minPtsPerAng=" + minPtsPerAng);
+this.setRanges(this.params.solvent_ptsPerAngstrom, this.params.solvent_gridMax, minPtsPerAng);
+this.volumeData.getYzCount();
+this.margin = this.volumeData.maxGrid * 2.0;
+}if (this.bsNearby != null) this.bsMySelected.or(this.bsNearby);
+} else if (!isMapData) {
+this.setVolumeData();
+}if (!this.doCalculateTroughs) {
+if (isMapData) {
+this.precalculateVoxelData = false;
+this.volumeData.sr = this;
+} else if (!this.isCavity) {
+this.isProgressive = this.isXLowToHigh = true;
+}}if (this.thisAtomSet == null) this.thisAtomSet = JU.BSUtil.setAll(this.myAtomCount);
+}, "~B");
+Clazz.overrideMethod(c$, "generateCube",
+function(){
+if (this.isCavity && this.params.theProperty != null) return;
+if (this.isCavity && this.dataType != 1207 && this.dataType != 1208) {
+this.params.vertexSource = null;
+this.newVoxelDataCube();
+this.resetVoxelData(3.4028235E38);
+this.markSphereVoxels(this.cavityRadius, this.params.distance);
+this.generateSolventCavity();
+this.resetVoxelData(3.4028235E38);
+this.markSphereVoxels(0, NaN);
+} else {
+this.voxelSource = Clazz.newIntArray (this.volumeData.nPoints, 0);
+this.generateSolventCube();
+}this.unsetVoxelData();
+var info = this.params.slabInfo;
+if (info != null) for (var i = 0; i < info.size(); i++) if ((info.get(i)[2]).booleanValue() && Clazz.instanceOf(info.get(i)[0],"JU.P4")) {
+this.volumeData.capData(info.get(i)[0], this.params.cutoff);
+info.removeItemAt(i--);
+}
+});
+Clazz.overrideMethod(c$, "getSurfacePointAndFraction",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA0, vB0, fReturn, ptReturn){
+var vA = this.marchingCubes.getLinearOffset(x, y, z, vA0);
+var vB = this.marchingCubes.getLinearOffset(x, y, z, vB0);
+this.isSurfacePoint = (this.bsSurfaceVoxels != null && (this.bsSurfaceVoxels.get(vA) || this.bsSurfaceVoxels.get(vB)));
+if (this.voxelSource != null) {
+var vs = Math.abs(Float.isNaN(valueB) || valueA < valueB ? this.voxelSource[vA] : this.voxelSource[vB]);
+if (vs > 0) this.iAtomSurface = this.atomIndex[vs - 1];
+}if (J.jvxl.readers.IsoSolventReader.testLinear || this.voxelSource == null || this.voxelSource[vA] == 0 || this.voxelSource[vA] != this.voxelSource[vB]) return this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+var fraction = fReturn[0] = JU.MeshSurface.getSphericalInterpolationFraction((this.voxelSource[vA] < 0 ? this.sr : this.atomRadius[this.voxelSource[vA] - 1]), valueA, valueB, edgeVector.length());
+ptReturn.scaleAdd2(fraction, edgeVector, pointA);
+var diff = valueB - valueA;
+return valueA + fraction * diff;
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.overrideMethod(c$, "addVertexCopy",
+function(vertexXYZ, value, assocVertex, asCopy){
+var i = this.addVC(vertexXYZ, value, assocVertex, asCopy);
+if (i < 0) return i;
+if (this.isSurfacePoint) this.bsSurfacePoints.set(i);
+if (this.params.vertexSource != null) this.params.vertexSource[i] = this.iAtomSurface;
+return i;
+}, "JU.T3,~N,~N,~B");
+Clazz.overrideMethod(c$, "selectPocket",
+function(doExclude){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+var v = this.meshData.vs;
+var nVertices = this.meshData.vc;
+var vv = this.meshData.vvs;
+var nDots = this.dots.length;
+for (var i = 0; i < nVertices; i++) {
+for (var j = 0; j < nDots; j++) {
+if (this.dots[j].distance(v[i]) < this.envelopeRadius) {
+vv[i] = NaN;
+continue;
+}}
+}
+this.meshData.getSurfaceSet();
+var nSets = this.meshData.nSets;
+var pocketSet = JU.BS.newN(nSets);
+var ss;
+for (var i = 0; i < nSets; i++) if ((ss = this.meshData.surfaceSet[i]) != null) for (var j = ss.nextSetBit(0); j >= 0; j = ss.nextSetBit(j + 1)) if (Float.isNaN(this.meshData.vvs[j])) {
+pocketSet.set(i);
+break;
+}
+
+for (var i = 0; i < nSets; i++) if (this.meshData.surfaceSet[i] != null && pocketSet.get(i) == doExclude) this.meshData.invalidateSurfaceSet(i);
+
+this.updateSurfaceData();
+if (!doExclude) this.meshData.surfaceSet = null;
+if (this.meshDataServer != null) {
+this.meshDataServer.fillMeshData(this.meshData, 3, null);
+this.meshData = new J.jvxl.data.MeshData();
+}}, "~B");
+Clazz.overrideMethod(c$, "postProcessVertices",
+function(){
+this.setVertexSource();
+if (this.doCalculateTroughs && this.bsSurfacePoints != null) {
+var bsAll = new JU.BS();
+var bsSurfaces = this.meshData.getSurfaceSet();
+var bsSources = null;
+var volumes = (this.isPocket ? null : J.jvxl.data.MeshData.calculateVolumeOrArea(this.meshData, null, false, false));
+var minVolume = (this.isCavity ? (1.5 * 3.141592653589793 * Math.pow(this.sr, 3)) : 0);
+var maxVolume = 0;
+var maxIsNegative = false;
+if (volumes != null && !this.isCavity) for (var i = 0; i < this.meshData.nSets; i++) {
+var v = volumes[i];
+if (Math.abs(v) > maxVolume) {
+maxVolume = Math.abs(v);
+maxIsNegative = (v < 0);
+}}
+var factor = (maxIsNegative ? -1 : 1);
+for (var i = 0; i < this.meshData.nSets; i++) {
+var bss = bsSurfaces[i];
+if (bss.intersects(this.bsSurfacePoints)) {
+if (volumes == null || volumes[i] * factor > minVolume) if (this.params.vertexSource != null) {
+var bs = new JU.BS();
+if (bsSources == null) bsSources = new Array(bsSurfaces.length);
+for (var j = bss.nextSetBit(0); j >= 0; j = bss.nextSetBit(j + 1)) {
+var iatom = this.params.vertexSource[j];
+if (iatom < 0) continue;
+if (bsAll.get(iatom)) {
+this.meshData.invalidateSurfaceSet(i);
+break;
+}bs.set(iatom);
+}
+bsAll.or(bs);
+continue;
+}}this.meshData.invalidateSurfaceSet(i);
+}
+this.updateSurfaceData();
+if (this.meshDataServer != null) {
+this.meshDataServer.fillMeshData(this.meshData, 3, null);
+this.meshData = new J.jvxl.data.MeshData();
+}}if (this.params.thePlane != null && this.params.slabInfo == null) this.params.addSlabInfo(JU.TempArray.getSlabWithinRange(-100, 0));
+});
+Clazz.defineMethod(c$, "generateSolventCavity",
+function(){
+var bs = JU.BS.newN(this.nPointsX * this.nPointsY * this.nPointsZ);
+var i = 0;
+var nDots = this.dots.length;
+var n = 0;
+var d;
+var r2 = this.envelopeRadius;
+for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) {
+out : for (var z = 0; z < this.nPointsZ; ++z, ++i) if ((d = this.voxelData[x][y][z]) < 3.4028235E38 && d >= this.cavityRadius) {
+this.volumeData.voxelPtToXYZ(x, y, z, this.ptV);
+for (var j = 0; j < nDots; j++) {
+if (this.dots[j].distance(this.ptV) < r2) continue out;
+}
+bs.set(i);
+n++;
+}
+}
+
+JU.Logger.info("cavities include " + n + " voxel points");
+this.atomRadius = Clazz.newFloatArray (n, 0);
+this.atomXyzTruncated = new Array(n);
+for (var x = 0, ipt = 0, apt = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) if (bs.get(ipt++)) {
+this.volumeData.voxelPtToXYZ(x, y, z, (this.atomXyzTruncated[apt] = new JU.P3()));
+this.atomRadius[apt++] = this.voxelData[x][y][z];
+}
+
+
+this.myAtomCount = this.firstNearbyAtom = n;
+this.thisAtomSet = JU.BSUtil.setAll(this.myAtomCount);
+this.rs = null;
+this.setRadii();
+});
+Clazz.defineMethod(c$, "generateSolventCube",
+function(){
+if (this.dataType == 1207) return;
+this.params.vertexSource = Clazz.newIntArray (this.volumeData.nPoints, 0);
+this.bsSurfaceDone = new JU.BS();
+this.bsSurfaceVoxels = new JU.BS();
+this.bsSurfacePoints = new JU.BS();
+if (this.doCalculateTroughs) {
+this.iter = this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected, true, false, false);
+this.vEdges = new JU.Lst();
+this.bsLocale = new Array(this.myAtomCount);
+this.htEdges = new java.util.Hashtable();
+this.getEdges();
+JU.Logger.info(this.vEdges.size() + " edges");
+this.vFaces = new JU.Lst();
+this.getFaces();
+JU.Logger.info(this.vFaces.size() + " faces");
+this.bsLocale = null;
+this.htEdges = null;
+this.iter.release();
+this.iter = null;
+this.newVoxelDataCube();
+this.resetVoxelData(3.4028235E38);
+this.markFaceVoxels(true);
+this.markToroidVoxels();
+this.validSpheres.or(this.noFaceSpheres);
+this.vEdges = null;
+this.markFaceVoxels(false);
+this.vFaces = null;
+} else {
+this.newVoxelDataCube();
+this.resetVoxelData(3.4028235E38);
+}this.markSphereVoxels(0, this.doCalculateTroughs ? 3.4028235E38 : this.params.distance);
+this.noFaceSpheres = null;
+this.validSpheres = null;
+});
+Clazz.defineMethod(c$, "getEdges",
+function(){
+for (var iatomA = 0; iatomA < this.myAtomCount; iatomA++) this.bsLocale[iatomA] = new JU.BS();
+
+for (var iatomA = 0; iatomA < this.myAtomCount; iatomA++) {
+var ptA = this.atomXyzTruncated[iatomA];
+var rA = this.rs[iatomA];
+this.sg.atomDataServer.setIteratorForAtom(this.iter, this.atomIndex[iatomA], rA + this.maxRS);
+while (this.iter.hasNext()) {
+var iB = this.iter.next();
+var iatomB = this.myIndex[iB];
+if (iatomA >= this.firstNearbyAtom && iatomB >= this.firstNearbyAtom) continue;
+var ptB = this.atomXyzTruncated[iatomB];
+var rB = this.rs[iatomB];
+var dAB = ptA.distance(ptB);
+if (dAB >= rA + rB) continue;
+var edge = Clazz.innerTypeInstance(J.jvxl.readers.IsoSolventReader.Edge, this, null, this, iatomA, iatomB, dAB);
+this.vEdges.addLast(edge);
+this.bsLocale[iatomA].set(iatomB);
+this.bsLocale[iatomB].set(iatomA);
+this.htEdges.put(edge.toString(), edge);
+}
+}
+});
+Clazz.defineMethod(c$, "findEdge",
+function(i, j){
+return this.htEdges.get(i < j ? i + "_" + j : j + "_" + i);
+}, "~N,~N");
+Clazz.defineMethod(c$, "getFaces",
+function(){
+var bs = new JU.BS();
+this.params.surfaceAtoms = this.validSpheres = new JU.BS();
+this.noFaceSpheres = JU.BSUtil.setAll(this.myAtomCount);
+for (var i = this.vEdges.size(); --i >= 0; ) {
+var edge = this.vEdges.get(i);
+var ia = edge.ia;
+var ib = edge.ib;
+bs.clearAll();
+bs.or(this.bsLocale[ia]);
+bs.and(this.bsLocale[ib]);
+for (var ic = bs.nextSetBit(ib + 1); ic >= 0; ic = bs.nextSetBit(ic + 1)) {
+if (this.getSolventPoints(edge, ia, ib, ic)) {
+var f;
+var isOK = false;
+if ((f = this.validateFace(ia, ib, ic, edge, this.ptS1)) != null) {
+this.vFaces.addLast(f);
+isOK = true;
+}if ((f = this.validateFace(ia, ib, ic, edge, this.ptS2)) != null) {
+this.vFaces.addLast(f);
+isOK = true;
+}if (isOK) {
+this.noFaceSpheres.clear(ia);
+this.noFaceSpheres.clear(ib);
+this.noFaceSpheres.clear(ic);
+}}}
+}
+});
+Clazz.defineMethod(c$, "validateFace",
+function(ia, ib, ic, edge, ptS){
+this.sg.atomDataServer.setIteratorForPoint(this.iter, this.modelIndex, ptS, this.maxRS);
+var isValid = true;
+while (this.iter.hasNext()) {
+var iia = this.iter.next();
+var iatom = this.myIndex[iia];
+if (iatom == ia || iatom == ib || iatom == ic) continue;
+var d = this.atomData.atoms[iia].distance(ptS);
+if (d < this.atomData.atomRadius[iia] + this.sr) {
+isValid = false;
+break;
+}}
+var bc = this.findEdge(ib, ic);
+var ca = this.findEdge(ia, ic);
+var f = (isValid ? Clazz.innerTypeInstance(J.jvxl.readers.IsoSolventReader.Face, this, null, ia, ib, ic, ptS) : null);
+edge.addFace(f);
+bc.addFace(f);
+ca.addFace(f);
+if (!isValid) return null;
+this.validSpheres.set(ia);
+this.validSpheres.set(ib);
+this.validSpheres.set(ic);
+return f;
+}, "~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");
+Clazz.defineMethod(c$, "markFaceVoxels",
+function(firstPass){
+var bsThisPass = new JU.BS();
+var v0 = this.volumetricVectors[0];
+var v1 = this.volumetricVectors[1];
+var v2 = this.volumetricVectors[2];
+for (var fi = this.vFaces.size(); --fi >= 0; ) {
+var f = this.vFaces.get(fi);
+var ptA = this.atomXyzTruncated[f.ia];
+var ptB = this.atomXyzTruncated[f.ib];
+var ptC = this.atomXyzTruncated[f.ic];
+var ptS = f.pS;
+this.setGridLimitsForAtom(ptS, this.sr, this.pt0, this.pt1);
+this.volumeData.voxelPtToXYZ(this.pt0.x, this.pt0.y, this.pt0.z, this.ptV);
+for (var i = this.pt0.x; i < this.pt1.x; i++, this.ptV.add2(v0, this.ptY0)) {
+this.ptY0.setT(this.ptV);
+for (var j = this.pt0.y; j < this.pt1.y; j++, this.ptV.add2(v1, this.ptZ0)) {
+this.ptZ0.setT(this.ptV);
+for (var k = this.pt0.z; k < this.pt1.z; k++, this.ptV.add(v2)) {
+var value = this.sr - this.ptV.distance(ptS);
+var v = this.voxelData[i][j][k];
+var ipt = this.volumeData.getPointIndex(i, j, k);
+if (firstPass && value > 0) this.bsSurfaceDone.set(ipt);
+if (JU.Measure.isInTetrahedron(this.ptV, ptA, ptB, ptC, ptS, this.plane, this.vTemp, this.vTemp2, false)) {
+if (!firstPass ? !this.bsSurfaceDone.get(ipt) && value < 0 && value > -this.volumeData.maxGrid * 1.8 && (value > v) == bsThisPass.get(ipt) : (value > 0 && (v < 0 || v == 3.4028235E38 || (value > v) == bsThisPass.get(ipt)))) {
+bsThisPass.set(ipt);
+this.setVoxel(i, j, k, ipt, value);
+if (this.voxelSource != null) this.voxelSource[ipt] = -1 - f.ia;
+if (value > 0) {
+this.bsSurfaceVoxels.set(ipt);
+}}}}
+}
+}
+}
+}, "~B");
+Clazz.defineMethod(c$, "markToroidVoxels",
+function(){
+var v0 = this.volumetricVectors[0];
+var v1 = this.volumetricVectors[1];
+var v2 = this.volumetricVectors[2];
+for (var ei = this.vEdges.size(); --ei >= 0; ) {
+var edge = this.vEdges.get(ei);
+if (!edge.isValid()) continue;
+var ia = edge.ia;
+var ib = edge.ib;
+var ptA = this.atomXyzTruncated[ia];
+var ptB = this.atomXyzTruncated[ib];
+this.rAS = this.rs[ia];
+this.rBS = this.rs[ib];
+this.rAS2 = this.rs2[ia];
+this.rBS2 = this.rs2[ib];
+this.dAB = edge.d;
+this.dAB2 = edge.d2;
+this.ecosASB2 = edge.cosASB2;
+this.setGridLimitsForAtom(edge, edge.maxr, this.pt0, this.pt1);
+this.volumeData.voxelPtToXYZ(this.pt0.x, this.pt0.y, this.pt0.z, this.ptV);
+for (var i = this.pt0.x; i < this.pt1.x; i++, this.ptV.add2(v0, this.ptY0)) {
+this.ptY0.setT(this.ptV);
+for (var j = this.pt0.y; j < this.pt1.y; j++, this.ptV.add2(v1, this.ptZ0)) {
+this.ptZ0.setT(this.ptV);
+for (var k = this.pt0.z; k < this.pt1.z; k++, this.ptV.add(v2)) {
+var dVS = this.checkSpecialVoxel(ptA, ptB, this.ptV);
+if (Float.isNaN(dVS)) continue;
+var value = this.sr - dVS;
+if (value < this.voxelData[i][j][k]) {
+var ipt = this.volumeData.getPointIndex(i, j, k);
+this.setVoxel(i, j, k, ipt, value);
+if (this.voxelSource != null) this.voxelSource[ipt] = -1 - ia;
+}}
+}
+}
+}
+});
+Clazz.overrideMethod(c$, "unsetVoxelData",
+function(){
+if (!this.havePlane) {
+this.unsetVoxelData2();
+return;
+}if (this.isProgressive) for (var i = 0; i < this.yzCount; i++) {
+if (this.thisPlane[i] < 0.001) {
+} else {
+this.thisPlane[i] = 0.001;
+}}
+ else for (var x = 0; x < this.nPointsX; ++x) for (var y = 0; y < this.nPointsY; ++y) for (var z = 0; z < this.nPointsZ; ++z) if (this.voxelData[x][y][z] < 0.001) {
+} else {
+this.voxelData[x][y][z] = 0.001;
+}
+
+
+});
+Clazz.defineMethod(c$, "getSolventPoints",
+function(edge, ia, ib, ic){
+var rAS = this.rs[ia];
+var v = edge.v;
+var cosAngleBAS = (edge.d2 + this.rs2[ia] - this.rs2[ib]) / (2 * edge.d * rAS);
+var angleBAS = Math.acos(cosAngleBAS);
+this.p.scaleAdd2(cosAngleBAS * rAS, v, this.atomXyzTruncated[ia]);
+JU.Measure.getPlaneThroughPoint(this.p, v, this.plane);
+var dPS = (Math.sin(angleBAS) * rAS);
+var ptC = this.atomXyzTruncated[ic];
+var rCS = this.rs[ic];
+var dCT = JU.Measure.distanceToPlane(this.plane, ptC);
+if (Math.abs(dCT) >= rCS * 0.9) return false;
+this.ptTemp.scaleAdd2(-dCT, v, ptC);
+var dpT = this.p.distance(this.ptTemp);
+var dsp2 = dPS * dPS;
+var dST2 = this.rs2[ic] - dCT * dCT;
+var cosTheta = (dsp2 + dpT * dpT - dST2) / (2 * dPS * dpT);
+if (Math.abs(cosTheta) >= 0.99) return false;
+var vXS = this.vTemp2;
+vXS.sub2(this.ptTemp, this.p);
+vXS.normalize();
+this.ptTemp.scaleAdd2(dPS * cosTheta, vXS, this.p);
+vXS.cross(v, vXS);
+vXS.normalize();
+vXS.scale((Math.sqrt(1 - cosTheta * cosTheta) * dPS));
+this.ptS1.add2(this.ptTemp, vXS);
+this.ptS2.sub2(this.ptTemp, vXS);
+return true;
+}, "J.jvxl.readers.IsoSolventReader.Edge,~N,~N,~N");
+Clazz.defineMethod(c$, "checkSpecialVoxel",
+function(ptA, ptB, ptV){
+var dAV = ptA.distance(ptV);
+var dAV2 = ptA.distanceSquared(ptV);
+var f = this.rAS / dAV;
+if (f > 1) {
+this.p.set(ptA.x + (ptV.x - ptA.x) * f, ptA.y + (ptV.y - ptA.y) * f, ptA.z + (ptV.z - ptA.z) * f);
+return (ptB.distanceSquared(this.p) >= this.rBS2 ? NaN : this.solventDistance(this.rAS, this.rAS2, this.rBS2, dAV, dAV2, ptB.distanceSquared(ptV)));
+}var dBV = ptB.distance(ptV);
+if ((f = this.rBS / dBV) > 1) {
+this.p.set(ptB.x + (ptV.x - ptB.x) * f, ptB.y + (ptV.y - ptB.y) * f, ptB.z + (ptV.z - ptB.z) * f);
+return (ptA.distanceSquared(this.p) >= this.rAS2 ? NaN : this.solventDistance(this.rBS, this.rBS2, this.rAS2, dBV, dBV * dBV, dAV2));
+}return NaN;
+}, "JU.P3,JU.P3,JU.P3");
+Clazz.defineMethod(c$, "solventDistance",
+function(rAS, rAS2, rBS2, dAV, dAV2, dBV2){
+var angleVAB = Math.acos((dAV2 + this.dAB2 - dBV2) / (2 * dAV * this.dAB));
+var angleSAB = Math.acos((rAS2 + this.dAB2 - rBS2) / (2 * rAS * this.dAB));
+var dVS2 = (rAS2 + dAV2 - 2 * rAS * dAV * Math.cos(angleSAB - angleVAB));
+var dVS = Math.sqrt(dVS2);
+return (this.ecosASB2 < (rAS2 + dVS2 - dAV * dAV) / (dVS * rAS) ? dVS : NaN);
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "dumpLine",
+function(pt1, pt2, label, color){
+this.sg.log("draw ID \"x" + label + (this.nTest++) + "\" " + JU.P3.newP(pt1) + " " + JU.P3.newP(pt2) + " color " + color);
+}, "JU.P3,JU.T3,~S,~S");
+Clazz.defineMethod(c$, "dumpLine2",
+function(pt1, pt2, label, d, color1, color2){
+var pt = new JU.V3();
+pt.setT(pt2);
+pt.sub(pt1);
+pt.normalize();
+pt.scale(d);
+pt.add(pt1);
+this.sg.log("draw ID \"" + label + (this.nTest++) + "\" " + JU.P3.newP(pt1) + " " + JU.P3.newP(pt) + " color " + color1);
+this.sg.log("draw ID \"" + label + (this.nTest++) + "\"" + JU.P3.newP(pt) + " " + JU.P3.newP(pt2) + " color " + color2 + "\"" + label + "\"");
+}, "JU.P3,JU.P3,~S,~N,~S,~S");
+Clazz.defineMethod(c$, "dumpPoint",
+function(pt, label, color){
+this.sg.log("draw ID \"" + label + (this.nTest++) + "\"" + JU.P3.newP(pt) + " color " + color);
+}, "JU.P3,~S,~S");
+Clazz.overrideMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+if (this.contactPair != null) return pt.distance(this.contactPair.myAtoms[1]) - this.contactPair.radii[1];
+var value = 3.4028235E38;
+for (var iAtom = 0; iAtom < this.firstNearbyAtom; iAtom++) {
+var r = pt.distance(this.atomXyzTruncated[iAtom]) - this.rs[iAtom];
+if (r < value) value = r;
+}
+return (value == 3.4028235E38 ? NaN : value);
+}, "JU.T3,~B");
+Clazz.overrideMethod(c$, "discardTempData",
+function(discardAll){
+this.rs = null;
+this.rs2 = null;
+this.discardTempDataSR(discardAll);
+}, "~B");
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+if (this.yzCount == 0) {
+this.initPlanes();
+}this.thisX = x;
+this.thisPlane = this.yzPlanes[x % 2];
+if (this.contactPair == null) {
+this.resetPlane(3.4028235E38);
+this.thisAtomSet = this.bsAtomMinMax[x];
+this.markSphereVoxels(0, this.params.distance);
+this.unsetVoxelData();
+} else {
+this.markPlaneVoxels(this.contactPair.myAtoms[0], this.contactPair.radii[0]);
+}return this.thisPlane;
+}, "~N");
+c$.$IsoSolventReader$Edge$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.ia = 0;
+this.ib = 0;
+this.nFaces = 0;
+this.nInvalid = 0;
+this.d = 0;
+this.d2 = 0;
+this.maxr = 0;
+this.cosASB2 = 0;
+this.v = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers.IsoSolventReader, "Edge", JU.P3);
+Clazz.overrideConstructor(c$,
+function(r, ia, ib, d){
+this.ia = Math.min(ia, ib);
+this.ib = Math.max(ia, ib);
+this.d = d;
+this.d2 = d * d;
+this.maxr = Math.sqrt(this.d2 / 4 + Math.max(r.rs2[ia], r.rs2[ib]));
+this.ave(r.atomXyzTruncated[ia], r.atomXyzTruncated[ib]);
+this.cosASB2 = (r.rs2[ia] + r.rs2[ib] - this.d2) / (r.rs[ib] * r.rs[ia]);
+this.v = JU.V3.newVsub(r.atomXyzTruncated[ib], r.atomXyzTruncated[ia]);
+this.v.normalize();
+}, "J.jvxl.readers.IsoSolventReader,~N,~N,~N");
+Clazz.defineMethod(c$, "addFace",
+function(f){
+this.nFaces++;
+if (f == null) {
+this.nInvalid++;
+return;
+}}, "J.jvxl.readers.IsoSolventReader.Face");
+Clazz.defineMethod(c$, "isValid",
+function(){
+return (this.nFaces == 0 || this.nInvalid != this.nFaces);
+});
+Clazz.overrideMethod(c$, "toString",
+function(){
+return this.ia + "_" + this.ib;
+});
+/*eoif4*/})();
+};
+c$.$IsoSolventReader$Face$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.ia = 0;
+this.ib = 0;
+this.ic = 0;
+this.pS = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers.IsoSolventReader, "Face", null);
+Clazz.makeConstructor(c$,
+function(ia, ib, ic, pS){
+this.ia = ia;
+this.ib = ib;
+this.ic = ic;
+this.pS = JU.P3.newP(pS);
+}, "~N,~N,~N,JU.P3");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return this.ia + "_" + this.ib + "_" + this.ic + "_" + this.pS;
+});
+/*eoif4*/})();
+};
+c$.testLinear = false;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JaguarReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JaguarReader.js
new file mode 100755
index 000000000000..085f348f2022
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JaguarReader.js
@@ -0,0 +1,56 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.JaguarReader", ["JU.PT", "$.SB"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.extents = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "JaguarReader", J.jvxl.readers.VolumeFileReader);
+Clazz.prepareFields (c$, function(){
+this.extents = Clazz.newFloatArray (3, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.JaguarReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("Jaguar data\n");
+this.jvxlFileHeaderBuffer.append("\n");
+var atomLine;
+while ((atomLine = this.rd()) != null && atomLine.indexOf("origin=") < 0) {
+}
+var tokens = JU.PT.getTokensAt(atomLine, 0);
+if (tokens.length == 4 && tokens[0].equals("origin=")) {
+this.volumetricOrigin.set(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+J.jvxl.readers.VolumeFileReader.checkAtomLine(this.isXLowToHigh, this.isAngstroms, "0", "0 " + tokens[1] + " " + tokens[2] + " " + tokens[3], this.jvxlFileHeaderBuffer);
+if (!this.isAngstroms) this.volumetricOrigin.scale(0.5291772);
+}this.readExtents(0);
+this.readExtents(1);
+this.readExtents(2);
+tokens = JU.PT.getTokens(this.rd());
+this.voxelCounts[0] = this.parseIntStr(tokens[1]);
+this.voxelCounts[1] = this.parseIntStr(tokens[2]);
+this.voxelCounts[2] = this.parseIntStr(tokens[3]);
+var factor = (this.isAngstroms ? 1 : 0.5291772);
+var d = this.extents[0] / (this.voxelCounts[0] - 1);
+this.volumetricVectors[0].set(d * factor, 0, 0);
+this.jvxlFileHeaderBuffer.append(this.voxelCounts[0] + " " + d + " 0.0 0.0\n");
+d = this.extents[1] / (this.voxelCounts[1] - 1);
+this.volumetricVectors[1].set(0, d * factor, 0);
+this.jvxlFileHeaderBuffer.append(this.voxelCounts[1] + " 0.0 " + d + " 0.0\n");
+d = this.extents[2] / (this.voxelCounts[2] - 1);
+this.volumetricVectors[2].set(0, 0, d * factor);
+this.jvxlFileHeaderBuffer.append(this.voxelCounts[2] + " 0.0 0.0 " + d + "\n");
+this.rd();
+});
+Clazz.defineMethod(c$, "readExtents",
+function(voxelVectorIndex){
+var tokens = JU.PT.getTokens(this.rd());
+this.extents[voxelVectorIndex] = this.parseFloatStr(tokens[voxelVectorIndex + 1]);
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlReader.js
new file mode 100755
index 000000000000..4995b5cb715b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlReader.js
@@ -0,0 +1,195 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.JvxlXmlReader"], "J.jvxl.readers.JvxlReader", ["JU.P4", "$.PT", "$.SB", "J.jvxl.data.JvxlCoder", "J.jvxl.readers.VolumeFileReader", "JU.C", "$.Escape", "$.Logger"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "JvxlReader", J.jvxl.readers.JvxlXmlReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.JvxlReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2JXR(sg, br);
+this.isXmlFile = false;
+this.JVXL_VERSION = "2.0";
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB().append(this.skipComments(false));
+if (this.line == null || this.line.length == 0) this.line = "Line 1";
+this.jvxlFileHeaderBuffer.append(this.line).appendC('\n');
+if (this.rd() == null || this.line.length == 0) this.line = "Line 2";
+this.jvxlFileHeaderBuffer.append(this.line).appendC('\n');
+this.jvxlFileHeaderBuffer.append(this.skipComments(false));
+var atomLine = this.line;
+var tokens = JU.PT.getTokensAt(atomLine, 0);
+this.isXLowToHigh = false;
+this.negativeAtomCount = true;
+this.ac = 0;
+if (tokens[0] === "-0") {
+} else if (tokens[0].charAt(0) == '+') {
+this.isXLowToHigh = true;
+this.ac = this.parseIntStr(tokens[0].substring(1));
+} else {
+this.ac = -this.parseIntStr(tokens[0]);
+}if (this.ac == -2147483648) return;
+this.volumetricOrigin.set(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+this.isAngstroms = J.jvxl.readers.VolumeFileReader.checkAtomLine(this.isXLowToHigh, this.isAngstroms, null, atomLine, this.jvxlFileHeaderBuffer);
+if (!this.isAngstroms) this.volumetricOrigin.scale(0.5291772);
+this.readVoxelVector(0);
+this.readVoxelVector(1);
+this.readVoxelVector(2);
+for (var i = 0; i < this.ac; ++i) this.jvxlFileHeaderBuffer.append(this.rd() + "\n");
+
+this.skipComments(true);
+JU.Logger.info("Reading extra JVXL information line: " + this.line);
+this.nSurfaces = this.parseIntStr(this.line);
+if (!(this.isJvxl = (this.nSurfaces < 0))) return;
+this.nSurfaces = -this.nSurfaces;
+JU.Logger.info("jvxl file surfaces: " + this.nSurfaces);
+var ich;
+if ((ich = this.parseInt()) == -2147483648) {
+JU.Logger.info("using default edge fraction base and range");
+} else {
+this.edgeFractionBase = ich;
+this.edgeFractionRange = this.parseInt();
+}if ((ich = this.parseInt()) == -2147483648) {
+JU.Logger.info("using default color fraction base and range");
+} else {
+this.colorFractionBase = ich;
+this.colorFractionRange = this.parseInt();
+}this.cJvxlEdgeNaN = String.fromCharCode(this.edgeFractionBase + this.edgeFractionRange);
+this.vertexDataOnly = this.jvxlData.vertexDataOnly = (this.volumetricVectors[0].length() == 0);
+});
+Clazz.overrideMethod(c$, "jvxlReadFractionData",
+function(type, nPoints){
+var str = "";
+try {
+while (str.length < nPoints) {
+this.rd();
+str += J.jvxl.data.JvxlCoder.jvxlDecompressString(this.line);
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Error reading " + type + " data " + e);
+throw new NullPointerException();
+} else {
+throw e;
+}
+}
+return str;
+}, "~S,~N");
+Clazz.overrideMethod(c$, "gotoData",
+function(n, nPoints){
+if (n > 0) JU.Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
+this.vertexDataOnly = this.jvxlData.vertexDataOnly = (nPoints == 0);
+for (var i = 0; i < n; i++) {
+this.jvxlReadDefinitionLine(true);
+JU.Logger.info("JVXL skipping: jvxlSurfaceDataCount=" + this.surfaceDataCount + " jvxlEdgeDataCount=" + this.edgeDataCount + " jvxlDataIsColorMapped=" + this.jvxlDataIsColorMapped);
+this.jvxlSkipData(nPoints, true);
+}
+this.jvxlReadDefinitionLine(true);
+}, "~N,~N");
+Clazz.defineMethod(c$, "jvxlReadDefinitionLine",
+function(showMsg){
+var comment = this.skipComments(true);
+if (showMsg) JU.Logger.info("reading jvxl data set: " + comment + this.line);
+this.haveContourData = (comment.indexOf("+contourlines") >= 0);
+this.jvxlCutoff = this.parseFloatStr(this.line);
+JU.Logger.info("JVXL read: cutoff " + this.jvxlCutoff);
+this.jvxlCutoffRange = this.parseFloatArray( Clazz.newFloatArray (2, 0), "[", "]");
+var param1 = this.parseInt();
+var param2 = this.parseInt();
+var param3 = this.parseInt();
+if (param3 == -2147483648 || param3 == -1) param3 = 0;
+if (param1 == -1) {
+try {
+this.params.thePlane = JU.P4.new4(this.parseFloat(), this.parseFloat(), this.parseFloat(), this.parseFloat());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Error reading 4 floats for PLANE definition -- setting to 0 0 1 0 (z=0)");
+this.params.thePlane = JU.P4.new4(0, 0, 1, 0);
+} else {
+throw e;
+}
+}
+JU.Logger.info("JVXL read: plane " + this.params.thePlane);
+if (param2 == -1 && param3 < 0) param3 = -param3;
+} else {
+this.params.thePlane = null;
+}if (param1 < 0 && param2 != -1) {
+this.params.isContoured = (param3 != 0);
+var nContoursRead = this.parseInt();
+if (nContoursRead == -2147483648) {
+if (this.line.charAt(this.next[0]) == '[') {
+this.jvxlData.contourValues = this.params.contoursDiscrete = this.parseFloatArray(null, null, null);
+JU.Logger.info("JVXL read: contourValues " + JU.Escape.eAF(this.jvxlData.contourValues));
+this.jvxlData.contourColixes = this.params.contourColixes = JU.C.getColixArray(this.getQuotedStringNext());
+this.jvxlData.contourColors = JU.C.getHexCodes(this.jvxlData.contourColixes);
+JU.Logger.info("JVXL read: contourColixes " + this.jvxlData.contourColors);
+this.params.nContours = this.jvxlData.contourValues.length;
+}} else {
+if (nContoursRead < 0) {
+nContoursRead = -1 - nContoursRead;
+this.params.contourFromZero = false;
+}if (nContoursRead != 0 && this.params.nContours == 0) {
+this.params.nContours = nContoursRead;
+JU.Logger.info("JVXL read: contours " + this.params.nContours);
+}}} else {
+this.params.isContoured = false;
+}this.jvxlData.isJvxlPrecisionColor = (param1 == -1 && param2 == -2 || param3 < 0);
+this.params.isBicolorMap = (param1 > 0 && param2 < 0);
+this.jvxlDataIsColorMapped = (param3 != 0);
+if (this.jvxlDataIsColorMapped) this.jvxlData.colorScheme = "RGB";
+this.jvxlDataIs2dContour = (this.jvxlDataIsColorMapped && this.params.isContoured);
+if (this.params.isBicolorMap || this.params.colorBySign) this.jvxlCutoff = 0;
+this.surfaceDataCount = (param1 < -1 ? -1 - param1 : param1 > 0 ? param1 : 0);
+if (param1 == -1) this.edgeDataCount = 0;
+ else this.edgeDataCount = (param2 < -1 ? -param2 : param2 > 0 ? param2 : 0);
+this.colorDataCount = (this.params.isBicolorMap ? -param2 : param3 < -1 ? -param3 : param3 > 0 ? param3 : 0);
+if (this.params.colorBySign) this.params.isBicolorMap = true;
+var dataMin = NaN;
+var dataMax = NaN;
+var red = NaN;
+var blue = NaN;
+var insideOut = (this.line.indexOf("insideOut") >= 0);
+if (this.jvxlDataIsColorMapped) {
+dataMin = this.parseFloat();
+dataMax = this.parseFloat();
+red = this.parseFloat();
+blue = this.parseFloat();
+}this.jvxlSetColorRanges(dataMin, dataMax, red, blue, insideOut);
+}, "~B");
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapDataIgnored){
+this.thisInside = !this.params.isContoured;
+if (!this.readSurfaceDataXML()) this.readSurfaceDataJXR();
+}, "~B");
+Clazz.overrideMethod(c$, "jvxlSkipData",
+function(nPoints, doSkipColorData){
+if (this.surfaceDataCount > 0) this.jvxlSkipDataBlock(nPoints, true);
+if (this.edgeDataCount > 0) this.jvxlSkipDataBlock(this.edgeDataCount, false);
+if (this.jvxlDataIsColorMapped && doSkipColorData) this.jvxlSkipDataBlock(this.colorDataCount, false);
+}, "~N,~B");
+Clazz.defineMethod(c$, "jvxlSkipDataBlock",
+function(nPoints, isInt){
+var n = 0;
+while (n < nPoints) {
+this.rd();
+n += (isInt ? this.countData(this.line) : J.jvxl.data.JvxlCoder.jvxlDecompressString(this.line).length);
+}
+}, "~N,~B");
+Clazz.defineMethod(c$, "countData",
+function(str){
+var $private = Clazz.checkPrivateMethod (arguments);
+if ($private != null) {
+return $private.apply (this, arguments);
+}
+var count = 0;
+var n = this.parseIntStr(str);
+while (n != -2147483648) {
+count += n;
+n = this.parseIntNext(str);
+}
+return count;
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlXmlReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlXmlReader.js
new file mode 100755
index 000000000000..fa35f9ebf95f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/JvxlXmlReader.js
@@ -0,0 +1,700 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.JvxlXmlReader", ["java.util.Hashtable", "JU.AU", "$.BS", "$.CU", "$.Lst", "$.P3", "$.P4", "$.PT", "$.SB", "J.jvxl.data.JvxlCoder", "$.MeshData", "J.jvxl.readers.XmlReader", "J.shapesurface.IsosurfaceMesh", "JU.C", "$.ColorEncoder", "$.Escape", "$.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.JVXL_VERSION = "2.3";
+this.surfaceDataCount = 0;
+this.edgeDataCount = 0;
+this.colorDataCount = 0;
+this.excludedTriangleCount = 0;
+this.excludedVertexCount = 0;
+this.invalidatedVertexCount = 0;
+this.haveContourData = false;
+this.xr = null;
+this.isXmlFile = true;
+this.thisInside = false;
+this.tempDataXml = null;
+this.bsVoxelBitSet = null;
+this.includeValueNaN = true;
+this.valueCount = 0;
+this.valueMin = NaN;
+this.valueRange = NaN;
+this.fractionPtr = 0;
+this.colorPtr = 0;
+this.strFractionTemp = "";
+this.haveReadColorData = false;
+this.jvxlColorEncodingRead = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "JvxlXmlReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.JvxlXmlReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2JXR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2JXR",
+function(sg, br){
+this.init2VFR(sg, br);
+this.jvxlData.wasJvxl = this.isJvxl = true;
+this.isXLowToHigh = this.canDownsample = false;
+this.xr = new J.jvxl.readers.XmlReader(br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readVolumeData",
+function(isMapData){
+if (!this.readVolumeDataVFR(isMapData)) return false;
+this.strFractionTemp = this.jvxlEdgeDataRead;
+this.fractionPtr = 0;
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "gotoAndReadVoxelData",
+function(isMapData){
+this.initializeVolumetricData();
+if (this.nPointsX < 0 || this.nPointsY < 0 || this.nPointsZ < 0) return true;
+try {
+this.gotoData(this.params.fileIndex - 1, this.nPointsX * this.nPointsY * this.nPointsZ);
+if (this.vertexDataOnly) return true;
+this.volumeData.setMappingPlane(this.params.thePlane);
+this.readSurfaceData(isMapData);
+this.volumeData.setMappingPlane(null);
+if (this.edgeDataCount > 0) this.jvxlEdgeDataRead = this.jvxlReadFractionData("edge", this.edgeDataCount);
+this.params.bsExcluded = this.jvxlData.jvxlExcluded = new Array(4);
+this.hasColorData = (this.colorDataCount > 0);
+if (this.hasColorData) this.jvxlColorDataRead = this.jvxlReadFractionData("color", this.colorDataCount);
+if (this.excludedVertexCount > 0) {
+this.jvxlData.jvxlExcluded[0] = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedVertexData", null, false, false));
+if (this.xr.isNext("jvxlExcludedPlaneData")) this.jvxlData.jvxlExcluded[2] = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedPlaneData", null, false, false));
+}if (this.excludedTriangleCount > 0) this.jvxlData.jvxlExcluded[3] = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedTriangleData", null, false, false));
+if (this.invalidatedVertexCount > 0) this.jvxlData.jvxlExcluded[1] = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlInvalidatedVertexData", null, false, false));
+if (this.haveContourData) this.jvxlDecodeContourData(this.jvxlData, this.xr.getXmlData("jvxlContourData", null, false, false));
+if (this.jvxlDataIsColorMapped && this.jvxlData.nVertexColors > 0) {
+this.jvxlData.vertexColorMap = new java.util.Hashtable();
+var vdata = this.xr.getXmlData("jvxlVertexColorData", null, true, false);
+var baseColor = J.jvxl.readers.XmlReader.getXmlAttrib(vdata, "baseColor");
+this.jvxlData.baseColor = (baseColor.length > 0 ? baseColor : null);
+for (var i = 0; i < this.jvxlData.nVertexColors; i++) {
+var s = this.xr.getXmlData("jvxlColorMap", vdata, true, false);
+var color = J.jvxl.readers.XmlReader.getXmlAttrib(s, "color");
+var bs = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlColorMap", s, false, false));
+this.jvxlData.vertexColorMap.put(color, bs);
+}
+}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error(e.toString());
+return false;
+} else {
+throw e;
+}
+}
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var s = this.xr.getXmlDataLF("jvxlFileTitle", null, false, false, true);
+this.jvxlFileHeaderBuffer = JU.SB.newS(s == null ? "" : s);
+this.xr.toTag("jvxlVolumeData");
+var data = this.tempDataXml = this.xr.getXmlData("jvxlVolumeData", null, true, false);
+this.volumetricOrigin.setT(this.xr.getXmlPoint(data, "origin"));
+this.isAngstroms = true;
+this.readVector(0);
+this.readVector(1);
+this.readVector(2);
+this.line = this.xr.toTag("jvxlSurfaceSet");
+this.nSurfaces = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(this.line, "count"));
+JU.Logger.info("jvxl file surfaces: " + this.nSurfaces);
+JU.Logger.info("using default edge fraction base and range");
+JU.Logger.info("using default color fraction base and range");
+this.cJvxlEdgeNaN = String.fromCharCode(this.edgeFractionBase + this.edgeFractionRange);
+});
+Clazz.overrideMethod(c$, "getJVXLCutoff",
+function(){
+return this.params.cutoff;
+});
+Clazz.defineMethod(c$, "readVector",
+function(voxelVectorIndex){
+var data = this.xr.getXmlData("jvxlVolumeVector", this.tempDataXml, true, true);
+this.tempDataXml = this.tempDataXml.substring(this.tempDataXml.indexOf(data) + data.length);
+var n = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "count"));
+if (n == -2147483648) this.vertexDataOnly = true;
+this.voxelCounts[voxelVectorIndex] = (n < 0 ? 0 : n);
+this.volumetricVectors[voxelVectorIndex].setT(this.xr.getXmlPoint(data, "vector"));
+if (this.isAnisotropic) this.setVectorAnisotropy(this.volumetricVectors[voxelVectorIndex]);
+}, "~N");
+Clazz.overrideMethod(c$, "gotoData",
+function(n, nPoints){
+if (n > 0) JU.Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
+this.vertexDataOnly = this.jvxlData.vertexDataOnly = (nPoints == 0);
+for (var i = 0; i < n; i++) {
+this.jvxlSkipData(nPoints, true);
+}
+this.xr.toTag("jvxlSurface");
+this.jvxlReadSurfaceInfo();
+}, "~N,~N");
+Clazz.defineMethod(c$, "jvxlSkipData",
+function(nPoints, doSkipColorData){
+this.rd();
+this.xr.skipTag("jvxlSurface");
+}, "~N,~B");
+Clazz.defineMethod(c$, "jvxlReadSurfaceInfo",
+function(){
+var data = this.xr.getXmlData("jvxlSurfaceInfo", null, true, true);
+this.isXLowToHigh = J.jvxl.readers.XmlReader.getXmlAttrib(data, "isXLowToHigh").equals("true");
+var s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "cutoff");
+if (s.indexOf(" ") < 0) {
+this.jvxlCutoff = this.parseFloatStr(s);
+if (!Double.isNaN(this.jvxlCutoff)) JU.Logger.info("JVXL read: cutoff " + this.jvxlCutoff);
+} else {
+this.jvxlCutoffRange = this.parseFloatArrayStr(s);
+this.jvxlCutoff = this.jvxlCutoffRange[0];
+JU.Logger.info("JVXL read: cutoff " + JU.Escape.eAF(this.jvxlCutoffRange));
+}this.params.cutoff = this.jvxlCutoff;
+var nContourData = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nContourData"));
+this.haveContourData = (nContourData > 0);
+this.params.isContoured = this.jvxlData.isModelConnected = J.jvxl.readers.XmlReader.getXmlAttrib(data, "contoured").equals("true");
+this.params.isModelConnected = J.jvxl.readers.XmlReader.getXmlAttrib(data, "isModelConnected").equals("true");
+if (this.params.isContoured) {
+var nContoursRead = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nContours"));
+if (nContoursRead <= 0) {
+nContoursRead = 0;
+} else {
+if (this.params.thisContour < 0) this.params.thisContour = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "thisContour"));
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "contourValues");
+if (s.length > 0) {
+s = s.$replace('[', ' ').$replace(']', ' ');
+this.jvxlData.contourValues = this.params.contoursDiscrete = this.parseFloatArrayStr(s);
+JU.Logger.info("JVXL read: contourValues " + JU.Escape.eAF(this.jvxlData.contourValues));
+}s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "contourColors");
+if (s.length > 0) {
+this.jvxlData.contourColixes = this.params.contourColixes = JU.C.getColixArray(s);
+this.jvxlData.contourColors = JU.C.getHexCodes(this.jvxlData.contourColixes);
+JU.Logger.info("JVXL read: contourColixes " + JU.C.getHexCodes(this.jvxlData.contourColixes));
+}this.params.contourFromZero = J.jvxl.readers.XmlReader.getXmlAttrib(data, "contourFromZero").equals("true");
+}this.params.nContours = (this.haveContourData ? nContourData : nContoursRead);
+}this.jvxlData.nVertexColors = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nVertexColors"));
+this.params.isBicolorMap = J.jvxl.readers.XmlReader.getXmlAttrib(data, "bicolorMap").equals("true");
+if (this.params.isBicolorMap) {
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "colorPositive");
+if (s.length > 0 && this.params.colorRgb == -2147483648 && this.params.colorPos == -16776961) this.params.colorPos = JU.CU.getArgbFromString(s);
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "colorNegative");
+if (s.length > 0 && this.params.colorRgb == -2147483648 && this.params.colorNeg == -65536) this.params.colorNeg = JU.CU.getArgbFromString(s);
+}if (this.params.isBicolorMap || this.params.colorBySign) this.jvxlCutoff = 0;
+this.jvxlDataIsColorMapped = ((this.params.colorRgb == -2147483648 || this.params.colorRgb == 2147483647) && (this.params.isBicolorMap || J.jvxl.readers.XmlReader.getXmlAttrib(data, "colorMapped").equals("true")));
+this.jvxlData.isJvxlPrecisionColor = J.jvxl.readers.XmlReader.getXmlAttrib(data, "precisionColor").equals("true");
+this.jvxlData.jvxlDataIsColorDensity = this.params.colorDensity = (this.params.colorRgb == -2147483648 && J.jvxl.readers.XmlReader.getXmlAttrib(data, "colorDensity").equals("true"));
+if (this.jvxlData.jvxlDataIsColorDensity && Float.isNaN(this.params.pointSize)) {
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "pointSize");
+if (s.length > 0) this.jvxlData.pointSize = this.params.pointSize = this.parseFloatStr(s);
+}s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "allowVolumeRender");
+this.jvxlData.allowVolumeRender = this.params.allowVolumeRender = (s.length == 0 || s.equalsIgnoreCase("true"));
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "plane");
+if (s.indexOf("{") >= 0) {
+this.params.thePlane = null;
+this.params.mapLattice = null;
+try {
+this.params.thePlane = JU.Escape.uP(s);
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "maplattice");
+JU.Logger.info("JVXL read: plane " + this.params.thePlane);
+if (s.indexOf("{") >= 0) {
+this.params.mapLattice = JU.Escape.uP(s);
+JU.Logger.info("JVXL read: mapLattice " + this.params.mapLattice);
+}if (this.params.scale3d == 0) this.params.scale3d = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "scale3d"));
+if (Float.isNaN(this.params.scale3d)) this.params.scale3d = 0;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (this.params.thePlane == null) {
+JU.Logger.error("JVXL Error reading plane definition -- setting to 0 0 1 0 (z=0)");
+this.params.thePlane = JU.P4.new4(0, 0, 1, 0);
+} else {
+JU.Logger.error("JVXL Error reading mapLattice definition -- ignored");
+}} else {
+throw e;
+}
+}
+this.surfaceDataCount = 0;
+this.edgeDataCount = 0;
+} else {
+this.params.thePlane = null;
+this.surfaceDataCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nSurfaceInts"));
+this.edgeDataCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nBytesUncompressedEdgeData"));
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "fixedLattice");
+if (s.indexOf("{") >= 0) this.jvxlData.fixedLattice = JU.Escape.uP(s);
+}this.excludedVertexCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nExcludedVertexes"));
+this.excludedTriangleCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nExcludedTriangles"));
+this.invalidatedVertexCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nInvalidatedVertexes"));
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "slabInfo");
+if (s.length > 0) this.jvxlData.slabInfo = s;
+this.colorDataCount = Math.max(0, this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "nBytesUncompressedColorData")));
+this.jvxlDataIs2dContour = (this.params.thePlane != null && this.jvxlDataIsColorMapped);
+this.jvxlData.color = J.jvxl.readers.XmlReader.getXmlAttrib(data, "color");
+if (this.jvxlData.color.length == 0 || this.jvxlData.color.indexOf("null") >= 0) this.jvxlData.color = "orange";
+this.jvxlData.translucency = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "translucency"));
+if (Float.isNaN(this.jvxlData.translucency)) this.jvxlData.translucency = 0;
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "meshColor");
+if (s.length > 0) this.jvxlData.meshColor = s;
+s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "rendering");
+if (s.length > 0) this.jvxlData.rendering = s;
+this.jvxlData.colorScheme = J.jvxl.readers.XmlReader.getXmlAttrib(data, "colorScheme");
+if (this.jvxlData.colorScheme.length == 0) this.jvxlData.colorScheme = (this.jvxlDataIsColorMapped ? "roygb" : null);
+if (this.jvxlData.thisSet == null) {
+var n = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "set"));
+if (n > 0) {
+this.jvxlData.thisSet = new JU.BS();
+this.jvxlData.thisSet.set(n - 1);
+}var a = J.jvxl.readers.XmlReader.getXmlAttrib(data, "subset");
+if (a != null && a.length > 2) {
+var sets = a.$replace('[', ' ').$replace(']', ' ').trim().$plit(" ");
+if (sets.length > 0) {
+this.jvxlData.thisSet = new JU.BS();
+for (var i = sets.length; --i >= 0; ) {
+this.jvxlData.thisSet.set(JU.PT.parseInt(sets[i]) - 1);
+}
+}}}this.jvxlData.slabValue = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "slabValue"));
+this.jvxlData.isSlabbable = (J.jvxl.readers.XmlReader.getXmlAttrib(data, "slabbable").equalsIgnoreCase("true"));
+this.jvxlData.diameter = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "diameter"));
+if (this.jvxlData.diameter == -2147483648) this.jvxlData.diameter = 0;
+if (this.jvxlDataIs2dContour) this.params.isContoured = true;
+if (this.params.colorBySign) this.params.isBicolorMap = true;
+var insideOut = J.jvxl.readers.XmlReader.getXmlAttrib(data, "insideOut").equals("true");
+var dataMin = NaN;
+var dataMax = NaN;
+var red = NaN;
+var blue = NaN;
+if (this.jvxlDataIsColorMapped) {
+dataMin = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "dataMinimum"));
+dataMax = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "dataMaximum"));
+red = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "valueMappedToRed"));
+blue = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "valueMappedToBlue"));
+if (Float.isNaN(dataMin)) {
+dataMin = red = -1.0;
+dataMax = blue = 1;
+}}this.jvxlSetColorRanges(dataMin, dataMax, red, blue, insideOut);
+});
+Clazz.defineMethod(c$, "jvxlSetColorRanges",
+function(dataMin, dataMax, red, blue, insideOut){
+if (this.jvxlDataIsColorMapped) {
+if (!Float.isNaN(dataMin) && !Float.isNaN(dataMax)) {
+if (dataMax == 0 && dataMin == 0) {
+dataMin = -1;
+dataMax = 1;
+}this.params.mappedDataMin = dataMin;
+this.params.mappedDataMax = dataMax;
+JU.Logger.info("JVXL read: data_min/max " + this.params.mappedDataMin + "/" + this.params.mappedDataMax);
+}if (!this.params.rangeDefined) if (!Float.isNaN(red) && !Float.isNaN(blue)) {
+if (red == 0 && blue == 0) {
+red = -1;
+blue = 1;
+}this.params.valueMappedToRed = Math.min(red, blue);
+this.params.valueMappedToBlue = Math.max(red, blue);
+this.params.isColorReversed = (red > blue);
+this.params.rangeDefined = true;
+} else {
+this.params.valueMappedToRed = 0;
+this.params.valueMappedToBlue = 1;
+this.params.rangeDefined = true;
+}JU.Logger.info("JVXL read: color red/blue: " + this.params.valueMappedToRed + "/" + this.params.valueMappedToBlue);
+}this.jvxlData.valueMappedToRed = this.params.valueMappedToRed;
+this.jvxlData.valueMappedToBlue = this.params.valueMappedToBlue;
+this.jvxlData.mappedDataMin = this.params.mappedDataMin;
+this.jvxlData.mappedDataMax = this.params.mappedDataMax;
+this.jvxlData.isColorReversed = this.params.isColorReversed;
+if (this.params.insideOut) insideOut = !insideOut;
+this.params.insideOut = this.jvxlData.insideOut = insideOut;
+}, "~N,~N,~N,~N,~B");
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapDataIgnored){
+this.thisInside = !this.params.isContoured;
+if (this.readSurfaceDataXML()) return;
+this.tempDataXml = this.xr.getXmlData("jvxlEdgeData", null, true, false);
+this.bsVoxelBitSet = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlEdgeData", this.tempDataXml, false, false));
+this.readSurfaceDataJXR();
+}, "~B");
+Clazz.defineMethod(c$, "readSurfaceDataXML",
+function(){
+if (this.vertexDataOnly) {
+this.getEncodedVertexData();
+return true;
+}if (this.params.thePlane != null) {
+this.volumeData.setDataDistanceToPlane(this.params.thePlane);
+this.setVolumeDataV(this.volumeData);
+this.params.cutoff = 0;
+this.jvxlData.setSurfaceInfo(this.params.thePlane, this.params.mapLattice, 0, "");
+this.jvxlData.scale3d = this.params.scale3d;
+return true;
+}return false;
+});
+Clazz.defineMethod(c$, "readSurfaceDataJXR",
+function(){
+this.readSurfaceDataVFR(false);
+this.volumeData.setMappingPlane(null);
+});
+Clazz.defineMethod(c$, "jvxlReadFractionData",
+function(type, nPoints){
+var str;
+try {
+if (type.equals("edge")) {
+str = J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml, "data"));
+} else {
+var data = this.xr.getXmlData("jvxlColorData", null, true, false);
+this.jvxlData.isJvxlPrecisionColor = J.jvxl.readers.JvxlXmlReader.getEncoding(data).endsWith("2");
+str = J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(data, "data"));
+}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Error reading " + type + " data " + e);
+throw new NullPointerException();
+} else {
+throw e;
+}
+}
+return str;
+}, "~S,~N");
+Clazz.overrideMethod(c$, "getVoxelBitSet",
+function(nPoints){
+if (this.bsVoxelBitSet != null) return this.bsVoxelBitSet;
+var bs = new JU.BS();
+var bsVoxelPtr = 0;
+if (this.surfaceDataCount <= 0) return bs;
+var nThisValue = 0;
+while (bsVoxelPtr < nPoints) {
+nThisValue = this.parseInt();
+if (nThisValue == -2147483648) {
+this.rd();
+if (this.line == null || (nThisValue = this.parseIntStr(this.line)) == -2147483648) {
+if (!this.endOfData) JU.Logger.error("end of file in JvxlReader?" + " line=" + this.line);
+this.endOfData = true;
+nThisValue = 10000;
+}}this.thisInside = !this.thisInside;
+++this.jvxlNSurfaceInts;
+if (this.thisInside) bs.setBits(bsVoxelPtr, bsVoxelPtr + nThisValue);
+bsVoxelPtr += nThisValue;
+}
+return bs;
+}, "~N");
+Clazz.overrideMethod(c$, "getSurfacePointAndFraction",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+if (this.edgeDataCount <= 0) return this.getSPFv(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+ptReturn.scaleAdd2(fReturn[0] = this.jvxlGetNextFraction(this.edgeFractionBase, this.edgeFractionRange, 0.5), edgeVector, pointA);
+if (Float.isNaN(this.valueMin)) this.setValueMinMax();
+return (this.valueCount == 0 || this.includeValueNaN && Float.isNaN(fReturn[0]) ? fReturn[0] : this.getNextValue());
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.defineMethod(c$, "getNextValue",
+function(){
+var fraction = NaN;
+while (this.colorPtr < this.valueCount && Float.isNaN(fraction)) {
+if (this.jvxlData.isJvxlPrecisionColor) {
+fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(this.jvxlColorDataRead.charAt(this.colorPtr).charCodeAt(0), this.jvxlColorDataRead.charAt((this.colorPtr++) + this.valueCount).charCodeAt(0), this.colorFractionBase, this.colorFractionRange);
+} else {
+fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.jvxlColorDataRead.charAt(this.colorPtr++).charCodeAt(0), this.colorFractionBase, this.colorFractionRange, 0.5);
+}break;
+}
+return this.valueMin + fraction * this.valueRange;
+});
+Clazz.defineMethod(c$, "setValueMinMax",
+function(){
+this.valueCount = this.jvxlColorDataRead.length;
+if (this.jvxlData.isJvxlPrecisionColor) this.valueCount /= 2;
+this.includeValueNaN = (this.valueCount != this.jvxlEdgeDataRead.length);
+this.valueMin = (!this.jvxlData.isJvxlPrecisionColor ? this.params.valueMappedToRed : this.params.mappedDataMin == 3.4028235E38 ? 0.0 : this.params.mappedDataMin);
+this.valueRange = (!this.jvxlData.isJvxlPrecisionColor ? this.params.valueMappedToBlue : this.params.mappedDataMin == 3.4028235E38 ? 1.0 : this.params.mappedDataMax) - this.valueMin;
+this.haveReadColorData = true;
+});
+Clazz.defineMethod(c$, "jvxlGetNextFraction",
+function(base, range, fracOffset){
+if (this.fractionPtr >= this.strFractionTemp.length) {
+if (!this.endOfData) JU.Logger.error("end of file reading compressed fraction data");
+this.endOfData = true;
+this.strFractionTemp = "" + String.fromCharCode(base);
+this.fractionPtr = 0;
+}return J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.strFractionTemp.charAt(this.fractionPtr++).charCodeAt(0), base, range, fracOffset);
+}, "~N,~N,~N");
+Clazz.overrideMethod(c$, "readColorData",
+function(){
+if (!this.jvxlDataIsColorMapped) return "";
+var vertexCount = this.jvxlData.vertexCount = this.meshData.vc;
+var colixes = this.meshData.vcs;
+var vertexValues = this.meshData.vvs;
+if ("none".equals(this.jvxlColorEncodingRead)) {
+this.jvxlData.vertexColors = Clazz.newIntArray (vertexCount, 0);
+var nextc = Clazz.newIntArray (1, 0);
+var n = JU.PT.parseIntNext(this.jvxlColorDataRead, nextc);
+n = Math.min(n, vertexCount);
+var tokens = JU.PT.getTokens(this.jvxlColorDataRead.substring(nextc[0]));
+var haveTranslucent = false;
+var trans = this.jvxlData.translucency;
+var lastColor = 0;
+for (var i = 0; i < n; i++) try {
+var c = J.jvxl.readers.JvxlXmlReader.getColor(tokens[i]);
+if (c == 0) c = lastColor;
+ else lastColor = c;
+colixes[i] = JU.C.getColixTranslucent(this.jvxlData.vertexColors[i] = c);
+if (JU.C.isColixTranslucent(colixes[i])) haveTranslucent = true;
+ else if (trans != 0) colixes[i] = JU.C.getColixTranslucent3(colixes[i], true, trans);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.info("JvxlXmlReader: Cannot interpret color code: " + tokens[i]);
+} else {
+throw e;
+}
+}
+
+if (haveTranslucent && trans == 0) {
+this.jvxlData.translucency = 0.5;
+}return "-";
+}if (this.params.colorEncoder == null) this.params.colorEncoder = new JU.ColorEncoder(null, null);
+this.params.colorEncoder.setColorScheme(null, false);
+this.params.colorEncoder.setRange(this.params.valueMappedToRed, this.params.valueMappedToBlue, this.params.isColorReversed);
+JU.Logger.info("JVXL reading color data mapped min/max: " + this.params.mappedDataMin + "/" + this.params.mappedDataMax + " for " + vertexCount + " vertices." + " using encoding keys " + this.colorFractionBase + " " + this.colorFractionRange);
+JU.Logger.info("mapping red-->blue for " + this.params.valueMappedToRed + " to " + this.params.valueMappedToBlue + " colorPrecision:" + this.jvxlData.isJvxlPrecisionColor);
+var getValues = (Float.isNaN(this.valueMin));
+if (getValues) this.setValueMinMax();
+var contourPlaneMinimumValue = 3.4028235E38;
+var contourPlaneMaximumValue = -3.4028235E38;
+if (colixes == null || colixes.length < vertexCount) this.meshData.vcs = colixes = Clazz.newShortArray (vertexCount, 0);
+var colixNeg = 0;
+var colixPos = 0;
+if (this.params.colorBySign) {
+colixPos = JU.C.getColix(this.params.isColorReversed ? this.params.colorNeg : this.params.colorPos);
+colixNeg = JU.C.getColix(this.params.isColorReversed ? this.params.colorPos : this.params.colorNeg);
+}var vertexIncrement = this.meshData.vertexIncrement;
+var needContourMinMax = (this.params.mappedDataMin == 3.4028235E38);
+for (var i = 0; i < vertexCount; i += vertexIncrement) {
+var value;
+if (getValues) value = vertexValues[i] = this.getNextValue();
+ else value = vertexValues[i];
+if (needContourMinMax) {
+if (value < contourPlaneMinimumValue) contourPlaneMinimumValue = value;
+if (value > contourPlaneMaximumValue) contourPlaneMaximumValue = value;
+}}
+if (needContourMinMax) {
+this.params.mappedDataMin = contourPlaneMinimumValue;
+this.params.mappedDataMax = contourPlaneMaximumValue;
+}if (this.jvxlData.colorScheme != null) {
+var setContourValue = (this.marchingSquares != null && this.params.isContoured);
+for (var i = 0; i < vertexCount; i += vertexIncrement) {
+var value = vertexValues[i];
+if (setContourValue) {
+this.marchingSquares.setContourData(i, value);
+continue;
+}var colix = (!this.params.colorBySign ? this.params.colorEncoder.getColorIndex(value) : (this.params.isColorReversed ? value > 0 : value <= 0) ? colixNeg : colixPos);
+colixes[i] = JU.C.getColixTranslucent3(colix, true, this.jvxlData.translucency);
+}
+}return this.jvxlColorDataRead + "\n";
+});
+c$.getColor = Clazz.defineMethod(c$, "getColor",
+function(c){
+var n = 0;
+try {
+switch ((c.charAt(0)).charCodeAt(0)) {
+case 91:
+n = JU.CU.getArgbFromString(c);
+break;
+case 48:
+n = JU.PT.parseIntRadix(c.substring(2), 16);
+break;
+default:
+n = JU.PT.parseIntRadix(c, 10);
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+return n;
+}, "~S");
+Clazz.defineMethod(c$, "getEncodedVertexData",
+function(){
+var sdata = this.xr.getXmlData("jvxlSurfaceData", null, true, false);
+this.jvxlDecodeVertexData(this.xr.getXmlData("jvxlVertexData", sdata, true, false), false);
+var tData = this.xr.getXmlData("jvxlTriangleData", sdata, true, false);
+var edgeData = this.xr.getXmlData("jvxlTriangleEdgeData", sdata, true, false);
+var polygonColorData = this.xr.getXmlData("jvxlPolygonColorData", sdata, false, false);
+this.jvxlDecodeTriangleData(tData, edgeData, polygonColorData);
+var cData = this.xr.getXmlData("jvxlColorData", sdata, true, false);
+this.jvxlColorEncodingRead = J.jvxl.readers.JvxlXmlReader.getEncoding(cData);
+this.jvxlData.isJvxlPrecisionColor = this.jvxlColorEncodingRead.endsWith("2");
+cData = this.getData(cData, "jvxlColorData");
+this.jvxlColorDataRead = (this.jvxlColorEncodingRead.equals("none") ? cData : J.jvxl.data.JvxlCoder.jvxlDecompressString(cData));
+this.jvxlDataIsColorMapped = ((this.params.colorRgb == -2147483648 || this.params.colorRgb == 2147483647) && this.jvxlColorDataRead.length > 0);
+if (this.haveContourData) this.jvxlDecodeContourData(this.jvxlData, this.xr.getXmlData("jvxlContourData", null, false, false));
+});
+Clazz.defineMethod(c$, "getData",
+function(sdata, name){
+var data = J.jvxl.readers.XmlReader.getXmlAttrib(sdata, "data");
+if (data.length == 0) data = this.xr.getXmlData(name, sdata, false, false);
+return data;
+}, "~S,~S");
+c$.getEncoding = Clazz.defineMethod(c$, "getEncoding",
+function(data){
+if (J.jvxl.readers.XmlReader.getXmlAttrib(data, "len").length > 0) return "";
+var s = J.jvxl.readers.XmlReader.getXmlAttrib(data, "encoding");
+return (s.length == 0 ? "none" : s);
+}, "~S");
+Clazz.defineMethod(c$, "jvxlDecodeVertexData",
+function(data, asArray){
+var vertexCount = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(data, "count"));
+if (!asArray) JU.Logger.info("Reading " + vertexCount + " vertices");
+var ptCount = vertexCount * 3;
+var vertices = (asArray ? new Array(vertexCount) : null);
+var fraction;
+var vData = J.jvxl.readers.XmlReader.getXmlAttrib(data, "data");
+var encoding = J.jvxl.readers.JvxlXmlReader.getEncoding(data);
+if ("none".equals(encoding)) {
+if (vData.length == 0) vData = this.xr.getXmlData("jvxlVertexData", data, false, false);
+var fdata = JU.PT.parseFloatArray(vData);
+if (fdata[0] != vertexCount * 3) JU.Logger.info("JvxlXmlReader: vertexData count=" + (Clazz.floatToInt(fdata[0])) + "; expected " + (vertexCount * 3));
+for (var i = 0, pt = 1; i < vertexCount; i++) {
+var p = JU.P3.new3(fdata[pt++], fdata[pt++], fdata[pt++]);
+if (asArray) vertices[i] = p;
+ else this.addVertexCopy(p, 0, i, false);
+}
+} else {
+var min = this.xr.getXmlPoint(data, "min");
+var range = this.xr.getXmlPoint(data, "max");
+range.sub(min);
+var colorFractionBase = this.jvxlData.colorFractionBase;
+var colorFractionRange = this.jvxlData.colorFractionRange;
+var s = J.jvxl.data.JvxlCoder.jvxlDecompressString(vData);
+if (s.length == 0) s = this.xr.getXmlData("jvxlVertexData", data, false, false);
+for (var i = 0, pt = -1; i < vertexCount; i++) {
+var p = new JU.P3();
+fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(s.charAt(++pt).charCodeAt(0), s.charAt(pt + ptCount).charCodeAt(0), colorFractionBase, colorFractionRange);
+p.x = min.x + fraction * range.x;
+fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(s.charAt(++pt).charCodeAt(0), s.charAt(pt + ptCount).charCodeAt(0), colorFractionBase, colorFractionRange);
+p.y = min.y + fraction * range.y;
+fraction = J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(s.charAt(++pt).charCodeAt(0), s.charAt(pt + ptCount).charCodeAt(0), colorFractionBase, colorFractionRange);
+p.z = min.z + fraction * range.z;
+if (asArray) vertices[i] = p;
+ else this.addVertexCopy(p, 0, i, false);
+}
+}return vertices;
+}, "~S,~B");
+Clazz.defineMethod(c$, "jvxlDecodeTriangleData",
+function(tdata, edgeData, colorData){
+var nTriangles = this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(tdata, "count"));
+if (nTriangles < 0) return;
+var nextc = Clazz.newIntArray (1, 0);
+var nColors = (colorData == null ? -1 : 1);
+var color = 0;
+JU.Logger.info("Reading " + nTriangles + " triangles");
+var encoding = J.jvxl.readers.JvxlXmlReader.getEncoding(tdata);
+tdata = this.getData(tdata, "jvxlTriangleData");
+var edata = this.getData(edgeData, "jvxlTriangleEdgeData");
+var vertex = Clazz.newIntArray (3, 0);
+var nextp = Clazz.newIntArray (1, 0);
+var nexte = null;
+var edgeMask = 7;
+var haveEdgeInfo;
+var haveEncoding = !"none".equals(encoding);
+if (haveEncoding) {
+tdata = J.jvxl.data.JvxlCoder.jvxlDecompressString(tdata);
+edata = J.jvxl.data.JvxlCoder.jvxlDecompressString(edata).trim();
+haveEdgeInfo = (edata.length == nTriangles);
+} else {
+var n = JU.PT.parseIntNext(tdata, nextp);
+haveEdgeInfo = (edata.length > 0);
+if (haveEdgeInfo) {
+nexte = Clazz.newIntArray (1, 0);
+JU.PT.parseIntNext(edata, nexte);
+} else if (n > 0) {
+JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count=" + n + "; expected " + nTriangles);
+}}for (var i = 0, v = 0, p = 0, pt = -1; i < nTriangles; ) {
+if (haveEncoding) {
+var ch = tdata.charAt(++pt);
+var diff;
+switch ((ch).charCodeAt(0)) {
+case 33:
+diff = 0;
+break;
+case 43:
+case 46:
+case 32:
+case 10:
+case 13:
+case 9:
+case 44:
+continue;
+case 45:
+case 48:
+case 49:
+case 50:
+case 51:
+case 52:
+case 53:
+case 54:
+case 55:
+case 56:
+case 57:
+nextp[0] = pt;
+diff = JU.PT.parseIntNext(tdata, nextp);
+pt = nextp[0] - 1;
+break;
+default:
+diff = ch.charCodeAt(0) - 92;
+}
+v += diff;
+} else {
+v = JU.PT.parseIntNext(tdata, nextp) - 1;
+}vertex[p] = v;
+if (++p == 3) {
+p = 0;
+if (haveEdgeInfo) {
+edgeMask = (nexte == null ? (edata.charAt(i)).charCodeAt(0) - 48 : JU.PT.parseIntNext(edata, nexte));
+if (edgeMask < 0 || edgeMask > 7) edgeMask = 7;
+}if (--nColors == 0) {
+nColors = (JU.PT.parseIntNext(colorData, nextc));
+var c = JU.PT.parseIntNext(colorData, nextc);
+if (c == -2147483648) nColors = 0;
+ else color = c | 0xFF000000;
+}this.addTriangleCheck(vertex[0], vertex[1], vertex[2], edgeMask, color, false, color);
+i++;
+}}
+}, "~S,~S,~S");
+Clazz.defineMethod(c$, "jvxlDecodeContourData",
+function(jvxlData, data){
+var vs = new JU.Lst();
+var values = new JU.SB();
+var colors = new JU.SB();
+var pt = -1;
+jvxlData.vContours = null;
+if (data == null) return;
+while ((pt = data.indexOf("= 0) {
+var v = new JU.Lst();
+var s = this.xr.getXmlData("jvxlContour", data.substring(pt), true, false);
+var value = this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(s, "value"));
+values.append(" ").appendF(value);
+var color = J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(s, "color"));
+var colix = JU.C.getColix(color);
+colors.append(" ").append(JU.Escape.escapeColor(color));
+var fData = J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(s, "data"));
+var bs = J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour", s, false, false));
+var n = bs.length();
+J.shapesurface.IsosurfaceMesh.setContourVector(v, n, bs, value, colix, color, JU.SB.newS(fData));
+vs.addLast(v);
+}
+var n = vs.size();
+if (n > 0) {
+jvxlData.vContours = JU.AU.createArrayOfArrayList(n);
+jvxlData.contourColixes = this.params.contourColixes = Clazz.newShortArray (n, 0);
+jvxlData.contourValues = this.params.contoursDiscrete = Clazz.newFloatArray (n, 0);
+for (var i = 0; i < n; i++) {
+jvxlData.vContours[i] = vs.get(i);
+jvxlData.contourValues[i] = (jvxlData.vContours[i].get(2)).floatValue();
+jvxlData.contourColixes[i] = (jvxlData.vContours[i].get(3))[0];
+}
+jvxlData.contourColors = JU.C.getHexCodes(jvxlData.contourColixes);
+JU.Logger.info("JVXL read: " + n + " discrete contours");
+JU.Logger.info("JVXL read: contour values: " + values);
+JU.Logger.info("JVXL read: contour colors: " + colors);
+}}, "J.jvxl.data.JvxlData,~S");
+Clazz.overrideMethod(c$, "postProcessVertices",
+function(){
+var bsInvalid = this.params.bsExcluded[1];
+if (bsInvalid != null) {
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshData.invalidateVertices(bsInvalid);
+if (this.meshDataServer != null) {
+this.meshDataServer.fillMeshData(this.meshData, 4, null);
+this.meshData = new J.jvxl.data.MeshData();
+}this.updateTriangles();
+}});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/KinemageReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/KinemageReader.js
new file mode 100755
index 000000000000..6aa0fe107c03
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/KinemageReader.js
@@ -0,0 +1,122 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PmeshReader"], "J.jvxl.readers.KinemageReader", ["JU.CU", "$.P3", "$.PT", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nDots = 0;
+this.vMin = -3.4028235E38;
+this.vMax = 3.4028235E38;
+this.pointType = 0;
+this.findString = null;
+this.lastAtom = "";
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "KinemageReader", J.jvxl.readers.PmeshReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.KinemageReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PR(sg, br);
+this.type = "kinemage";
+this.setHeader();
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+if (this.params.parameters != null && this.params.parameters.length >= 2) {
+this.vMin = this.params.parameters[1];
+this.vMax = (this.params.parameters.length >= 3 ? this.params.parameters[2] : this.vMin);
+this.pointType = (this.params.parameters.length >= 4 ? Clazz.floatToInt(this.params.parameters[3]) : 0);
+this.findString = this.params.calculationType;
+}return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readVertices",
+function(){
+this.rd();
+var n0;
+while (this.line != null) {
+if (this.line.length != 0 && this.line.charAt(0) == '@') {
+JU.Logger.info(this.line);
+if (this.line.indexOf("contact}") >= 0 || this.line.indexOf("overlap}") >= 0 || this.line.indexOf("H-bonds}") >= 0) {
+if (this.line.indexOf("@dotlist") == 0) {
+n0 = this.nDots;
+this.readDots();
+if (this.nDots > n0) JU.Logger.info("dots: " + (this.nDots - n0) + "/" + this.nDots);
+continue;
+} else if (this.line.indexOf("@vectorlist") == 0) {
+n0 = this.nPolygons;
+this.readVectors();
+if (this.nPolygons > n0) JU.Logger.info("lines: " + (this.nPolygons - n0) + "/" + this.nPolygons);
+continue;
+}}}this.rd();
+}
+return true;
+});
+Clazz.defineMethod(c$, "readDots",
+function(){
+var color = Clazz.newIntArray (1, 0);
+while (this.rd() != null && this.line.indexOf('@') < 0) {
+var i = this.getPoint(this.line, 2, color, true);
+if (i < 0) continue;
+this.nDots++;
+this.nTriangles = this.addTriangleCheck(i, i, i, 7, 0, false, color[0]);
+}
+});
+Clazz.defineMethod(c$, "readVectors",
+function(){
+var color = Clazz.newIntArray (1, 0);
+while (this.rd() != null && this.line.indexOf('@') < 0) {
+var ia = this.getPoint(this.line, 3, color, true);
+var ib = this.getPoint(this.line.substring(this.line.lastIndexOf('{')), 2, color, false);
+if (ia < 0 || ib < 0) continue;
+this.nPolygons++;
+this.nTriangles = this.addTriangleCheck(ia, ib, ib, 7, 0, false, color[0]);
+}
+});
+Clazz.defineMethod(c$, "getPoint",
+function(line, i, retColor, checkType){
+if (this.findString != null) {
+var atom = line.substring(0, line.indexOf("}") + 1);
+if (atom.length < 4) atom = this.lastAtom;
+ else this.lastAtom = atom;
+if (atom.indexOf(this.findString) < 0) return -1;
+}var tokens = JU.PT.getTokens(line.substring(line.indexOf("}") + 1));
+var value = this.assignValueFromGapColorForKin(tokens[0]);
+if (Float.isNaN(value)) return -1;
+if (checkType && this.pointType != 0) {
+switch ((tokens[i - 1].charAt(1)).charCodeAt(0)) {
+case 77:
+if (this.pointType != 1) return -1;
+break;
+case 83:
+if (this.pointType != 2) return -1;
+break;
+case 80:
+if (this.pointType != 3) return -1;
+break;
+case 79:
+if (this.pointType != 4) return -1;
+break;
+default:
+return -1;
+}
+}retColor[0] = this.getColor(tokens[0]);
+tokens = JU.PT.getTokens(tokens[i].$replace(',', ' '));
+var pt = JU.P3.new3(JU.PT.parseFloat(tokens[0]), JU.PT.parseFloat(tokens[1]), JU.PT.parseFloat(tokens[2]));
+if (this.isAnisotropic) this.setVertexAnisotropy(pt);
+return this.addVertexCopy(pt, value, this.nVertices++, false);
+}, "~S,~N,~A,~B");
+Clazz.defineMethod(c$, "getColor",
+function(color){
+if (color.equals("sky")) color = "skyblue";
+ else if (color.equals("sea")) color = "seagreen";
+return JU.CU.getArgbFromString(color);
+}, "~S");
+Clazz.defineMethod(c$, "assignValueFromGapColorForKin",
+function(color){
+var value = (color.equals("greentint") ? 4 : color.equals("blue") ? 0.35 : color.equals("sky") ? 0.25 : color.equals("sea") ? 0.15 : color.equals("green") ? 0.0 : color.equals("yellowtint") ? -0.1 : color.equals("yellow") ? -0.2 : color.equals("orange") ? -0.3 : color.equals("red") ? -0.4 : -0.5);
+return (value >= this.vMin && value <= this.vMax ? value : NaN);
+}, "~S");
+Clazz.overrideMethod(c$, "readPolygons",
+function(){
+return true;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MapFileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MapFileReader.js
new file mode 100755
index 000000000000..f1e8ed831d77
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MapFileReader.js
@@ -0,0 +1,108 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader", "JU.P3"], "J.jvxl.readers.MapFileReader", ["JU.Logger", "$.SimpleUnitCell"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.dmin = 3.4028235E38;
+this.dmax = 0;
+this.dmean = 0;
+this.drange = 0;
+this.mapc = 0;
+this.mapr = 0;
+this.maps = 0;
+this.n0 = 0;
+this.n1 = 0;
+this.n2 = 0;
+this.mode = 0;
+this.xyzStart = null;
+this.na = 0;
+this.nb = 0;
+this.nc = 0;
+this.a = 0;
+this.b = 0;
+this.c = 0;
+this.alpha = 0;
+this.beta = 0;
+this.gamma = 0;
+this.origin = null;
+this.vectors = null;
+this.xIndex = -1;
+this.yIndex = 0;
+this.zIndex = 0;
+this.p3 = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "MapFileReader", J.jvxl.readers.VolumeFileReader);
+Clazz.prepareFields (c$, function(){
+this.xyzStart = Clazz.newFloatArray (3, 0);
+this.origin = new JU.P3();
+this.vectors = new Array(3);
+this.p3 = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.MapFileReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2MFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2MFR",
+function(sg, br){
+this.init2VFR(sg, br);
+this.isAngstroms = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "checkInsideOut",
+function(mapc, mapr, maps){
+if (this.params.thePlane == null) this.params.insideOut = (";123;231;312;".indexOf(";" + mapc + mapr + maps) >= 0);
+}, "~N,~N,~N");
+Clazz.defineMethod(c$, "getVectorsAndOrigin",
+function(){
+this.checkInsideOut(this.mapc, this.mapr, this.maps);
+JU.Logger.info("grid parameters: nx,ny,nz: " + this.n0 + "," + this.n1 + "," + this.n2);
+JU.Logger.info("grid parameters: nxStart,nyStart,nzStart: " + this.xyzStart[0] + "," + this.xyzStart[1] + "," + this.xyzStart[2]);
+JU.Logger.info("grid parameters: mx,my,mz: " + this.na + "," + this.nb + "," + this.nc);
+JU.Logger.info("grid parameters: a,b,c,alpha,beta,gamma: " + this.a + "," + this.b + "," + this.c + "," + this.alpha + "," + this.beta + "," + this.gamma);
+JU.Logger.info("grid parameters: mapc,mapr,maps: " + this.mapc + "," + this.mapr + "," + this.maps);
+JU.Logger.info("grid parameters: originX,Y,Z: " + this.origin);
+var unitCell = JU.SimpleUnitCell.newA( Clazz.newFloatArray(-1, [this.a / this.na, this.b / this.nb, this.c / this.nc, this.alpha, this.beta, this.gamma]));
+this.vectors[0] = JU.P3.new3(1, 0, 0);
+this.vectors[1] = JU.P3.new3(0, 1, 0);
+this.vectors[2] = JU.P3.new3(0, 0, 1);
+unitCell.toCartesian(this.vectors[0], false);
+unitCell.toCartesian(this.vectors[1], false);
+unitCell.toCartesian(this.vectors[2], false);
+JU.Logger.info("Jmol unit cell vectors:");
+JU.Logger.info(" a: " + this.vectors[0]);
+JU.Logger.info(" b: " + this.vectors[1]);
+JU.Logger.info(" c: " + this.vectors[2]);
+this.voxelCounts[0] = this.n2;
+this.voxelCounts[1] = this.n1;
+this.voxelCounts[2] = this.n0;
+this.volumetricVectors[0].setT(this.vectors[this.maps - 1]);
+this.volumetricVectors[1].setT(this.vectors[this.mapr - 1]);
+this.volumetricVectors[2].setT(this.vectors[this.mapc - 1]);
+if (this.origin.x == 0 && this.origin.y == 0 && this.origin.z == 0) {
+if (this.xIndex == -1) {
+var xyz2crs = Clazz.newIntArray (3, 0);
+xyz2crs[this.mapc - 1] = 0;
+xyz2crs[this.mapr - 1] = 1;
+xyz2crs[this.maps - 1] = 2;
+this.xIndex = xyz2crs[0];
+this.yIndex = xyz2crs[1];
+this.zIndex = xyz2crs[2];
+}this.origin.scaleAdd2(this.xyzStart[this.xIndex], this.vectors[0], this.origin);
+this.origin.scaleAdd2(this.xyzStart[this.yIndex], this.vectors[1], this.origin);
+this.origin.scaleAdd2(this.xyzStart[this.zIndex], this.vectors[2], this.origin);
+}this.volumetricOrigin.setT(this.origin);
+JU.Logger.info("Jmol grid origin in Cartesian coordinates: " + this.origin);
+JU.Logger.info("Use isosurface OFFSET {x y z} if you want to shift it.\n");
+this.p3.set(this.na, this.nb, this.nc);
+unitCell.toCartesian(this.p3, true);
+this.p3.add(this.origin);
+JU.Logger.info("boundbox corners " + this.origin + " " + this.p3 + ";draw bbox boundbox mesh nofill");
+});
+Clazz.defineMethod(c$, "setCutoffAutomatic",
+function(){
+if (this.params.thePlane == null && this.params.cutoffAutomatic) {
+this.params.cutoff = -1.0;
+JU.Logger.info("MapReader: setting cutoff to default value of " + this.params.cutoff + (this.boundingBox == null ? " (no BOUNDBOX parameter)\n" : "\n"));
+}});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MrcBinaryReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MrcBinaryReader.js
new file mode 100755
index 000000000000..8ceaf1bd45d7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MrcBinaryReader.js
@@ -0,0 +1,178 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.MapFileReader"], "J.jvxl.readers.MrcBinaryReader", ["JU.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.labels = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "MrcBinaryReader", J.jvxl.readers.MapFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.MrcBinaryReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+var fileName = (sg.getReaderData())[0];
+this.init2MFR(sg, br);
+this.binarydoc = this.newBinaryDocument();
+this.setStream(fileName, true);
+this.nSurfaces = 1;
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.allowSigma = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var ispg;
+var nsymbt;
+var extra = Clazz.newByteArray (100, 0);
+var map = Clazz.newByteArray (4, 0);
+var machst = Clazz.newByteArray (4, 0);
+var rmsDeviation;
+var nlabel;
+this.n0 = this.binarydoc.readInt();
+if (this.n0 < 0 || this.n0 > 256) {
+this.setStream(null, false);
+this.n0 = this.binarydoc.swapBytesI(this.n0);
+if (this.n0 < 0 || this.n0 > 1000) {
+JU.Logger.info("nx=" + this.n0 + " not displayable as MRC file");
+throw new Exception("MRC file type not readable");
+}JU.Logger.info("reading little-endian MRC file");
+}this.n1 = this.binarydoc.readInt();
+this.n2 = this.binarydoc.readInt();
+this.mode = this.binarydoc.readInt();
+if (this.mode < 0 || this.mode > 6) {
+this.setStream(null, false);
+this.n0 = this.binarydoc.swapBytesI(this.n0);
+this.n1 = this.binarydoc.swapBytesI(this.n1);
+this.n2 = this.binarydoc.swapBytesI(this.n2);
+this.mode = this.binarydoc.swapBytesI(this.mode);
+}JU.Logger.info("MRC header: mode: " + this.mode);
+JU.Logger.info("MRC header: nx ny nz: " + this.n0 + " " + this.n1 + " " + this.n2);
+this.xyzStart[0] = this.binarydoc.readInt();
+this.xyzStart[1] = this.binarydoc.readInt();
+this.xyzStart[2] = this.binarydoc.readInt();
+JU.Logger.info("MRC header: nxyzStart: " + this.xyzStart[0] + " " + this.xyzStart[1] + " " + this.xyzStart[2]);
+this.na = this.binarydoc.readInt();
+this.nb = this.binarydoc.readInt();
+this.nc = this.binarydoc.readInt();
+if (this.na == 0) this.na = this.n0 - 1;
+if (this.nb == 0) this.nb = this.n1 - 1;
+if (this.nc == 0) this.nc = this.n2 - 1;
+JU.Logger.info("MRC header: na nb nc: " + this.na + " " + this.nb + " " + this.nc);
+this.a = this.binarydoc.readFloat();
+this.b = this.binarydoc.readFloat();
+this.c = this.binarydoc.readFloat();
+this.alpha = this.binarydoc.readFloat();
+this.beta = this.binarydoc.readFloat();
+this.gamma = this.binarydoc.readFloat();
+if (this.alpha == 0) {
+this.alpha = this.beta = this.gamma = 90;
+JU.Logger.info("MRC header: alpha,beta,gamma 0 changed to 90,90,90");
+JU.Logger.info("MRC header: alpha,beta,gamma 0 reversing insideOut sense");
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+}this.mapc = this.binarydoc.readInt();
+this.mapr = this.binarydoc.readInt();
+this.maps = this.binarydoc.readInt();
+if (this.mapc == 2 && this.mapr == 1 && this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+var s = "" + this.mapc + this.mapr + this.maps;
+JU.Logger.info("MRC header: mapc mapr maps: " + s);
+if (this.params.thePlane == null && "21321".indexOf(s) >= 1) {
+JU.Logger.info("MRC header: data are xy-reversed");
+this.params.dataXYReversed = true;
+}this.dmin = this.binarydoc.readFloat();
+this.dmax = this.binarydoc.readFloat();
+this.dmean = this.binarydoc.readFloat();
+JU.Logger.info("MRC header: dmin,dmax,dmean: " + this.dmin + "," + this.dmax + "," + this.dmean);
+ispg = this.binarydoc.readInt();
+nsymbt = this.binarydoc.readInt();
+JU.Logger.info("MRC header: ispg,nsymbt: " + ispg + "," + nsymbt);
+this.binarydoc.readByteArray(extra, 0, extra.length);
+this.origin.x = this.binarydoc.readFloat();
+this.origin.y = this.binarydoc.readFloat();
+this.origin.z = this.binarydoc.readFloat();
+JU.Logger.info("MRC header: origin: " + this.origin);
+this.binarydoc.readByteArray(map, 0, map.length);
+this.binarydoc.readByteArray(machst, 0, machst.length);
+rmsDeviation = this.binarydoc.readFloat();
+JU.Logger.info("MRC header: rms: " + rmsDeviation);
+nlabel = this.binarydoc.readInt();
+JU.Logger.info("MRC header: labels: " + nlabel);
+this.labels = new Array(nlabel);
+if (nlabel > 0) this.labels[0] = "Jmol MrcBinaryReader";
+for (var i = 0; i < 10; i++) {
+s = this.binarydoc.readString(80).trim();
+if (i < nlabel) {
+this.labels[i] = s;
+JU.Logger.info(this.labels[i]);
+}}
+for (var i = 0; i < nsymbt; i += 80) {
+var position = this.binarydoc.getPosition();
+s = this.binarydoc.readString(80).trim();
+if (s.indexOf('\0') != s.lastIndexOf('\0')) {
+JU.Logger.error("File indicates " + nsymbt + " symmetry lines, but " + i + " found!");
+this.binarydoc.seek(position);
+break;
+}JU.Logger.info("MRC file symmetry information: " + s);
+}
+JU.Logger.info("MRC header: bytes read: " + this.binarydoc.getPosition() + "\n");
+this.getVectorsAndOrigin();
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("MRC DATA ").append(nlabel > 0 ? this.labels[0] : "").append("\n");
+this.jvxlFileHeaderBuffer.append("see http://ami.scripps.edu/software/mrctools/mrc_specification.php\n");
+if (this.params.thePlane == null && (this.params.cutoffAutomatic || !Float.isNaN(this.params.sigma))) {
+var sigma = (this.params.sigma < 0 || Float.isNaN(this.params.sigma) ? 1 : this.params.sigma);
+this.params.cutoff = rmsDeviation * sigma + this.dmean;
+s = "cutoff set to " + this.params.cutoff + " (mean + rmsDeviation*sigma = " + this.dmean + " + " + rmsDeviation + "*" + sigma + ")";
+JU.Logger.info(s);
+this.jvxlFileHeaderBuffer.append(s + "\n");
+}});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+var voxelValue;
+switch (this.mode) {
+case 0:
+voxelValue = this.binarydoc.readByte();
+break;
+case 1:
+voxelValue = this.binarydoc.readShort();
+break;
+default:
+case 2:
+voxelValue = this.binarydoc.readFloat();
+break;
+case 3:
+voxelValue = this.binarydoc.readShort();
+this.binarydoc.readShort();
+break;
+case 4:
+voxelValue = this.binarydoc.readFloat();
+this.binarydoc.readFloat();
+break;
+case 6:
+voxelValue = this.binarydoc.readUnsignedShort();
+break;
+}
+this.nBytes = this.binarydoc.getPosition();
+return voxelValue;
+});
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+for (var i = 0; i < nPoints; i++) switch (this.mode) {
+case 0:
+this.binarydoc.readByte();
+break;
+case 1:
+case 6:
+this.binarydoc.readByteArray(J.jvxl.readers.MrcBinaryReader.b8, 0, 2);
+break;
+default:
+case 2:
+case 3:
+this.binarydoc.readByteArray(J.jvxl.readers.MrcBinaryReader.b8, 0, 4);
+break;
+case 4:
+this.binarydoc.readByteArray(J.jvxl.readers.MrcBinaryReader.b8, 0, 8);
+break;
+}
+
+}, "~N");
+c$.b8 = Clazz.newByteArray (8, 0);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MsmsReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MsmsReader.js
new file mode 100755
index 000000000000..f08b414b3ff9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/MsmsReader.js
@@ -0,0 +1,54 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PmeshReader"], "J.jvxl.readers.MsmsReader", ["JU.PT", "$.Rdr", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.fileName = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "MsmsReader", J.jvxl.readers.PmeshReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.MsmsReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PFR(sg, br);
+this.fileName = (sg.getReaderData())[0];
+if (this.fileName == null) return;
+this.type = "msms";
+this.onePerLine = true;
+this.fixedCount = 3;
+this.vertexBase = 1;
+this.setHeader();
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readVertices",
+function(){
+this.skipHeader();
+return this.readVerticesPM();
+});
+Clazz.overrideMethod(c$, "readPolygons",
+function(){
+this.br.close();
+this.fileName = JU.PT.rep(this.fileName, ".vert", ".face");
+JU.Logger.info("reading from file " + this.fileName);
+try {
+this.br = JU.Rdr.getBufferedReader(this.sg.atomDataServer.getBufferedInputStream(this.fileName), null);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.info("Note: file " + this.fileName + " was not found");
+this.br = null;
+return true;
+} else {
+throw e;
+}
+}
+this.sg.addRequiredFile(this.fileName);
+this.skipHeader();
+return this.readPolygonsPM();
+});
+Clazz.defineMethod(c$, "skipHeader",
+function(){
+while (this.rd() != null && this.line.indexOf("#") >= 0) {
+}
+this.tokens = this.getTokens();
+this.iToken = 0;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/NffReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/NffReader.js
new file mode 100755
index 000000000000..32225a0547d9
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/NffReader.js
@@ -0,0 +1,75 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PolygonFileReader", "java.util.Hashtable", "JU.P3"], "J.jvxl.readers.NffReader", ["JU.CU", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nPolygons = 0;
+this.vertexMap = null;
+this.pt = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "NffReader", J.jvxl.readers.PolygonFileReader);
+Clazz.prepareFields (c$, function(){
+this.vertexMap = new java.util.Hashtable();
+this.pt = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.NffReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "setHeader",
+function(){
+this.jvxlFileHeaderBuffer.append("NFF file format\nvertices and triangles only\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+});
+Clazz.overrideMethod(c$, "getSurfaceData",
+function(){
+if (this.readVerticesAndPolygons()) JU.Logger.info("NFF file contains " + this.nVertices + " vertices and " + this.nTriangles + " triangles");
+ else JU.Logger.error(this.params.fileName + ": Error reading Nff data ");
+});
+Clazz.defineMethod(c$, "readVerticesAndPolygons",
+function(){
+var color = 0xFF0000;
+try {
+while (this.rd() != null) {
+if (this.line.length == 0) continue;
+var tokens = this.getTokens();
+switch ((this.line.charAt(0)).charCodeAt(0)) {
+case 35:
+this.vertexMap.clear();
+continue;
+case 102:
+color = JU.CU.colorTriadToFFRGB(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
+continue;
+case 112:
+if (this.line.equals("pp 3")) {
+var i1 = this.getVertex();
+var i2 = this.getVertex();
+var i3 = this.getVertex();
+this.nTriangles++;
+this.addTriangleCheck(i1, i2, i3, 7, 0, false, color);
+}continue;
+}
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+return true;
+});
+Clazz.defineMethod(c$, "getVertex",
+function(){
+var i = this.vertexMap.get(this.rd());
+if (i == null) {
+var tokens = this.getTokens();
+this.pt.set(this.parseFloatStr(tokens[0]), this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]));
+if (!Float.isNaN(this.params.scale)) this.pt.scale(this.params.scale);
+if (this.isAnisotropic) this.setVertexAnisotropy(this.pt);
+i = Integer.$valueOf(this.addVertexCopy(this.pt, 0, this.nVertices++, true));
+this.vertexMap.put(this.line, i);
+}return i.intValue();
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ObjReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ObjReader.js
new file mode 100755
index 000000000000..05bed82d8a9f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/ObjReader.js
@@ -0,0 +1,100 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PmeshReader"], "J.jvxl.readers.ObjReader", ["java.util.Hashtable", "JU.BS", "$.CU", "$.P3", "$.PT"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "ObjReader", J.jvxl.readers.PmeshReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.ObjReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PR(sg, br);
+this.type = "obj";
+this.setHeader();
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readVertices",
+function(){
+this.pmeshError = "pmesh ERROR: invalid vertex/face list";
+var pt = new JU.P3();
+var color = 0;
+var ia;
+var ib;
+var ic;
+var id = 0;
+var i = 0;
+var nPts = 0;
+var htPymol = new java.util.Hashtable();
+var ipt = null;
+var spt = null;
+var pymolMap = Clazz.newIntArray (3, 0);
+var bsOK = new JU.BS();
+while (this.rd() != null) {
+if (this.line.length < 2 || this.line.charAt(1) != ' ') {
+if (this.params.readAllData && this.line.startsWith("usemtl")) color = JU.CU.getArgbFromString("[x" + this.line.substring(8) + "]");
+continue;
+}switch ((this.line.charAt(0)).charCodeAt(0)) {
+case 118:
+this.next[0] = 2;
+pt.set(JU.PT.parseFloatNext(this.line, this.next), JU.PT.parseFloatNext(this.line, this.next), JU.PT.parseFloatNext(this.line, this.next));
+var addHt = false;
+if (htPymol == null) {
+i = this.nVertices;
+} else if ((ipt = htPymol.get(spt = "" + pt)) == null) {
+addHt = true;
+i = this.nVertices;
+} else {
+i = ipt.intValue();
+}var j = i;
+if (i == this.nVertices) {
+if (this.isAnisotropic) this.setVertexAnisotropy(pt);
+j = this.addVertexCopy(pt, 0, this.nVertices++, true);
+if (j >= 0) bsOK.set(i);
+}pymolMap[nPts % 3] = j;
+if (addHt) htPymol.put(spt, Integer.$valueOf(i));
+nPts++;
+if (htPymol != null && nPts > 3) htPymol = null;
+break;
+case 102:
+if (nPts == 3 && this.line.indexOf("//") < 0) htPymol = null;
+nPts = 0;
+this.nPolygons++;
+var tokens = JU.PT.getTokens(this.line);
+var vertexCount = tokens.length - 1;
+if (vertexCount == 4) htPymol = null;
+if (htPymol == null) {
+ia = JU.PT.parseInt(tokens[1]) - 1;
+ib = JU.PT.parseInt(tokens[2]) - 1;
+ic = JU.PT.parseInt(tokens[3]) - 1;
+this.pmeshError = " " + ia + " " + ib + " " + ic + " " + this.line;
+if (!bsOK.get(ia) || !bsOK.get(ib) || !bsOK.get(ic)) continue;
+if (vertexCount == 4) {
+id = JU.PT.parseInt(tokens[4]) - 1;
+var isOK = (bsOK.get(id));
+this.nTriangles = this.addTriangleCheck(ia, ib, ic, (isOK ? 3 : 7), 0, false, color);
+if (isOK) this.nTriangles = this.addTriangleCheck(ia, ic, id, 6, 0, false, color);
+continue;
+}} else {
+ia = pymolMap[0];
+ib = pymolMap[1];
+ic = pymolMap[2];
+if (ia < 0 || ib < 0 || ic < 0) continue;
+}this.nTriangles = this.addTriangleCheck(ia, ib, ic, 7, 0, false, color);
+break;
+case 103:
+htPymol = null;
+if (this.params.readAllData) try {
+color = JU.PT.parseIntRadix(this.line.substring(3), 16);
+} catch (e) {
+color = 0;
+}
+break;
+}
+}
+this.pmeshError = null;
+return true;
+});
+Clazz.overrideMethod(c$, "readPolygons",
+function(){
+return true;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Parameters.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Parameters.js
new file mode 100755
index 000000000000..d5110f73d9a4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Parameters.js
@@ -0,0 +1,549 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(null, "J.jvxl.readers.Parameters", ["java.util.Hashtable", "JU.A4", "$.Lst", "$.M3", "$.P3", "$.P4", "$.V3", "JU.Escape", "$.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.state = 0;
+this.testFlags = 0;
+this.logMessages = false;
+this.logCompression = false;
+this.logCube = false;
+this.isSilent = false;
+this.assocCutoff = 0.3;
+this.dataType = 0;
+this.surfaceType = 0;
+this.calculationType = "";
+this.atomRadiusData = null;
+this.addHydrogens = false;
+this.solventRadius = 0;
+this.solventExtendedAtomRadius = 0;
+this.propertySmoothing = false;
+this.propertySmoothingPower = 4;
+this.envelopeRadius = 0;
+this.cavityRadius = 0;
+this.isCavity = false;
+this.pocket = null;
+this.minSet = 0;
+this.slabInfo = null;
+this.slabPlaneOffset = NaN;
+this.theProperty = null;
+this.solvent_ptsPerAngstrom = 4;
+this.solvent_gridMax = 60;
+this.plane_ptsPerAngstrom = 4;
+this.plane_gridMax = 81;
+this.colorBySign = false;
+this.colorByPhase = false;
+this.colorBySets = false;
+this.colorRgb = 0;
+this.colorNeg = 0;
+this.colorPos = 0;
+this.colorPosLCAO = 0;
+this.colorNegLCAO = 0;
+this.colorPhase = 0;
+this.colorDensity = false;
+this.iAddGridPoints = false;
+this.atomIndex = 0;
+this.isAngstroms = false;
+this.scale = 0;
+this.scale3d = 0;
+this.anisotropy = null;
+this.isAnisotropic = false;
+this.eccentricityMatrix = null;
+this.eccentricityMatrixInverse = null;
+this.isEccentric = false;
+this.eccentricityScale = 0;
+this.eccentricityRatio = 0;
+this.aniosU = null;
+this.anisoB = null;
+this.lcaoType = null;
+this.functionInfo = null;
+this.psi_n = 2;
+this.psi_l = 1;
+this.psi_m = 1;
+this.psi_Znuc = 1;
+this.psi_ptsPerAngstrom = 5;
+this.psi_monteCarloCount = 0;
+this.mep_gridMax = 40;
+this.mep_ptsPerAngstrom = 3;
+this.mep_marginAngstroms = 1;
+this.mep_calcType = -1;
+this.qmOrbitalType = 0;
+this.qmOrbitalCount = 0;
+this.moData = null;
+this.qm_gridMax = 80;
+this.qm_ptsPerAngstrom = 10;
+this.qm_marginAngstroms = 1;
+this.qm_nAtoms = 0;
+this.qm_moNumber = 2147483647;
+this.qm_moLinearCombination = null;
+this.center = null;
+this.point = null;
+this.distance = 0;
+this.allowVolumeRender = false;
+this.script = null;
+this.bsSelected = null;
+this.bsIgnore = null;
+this.bsSolvent = null;
+this.func = null;
+this.title = null;
+this.blockCubeData = false;
+this.readAllData = false;
+this.fileIndex = -1;
+this.fileName = null;
+this.modelIndex = -1;
+this.modelInvRotation = null;
+this.isXLowToHigh = false;
+this.insideOut = false;
+this.dataXYReversed = false;
+this.cutoff = 3.4028235E38;
+this.cutoffRange = null;
+this.sigma = 3.4028235E38;
+this.cutoffAutomatic = true;
+this.isCutoffAbsolute = false;
+this.isPositiveOnly = false;
+this.rangeAll = false;
+this.rangeSelected = false;
+this.rangeDefined = false;
+this.valueMappedToRed = 0;
+this.valueMappedToBlue = 0;
+this.mappedDataMin = 0;
+this.mappedDataMax = 0;
+this.isColorReversed = false;
+this.isBicolorMap = false;
+this.isSquared = false;
+this.isSquaredLinear = false;
+this.thePlane = null;
+this.isContoured = false;
+this.nContours = 0;
+this.thisContour = 0;
+this.contourFromZero = false;
+this.parameters = null;
+this.resolution = 0;
+this.downsampleFactor = 0;
+this.maxSet = 0;
+this.contoursDiscrete = null;
+this.contourColixes = null;
+this.contourIncrements = null;
+this.boundingBox = null;
+this.bsExcluded = null;
+this.contourType = 0;
+this.colorSchemeTranslucent = false;
+this.colorEncoder = null;
+this.usePropertyForColorRange = true;
+this.isPeriodic = false;
+this.doFullMolecular = false;
+this.propertyDistanceMax = 2147483647;
+this.randomSeed = 0;
+this.fullyLit = false;
+this.vertexSource = null;
+this.intersection = null;
+this.origin = null;
+this.steps = null;
+this.points = null;
+this.volumeData = null;
+this.contactPair = null;
+this.mapLattice = null;
+this.extendGrid = 0;
+this.isMapped = false;
+this.showTiming = false;
+this.pointSize = 0;
+this.probes = null;
+this.isModelConnected = false;
+this.surfaceAtoms = null;
+this.filesData = null;
+this.probeValues = null;
+this.sbOut = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "Parameters", null);
+Clazz.prepareFields (c$, function(){
+this.anisotropy = Clazz.newFloatArray (3, 0);
+});
+Clazz.defineMethod(c$, "initialize",
+function(){
+this.addHydrogens = false;
+this.allowVolumeRender = true;
+this.atomRadiusData = null;
+this.atomIndex = -1;
+this.blockCubeData = false;
+this.boundingBox = null;
+this.bsExcluded = new Array(4);
+this.bsIgnore = null;
+this.bsSelected = null;
+this.bsSolvent = null;
+this.calculationType = "";
+this.center = new JU.P3();
+this.resetForMapping(true);
+this.colorBySign = this.colorByPhase = this.colorBySets = false;
+this.colorEncoder = null;
+this.colorNeg = -65536;
+this.colorNegLCAO = -8388480;
+this.colorPos = -16776961;
+this.colorPosLCAO = -23296;
+this.colorRgb = -2147483648;
+this.colorSchemeTranslucent = false;
+this.contactPair = null;
+this.contourIncrements = null;
+this.contoursDiscrete = null;
+this.contourColixes = null;
+this.contourFromZero = true;
+this.cutoff = 3.4028235E38;
+this.cutoffAutomatic = true;
+this.dataXYReversed = false;
+this.distance = 3.4028235E38;
+this.doFullMolecular = false;
+this.envelopeRadius = 10;
+this.extendGrid = 0;
+this.fileIndex = 1;
+this.readAllData = true;
+this.fileName = "";
+this.filesData = null;
+this.fullyLit = false;
+this.functionInfo = null;
+this.iAddGridPoints = false;
+this.insideOut = false;
+this.isAngstroms = false;
+this.isBicolorMap = this.isCutoffAbsolute = this.isPositiveOnly = false;
+this.isCavity = false;
+this.isColorReversed = false;
+this.isModelConnected = false;
+this.isSquared = false;
+this.isSquaredLinear = false;
+this.isContoured = false;
+this.isEccentric = false;
+this.isMapped = false;
+this.isPeriodic = false;
+this.isSilent = false;
+this.logCube = this.logCompression = false;
+this.logMessages = JU.Logger.debugging;
+this.mapLattice = null;
+this.mep_calcType = -1;
+this.minSet = 0;
+this.modelIndex = -1;
+this.modelInvRotation = null;
+this.nContours = 0;
+this.pocket = null;
+this.pointSize = NaN;
+this.probes = null;
+this.probeValues = null;
+this.propertyDistanceMax = 2147483647;
+this.propertySmoothing = false;
+this.propertySmoothingPower = 4;
+this.rangeDefined = false;
+this.rangeAll = false;
+this.rangeSelected = false;
+this.resolution = 3.4028235E38;
+this.scale = NaN;
+this.scale3d = 0;
+this.sigma = NaN;
+this.slabInfo = null;
+this.solventExtendedAtomRadius = 0;
+this.state = 1;
+this.testFlags = 0;
+this.thePlane = null;
+this.theProperty = null;
+this.thisContour = -1;
+this.title = null;
+this.usePropertyForColorRange = true;
+this.vertexSource = null;
+});
+Clazz.defineMethod(c$, "resetForMapping",
+function(haveSurface){
+if (!haveSurface) this.state = 2;
+this.center.x = NaN;
+this.colorDensity = false;
+this.func = null;
+this.intersection = null;
+this.isAnisotropic = false;
+this.isMapped = true;
+this.mappedDataMin = 3.4028235E38;
+this.origin = null;
+this.parameters = null;
+this.points = null;
+this.qmOrbitalType = 0;
+this.steps = null;
+this.volumeData = null;
+}, "~B");
+Clazz.defineMethod(c$, "setAnisotropy",
+function(pt){
+this.anisotropy[0] = pt.x;
+this.anisotropy[1] = pt.y;
+this.anisotropy[2] = pt.z;
+this.isAnisotropic = true;
+if (Float.isNaN(this.center.x)) this.center.set(0, 0, 0);
+}, "JU.P3");
+Clazz.defineMethod(c$, "setEccentricity",
+function(info){
+var ecc = JU.V3.new3(info.x, info.y, info.z);
+var c = (this.scale > 0 ? this.scale : info.w < 0 ? 1 : ecc.length());
+var fab_c = Math.abs(info.w);
+ecc.normalize();
+var z = JU.V3.new3(0, 0, 1);
+ecc.add(z);
+ecc.normalize();
+if (Float.isNaN(ecc.x)) ecc.set(1, 0, 0);
+this.eccentricityMatrixInverse = new JU.M3();
+this.eccentricityMatrixInverse.invertM(this.eccentricityMatrix = new JU.M3().setAA(JU.A4.newVA(ecc, 3.141592653589793)));
+this.isEccentric = this.isAnisotropic = true;
+this.eccentricityScale = c;
+this.eccentricityRatio = fab_c;
+if (fab_c > 1) this.eccentricityScale *= fab_c;
+this.anisotropy[0] = fab_c * c;
+this.anisotropy[1] = fab_c * c;
+this.anisotropy[2] = c;
+if (Float.isNaN(this.center.x)) this.center.set(0, 0, 0);
+}, "JU.P4");
+Clazz.defineMethod(c$, "setPlane",
+function(plane){
+this.thePlane = plane;
+if (this.thePlane.x == 0 && this.thePlane.y == 0 && this.thePlane.z == 0) this.thePlane.z = 1;
+this.isContoured = true;
+}, "JU.P4");
+Clazz.defineMethod(c$, "setSphere",
+function(radius, isGeodesic){
+this.dataType = (isGeodesic ? 74 : 65);
+this.distance = radius;
+this.setEccentricity(JU.P4.new4(0, 0, 1, 1));
+this.cutoff = 1.4E-45;
+this.isCutoffAbsolute = false;
+this.isSilent = !this.logMessages;
+this.script = this.getScriptParams() + " SPHERE " + radius + ";";
+}, "~N,~B");
+Clazz.defineMethod(c$, "setEllipsoidP4",
+function(v){
+this.dataType = 66;
+this.distance = 1;
+this.setEccentricity(v);
+this.cutoff = 1.4E-45;
+this.isCutoffAbsolute = false;
+this.isSilent = !this.logMessages;
+}, "JU.P4");
+Clazz.defineMethod(c$, "setEllipsoidAF",
+function(bList){
+this.anisoB = bList;
+this.dataType = 67;
+this.distance = 0.3 * (Float.isNaN(this.scale) ? 1 : this.scale);
+this.cutoff = 1.4E-45;
+this.isCutoffAbsolute = false;
+this.isSilent = !this.logMessages;
+if (Float.isNaN(this.center.x)) this.center.set(0, 0, 0);
+if (this.resolution == 3.4028235E38) this.resolution = 6;
+}, "~A");
+Clazz.defineMethod(c$, "setLobe",
+function(v){
+this.dataType = 68;
+this.setEccentricity(v);
+if (this.cutoff == 3.4028235E38) {
+this.cutoff = 0.14;
+if (this.isSquared) this.cutoff = this.cutoff * this.cutoff;
+}this.isSilent = !this.logMessages;
+this.script = this.getScriptParams() + " LOBE {" + v.x + " " + v.y + " " + v.z + " " + v.w + "};";
+}, "JU.P4");
+Clazz.defineMethod(c$, "getScriptParams",
+function(){
+return " center " + JU.Escape.eP(this.center) + (Float.isNaN(this.scale) ? "" : " scale " + this.scale);
+});
+Clazz.defineMethod(c$, "setLp",
+function(v){
+this.dataType = 70;
+this.setEccentricity(v);
+if (this.cutoff == 3.4028235E38) {
+this.cutoff = 0.14;
+if (this.isSquared) this.cutoff = this.cutoff * this.cutoff;
+}this.isSilent = !this.logMessages;
+this.script = " center " + JU.Escape.eP(this.center) + (Float.isNaN(this.scale) ? "" : " scale " + this.scale) + " LP {" + v.x + " " + v.y + " " + v.z + " " + v.w + "};";
+}, "JU.P4");
+Clazz.defineMethod(c$, "setRadical",
+function(v){
+this.dataType = 71;
+this.setEccentricity(v);
+if (this.cutoff == 3.4028235E38) {
+this.cutoff = 0.14;
+if (this.isSquared) this.cutoff = this.cutoff * this.cutoff;
+}this.isSilent = !this.logMessages;
+this.script = " center " + JU.Escape.eP(this.center) + (Float.isNaN(this.scale) ? "" : " scale " + this.scale) + " RAD {" + v.x + " " + v.y + " " + v.z + " " + v.w + "};";
+}, "JU.P4");
+Clazz.defineMethod(c$, "setLcao",
+function(type, colorPtr){
+this.lcaoType = type;
+if (colorPtr == 1) this.colorPosLCAO = this.colorNegLCAO;
+this.isSilent = !this.logMessages;
+}, "~S,~N");
+Clazz.defineMethod(c$, "setSolvent",
+function(propertyName, radius){
+this.isEccentric = this.isAnisotropic = false;
+this.solventRadius = Math.abs(radius);
+this.dataType = (this.intersection != null ? 1333 : "nomap" === propertyName ? 1207 : "molecular" === propertyName ? 1203 : "sasurface" === propertyName || this.solventRadius == 0 ? 1196 : 1195);
+if (this.state < 2 && (this.cutoffAutomatic || !this.colorDensity) && (this.intersection == null || this.cutoff == 3.4028235E38)) this.cutoff = 0.0;
+switch (this.dataType) {
+case 1333:
+this.calculationType = "VDW intersection";
+break;
+case 1207:
+this.calculationType = "unmapped plane";
+break;
+case 1203:
+this.calculationType = "molecular surface with radius " + this.solventRadius;
+if (this.minSet == 0) this.minSet = 50;
+break;
+case 1195:
+this.calculationType = "solvent-excluded surface with radius " + this.solventRadius;
+if (this.minSet == 0) this.minSet = 50;
+break;
+case 1196:
+this.calculationType = "solvent-accessible surface with radius " + this.solventRadius;
+if (this.minSet == 0) this.minSet = 50;
+break;
+}
+switch (this.dataType) {
+case 1207:
+this.solventExtendedAtomRadius = this.solventRadius;
+this.solventRadius = 0;
+this.isContoured = false;
+break;
+case 1203:
+this.solventExtendedAtomRadius = 0;
+break;
+case 1195:
+this.solventExtendedAtomRadius = 0;
+if (this.bsIgnore == null) this.bsIgnore = this.bsSolvent;
+ else if (this.bsSolvent != null) this.bsIgnore.or(this.bsSolvent);
+break;
+case 1196:
+this.solventExtendedAtomRadius = this.solventRadius;
+this.solventRadius = 0;
+if (this.bsIgnore == null) this.bsIgnore = this.bsSolvent;
+ else if (this.bsSolvent != null) this.bsIgnore.or(this.bsSolvent);
+break;
+}
+}, "~S,~N");
+Clazz.defineMethod(c$, "setFunctionXY",
+function(value){
+this.dataType = 8;
+this.functionInfo = value;
+this.cutoff = 1.4E-45;
+this.isEccentric = this.isAnisotropic = false;
+}, "JU.Lst");
+Clazz.defineMethod(c$, "setFunctionXYZ",
+function(value){
+this.dataType = 9;
+this.functionInfo = value;
+if (this.cutoff == 3.4028235E38) this.cutoff = 1.4E-45;
+this.isEccentric = this.isAnisotropic = false;
+}, "JU.Lst");
+Clazz.defineMethod(c$, "setAtomicOrbital",
+function(nlmZprs){
+this.dataType = 1294;
+this.setEccentricity(JU.P4.new4(0, 0, 1, 1));
+this.psi_n = Clazz.floatToInt(nlmZprs[0]);
+this.psi_l = Clazz.floatToInt(nlmZprs[1]);
+this.psi_m = Clazz.floatToInt(nlmZprs[2]);
+this.psi_Znuc = nlmZprs[3];
+this.psi_monteCarloCount = Clazz.floatToInt(nlmZprs[4]);
+this.distance = nlmZprs[5];
+if (this.distance != 0 || this.thePlane != null) this.allowVolumeRender = false;
+this.randomSeed = Clazz.floatToInt(nlmZprs[6]);
+this.psi_ptsPerAngstrom = 10;
+if (this.cutoff == 3.4028235E38 || this.cutoff == 0.14) {
+this.cutoff = (this.psi_monteCarloCount > 0 ? 0 : 0.04);
+if (this.isSquared) this.cutoff = this.cutoff * this.cutoff;
+}this.isCutoffAbsolute = true;
+if (this.state < 2 && this.thePlane == null && this.colorBySign) this.isBicolorMap = true;
+return (this.psi_Znuc > 0 && Math.abs(this.psi_m) <= this.psi_l && this.psi_l < this.psi_n);
+}, "~A");
+Clazz.defineMethod(c$, "setMep",
+function(charges, isMLP){
+this.dataType = (isMLP ? 1329 : 1328);
+this.theProperty = charges;
+this.usePropertyForColorRange = false;
+this.isEccentric = this.isAnisotropic = false;
+if (this.cutoff == 3.4028235E38) {
+this.cutoff = 0.1;
+if (this.isSquared) this.cutoff = this.cutoff * this.cutoff;
+}this.isCutoffAbsolute = (this.cutoff > 0 && !this.isPositiveOnly);
+this.contourFromZero = false;
+if (this.state >= 2 || this.thePlane != null) {
+if (!this.rangeDefined && !this.rangeAll) {
+this.valueMappedToRed = -0.1;
+this.valueMappedToBlue = 0.1;
+this.rangeDefined = true;
+}} else {
+this.colorBySign = true;
+this.isBicolorMap = true;
+}}, "~A,~B");
+Clazz.defineMethod(c$, "setNci",
+function(isPromolecular){
+this.fullyLit = true;
+this.qm_gridMax = 200;
+if (isPromolecular) this.dataType = 1844;
+this.qm_marginAngstroms = 2;
+this.qmOrbitalType = (isPromolecular ? 3 : 4);
+if (isPromolecular) {
+if (this.parameters == null || this.parameters.length < 2) this.parameters = Clazz.newFloatArray(-1, [this.cutoff, 2]);
+}if (this.cutoff == 3.4028235E38 || this.cutoff == 0) this.cutoff = 0.3;
+if (this.isSquared) this.cutoff *= this.cutoff;
+if (this.title == null) this.title = new Array(0);
+this.moData = new java.util.Hashtable();
+}, "~B");
+Clazz.defineMethod(c$, "setMO",
+function(iMo, linearCombination){
+this.isModelConnected = true;
+this.qm_moLinearCombination = linearCombination;
+this.qm_moNumber = (linearCombination == null ? Math.abs(iMo) : Clazz.floatToInt(linearCombination[1]));
+this.qmOrbitalType = (this.moData.containsKey("haveVolumeData") ? 5 : this.moData.containsKey("gaussians") ? 1 : this.moData.containsKey("slaters") ? 2 : 0);
+var isElectronDensity = (iMo <= 0 && linearCombination == null);
+if (this.qmOrbitalType == 0) {
+JU.Logger.error("MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?)");
+this.title = Clazz.newArray(-1, ["no basis functions found in file"]);
+} else {
+var mos = this.moData.get("mos");
+this.qmOrbitalCount = mos.size();
+this.calculationType = this.moData.get("calculationType");
+this.calculationType = "Molecular orbital #" + this.qm_moNumber + "/" + this.qmOrbitalCount + " " + (this.calculationType == null ? "" : this.calculationType);
+if (!isElectronDensity) {
+if (this.title == null) {
+this.title = new Array(5);
+this.title[0] = "%F";
+this.title[1] = "Model %M MO %I/%N %T";
+this.title[2] = "?Energy = %E %U";
+this.title[3] = "?Symmetry = %S";
+this.title[4] = "?Occupancy = %O";
+}}}this.dataType = 1837;
+if (this.cutoff == 3.4028235E38) {
+this.cutoff = (isElectronDensity ? 0.01 : 0.05);
+}if (this.isSquared || this.isSquaredLinear) this.cutoff = this.cutoff * this.cutoff;
+this.isEccentric = this.isAnisotropic = false;
+this.isCutoffAbsolute = (this.cutoff > 0 && !this.isPositiveOnly);
+if (this.state >= 2 || this.thePlane != null) return;
+this.colorBySign = true;
+if (this.colorByPhase && this.colorPhase == 0) this.colorByPhase = false;
+this.isBicolorMap = true;
+}, "~N,~A");
+Clazz.defineMethod(c$, "setMapRanges",
+function(surfaceReader, haveData){
+if (!this.colorDensity) if (this.colorByPhase || this.colorBySign || (this.thePlane != null || this.isBicolorMap) && !this.isContoured) {
+this.mappedDataMin = -1;
+this.mappedDataMax = 1;
+}if (this.mappedDataMin == 3.4028235E38 || this.mappedDataMin == this.mappedDataMax) {
+var minMax = surfaceReader.getMinMaxMappedValues(haveData);
+System.out.println("parameters - setmapranges " + minMax[0] + " " + minMax[1]);
+this.mappedDataMin = minMax[0];
+this.mappedDataMax = minMax[1];
+}if (this.mappedDataMin == 0 && this.mappedDataMax == 0) {
+this.mappedDataMin = -1;
+this.mappedDataMax = 1;
+}if (!this.rangeDefined) {
+this.valueMappedToRed = this.mappedDataMin;
+this.valueMappedToBlue = this.mappedDataMax;
+}}, "J.jvxl.readers.SurfaceReader,~B");
+Clazz.defineMethod(c$, "addSlabInfo",
+function(slabObject){
+if (this.slabInfo == null) this.slabInfo = new JU.Lst();
+this.slabInfo.addLast(slabObject);
+}, "~A");
+Clazz.defineMethod(c$, "isInsideOut",
+function(){
+return this.insideOut != this.dataXYReversed;
+});
+Clazz.defineMethod(c$, "isFullyLit",
+function(){
+return (this.thePlane != null || this.fullyLit);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PeriodicVolumeFileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PeriodicVolumeFileReader.js
new file mode 100755
index 000000000000..62390a42e831
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PeriodicVolumeFileReader.js
@@ -0,0 +1,62 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.PeriodicVolumeFileReader", null, function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "PeriodicVolumeFileReader", J.jvxl.readers.VolumeFileReader);
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+this.initializeSurfaceData();
+this.newVoxelDataCube();
+this.getPeriodicVoxels();
+if (this.params.extendGrid != 0) {
+var n = Clazz.newIntArray (3, 0);
+var nx = this.nPointsX - 1;
+var ny = this.nPointsY - 1;
+var nz = this.nPointsZ - 1;
+for (var i = 0; i < 3; i++) {
+var vi = this.voxelCounts[i] - 1;
+n[i] = Clazz.floatToInt(vi * this.params.extendGrid);
+this.volumetricOrigin.scaleAdd2(-n[i], this.volumetricVectors[i], this.volumetricOrigin);
+vi += 2 * n[i];
+while (n[i] > 0) n[i] -= this.voxelCounts[i] - 1;
+
+this.voxelCounts[i] = vi + 1;
+}
+this.nPointsX = this.voxelCounts[0];
+this.nPointsY = this.voxelCounts[1];
+this.nPointsZ = this.voxelCounts[2];
+var vd = Clazz.newFloatArray (this.nPointsX, this.nPointsY, this.nPointsZ, 0);
+for (var i = this.nPointsX; --i >= 0; ) for (var j = this.nPointsY; --j >= 0; ) for (var k = this.nPointsZ; --k >= 0; ) {
+vd[i][j][k] = this.voxelData[(i - n[0]) % nx][(j - n[1]) % ny][(k - n[2]) % nz];
+}
+
+
+this.voxelData = vd;
+} else {
+var n;
+n = this.nPointsX - 1;
+for (var i = 0; i < this.nPointsY; ++i) for (var j = 0; j < this.nPointsZ; ++j) this.voxelData[n][i][j] = this.voxelData[0][i][j];
+
+
+n = this.nPointsY - 1;
+for (var i = 0; i < this.nPointsX; ++i) for (var j = 0; j < this.nPointsZ; ++j) this.voxelData[i][n][j] = this.voxelData[i][0][j];
+
+
+n = this.nPointsZ - 1;
+for (var i = 0; i < this.nPointsX; ++i) for (var j = 0; j < this.nPointsY; ++j) this.voxelData[i][j][n] = this.voxelData[i][j][0];
+
+
+}if (isMapData && this.volumeData.hasPlane()) {
+this.volumeData.setVoxelMap();
+for (var x = 0; x < this.nPointsX; ++x) {
+for (var y = 0; y < this.nPointsY; ++y) {
+for (var z = 0; z < this.nPointsZ; ++z) {
+var f = this.volumeData.getToPlaneParameter();
+if (this.volumeData.isNearPlane(x, y, z, f)) this.volumeData.setVoxelMapValue(x, y, z, this.voxelData[x][y][z]);
+}
+}
+}
+this.voxelData = null;
+}this.volumeData.setVoxelDataAsArray(this.voxelData);
+if (this.dataMin > this.params.cutoff) this.params.cutoff = 2 * this.dataMin;
+}, "~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PltFormattedReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PltFormattedReader.js
new file mode 100755
index 000000000000..b1db471fef75
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PltFormattedReader.js
@@ -0,0 +1,40 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.PltFormattedReader", ["JU.SB", "JV.Viewer"], function(){
+var c$ = Clazz.declareType(J.jvxl.readers, "PltFormattedReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.PltFormattedReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+this.isAngstroms = true;
+this.jvxlData.wasCubic = true;
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var n1 = this.parseIntStr(this.rd());
+var n2 = this.parseInt();
+this.nPointsX = this.parseIntStr(this.rd());
+this.nPointsY = this.parseInt();
+this.nPointsZ = this.parseInt();
+this.jvxlFileHeaderBuffer.append("Plt formatted data (" + n1 + "," + n2 + ") " + this.nPointsX + " x " + this.nPointsY + " x " + this.nPointsZ + " \nJmol " + JV.Viewer.getJmolVersion() + '\n');
+this.volumetricOrigin.set(0, 0, 0);
+var xmin = this.parseFloatStr(this.rd().substring(0, 12));
+var xmax = this.parseFloatRange(this.line, 12, 24);
+var ymin = this.parseFloatRange(this.line, 24, 36);
+var ymax = this.parseFloatRange(this.line, 36, 48);
+var zmin = this.parseFloatRange(this.line, 48, 60);
+var zmax = this.parseFloatRange(this.line, 60, 72);
+this.volumetricOrigin.set(xmin, ymin, zmin);
+this.voxelCounts[0] = this.nPointsX;
+this.voxelCounts[1] = this.nPointsY;
+this.voxelCounts[2] = this.nPointsZ;
+this.volumetricVectors[0].set(0, 0, (xmax - xmin) / this.nPointsX);
+this.volumetricVectors[1].set(0, (ymax - ymin) / this.nPointsY, 0);
+this.volumetricVectors[2].set((zmax - zmin) / this.nPointsZ, 0, 0);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Pmesh4Reader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Pmesh4Reader.js
new file mode 100755
index 000000000000..4e3b68b015b2
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Pmesh4Reader.js
@@ -0,0 +1,102 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PolygonFileReader"], "J.jvxl.readers.Pmesh4Reader", ["JU.CU", "$.P4", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nPolygons = 0;
+this.pmeshError = null;
+this.type = null;
+this.color = 0;
+this.transparency = 0;
+this.nX = 0;
+this.nY = 0;
+this.tokens = null;
+this.iToken = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "Pmesh4Reader", J.jvxl.readers.PolygonFileReader);
+Clazz.prepareFields (c$, function(){
+this.tokens = new Array(0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.Pmesh4Reader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PFR(sg, br);
+var fileName = (sg.getReaderData())[0];
+if (fileName == null) return;
+this.params.fullyLit = true;
+this.type = "pmesh4";
+this.jvxlFileHeaderBuffer.append(this.type + " file format\nvertices and triangles only\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "getSurfaceData",
+function(){
+this.rd();
+if (this.readVerticesAndPolygons()) JU.Logger.info(this.type + " file contains " + this.nVertices + " 4D vertices and " + this.nPolygons + " polygons for " + this.nTriangles + " triangles");
+ else JU.Logger.error(this.params.fileName + ": " + (this.pmeshError == null ? "Error reading pmesh4 data " : this.pmeshError));
+});
+Clazz.defineMethod(c$, "readVerticesAndPolygons",
+function(){
+try {
+this.readColor();
+this.nY = this.getInt();
+this.nX = this.getInt();
+this.readVertices();
+this.createMesh();
+return true;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (this.pmeshError == null) this.pmeshError = this.type + " ERROR: " + e;
+} else {
+throw e;
+}
+}
+return false;
+});
+Clazz.defineMethod(c$, "readColor",
+function(){
+this.color = JU.CU.colorTriadToFFRGB(this.getFloat(), this.getFloat(), this.getFloat());
+this.transparency = this.getFloat();
+});
+Clazz.defineMethod(c$, "readVertices",
+function(){
+this.nVertices = this.nX * this.nY;
+this.iToken = 2147483647;
+this.pmeshError = this.type + " ERROR: invalid vertex list";
+for (var i = 0; i < this.nVertices; i++) {
+var pt = JU.P4.new4(this.getFloat(), this.getFloat(), this.getFloat(), this.getFloat());
+if (JU.Logger.debugging) JU.Logger.debug(i + ": " + pt);
+this.addVertexCopy(pt, 0, i, false);
+this.iToken = 2147483647;
+}
+this.pmeshError = null;
+return true;
+});
+Clazz.defineMethod(c$, "createMesh",
+function(){
+for (var i = 0; i < this.nX - 1; i++) {
+for (var j = 0; j < this.nY - 1; j++) {
+this.nTriangles += 2;
+this.addTriangleCheck(i * this.nY + j, (i + 1) * this.nY + j, (i + 1) * this.nY + j + 1, 3, 0, false, this.color);
+this.addTriangleCheck((i + 1) * this.nY + j + 1, i * this.nY + j + 1, i * this.nY + j, 3, 0, false, this.color);
+}
+}
+});
+Clazz.defineMethod(c$, "nextToken",
+function(){
+while (this.iToken >= this.tokens.length) {
+this.iToken = 0;
+this.rd();
+this.tokens = this.getTokens();
+}
+return this.tokens[this.iToken++];
+});
+Clazz.defineMethod(c$, "getInt",
+function(){
+return this.parseIntStr(this.nextToken());
+});
+Clazz.defineMethod(c$, "getFloat",
+function(){
+return this.parseFloatStr(this.nextToken());
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PmeshReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PmeshReader.js
new file mode 100755
index 000000000000..f8067324569b
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PmeshReader.js
@@ -0,0 +1,205 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PolygonFileReader"], "J.jvxl.readers.PmeshReader", ["JU.CU", "$.P3", "$.PT", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isBinary = false;
+this.nPolygons = 0;
+this.pmeshError = null;
+this.type = null;
+this.isClosedFace = false;
+this.fixedCount = 0;
+this.onePerLine = false;
+this.vertexBase = 0;
+this.vertexMap = null;
+this.tokens = null;
+this.iToken = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "PmeshReader", J.jvxl.readers.PolygonFileReader);
+Clazz.prepareFields (c$, function(){
+this.tokens = new Array(0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.PmeshReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2PR",
+function(sg, br){
+this.init2PFR(sg, br);
+var fileName = (sg.getReaderData())[0];
+if (fileName == null) return;
+this.type = "pmesh";
+this.setHeader();
+this.isBinary = this.checkBinary(fileName);
+this.isClosedFace = !this.isBinary;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "setHeader",
+function(){
+this.jvxlFileHeaderBuffer.append(this.type + " file format\nvertices and triangles only\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+});
+Clazz.defineMethod(c$, "checkBinary",
+function(fileName){
+try {
+this.br.mark(4);
+var buf = Clazz.newCharArray (5, '\0');
+this.br.read(buf, 0, 5);
+if (( String.instantialize(buf)).startsWith("PM\u0001\u0000")) {
+this.br.close();
+this.binarydoc = this.newBinaryDocument();
+this.setStream(fileName, (buf[4] == '\0'));
+return true;
+}this.br.reset();
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(e);
+} else {
+throw e;
+}
+}
+return false;
+}, "~S");
+Clazz.overrideMethod(c$, "getSurfaceData",
+function(){
+if (this.readVerticesAndPolygons()) JU.Logger.info((this.isBinary ? "binary " : "") + this.type + " file contains " + this.nVertices + " vertices and " + this.nPolygons + " polygons for " + this.nTriangles + " triangles");
+ else JU.Logger.error(this.params.fileName + ": " + (this.pmeshError == null ? "Error reading pmesh data " : this.pmeshError));
+});
+Clazz.defineMethod(c$, "readVerticesAndPolygons",
+function(){
+try {
+if (this.isBinary && !this.readBinaryHeader()) return false;
+if (this.readVertices() && this.readPolygons()) return true;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (this.pmeshError == null) this.pmeshError = this.type + " ERROR: " + e;
+} else {
+throw e;
+}
+}
+return false;
+});
+Clazz.defineMethod(c$, "readBinaryHeader",
+function(){
+this.pmeshError = "could not read binary Pmesh file header";
+try {
+var ignored = Clazz.newByteArray (64, 0);
+this.binarydoc.readByteArray(ignored, 0, 8);
+this.nVertices = this.binarydoc.readInt();
+this.nPolygons = this.binarydoc.readInt();
+this.binarydoc.readByteArray(ignored, 0, 64);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+this.pmeshError += " " + e.toString();
+this.binarydoc.close();
+return false;
+} else {
+throw e;
+}
+}
+this.pmeshError = null;
+return true;
+});
+Clazz.defineMethod(c$, "readVertices",
+function(){
+return this.readVerticesPM();
+});
+Clazz.defineMethod(c$, "readVerticesPM",
+function(){
+this.pmeshError = this.type + " ERROR: vertex count must be positive";
+if (!this.isBinary) {
+this.nVertices = this.getInt();
+if (this.nVertices == -2147483648) this.nVertices = this.getInt();
+}if (this.onePerLine) this.iToken = 2147483647;
+if (this.nVertices <= 0) {
+this.pmeshError += " (" + this.nVertices + ")";
+return false;
+}this.pmeshError = this.type + " ERROR: invalid vertex list";
+this.vertexMap = Clazz.newIntArray (this.nVertices, 0);
+for (var i = 0; i < this.nVertices; i++) {
+var pt = JU.P3.new3(this.getFloat(), this.getFloat(), this.getFloat());
+if (this.isAnisotropic) this.setVertexAnisotropy(pt);
+if (JU.Logger.debugging) JU.Logger.debug(i + ": " + pt);
+this.vertexMap[i] = this.addVertexCopy(pt, 0, i, false);
+if (this.onePerLine) this.iToken = 2147483647;
+}
+this.pmeshError = null;
+return true;
+});
+Clazz.defineMethod(c$, "readPolygons",
+function(){
+return this.readPolygonsPM();
+});
+Clazz.defineMethod(c$, "readPolygonsPM",
+function(){
+this.pmeshError = this.type + " ERROR: polygon count must be zero or positive";
+if (!this.isBinary) this.nPolygons = this.getInt();
+if (this.onePerLine) this.iToken = 2147483647;
+var vertices = Clazz.newIntArray (5, 0);
+if (this.nPolygons == -1) this.nPolygons = 2147483647;
+var nread = 0;
+for (var iPoly = 0; iPoly < this.nPolygons; iPoly++) {
+var intCount = (this.fixedCount == 0 ? this.getInt() : this.fixedCount);
+if (intCount == 0) break;
+nread++;
+var haveColor = (intCount < 0);
+if (haveColor) intCount = -intCount;
+var vertexCount = intCount - (intCount > 3 && this.isClosedFace ? 1 : 0);
+if (vertexCount < 1 || vertexCount > 4) {
+this.pmeshError = this.type + " ERROR: bad polygon (must have 1-4 vertices) at #" + (iPoly + 1);
+return false;
+}var isOK = true;
+for (var i = 0; i < intCount; ++i) {
+if ((vertices[i] = this.getInt() - this.vertexBase) < 0 || vertices[i] >= this.nVertices) {
+this.pmeshError = this.type + " ERROR: invalid vertex index: " + vertices[i];
+return false;
+}if ((vertices[i] = this.vertexMap[vertices[i]]) < 0) isOK = false;
+}
+if (this.onePerLine) this.iToken = 2147483647;
+if (!isOK) continue;
+if (vertexCount < 3) for (var i = vertexCount; i < 3; ++i) vertices[i] = vertices[i - 1];
+
+var color = 0;
+if (haveColor) {
+if (this.isBinary) {
+color = this.getInt();
+} else {
+var c = this.nextToken();
+try {
+color = (c.startsWith("0x") ? JU.PT.parseIntRadix(c.substring(2), 16) : this.parseIntStr(c));
+} catch (e) {
+color = -2147483648;
+}
+if (color == -2147483648) color = JU.CU.getArgbFromString(c);
+}color |= 0xFF000000;
+}if (vertexCount == 4) {
+this.nTriangles += 2;
+this.addTriangleCheck(vertices[0], vertices[1], vertices[3], 5, 0, false, color);
+this.addTriangleCheck(vertices[1], vertices[2], vertices[3], 3, 0, false, color);
+} else {
+this.nTriangles++;
+this.addTriangleCheck(vertices[0], vertices[1], vertices[2], 7, 0, false, color);
+}}
+if (this.isBinary) this.nBytes = this.binarydoc.getPosition();
+this.nPolygons = nread;
+return true;
+});
+Clazz.defineMethod(c$, "nextToken",
+function(){
+while (this.iToken >= this.tokens.length) {
+this.iToken = 0;
+this.rd();
+this.tokens = this.getTokens();
+}
+return this.tokens[this.iToken++];
+});
+Clazz.defineMethod(c$, "getInt",
+function(){
+return (this.isBinary ? this.binarydoc.readInt() : this.parseIntStr(this.nextToken()));
+});
+Clazz.defineMethod(c$, "getFloat",
+function(){
+return (this.isBinary ? this.binarydoc.readFloat() : this.parseFloatStr(this.nextToken()));
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PolygonFileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PolygonFileReader.js
new file mode 100755
index 000000000000..0b408295fc68
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PolygonFileReader.js
@@ -0,0 +1,31 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.SurfaceFileReader"], "J.jvxl.readers.PolygonFileReader", ["java.util.Date", "JU.SB"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nVertices = 0;
+this.nTriangles = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "PolygonFileReader", J.jvxl.readers.SurfaceFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.PolygonFileReader, []);
+});
+Clazz.defineMethod(c$, "init2PFR",
+function(sg, br){
+this.init2SFR(sg, br);
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("#created ").append("" + new java.util.Date()).append("\n");
+this.vertexDataOnly = true;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readVolumeData",
+function(isMapData){
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+this.getSurfaceData();
+}, "~B");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PyMOLMeshReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PyMOLMeshReader.js
new file mode 100755
index 000000000000..2ca1e15f6633
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/PyMOLMeshReader.js
@@ -0,0 +1,127 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.MapFileReader"], "J.jvxl.readers.PyMOLMeshReader", ["JU.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.data = null;
+this.voxelList = null;
+this.surfaceName = null;
+this.pymolType = 0;
+this.isMesh = false;
+this.pt = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "PyMOLMeshReader", J.jvxl.readers.MapFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.PyMOLMeshReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, brNull){
+this.init2MFR(sg, null);
+this.allowSigma = true;
+this.nSurfaces = 1;
+var map = sg.getReaderData();
+this.data = map.get(this.params.calculationType);
+if (this.data == null) return;
+this.pymolType = Clazz.floatToInt(this.getFloat(J.jvxl.readers.PyMOLMeshReader.getList(this.data, 0), 0));
+this.isMesh = (this.pymolType == 3);
+this.surfaceName = this.data.get(this.data.size() - 1);
+JU.Logger.info("PyMOLMeshReader for " + this.params.calculationType + " pymolType=" + this.pymolType + "; isMesh=" + this.isMesh + " surfaceName=" + this.surfaceName);
+this.data = J.jvxl.readers.PyMOLMeshReader.getList(J.jvxl.readers.PyMOLMeshReader.getList(this.data, 2), 0);
+if (this.isMesh && this.params.thePlane == null && this.params.cutoffAutomatic) {
+this.params.cutoff = this.getFloat(this.data, 8);
+this.params.cutoffAutomatic = false;
+}if (this.isMesh) this.data = J.jvxl.readers.PyMOLMeshReader.getList(J.jvxl.readers.PyMOLMeshReader.getList(map.get(this.surfaceName), 2), 0);
+this.voxelList = J.jvxl.readers.PyMOLMeshReader.getList(J.jvxl.readers.PyMOLMeshReader.getList(J.jvxl.readers.PyMOLMeshReader.getList(this.data, 14), 2), 6);
+JU.Logger.info("PyMOLMeshReader: Number of grid points = " + this.voxelList.size());
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+c$.getList = Clazz.defineMethod(c$, "getList",
+function(list, i){
+return list.get(i);
+}, "JU.Lst,~N");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+var t;
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("PyMOL surface reader\n");
+this.jvxlFileHeaderBuffer.append(this.surfaceName + " (" + this.params.calculationType + ")\n");
+var s = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 1);
+t = J.jvxl.readers.PyMOLMeshReader.getList(s, 0);
+var haveUnitCell = false;
+if (t != null) {
+if (t.size() < 3) t = J.jvxl.readers.PyMOLMeshReader.getList(s = J.jvxl.readers.PyMOLMeshReader.getList(s, 0), 0);
+this.a = this.getFloat(t, 0);
+haveUnitCell = (this.a != 1);
+if (haveUnitCell) {
+this.b = this.getFloat(t, 1);
+this.c = this.getFloat(t, 2);
+t = J.jvxl.readers.PyMOLMeshReader.getList(s, 1);
+this.alpha = this.getFloat(t, 0);
+this.beta = this.getFloat(t, 1);
+this.gamma = this.getFloat(t, 2);
+}}t = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 7);
+this.origin.set(this.getFloat(t, 0), this.getFloat(t, 1), this.getFloat(t, 2));
+t = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 10);
+this.na = Clazz.floatToInt(this.getFloat(t, 0));
+this.nb = Clazz.floatToInt(this.getFloat(t, 1));
+this.nc = Clazz.floatToInt(this.getFloat(t, 2));
+t = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 11);
+this.xyzStart[0] = this.getFloat(t, 0);
+this.xyzStart[1] = this.getFloat(t, 1);
+this.xyzStart[2] = this.getFloat(t, 2);
+t = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 13);
+this.n2 = Clazz.floatToInt(this.getFloat(t, 0));
+this.n1 = Clazz.floatToInt(this.getFloat(t, 1));
+this.n0 = Clazz.floatToInt(this.getFloat(t, 2));
+if (!haveUnitCell) {
+this.na = this.n2 - 1;
+this.nb = this.n1 - 1;
+this.nc = this.n0 - 1;
+t = J.jvxl.readers.PyMOLMeshReader.getList(this.data, 8);
+this.a = this.getFloat(t, 0) - this.origin.x;
+this.b = this.getFloat(t, 1) - this.origin.y;
+this.c = this.getFloat(t, 2) - this.origin.z;
+this.alpha = this.beta = this.gamma = 90;
+}this.mapc = 3;
+this.mapr = 2;
+this.maps = 1;
+this.getVectorsAndOrigin();
+this.setCutoffAutomatic();
+});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+return this.getFloat(this.voxelList, this.pt++);
+});
+Clazz.defineMethod(c$, "getFloat",
+function(list, i){
+return (list.get(i)).floatValue();
+}, "JU.Lst,~N");
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+}, "~N");
+Clazz.overrideMethod(c$, "setCutoffAutomatic",
+function(){
+if (this.params.thePlane != null) return;
+if (Float.isNaN(this.params.sigma)) {
+if (!this.params.cutoffAutomatic) return;
+this.params.cutoff = (this.boundingBox == null ? 3.0 : 1.6);
+if (this.dmin != 3.4028235E38) {
+if (this.params.cutoff > this.dmax) this.params.cutoff = this.dmax / 4;
+}} else {
+this.params.cutoff = this.calculateCutoff();
+}JU.Logger.info("MapReader: setting cutoff to default value of " + this.params.cutoff + (this.boundingBox == null ? " (no BOUNDBOX parameter)\n" : "\n"));
+});
+Clazz.defineMethod(c$, "calculateCutoff",
+function(){
+var n = this.voxelList.size();
+var sum = 0;
+var sum2 = 0;
+for (var i = 0; i < n; i++) {
+var v = this.getFloat(this.voxelList, i);
+sum += v;
+sum2 += v * v;
+}
+var mean = sum / n;
+var rmsd = Math.sqrt(sum2 / n);
+JU.Logger.info("PyMOLMeshReader rmsd=" + rmsd + " mean=" + mean);
+return this.params.sigma * rmsd + mean;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Ras3DReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Ras3DReader.js
new file mode 100755
index 000000000000..c5b266743214
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/Ras3DReader.js
@@ -0,0 +1,97 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PolygonFileReader"], "J.jvxl.readers.Ras3DReader", ["java.util.Hashtable", "JU.CU", "$.P3", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.pmeshError = null;
+this.type = null;
+this.asQuads = false;
+this.nPolygons = 0;
+this.htVertices = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "Ras3DReader", J.jvxl.readers.PolygonFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.Ras3DReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2PR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2PR",
+function(sg, br){
+this.init2PFR(sg, br);
+var fileName = (sg.getReaderData())[0];
+if (fileName == null) return;
+this.type = "ras3d";
+this.setHeader();
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "setHeader",
+function(){
+this.jvxlFileHeaderBuffer.append(this.type + " file format\nvertices and triangles only\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+});
+Clazz.overrideMethod(c$, "getSurfaceData",
+function(){
+if (this.readVerticesAndPolygons()) JU.Logger.info(this.type + " file contains " + this.nVertices + " vertices and " + this.nPolygons + " polygons for " + this.nTriangles + " triangles");
+ else JU.Logger.error(this.params.fileName + ": " + (this.pmeshError == null ? "Error reading pmesh data " : this.pmeshError));
+});
+Clazz.defineMethod(c$, "readVerticesAndPolygons",
+function(){
+try {
+if (this.readVertices()) return true;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (this.pmeshError == null) this.pmeshError = this.type + " ERROR: " + e;
+} else {
+throw e;
+}
+}
+return false;
+});
+Clazz.defineMethod(c$, "readVertices",
+function(){
+this.htVertices = new java.util.Hashtable();
+var v0 = Clazz.newIntArray (3, 0);
+var v1 = Clazz.newIntArray (3, 0);
+var v2;
+var c0 = 0;
+var c1 = 0;
+var c2;
+if (this.rd().indexOf("DSSR") >= 0) this.asQuads = true;
+while (this.rd() != null) {
+while (!this.line.equals("1")) {
+this.rd();
+}
+this.rd();
+var tokens = this.getTokens();
+v0[0] = this.getPoint(tokens, 0);
+v0[1] = this.getPoint(tokens, 3);
+v0[2] = this.getPoint(tokens, 6);
+this.nTriangles++;
+c0 = JU.CU.colorTriadToFFRGB(this.parseFloatStr(tokens[9]), this.parseFloatStr(tokens[10]), this.parseFloatStr(tokens[11]));
+if (this.asQuads) {
+if (this.nTriangles % 2 == 1) {
+v2 = v1;
+v1 = v0;
+v0 = v2;
+c2 = c1;
+c1 = c0;
+c0 = c2;
+continue;
+}this.addTriangleCheck(v0[0], v0[1], v0[2], 6, 0, false, c0);
+this.addTriangleCheck(v1[0], v1[1], v1[2], 3, 0, false, c1);
+} else {
+this.addTriangleCheck(v0[0], v0[1], v0[2], 7, 0, false, c0);
+}this.nPolygons++;
+}
+return true;
+});
+Clazz.defineMethod(c$, "getPoint",
+function(tokens, i){
+var key = tokens[i] + ";" + tokens[i + 1] + ";" + tokens[i + 2];
+var v = this.htVertices.get(key);
+if (v == null) {
+this.addVertexCopy(JU.P3.new3(this.parseFloatStr(tokens[i]), this.parseFloatStr(tokens[i + 1]), this.parseFloatStr(tokens[i + 2])), 0, this.nVertices, false);
+this.htVertices.put(key, v = Integer.$valueOf(this.nVertices++));
+}return v.intValue();
+}, "~A,~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceFileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceFileReader.js
new file mode 100755
index 000000000000..46d6ef833c96
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceFileReader.js
@@ -0,0 +1,140 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.SurfaceReader"], "J.jvxl.readers.SurfaceFileReader", ["JU.PT", "$.Rdr", "J.api.Interface"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.br = null;
+this.binarydoc = null;
+this.out = null;
+this.line = null;
+this.next = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "SurfaceFileReader", J.jvxl.readers.SurfaceReader);
+Clazz.prepareFields (c$, function(){
+this.next = Clazz.newIntArray (1, 0);
+});
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.SurfaceFileReader, []);
+});
+Clazz.defineMethod(c$, "setStream",
+function(fileName, isBigEndian){
+if (fileName == null) this.binarydoc.setStream(null, isBigEndian);
+ else try {
+if (Clazz.instanceOf(this.br,"JU.Rdr.StreamReader")) {
+var stream = (this.br).getStream();
+stream.reset();
+this.binarydoc.setStream(stream, true);
+}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println("BCifDensityReader " + e);
+this.binarydoc.setStream(this.sg.atomDataServer.getBufferedInputStream(fileName), isBigEndian);
+} else {
+throw e;
+}
+}
+}, "~S,~B");
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initSR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "init2",
+function(sg, br){
+this.init2SFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2SFR",
+function(sg, br){
+this.br = br;
+this.init(sg);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "newBinaryDocument",
+function(){
+return J.api.Interface.getInterface("JU.BinaryDocument", this.sg.atomDataServer, "file");
+});
+Clazz.overrideMethod(c$, "setOutputChannel",
+function(out){
+if (this.binarydoc == null) this.out = out;
+ else this.sg.setOutputChannel(this.binarydoc, out);
+}, "JU.OC");
+Clazz.overrideMethod(c$, "closeReader",
+function(){
+this.closeReaderSFR();
+});
+Clazz.defineMethod(c$, "closeReaderSFR",
+function(){
+if (this.br != null) try {
+this.br.close();
+} catch (e) {
+if (Clazz.exceptionOf(e,"java.io.IOException")){
+} else {
+throw e;
+}
+}
+if (this.out != null) this.out.closeChannel();
+if (this.binarydoc != null) this.binarydoc.close();
+});
+Clazz.overrideMethod(c$, "discardTempData",
+function(discardAll){
+this.closeReader();
+this.discardTempDataSR(discardAll);
+}, "~B");
+Clazz.defineMethod(c$, "getTokens",
+function(){
+return JU.PT.getTokensAt(this.line, 0);
+});
+Clazz.defineMethod(c$, "parseFloat",
+function(){
+return JU.PT.parseFloatNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "parseFloatStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseFloatNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseFloatRange",
+function(s, iStart, iEnd){
+this.next[0] = iStart;
+return JU.PT.parseFloatRange(s, iEnd, this.next);
+}, "~S,~N,~N");
+Clazz.defineMethod(c$, "parseInt",
+function(){
+return JU.PT.parseIntNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "parseIntStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseIntNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseIntNext",
+function(s){
+return JU.PT.parseIntNext(s, this.next);
+}, "~S");
+Clazz.defineMethod(c$, "parseFloatArrayStr",
+function(s){
+this.next[0] = 0;
+return JU.PT.parseFloatArrayNext(s, this.next, null, null, null);
+}, "~S");
+Clazz.defineMethod(c$, "parseFloatArray",
+function(a, strStart, strEnd){
+return JU.PT.parseFloatArrayNext(this.line, this.next, a, strStart, strEnd);
+}, "~A,~S,~S");
+Clazz.defineMethod(c$, "getQuotedStringNext",
+function(){
+return JU.PT.getQuotedStringNext(this.line, this.next);
+});
+Clazz.defineMethod(c$, "skipTo",
+function(info, what){
+if (info != null) while (this.rd().indexOf(info) < 0) {
+}
+if (what != null) this.next[0] = this.line.indexOf(what) + what.length + 2;
+}, "~S,~S");
+Clazz.defineMethod(c$, "rd",
+function(){
+this.line = this.br.readLine();
+if (this.line != null) {
+this.nBytes += this.line.length;
+if (this.out != null) {
+var b = this.line.getBytes();
+this.out.write(b, 0, b.length);
+this.out.writeByteAsInt(0x0A);
+}}return this.line;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceGenerator.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceGenerator.js
new file mode 100755
index 000000000000..a9baf010d6ed
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceGenerator.js
@@ -0,0 +1,866 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["JU.P3", "$.V3"], "J.jvxl.readers.SurfaceGenerator", ["JU.AU", "$.BS", "$.Measure", "$.P4", "$.PT", "$.Rdr", "$.SB", "J.jvxl.data.JvxlCoder", "$.JvxlData", "$.MeshData", "$.VolumeData", "J.jvxl.readers.Parameters", "$.SurfaceReader", "JU.Logger", "JV.FileManager"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.params = null;
+this.jvxlData = null;
+this.meshData = null;
+this.volumeDataTemp = null;
+this.meshDataServer = null;
+this.atomDataServer = null;
+this.marchingSquares = null;
+this.version = null;
+this.isValid = true;
+this.fileType = null;
+this.bsVdw = null;
+this.colorPtr = 0;
+this.surfaceReader = null;
+this.out = null;
+this.readerData = null;
+this.vAB = null;
+this.vNorm = null;
+this.ptRef = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "SurfaceGenerator", null);
+Clazz.prepareFields (c$, function(){
+this.vAB = new JU.V3();
+this.vNorm = new JU.V3();
+this.ptRef = JU.P3.new3(0, 0, 1e15);
+});
+Clazz.makeConstructor(c$,
+function(atomDataServer, meshDataServer, meshData, jvxlData){
+this.atomDataServer = atomDataServer;
+this.meshDataServer = meshDataServer;
+this.params = new J.jvxl.readers.Parameters();
+this.meshData = (meshData == null ? new J.jvxl.data.MeshData() : meshData);
+this.jvxlData = (jvxlData == null ? new J.jvxl.data.JvxlData() : jvxlData);
+this.volumeDataTemp = new J.jvxl.data.VolumeData();
+this.initializeIsosurface();
+}, "J.atomdata.AtomDataServer,J.jvxl.api.MeshDataServer,J.jvxl.data.MeshData,J.jvxl.data.JvxlData");
+Clazz.defineMethod(c$, "setJvxlData",
+function(jvxlData){
+this.jvxlData = jvxlData;
+if (jvxlData != null) jvxlData.version = this.version;
+}, "J.jvxl.data.JvxlData");
+Clazz.defineMethod(c$, "setProp",
+function(propertyName, value, bs){
+if ("debug" === propertyName) {
+var TF = (value).booleanValue();
+this.params.logMessages = TF;
+this.params.logCube = TF;
+return true;
+}if ("init" === propertyName) {
+this.initializeIsosurface();
+if (Clazz.instanceOf(value,"J.jvxl.readers.Parameters")) {
+this.params = value;
+} else {
+this.params.script = value;
+if (this.params.script != null && this.params.script.indexOf(";#") >= 0) {
+this.params.script = JU.PT.rep(this.params.script, ";#", "; #");
+}}return false;
+}if ("silent" === propertyName) {
+this.params.isSilent = true;
+return true;
+}if ("map" === propertyName) {
+this.params.resetForMapping((value).booleanValue());
+if (this.surfaceReader != null) this.surfaceReader.minMax = null;
+return true;
+}if ("finalize" === propertyName) {
+this.initializeIsosurface();
+return true;
+}if ("clear" === propertyName) {
+if (this.surfaceReader != null) this.surfaceReader.discardTempData(true);
+return false;
+}if ("fileIndex" === propertyName) {
+this.params.fileIndex = (value).intValue();
+if (this.params.fileIndex < 0) this.params.fileIndex = 0;
+this.params.readAllData = false;
+return true;
+}if ("blockData" === propertyName) {
+this.params.blockCubeData = (value).booleanValue();
+return true;
+}if ("withinPoints" === propertyName) {
+this.params.boundingBox = (value)[1];
+return true;
+}if ("boundingBox" === propertyName) {
+var pts = value;
+this.params.boundingBox = Clazz.newArray(-1, [JU.P3.newP(pts[0]), JU.P3.newP(pts[pts.length - 1])]);
+return true;
+}if ("func" === propertyName) {
+this.params.func = value;
+return true;
+}if ("intersection" === propertyName) {
+this.params.intersection = value;
+return true;
+}if ("bsSolvent" === propertyName) {
+this.params.bsSolvent = value;
+return true;
+}if ("select" === propertyName) {
+this.params.bsSelected = value;
+return true;
+}if ("ignore" === propertyName) {
+this.params.bsIgnore = value;
+return true;
+}if ("propertySmoothing" === propertyName) {
+this.params.propertySmoothing = (value).booleanValue();
+return true;
+}if ("propertyDistanceMax" === propertyName) {
+this.params.propertyDistanceMax = (value).floatValue();
+return true;
+}if ("propertySmoothingPower" === propertyName) {
+this.params.propertySmoothingPower = (value).intValue();
+return true;
+}if ("title" === propertyName) {
+if (value == null) {
+this.params.title = null;
+return true;
+} else if (JU.AU.isAS(value)) {
+this.params.title = value;
+if (JU.Logger.debugging) for (var i = 0; i < this.params.title.length; i++) if (this.params.title[i].length > 0) JU.Logger.info(this.params.title[i]);
+
+}return true;
+}if ("sigma" === propertyName) {
+this.params.cutoff = this.params.sigma = (value).floatValue();
+this.params.cutoffRange = null;
+this.params.cutoffAutomatic = false;
+return true;
+}if ("cutoff" === propertyName) {
+this.params.cutoff = (value).floatValue();
+this.params.cutoffRange = null;
+this.params.isPositiveOnly = false;
+this.params.cutoffAutomatic = false;
+return true;
+}if ("cutoffPositive" === propertyName) {
+this.params.cutoff = (value).floatValue();
+this.params.cutoffRange = null;
+this.params.isPositiveOnly = true;
+this.params.isCutoffAbsolute = false;
+this.params.cutoffAutomatic = false;
+return true;
+}if ("cutoffRange" === propertyName) {
+this.params.cutoffRange = value;
+this.params.cutoff = this.params.cutoffRange[0];
+this.params.isPositiveOnly = false;
+this.params.cutoffAutomatic = false;
+return true;
+}if ("parameters" === propertyName) {
+this.params.parameters = JU.AU.ensureLengthA(value, 2);
+if (this.params.parameters.length > 0 && this.params.parameters[0] != 0) this.params.cutoff = this.params.parameters[0];
+return true;
+}if ("cap" === propertyName || "slab" === propertyName) {
+if (value != null) this.params.addSlabInfo(value);
+return true;
+}if ("scale" === propertyName) {
+this.params.scale = (value).floatValue();
+return true;
+}if ("scale3d" === propertyName) {
+this.params.scale3d = (value).floatValue();
+return true;
+}if ("angstroms" === propertyName) {
+this.params.isAngstroms = true;
+return true;
+}if ("resolution" === propertyName) {
+var resolution = (value).floatValue();
+this.params.resolution = (resolution > 0 ? resolution : 3.4028235E38);
+return true;
+}if ("downsample" === propertyName) {
+var rate = (value).intValue();
+this.params.downsampleFactor = (rate >= 0 ? rate : 0);
+return true;
+}if ("anisotropy" === propertyName) {
+if ((this.params.dataType & 32) == 0) this.params.setAnisotropy(value);
+return true;
+}if ("eccentricity" === propertyName) {
+this.params.setEccentricity(value);
+return true;
+}if ("addHydrogens" === propertyName) {
+this.params.addHydrogens = (value).booleanValue();
+return true;
+}if ("squareData" === propertyName) {
+this.params.isSquared = (value == null ? false : (value).booleanValue());
+return true;
+}if ("squareLinear" === propertyName) {
+this.params.isSquaredLinear = (value == null ? false : (value).booleanValue());
+return true;
+}if ("gridPoints" === propertyName) {
+this.params.iAddGridPoints = true;
+return true;
+}if ("atomIndex" === propertyName) {
+this.params.atomIndex = (value).intValue();
+return true;
+}if ("insideOut" === propertyName) {
+this.params.insideOut = true;
+return true;
+}if ("sign" === propertyName) {
+this.params.isCutoffAbsolute = !this.params.isPositiveOnly;
+this.params.colorBySign = true;
+this.colorPtr = 0;
+return true;
+}if ("colorRGB" === propertyName) {
+var rgb = (value).intValue();
+this.params.colorRgb = this.params.colorPos = this.params.colorPosLCAO = rgb;
+if (this.colorPtr++ == 0) {
+this.params.colorNeg = this.params.colorNegLCAO = rgb;
+} else {
+this.params.colorRgb = 2147483647;
+}return true;
+}if ("monteCarloCount" === propertyName) {
+this.params.psi_monteCarloCount = (value).intValue();
+return true;
+}if ("rangeAll" === propertyName) {
+this.params.rangeAll = true;
+return true;
+}if ("rangeSelected" === propertyName) {
+this.params.rangeSelected = true;
+return true;
+}if ("red" === propertyName) {
+this.params.valueMappedToRed = (value).floatValue();
+return true;
+}if ("blue" === propertyName) {
+this.params.valueMappedToBlue = (value).floatValue();
+if (this.params.valueMappedToRed > this.params.valueMappedToBlue) {
+var f = this.params.valueMappedToRed;
+this.params.valueMappedToRed = this.params.valueMappedToBlue;
+this.params.valueMappedToBlue = f;
+this.params.isColorReversed = !this.params.isColorReversed;
+}this.params.rangeDefined = true;
+this.params.rangeAll = false;
+return true;
+}if ("reverseColor" === propertyName) {
+this.params.isColorReversed = true;
+return true;
+}if ("setColorScheme" === propertyName) {
+this.getSurfaceSets();
+this.params.colorBySets = true;
+this.mapSurface();
+return true;
+}if ("center" === propertyName) {
+this.params.center.setT(value);
+return true;
+}if ("origin" === propertyName) {
+this.params.origin = value;
+return true;
+}if ("step" === propertyName) {
+this.params.steps = value;
+return true;
+}if ("modelInvRotation" === propertyName) {
+this.params.modelInvRotation = value;
+return true;
+}if ("point" === propertyName) {
+this.params.points = value;
+return true;
+}if ("withinDistance" === propertyName) {
+this.params.distance = (value).floatValue();
+return true;
+}if ("withinPoint" === propertyName) {
+this.params.point = value;
+return true;
+}if ("progressive" === propertyName) {
+this.params.isXLowToHigh = true;
+return true;
+}if ("phase" === propertyName) {
+var color = value;
+this.params.isCutoffAbsolute = true;
+this.params.colorBySign = true;
+this.params.colorByPhase = true;
+this.params.colorPhase = J.jvxl.readers.SurfaceReader.getColorPhaseIndex(color);
+if (this.params.colorPhase < 0) {
+JU.Logger.warn(" invalid color phase: " + color);
+this.params.colorPhase = 0;
+}this.params.colorByPhase = this.params.colorPhase != 0;
+if (this.params.state >= 2) {
+this.params.dataType = this.params.surfaceType;
+this.params.state = 3;
+this.params.isBicolorMap = true;
+this.surfaceReader.applyColorScale();
+}return true;
+}if ("radius" === propertyName) {
+JU.Logger.info("solvent probe radius set to " + value);
+this.params.atomRadiusData = value;
+return true;
+}if ("envelopeRadius" === propertyName) {
+this.params.envelopeRadius = (value).floatValue();
+return true;
+}if ("cavityRadius" === propertyName) {
+this.params.cavityRadius = (value).floatValue();
+return true;
+}if ("cavity" === propertyName) {
+this.params.isCavity = true;
+return true;
+}if ("doFullMolecular" === propertyName) {
+this.params.doFullMolecular = true;
+return true;
+}if ("pocket" === propertyName) {
+this.params.pocket = value;
+this.params.fullyLit = this.params.pocket.booleanValue();
+return true;
+}if ("minset" === propertyName) {
+this.params.minSet = (value).intValue();
+return true;
+}if ("maxset" === propertyName) {
+this.params.maxSet = (value).intValue();
+return true;
+}if ("plane" === propertyName) {
+this.params.setPlane(value);
+return true;
+}if ("contour" === propertyName) {
+this.params.isContoured = true;
+var n;
+if (JU.AU.isAF(value)) {
+this.params.contoursDiscrete = value;
+this.params.nContours = this.params.contoursDiscrete.length;
+} else if (Clazz.instanceOf(value,"JU.P3")) {
+var pt = this.params.contourIncrements = value;
+var from = pt.x;
+var to = pt.y;
+var step = pt.z;
+if (step <= 0) step = 1;
+n = 0;
+for (var p = from; p <= to + step / 10; p += step, n++) {
+}
+this.params.contoursDiscrete = Clazz.newFloatArray (n, 0);
+var p = from;
+for (var i = 0; i < n; i++, p += step) {
+this.params.contoursDiscrete[i] = p;
+}
+this.params.nContours = n;
+} else {
+n = (value).intValue();
+this.params.thisContour = 0;
+if (n == 0) this.params.nContours = 9;
+ else if (n > 0) this.params.nContours = n;
+ else this.params.thisContour = -n;
+}return true;
+}if ("colorDiscrete" === propertyName) {
+this.params.contourColixes = value;
+return true;
+}if ("colorDensity" === propertyName) {
+this.params.colorDensity = true;
+if (value != null) this.params.pointSize = (value).floatValue();
+return false;
+}if ("fullPlane" === propertyName) {
+this.params.contourFromZero = !(value).booleanValue();
+return true;
+}if ("mapLattice" === propertyName) {
+this.params.mapLattice = value;
+return true;
+}if ("extendGrid" === propertyName) {
+this.params.extendGrid = (value).floatValue();
+return true;
+}if ("property" === propertyName) {
+this.params.dataType = 1208;
+this.params.theProperty = value;
+this.mapSurface();
+return true;
+}if ("sphere" === propertyName) {
+this.params.setSphere((value).floatValue(), false);
+this.readerData = Float.$valueOf(this.params.distance);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("geodesic" === propertyName) {
+this.params.setSphere((value).floatValue(), true);
+this.readerData = Float.$valueOf(this.params.distance);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("ellipsoid" === propertyName) {
+if (Clazz.instanceOf(value,"JU.P4")) this.params.setEllipsoidP4(value);
+ else if (JU.AU.isAF(value)) this.params.setEllipsoidAF(value);
+ else return true;
+this.readerData = Float.$valueOf(this.params.distance);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("ellipsoid3" === propertyName) {
+this.params.setEllipsoidAF(value);
+this.readerData = Float.$valueOf(this.params.distance);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("lp" === propertyName) {
+this.params.setLp(value);
+this.readerData = Clazz.newFloatArray(-1, [3, 2, 0, 15, 0]);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("rad" === propertyName) {
+this.params.setRadical(value);
+this.readerData = Clazz.newFloatArray(-1, [3, 2, 0, 15, 0]);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("lobe" === propertyName) {
+this.params.setLobe(value);
+this.readerData = Clazz.newFloatArray(-1, [3, 2, 0, 15, 0]);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.generateSurface();
+return true;
+}if ("hydrogenOrbital" === propertyName) {
+if (!this.params.setAtomicOrbital(value)) {
+this.isValid = false;
+return true;
+}this.readerData = Clazz.newFloatArray(-1, [this.params.psi_n, this.params.psi_l, this.params.psi_m, this.params.psi_Znuc, this.params.psi_monteCarloCount]);
+this.surfaceReader = this.newReader("IsoShapeReader");
+this.processState();
+return true;
+}if ("functionXY" === propertyName) {
+this.params.setFunctionXY(value);
+if (this.params.isContoured) this.volumeDataTemp.setPlaneParameters(this.params.thePlane == null ? this.params.thePlane = JU.P4.new4(0, 0, 1, 0) : this.params.thePlane);
+if ((this.params.functionInfo.get(0)).indexOf("_xyz") >= 0) this.getFunctionZfromXY();
+this.processState();
+return true;
+}if ("functionXYZ" === propertyName) {
+this.params.setFunctionXYZ(value);
+this.processState();
+return true;
+}if ("lcaoType" === propertyName) {
+this.params.setLcao(value, this.colorPtr);
+return true;
+}if ("lcaoCartoonCenter" === propertyName) {
+if (++this.params.state != 2) return true;
+if (Float.isNaN(this.params.center.x)) this.params.center.setT(value);
+return false;
+}if ("molecular" === propertyName || "solvent" === propertyName || "sasurface" === propertyName || "nomap" === propertyName) {
+this.params.setSolvent(propertyName, (value).floatValue());
+if (!this.params.isSilent) JU.Logger.info(this.params.calculationType);
+this.processState();
+return true;
+}if ("moData" === propertyName) {
+this.params.moData = value;
+return true;
+}if ("mepCalcType" === propertyName) {
+this.params.mep_calcType = (value).intValue();
+return true;
+}if ("mep" === propertyName) {
+this.params.setMep(value, false);
+this.processState();
+return true;
+}if ("mlp" === propertyName) {
+this.params.setMep(value, true);
+this.processState();
+return true;
+}if ("nci" === propertyName) {
+var isPromolecular = (value).booleanValue();
+this.params.setNci(isPromolecular);
+if (isPromolecular) this.processState();
+return true;
+}if ("calculationType" === propertyName) {
+this.params.calculationType = value;
+return true;
+}if ("charges" === propertyName) {
+this.params.theProperty = value;
+return true;
+}if ("randomSeed" === propertyName) {
+this.params.randomSeed = (value).intValue();
+return true;
+}if ("molecularOrbital" === propertyName) {
+var iMo = 0;
+var linearCombination = null;
+if (Clazz.instanceOf(value, Integer)) {
+iMo = (value).intValue();
+} else {
+linearCombination = value;
+}this.params.setMO(iMo, linearCombination);
+JU.Logger.info(this.params.calculationType);
+this.processState();
+return true;
+}if ("fileType" === propertyName) {
+this.fileType = value;
+return true;
+}if ("fileName" === propertyName) {
+this.params.fileName = value;
+return true;
+}if ("filesData" === propertyName) {
+this.params.filesData = value;
+return true;
+}if ("outputChannel" === propertyName) {
+this.out = value;
+return true;
+}if ("readFile" === propertyName) {
+if ((this.surfaceReader = this.setFileData(this.atomDataServer, value)) == null) {
+JU.Logger.error("Could not set the surface data");
+return true;
+}this.surfaceReader.setOutputChannel(this.out);
+this.generateSurface();
+return true;
+}if ("mapColor" === propertyName) {
+if ((this.surfaceReader = this.setFileData(this.atomDataServer, value)) == null) {
+JU.Logger.error("Could not set the mapping data");
+return true;
+}this.surfaceReader.setOutputChannel(this.out);
+this.mapSurface();
+return true;
+}if ("getSurfaceSets" === propertyName) {
+this.getSurfaceSets();
+return true;
+}if ("periodic" === propertyName) {
+this.params.isPeriodic = true;
+}return false;
+}, "~S,~O,JU.BS");
+Clazz.defineMethod(c$, "newReader",
+function(name){
+var sr = J.jvxl.readers.SurfaceGenerator.getInterface(name);
+if (sr != null) sr.init(this);
+return sr;
+}, "~S");
+Clazz.defineMethod(c$, "newReaderBr",
+function(name, br){
+var sr = J.jvxl.readers.SurfaceGenerator.getInterface(name);
+if (sr != null) sr.init2(this, br);
+return sr;
+}, "~S,java.io.BufferedReader");
+c$.getInterface = Clazz.defineMethod(c$, "getInterface",
+function(name){
+try {
+var x = Clazz._4Name("J.jvxl.readers." + name);
+return (x == null ? null : x.newInstance());
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Interface.java Error creating instance for " + name + ": \n" + e.toString());
+return null;
+} else {
+throw e;
+}
+}
+}, "~S");
+Clazz.defineMethod(c$, "getSurfaceSets",
+function(){
+if (this.meshDataServer == null) {
+this.meshData.getSurfaceSet();
+} else {
+this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshData.getSurfaceSet();
+this.meshDataServer.fillMeshData(this.meshData, 3, null);
+}});
+Clazz.defineMethod(c$, "processState",
+function(){
+if (this.params.state == 1 && this.params.thePlane != null) this.params.state++;
+if (this.params.state >= 2) {
+this.mapSurface();
+} else {
+this.generateSurface();
+}});
+Clazz.defineMethod(c$, "setReader",
+function(){
+this.readerData = null;
+if (this.surfaceReader != null) return !this.surfaceReader.vertexDataOnly;
+switch (this.params.dataType) {
+case 1207:
+this.surfaceReader = this.newReader("IsoPlaneReader");
+break;
+case 1208:
+this.surfaceReader = this.newReader("AtomPropertyMapper");
+break;
+case 1328:
+case 1329:
+this.readerData = (this.params.dataType == 1328 ? "Mep" : "Mlp");
+if (this.params.state == 3) {
+this.surfaceReader = this.newReader("AtomPropertyMapper");
+} else {
+this.surfaceReader = this.newReader("Iso" + this.readerData + "Reader");
+}break;
+case 1334:
+this.surfaceReader = this.newReader("IsoIntersectFileReader");
+break;
+case 1333:
+this.surfaceReader = this.newReader("IsoIntersectAtomReader");
+break;
+case 1195:
+case 1203:
+case 1196:
+this.surfaceReader = this.newReader("IsoSolventReader");
+break;
+case 1844:
+case 1837:
+this.surfaceReader = this.newReader("IsoMOReader");
+break;
+case 8:
+this.surfaceReader = this.newReader("IsoFxyReader");
+break;
+case 9:
+this.surfaceReader = this.newReader("IsoFxyzReader");
+break;
+}
+if (JU.Logger.debugging) JU.Logger.info("Using surface reader " + this.surfaceReader);
+if (this.params.isSilent && this.surfaceReader != null) this.surfaceReader.isQuiet = true;
+return true;
+});
+Clazz.defineMethod(c$, "generateSurface",
+function(){
+if (++this.params.state != 2) return;
+this.setReader();
+if (this.params.sbOut == null) this.params.sbOut = new JU.SB();
+this.jvxlData.sbOut = this.params.sbOut;
+var haveMeshDataServer = (this.meshDataServer != null);
+if (this.params.colorBySign) this.params.isBicolorMap = true;
+if (this.surfaceReader == null) {
+JU.Logger.error("surfaceReader is null for " + this.params.dataType);
+return;
+}if (!this.surfaceReader.createIsosurface(false)) {
+JU.Logger.error("Could not create isosurface");
+this.params.cutoff = NaN;
+this.params.cutoffRange = null;
+this.surfaceReader.closeReader();
+return;
+}if (this.params.probes != null) {
+for (var i = this.params.probeValues.length; --i >= 0; ) {
+this.params.probeValues[i] = this.surfaceReader.getValueAtPoint(this.params.probes[i], false);
+}
+}if (this.params.pocket != null && haveMeshDataServer) this.surfaceReader.selectPocket(!this.params.pocket.booleanValue());
+if (this.params.minSet > 0) this.surfaceReader.excludeMinimumSet();
+if (this.params.maxSet > 0) this.surfaceReader.excludeMaximumSet();
+if (this.params.slabInfo != null) this.surfaceReader.slabIsosurface(this.params.slabInfo);
+if (haveMeshDataServer && this.meshDataServer.notifySurfaceGenerationCompleted()) this.surfaceReader.hasColorData = false;
+if (this.jvxlData.thisSet != null) this.getSurfaceSets();
+if (this.jvxlData.jvxlDataIs2dContour) {
+this.surfaceReader.colorIsosurface();
+this.params.state = 3;
+}if (this.jvxlData.jvxlDataIsColorDensity) {
+this.params.state = 3;
+}if (this.params.colorBySign || this.params.isBicolorMap) {
+this.params.state = 3;
+this.surfaceReader.applyColorScale();
+}if (this.jvxlData.vertexColorMap != null) {
+this.jvxlData.vertexColorMap = null;
+this.surfaceReader.hasColorData = false;
+}this.surfaceReader.jvxlUpdateInfo();
+this.marchingSquares = this.surfaceReader.marchingSquares;
+this.surfaceReader.discardTempData(false);
+this.params.mappedDataMin = 3.4028235E38;
+this.surfaceReader.closeReader();
+if (this.params.state != 3 && (this.surfaceReader.hasColorData || this.params.colorDensity)) {
+this.params.state = 3;
+this.colorIsosurface();
+}this.surfaceReader = null;
+});
+Clazz.defineMethod(c$, "mapSurface",
+function(){
+if (this.params.state == 1 && this.params.thePlane != null) this.params.state++;
+if (++this.params.state < 3) return;
+if (!this.setReader()) return;
+if (this.params.isPeriodic) this.surfaceReader.volumeData.isPeriodic = true;
+if (this.params.thePlane != null) {
+var isSquared = this.params.isSquared;
+this.params.isSquared = false;
+this.params.cutoff = 0;
+this.params.cutoffRange = null;
+this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);
+this.surfaceReader.createIsosurface(!this.params.isPeriodic);
+this.surfaceReader.volumeData.setMappingPlane(null);
+if (this.meshDataServer != null) this.meshDataServer.notifySurfaceGenerationCompleted();
+if (this.params.dataType == 1207) {
+this.surfaceReader.discardTempData(true);
+return;
+}this.params.isSquared = isSquared;
+this.params.mappedDataMin = 3.4028235E38;
+this.surfaceReader.readVolumeData(true);
+if (this.params.mapLattice != null) this.surfaceReader.volumeData.isPeriodic = true;
+} else if (!this.params.colorBySets && !this.params.colorDensity) {
+this.surfaceReader.readAndSetVolumeParameters(true);
+this.params.mappedDataMin = 3.4028235E38;
+this.surfaceReader.readVolumeData(true);
+}this.colorIsosurface();
+this.surfaceReader.closeReader();
+this.surfaceReader = null;
+});
+Clazz.defineMethod(c$, "colorIsosurface",
+function(){
+this.surfaceReader.colorIsosurface();
+this.surfaceReader.jvxlUpdateInfo();
+this.surfaceReader.updateTriangles();
+this.surfaceReader.discardTempData(true);
+if (this.meshDataServer != null) this.meshDataServer.notifySurfaceMappingCompleted();
+});
+Clazz.defineMethod(c$, "getProperty",
+function(property, index){
+if (property === "jvxlFileData") return J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData, null, this.params.title, "", true, index, null, null);
+if (property === "jvxlFileInfo") return J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);
+return null;
+}, "~S,~N");
+Clazz.defineMethod(c$, "setFileData",
+function(vwr, value){
+var fileType = this.fileType;
+this.fileType = null;
+if (Clazz.instanceOf(value,"java.util.Map")) {
+var map = value;
+if (map.containsKey("__pymolSurfaceData__")) {
+this.readerData = map;
+return this.newReaderBr("PyMOLMeshReader", null);
+}value = map.get("volumeData");
+}if (Clazz.instanceOf(value,"J.jvxl.data.VolumeData")) {
+this.volumeDataTemp = value;
+return this.newReader("VolumeDataReader");
+}var data = null;
+if ((typeof(value)=='string')) {
+data = value;
+value = JU.Rdr.getBR(value);
+}if (Clazz.instanceOf(value,Array)) {
+var a = (value)[0];
+var b = new Array(a.length);
+for (var i = 0; i < a.length; i++) {
+this.fileType = fileType;
+b[i] = this.setFileData(vwr, a[i]);
+}
+(value)[0] = b;
+this.readerData = value;
+return this.newReader("IsoIntersectGridReader");
+}var br = value;
+if (fileType == null) fileType = JV.FileManager.determineSurfaceFileType(br);
+if (fileType != null && fileType.startsWith("UPPSALA")) {
+var fname = this.params.fileName;
+fname = fname.substring(0, fname.indexOf("/", 10));
+fname += JU.PT.getQuotedStringAt(fileType, fileType.indexOf("A HREF") + 1);
+this.params.fileName = fname;
+value = this.atomDataServer.getBufferedInputStream(fname);
+if (value == null) {
+JU.Logger.error("Isosurface: could not open file " + fname);
+return null;
+}try {
+br = JU.Rdr.getBufferedReader(value, null);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+fileType = JV.FileManager.determineSurfaceFileType(br);
+}if (fileType == null) fileType = "UNKNOWN";
+JU.Logger.info("data file type was determined to be " + fileType);
+if (fileType.equals("Jvxl+")) return this.newReaderBr("JvxlReader", br);
+this.readerData = Clazz.newArray(-1, [this.params.fileName, data]);
+if ("MRC DELPHI DSN6".indexOf(fileType.toUpperCase()) >= 0) {
+fileType += "Binary";
+}return this.newReaderBr(fileType + "Reader", br);
+}, "JV.Viewer,~O");
+Clazz.defineMethod(c$, "getReaderData",
+function(){
+var o = this.readerData;
+this.readerData = null;
+return o;
+});
+Clazz.defineMethod(c$, "initializeIsosurface",
+function(){
+this.params.initialize();
+this.colorPtr = 0;
+this.surfaceReader = null;
+this.marchingSquares = null;
+this.initState();
+});
+Clazz.defineMethod(c$, "initState",
+function(){
+this.params.state = 1;
+this.params.dataType = this.params.surfaceType = 0;
+});
+Clazz.defineMethod(c$, "setLcao",
+function(){
+this.params.colorPos = this.params.colorPosLCAO;
+this.params.colorNeg = this.params.colorNegLCAO;
+return this.params.lcaoType;
+});
+Clazz.defineMethod(c$, "getFunctionZfromXY",
+function(){
+var origin = this.params.functionInfo.get(1);
+var counts = Clazz.newIntArray (3, 0);
+var nearest = Clazz.newIntArray (3, 0);
+var vectors = new Array(3);
+for (var i = 0; i < 3; i++) {
+var info = this.params.functionInfo.get(i + 2);
+counts[i] = Math.abs(Clazz.floatToInt(info.x));
+vectors[i] = JU.V3.new3(info.y, info.z, info.w);
+}
+var nx = counts[0];
+var ny = counts[1];
+var pt = new JU.P3();
+var pta = new JU.P3();
+var ptb = new JU.P3();
+var ptc = new JU.P3();
+var data = this.params.functionInfo.get(5);
+var data2 = Clazz.newFloatArray (nx, ny, 0);
+var d;
+for (var i = 0; i < nx; i++) for (var j = 0; j < ny; j++) {
+pt.scaleAdd2(i, vectors[0], origin);
+pt.scaleAdd2(j, vectors[1], pt);
+var dist = J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(pt.x, pt.y, data, nearest);
+pta.set((d = data[nearest[0]])[0], d[1], d[2]);
+if (dist < 0.00001) {
+pt.z = d[2];
+} else {
+ptb.set((d = data[nearest[1]])[0], d[1], d[2]);
+ptc.set((d = data[nearest[2]])[0], d[1], d[2]);
+pt.z = this.distanceVerticalToPlane(pt.x, pt.y, pta, ptb, ptc);
+}data2[i][j] = pt.z;
+}
+
+this.params.functionInfo.set(5, data2);
+});
+Clazz.defineMethod(c$, "distanceVerticalToPlane",
+function(x, y, pta, ptb, ptc){
+var d = JU.Measure.getDirectedNormalThroughPoints(pta, ptb, ptc, this.ptRef, this.vNorm, this.vAB);
+return (this.vNorm.x * x + this.vNorm.y * y + d) / -this.vNorm.z;
+}, "~N,~N,JU.P3,JU.P3,JU.P3");
+c$.findNearestThreePoints = Clazz.defineMethod(c$, "findNearestThreePoints",
+function(x, y, xyz, result){
+var d;
+var dist1;
+var dist2;
+var dist3;
+var i1;
+var i2;
+var i3;
+i1 = i2 = i3 = -1;
+dist1 = dist2 = dist3 = 3.4028235E38;
+for (var i = xyz.length; --i >= 0; ) {
+d = (d = xyz[i][0] - x) * d + (d = xyz[i][1] - y) * d;
+if (d < dist1) {
+dist3 = dist2;
+dist2 = dist1;
+dist1 = d;
+i3 = i2;
+i2 = i1;
+i1 = i;
+} else if (d < dist2) {
+dist3 = dist2;
+dist2 = d;
+i3 = i2;
+i2 = i;
+} else if (d < dist3) {
+dist3 = d;
+i3 = i;
+}}
+result[0] = i1;
+result[1] = i2;
+result[2] = i3;
+return dist1;
+}, "~N,~N,~A,~A");
+Clazz.defineMethod(c$, "addRequiredFile",
+function(fileName){
+if (this.meshDataServer == null) return;
+this.meshDataServer.addRequiredFile(fileName);
+}, "~S");
+Clazz.defineMethod(c$, "setRequiredFile",
+function(oldName, fileName){
+if (this.meshDataServer == null) return;
+this.meshDataServer.setRequiredFile(oldName, fileName);
+}, "~S,~S");
+Clazz.defineMethod(c$, "log",
+function(msg){
+if (this.atomDataServer == null) System.out.println(msg);
+ else this.atomDataServer.log(msg);
+}, "~S");
+Clazz.defineMethod(c$, "setOutputChannel",
+function(binaryDoc, out){
+if (this.meshDataServer == null) return;
+this.meshDataServer.setOutputChannel(binaryDoc, out);
+}, "javajs.api.GenericBinaryDocument,JU.OC");
+Clazz.defineMethod(c$, "fillAtomData",
+function(atomData, mode){
+if ((mode & 2) != 0 && atomData.bsSelected != null) {
+if (this.bsVdw == null) this.bsVdw = new JU.BS();
+this.bsVdw.or(atomData.bsSelected);
+}this.atomDataServer.fillAtomData(atomData, mode);
+}, "J.atomdata.AtomData,~N");
+Clazz.defineMethod(c$, "getOriginVaVbVc",
+function(){
+return (this.surfaceReader.volumeData == null ? null : this.surfaceReader.volumeData.oabc);
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceReader.js
new file mode 100755
index 000000000000..14aaf0e698d7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/SurfaceReader.js
@@ -0,0 +1,649 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.api.VertexDataServer", "JU.P3"], "J.jvxl.readers.SurfaceReader", ["JU.AU", "$.BS", "J.jvxl.calc.MarchingCubes", "$.MarchingSquares", "J.jvxl.data.JvxlCoder", "$.MeshData", "JU.BoxInfo", "$.C", "$.ColorEncoder", "$.Escape", "$.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.sg = null;
+this.meshDataServer = null;
+this.params = null;
+this.meshData = null;
+this.jvxlData = null;
+this.volumeData = null;
+this.edgeData = null;
+this.haveSurfaceAtoms = false;
+this.allowSigma = false;
+this.isProgressive = false;
+this.isXLowToHigh = false;
+this.assocCutoff = 0.3;
+this.isQuiet = false;
+this.isPeriodic = false;
+this.vertexDataOnly = false;
+this.hasColorData = false;
+this.dataMin = 3.4028235E38;
+this.dataMax = -3.4028235E38;
+this.dataMean = 0;
+this.xyzMin = null;
+this.xyzMax = null;
+this.center = null;
+this.anisotropy = null;
+this.isAnisotropic = false;
+this.eccentricityMatrix = null;
+this.eccentricityMatrixInverse = null;
+this.isEccentric = false;
+this.eccentricityScale = 0;
+this.eccentricityRatio = 0;
+this.edgeCount = 0;
+this.volumetricOrigin = null;
+this.volumetricVectors = null;
+this.voxelCounts = null;
+this.voxelData = null;
+this.nBytes = 0;
+this.nDataPoints = 0;
+this.nPointsX = 0;
+this.nPointsY = 0;
+this.nPointsZ = 0;
+this.isJvxl = false;
+this.edgeFractionBase = 0;
+this.edgeFractionRange = 0;
+this.colorFractionBase = 0;
+this.colorFractionRange = 0;
+this.jvxlFileHeaderBuffer = null;
+this.fractionData = null;
+this.jvxlEdgeDataRead = "";
+this.jvxlColorDataRead = "";
+this.jvxlVoxelBitSet = null;
+this.jvxlDataIsColorMapped = false;
+this.jvxlDataIsPrecisionColor = false;
+this.jvxlDataIs2dContour = false;
+this.jvxlDataIsColorDensity = false;
+this.jvxlCutoff = 0;
+this.jvxlCutoffRange = null;
+this.jvxlNSurfaceInts = 0;
+this.cJvxlEdgeNaN = '\0';
+this.contourVertexCount = 0;
+this.marchingSquares = null;
+this.marchingCubes = null;
+this.yzPlanes = null;
+this.yzCount = 0;
+this.qpc = null;
+this.ptTemp = null;
+this.minMax = null;
+this.haveSetAnisotropy = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "SurfaceReader", null, J.jvxl.api.VertexDataServer);
+Clazz.prepareFields (c$, function(){
+this.ptTemp = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+Clazz.defineMethod(c$, "initSR",
+function(sg){
+this.sg = sg;
+this.params = sg.params;
+this.assocCutoff = this.params.assocCutoff;
+this.isXLowToHigh = this.params.isXLowToHigh;
+this.center = this.params.center;
+this.anisotropy = this.params.anisotropy;
+this.isAnisotropic = this.params.isAnisotropic;
+this.eccentricityMatrix = this.params.eccentricityMatrix;
+this.eccentricityMatrixInverse = this.params.eccentricityMatrixInverse;
+this.isEccentric = this.params.isEccentric;
+this.eccentricityScale = this.params.eccentricityScale;
+this.eccentricityRatio = this.params.eccentricityRatio;
+this.marchingSquares = sg.marchingSquares;
+this.meshData = sg.meshData;
+this.jvxlData = sg.jvxlData;
+this.setVolumeDataV(sg.volumeDataTemp);
+this.meshDataServer = sg.meshDataServer;
+this.cJvxlEdgeNaN = String.fromCharCode(125);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "setOutputChannel",
+function(out){
+}, "JU.OC");
+Clazz.defineMethod(c$, "newVoxelDataCube",
+function(){
+this.volumeData.setVoxelDataAsArray(this.voxelData = Clazz.newFloatArray (this.nPointsX, this.nPointsY, this.nPointsZ, 0));
+});
+Clazz.defineMethod(c$, "setVolumeDataV",
+function(v){
+this.nBytes = 0;
+this.volumetricOrigin = v.volumetricOrigin;
+this.volumetricVectors = v.volumetricVectors;
+this.voxelCounts = v.voxelCounts;
+this.voxelData = v.getVoxelData();
+this.volumeData = v;
+}, "J.jvxl.data.VolumeData");
+Clazz.defineMethod(c$, "jvxlUpdateInfo",
+function(){
+this.jvxlData.jvxlUpdateInfo(this.params.title, this.nBytes);
+});
+Clazz.defineMethod(c$, "readAndSetVolumeParameters",
+function(isMapData){
+if (!this.readVolumeParameters(isMapData)) return false;
+if (this.vertexDataOnly) return true;
+return (this.volumeData.setUnitVectors());
+}, "~B");
+Clazz.defineMethod(c$, "createIsosurface",
+function(justForPlane){
+this.resetIsosurface();
+if (this.params.showTiming) JU.Logger.startTimer("isosurface creation");
+this.jvxlData.cutoff = NaN;
+this.jvxlData.cutoffRange = null;
+if (!this.readAndSetVolumeParameters(justForPlane)) return false;
+if (!justForPlane && !Float.isNaN(this.params.sigma) && !this.allowSigma) {
+if (this.params.sigma > 0) JU.Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
+this.params.cutoff = 1.6;
+}if (this.params.sigma < 0) this.params.sigma = -this.params.sigma;
+this.nPointsX = this.voxelCounts[0];
+this.nPointsY = this.voxelCounts[1];
+this.nPointsZ = this.voxelCounts[2];
+this.jvxlData.isSlabbable = ((this.params.dataType & 1024) != 0);
+this.jvxlData.insideOut = this.params.isInsideOut();
+this.jvxlData.isBicolorMap = this.params.isBicolorMap;
+this.jvxlData.nPointsX = this.nPointsX;
+this.jvxlData.nPointsY = this.nPointsY;
+this.jvxlData.nPointsZ = this.nPointsZ;
+this.jvxlData.jvxlVolumeDataXml = this.volumeData.xmlData;
+this.jvxlData.voxelVolume = this.volumeData.voxelVolume;
+if (justForPlane) {
+this.volumeData.setMappingPlane(this.params.thePlane);
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.params.setMapRanges(this, false);
+this.generateSurfaceData();
+this.volumeData.setMappingPlane(null);
+} else {
+if (!this.readVolumeData(false)) return false;
+this.generateSurfaceData();
+}if (this.jvxlFileHeaderBuffer == null) {
+this.jvxlData.jvxlFileTitle = "";
+this.jvxlData.jvxlFileSource = null;
+this.jvxlData.jvxlFileMessage = null;
+} else {
+var s = this.jvxlFileHeaderBuffer.toString();
+var i = s.indexOf('\n', s.indexOf('\n', s.indexOf('\n') + 1) + 1) + 1;
+this.jvxlData.jvxlFileTitle = s.substring(0, i);
+this.jvxlData.jvxlFileSource = this.params.fileName;
+}if (this.params.contactPair == null) this.setBBoxAll();
+this.jvxlData.isValid = (this.xyzMin.x != 3.4028235E38);
+if (!this.params.isSilent) {
+if (!this.jvxlData.isValid) JU.Logger.error("no isosurface points were found!");
+ else JU.Logger.info("boundbox corners " + JU.Escape.eP(this.xyzMin) + " " + JU.Escape.eP(this.xyzMax));
+}this.jvxlData.boundingBox = Clazz.newArray(-1, [this.xyzMin, this.xyzMax]);
+this.jvxlData.dataMin = this.dataMin;
+this.jvxlData.dataMax = this.dataMax;
+this.jvxlData.cutoffRange = (this.isJvxl ? this.jvxlCutoffRange : this.params.cutoffRange);
+this.jvxlData.cutoff = (this.jvxlCutoffRange != null ? this.jvxlData.cutoffRange[0] : this.isJvxl ? this.jvxlCutoff : this.params.cutoff);
+this.jvxlData.isCutoffAbsolute = this.params.isCutoffAbsolute;
+this.jvxlData.isModelConnected = this.params.isModelConnected;
+this.jvxlData.pointsPerAngstrom = 1 / this.volumeData.volumetricVectorLengths[0];
+this.jvxlData.jvxlColorData = "";
+this.jvxlData.jvxlPlane = this.params.thePlane;
+this.jvxlData.jvxlEdgeData = this.edgeData;
+this.jvxlData.isBicolorMap = this.params.isBicolorMap;
+this.jvxlData.isContoured = this.params.isContoured;
+this.jvxlData.colorDensity = this.params.colorDensity;
+this.jvxlData.pointSize = this.params.pointSize;
+if (this.jvxlData.vContours != null) this.params.nContours = this.jvxlData.vContours.length;
+this.jvxlData.nContours = (this.params.contourFromZero ? this.params.nContours : -1 - this.params.nContours);
+this.jvxlData.thisContour = this.params.thisContour;
+this.jvxlData.nEdges = this.edgeCount;
+this.jvxlData.edgeFractionBase = this.edgeFractionBase;
+this.jvxlData.edgeFractionRange = this.edgeFractionRange;
+this.jvxlData.colorFractionBase = this.colorFractionBase;
+this.jvxlData.colorFractionRange = this.colorFractionRange;
+this.jvxlData.jvxlDataIs2dContour = this.jvxlDataIs2dContour;
+this.jvxlData.jvxlDataIsColorMapped = this.jvxlDataIsColorMapped;
+this.jvxlData.jvxlDataIsColorDensity = this.jvxlDataIsColorDensity;
+this.jvxlData.isXLowToHigh = this.isXLowToHigh;
+this.jvxlData.vertexDataOnly = this.vertexDataOnly;
+this.jvxlData.saveVertexCount = 0;
+if (this.jvxlDataIsColorMapped || this.jvxlData.nVertexColors > 0) {
+if (this.meshDataServer != null) {
+this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshDataServer.fillMeshData(this.meshData, 2, null);
+}this.jvxlData.jvxlColorData = this.readColorData();
+this.updateSurfaceData();
+if (this.meshDataServer != null) this.meshDataServer.notifySurfaceMappingCompleted();
+}if (this.params.showTiming) JU.Logger.checkTimer("isosurface creation", false);
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "resetIsosurface",
+function(){
+this.meshData = new J.jvxl.data.MeshData();
+this.xyzMin = this.xyzMax = null;
+this.jvxlData.isBicolorMap = this.params.isBicolorMap;
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(null, 0, null);
+this.contourVertexCount = 0;
+if (this.params.cutoff == 3.4028235E38) this.params.cutoff = 0.02;
+this.jvxlData.jvxlSurfaceData = "";
+this.jvxlData.jvxlEdgeData = "";
+this.jvxlData.jvxlColorData = "";
+this.edgeCount = 0;
+this.edgeFractionBase = 35;
+this.edgeFractionRange = 90;
+this.colorFractionBase = 35;
+this.colorFractionRange = 90;
+this.params.mappedDataMin = 3.4028235E38;
+});
+Clazz.defineMethod(c$, "discardTempData",
+function(discardAll){
+this.discardTempDataSR(discardAll);
+}, "~B");
+Clazz.defineMethod(c$, "discardTempDataSR",
+function(discardAll){
+if (!discardAll) return;
+this.voxelData = null;
+this.sg.marchingSquares = this.marchingSquares = null;
+this.marchingCubes = null;
+}, "~B");
+Clazz.defineMethod(c$, "initializeVolumetricData",
+function(){
+this.nPointsX = this.voxelCounts[0];
+this.nPointsY = this.voxelCounts[1];
+this.nPointsZ = this.voxelCounts[2];
+this.setVolumeDataV(this.volumeData);
+});
+Clazz.defineMethod(c$, "gotoAndReadVoxelData",
+function(isMapData){
+this.initializeVolumetricData();
+if (this.nPointsX > 0 && this.nPointsY > 0 && this.nPointsZ > 0) try {
+this.gotoData(this.params.fileIndex - 1, this.nPointsX * this.nPointsY * this.nPointsZ);
+this.readSurfaceData(isMapData);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error(e.toString());
+return false;
+} else {
+throw e;
+}
+}
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "gotoData",
+function(n, nPoints){
+}, "~N,~N");
+Clazz.defineMethod(c$, "readColorData",
+function(){
+if (this.jvxlData.vertexColors == null) return "";
+var vertexCount = this.jvxlData.vertexCount;
+var colixes = this.meshData.vcs;
+var vertexValues = this.meshData.vvs;
+if (colixes == null || colixes.length < vertexCount) this.meshData.vcs = colixes = Clazz.newShortArray (vertexCount, 0);
+if (vertexValues == null || vertexValues.length < vertexCount) this.meshData.vvs = vertexValues = Clazz.newFloatArray (vertexCount, 0);
+for (var i = 0; i < vertexCount; i++) colixes[i] = JU.C.getColix(this.jvxlData.vertexColors[i]);
+
+return "-";
+});
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+return this.getPlaneSR(x);
+}, "~N");
+Clazz.defineMethod(c$, "getPlaneSR",
+function(x){
+if (this.yzCount == 0) this.initPlanes();
+if (this.qpc != null) this.qpc.getPlane(x, this.yzPlanes[x % 2]);
+return this.yzPlanes[x % 2];
+}, "~N");
+Clazz.defineMethod(c$, "initPlanes",
+function(){
+this.yzCount = this.nPointsY * this.nPointsZ;
+if (!this.isQuiet) JU.Logger.info("reading data progressively -- yzCount = " + this.yzCount);
+this.yzPlanes = JU.AU.newFloat2(2);
+this.yzPlanes[0] = Clazz.newFloatArray (this.yzCount, 0);
+this.yzPlanes[1] = Clazz.newFloatArray (this.yzCount, 0);
+});
+Clazz.overrideMethod(c$, "getValue",
+function(x, y, z, ptyz){
+return this.getValue2(x, y, z, ptyz);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "getValue2",
+function(x, y, z, ptyz){
+return (this.yzPlanes == null ? this.voxelData[x][y][z] : this.yzPlanes[x % 2][ptyz]);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "generateSurfaceData",
+function(){
+this.edgeData = "";
+if (this.vertexDataOnly) {
+try {
+this.readSurfaceData(false);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(e.toString());
+JU.Logger.error("Exception in SurfaceReader::readSurfaceData: " + e.toString());
+} else {
+throw e;
+}
+}
+return;
+}this.contourVertexCount = 0;
+var contourType = -1;
+this.marchingSquares = null;
+if (this.params.thePlane != null || this.params.isContoured) {
+this.marchingSquares = new J.jvxl.calc.MarchingSquares(this, this.volumeData, this.params.thePlane, this.params.contoursDiscrete, this.params.nContours, this.params.thisContour, this.params.contourFromZero);
+contourType = this.marchingSquares.contourType;
+this.marchingSquares.setMinMax(this.params.valueMappedToRed, this.params.valueMappedToBlue);
+}this.params.contourType = contourType;
+this.params.isXLowToHigh = this.isXLowToHigh;
+this.marchingCubes = new J.jvxl.calc.MarchingCubes(this, this.volumeData, this.params, this.jvxlVoxelBitSet);
+var data = this.marchingCubes.getEdgeData();
+if (this.params.thePlane == null) this.edgeData = data;
+this.jvxlData.setSurfaceInfoFromBitSetPts(this.marchingCubes.bsVoxels, this.params.thePlane, this.params.mapLattice);
+this.jvxlData.jvxlExcluded = this.params.bsExcluded;
+if (this.isJvxl) this.edgeData = this.jvxlEdgeDataRead;
+this.postProcessVertices();
+});
+Clazz.defineMethod(c$, "postProcessVertices",
+function(){
+});
+Clazz.overrideMethod(c$, "getSurfacePointIndexAndFraction",
+function(cutoff, isCutoffAbsolute, x, y, z, offset, vA, vB, valueA, valueB, pointA, edgeVector, isContourType, fReturn){
+var thisValue = this.getSurfacePointAndFraction(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, this.ptTemp);
+if (this.marchingSquares != null && this.params.isContoured) return this.marchingSquares.addContourVertex(this.ptTemp, cutoff);
+var assocVertex = (this.assocCutoff > 0 ? (fReturn[0] < this.assocCutoff ? vA : fReturn[0] > 1 - this.assocCutoff ? vB : -1) : -1);
+if (assocVertex >= 0) assocVertex = this.marchingCubes.getLinearOffset(x, y, z, assocVertex);
+var n = this.addVertexCopy(this.ptTemp, thisValue, assocVertex, true);
+if (n >= 0 && this.params.iAddGridPoints) {
+this.marchingCubes.calcVertexPoint(x, y, z, vB, this.ptTemp);
+this.addVertexCopy(valueA < valueB ? pointA : this.ptTemp, Math.min(valueA, valueB), -3, true);
+this.addVertexCopy(valueA < valueB ? this.ptTemp : pointA, Math.max(valueA, valueB), -3, true);
+}return n;
+}, "~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");
+Clazz.defineMethod(c$, "getSurfacePointAndFraction",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+return this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.defineMethod(c$, "getSPF",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+var diff = valueB - valueA;
+var fraction = (cutoff - valueA) / diff;
+if (isCutoffAbsolute && (fraction < 0 || fraction > 1)) fraction = (-cutoff - valueA) / diff;
+if (fraction < 0 || fraction > 1) {
+fraction = NaN;
+}fReturn[0] = fraction;
+ptReturn.scaleAdd2(fraction, edgeVector, pointA);
+return valueA + fraction * diff;
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.defineMethod(c$, "addVertexCopy",
+function(vertexXYZ, value, assocVertex, asCopy){
+return this.addVC(vertexXYZ, value, assocVertex, asCopy);
+}, "JU.T3,~N,~N,~B");
+Clazz.defineMethod(c$, "addVC",
+function(vertexXYZ, value, assocVertex, asCopy){
+return (Float.isNaN(value) && assocVertex != -3 ? -1 : this.meshDataServer == null ? this.meshData.addVertexCopy(vertexXYZ, value, assocVertex, asCopy) : this.meshDataServer.addVertexCopy(vertexXYZ, value, assocVertex, asCopy));
+}, "JU.T3,~N,~N,~B");
+Clazz.defineMethod(c$, "addTriangleCheck",
+function(iA, iB, iC, check, iContour, isAbsolute, color){
+if (this.marchingSquares != null && this.params.isContoured) {
+if (color == 0) return this.marchingSquares.addTriangle(iA, iB, iC, check, iContour);
+color = 0;
+}return (this.meshDataServer != null ? this.meshDataServer.addTriangleCheck(iA, iB, iC, check, iContour, isAbsolute, color) : isAbsolute && !J.jvxl.data.MeshData.checkCutoff(iA, iB, iC, this.meshData.vvs) ? -1 : this.meshData.addTriangleCheck(iA, iB, iC, check, iContour, color));
+}, "~N,~N,~N,~N,~N,~B,~N");
+Clazz.defineMethod(c$, "colorIsosurface",
+function(){
+if (this.params.isSquared && this.volumeData != null) this.volumeData.filterData(true, NaN);
+if (this.meshDataServer != null) {
+this.meshDataServer.fillMeshData(this.meshData, 1, null);
+}this.jvxlData.saveVertexCount = 0;
+if (this.params.isContoured && this.marchingSquares != null) {
+this.initializeMapping();
+this.params.setMapRanges(this, false);
+this.marchingSquares.setMinMax(this.params.valueMappedToRed, this.params.valueMappedToBlue);
+this.jvxlData.saveVertexCount = this.marchingSquares.contourVertexCount;
+this.contourVertexCount = this.marchingSquares.generateContourData(this.jvxlDataIs2dContour, (this.params.isSquared ? 1e-8 : 1e-4));
+this.jvxlData.contourValuesUsed = this.marchingSquares.contourValuesUsed;
+this.minMax = this.marchingSquares.getMinMax();
+if (this.meshDataServer != null) this.meshDataServer.notifySurfaceGenerationCompleted();
+this.finalizeMapping();
+}this.applyColorScale();
+this.jvxlData.nContours = (this.params.contourFromZero ? this.params.nContours : -1 - this.params.nContours);
+this.jvxlData.thisContour = this.params.thisContour;
+this.jvxlData.jvxlFileMessage = "mapped: min = " + this.params.valueMappedToRed + "; max = " + this.params.valueMappedToBlue;
+});
+Clazz.defineMethod(c$, "applyColorScale",
+function(){
+this.colorFractionBase = this.jvxlData.colorFractionBase = 35;
+this.colorFractionRange = this.jvxlData.colorFractionRange = 90;
+if (this.params.colorPhase == 0) this.params.colorPhase = 1;
+if (this.meshDataServer == null) {
+this.meshData.vcs = Clazz.newShortArray (this.meshData.vc, 0);
+} else {
+this.meshDataServer.fillMeshData(this.meshData, 1, null);
+if (this.params.contactPair == null) this.meshDataServer.fillMeshData(this.meshData, 2, null);
+}var saveColorData = (this.params.colorDensity || this.params.isBicolorMap || this.params.colorBySign || !this.params.colorByPhase);
+if (this.params.contactPair != null) saveColorData = false;
+this.jvxlData.isJvxlPrecisionColor = true;
+this.jvxlData.vertexCount = (this.contourVertexCount > 0 ? this.contourVertexCount : this.meshData.vc);
+this.jvxlData.minColorIndex = -1;
+this.jvxlData.maxColorIndex = 0;
+this.jvxlData.contourValues = this.params.contoursDiscrete;
+this.jvxlData.isColorReversed = this.params.isColorReversed;
+if (!this.params.colorDensity) if (this.params.isBicolorMap && !this.params.isContoured || this.params.colorBySign) {
+this.jvxlData.minColorIndex = JU.C.getColixTranslucent3(JU.C.getColix(this.params.isColorReversed ? this.params.colorPos : this.params.colorNeg), this.jvxlData.translucency != 0, this.jvxlData.translucency);
+this.jvxlData.maxColorIndex = JU.C.getColixTranslucent3(JU.C.getColix(this.params.isColorReversed ? this.params.colorNeg : this.params.colorPos), this.jvxlData.translucency != 0, this.jvxlData.translucency);
+}this.jvxlData.isTruncated = (this.jvxlData.minColorIndex >= 0 && !this.params.isContoured);
+var useMeshDataValues = this.jvxlDataIs2dContour || this.hasColorData || this.vertexDataOnly || this.params.colorDensity || this.params.isBicolorMap && !this.params.isContoured;
+if (!useMeshDataValues) {
+if (this.haveSurfaceAtoms && this.meshData.vertexSource == null) this.meshData.vertexSource = Clazz.newIntArray (this.meshData.vc, 0);
+var min = 3.4028235E38;
+var max = -3.4028235E38;
+var value;
+this.initializeMapping();
+for (var i = this.meshData.vc; --i >= this.meshData.mergeVertexCount0; ) {
+if (this.params.colorBySets) {
+value = this.meshData.vertexSets[i];
+} else if (this.params.colorByPhase) {
+value = this.getPhase(this.meshData.vs[i]);
+} else {
+var needSource = this.haveSurfaceAtoms;
+value = this.volumeData.lookupInterpolatedVoxelValue(this.meshData.vs[i], needSource);
+if (needSource) this.meshData.vertexSource[i] = this.getSurfaceAtomIndex();
+}if (value < min) min = value;
+if (value > max && value != 3.4028235E38) max = value;
+this.meshData.vvs[i] = value;
+}
+if (this.params.rangeSelected && this.minMax == null) this.minMax = Clazz.newFloatArray(-1, [min, max]);
+this.finalizeMapping();
+}this.params.setMapRanges(this, true);
+this.jvxlData.mappedDataMin = this.params.mappedDataMin;
+this.jvxlData.mappedDataMax = this.params.mappedDataMax;
+this.jvxlData.valueMappedToRed = this.params.valueMappedToRed;
+this.jvxlData.valueMappedToBlue = this.params.valueMappedToBlue;
+if (this.params.contactPair == null && this.jvxlData.vertexColors == null) this.colorData();
+J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData, (saveColorData ? this.meshData.vvs : null));
+if (this.haveSurfaceAtoms && this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 4, null);
+if (this.meshDataServer != null && this.params.colorBySets) this.meshDataServer.fillMeshData(this.meshData, 3, null);
+});
+Clazz.defineMethod(c$, "colorData",
+function(){
+var vertexValues = this.meshData.vvs;
+var vertexColixes = this.meshData.vcs;
+this.meshData.pcs = null;
+var valueBlue = this.jvxlData.valueMappedToBlue;
+var valueRed = this.jvxlData.valueMappedToRed;
+var minColorIndex = this.jvxlData.minColorIndex;
+var maxColorIndex = this.jvxlData.maxColorIndex;
+if (this.params.colorEncoder == null) this.params.colorEncoder = new JU.ColorEncoder(null, null);
+this.params.colorEncoder.setRange(this.params.valueMappedToRed, this.params.valueMappedToBlue, this.params.isColorReversed);
+for (var i = this.meshData.vc; --i >= 0; ) {
+var value = vertexValues[i];
+if (minColorIndex >= 0) {
+if (value <= 0) vertexColixes[i] = minColorIndex;
+ else if (value > 0) vertexColixes[i] = maxColorIndex;
+} else {
+if (value <= valueRed) value = valueRed;
+if (value >= valueBlue) value = valueBlue;
+vertexColixes[i] = this.params.colorEncoder.getColorIndex(value);
+}}
+if ((this.params.nContours > 0 || this.jvxlData.contourValues != null) && this.jvxlData.contourColixes == null) {
+var n = (this.jvxlData.contourValues == null ? this.params.nContours : this.jvxlData.contourValues.length);
+var colors = this.jvxlData.contourColixes = Clazz.newShortArray (n, 0);
+var values = this.jvxlData.contourValues;
+if (values == null) values = this.jvxlData.contourValuesUsed;
+if (this.jvxlData.contourValuesUsed == null) this.jvxlData.contourValuesUsed = (values == null ? Clazz.newFloatArray (n, 0) : values);
+var dv = (valueBlue - valueRed) / (n + 1);
+this.params.colorEncoder.setRange(this.params.valueMappedToRed, this.params.valueMappedToBlue, this.params.isColorReversed);
+for (var i = 0; i < n; i++) {
+var v = (values == null ? valueRed + (i + 1) * dv : values[i]);
+this.jvxlData.contourValuesUsed[i] = v;
+colors[i] = JU.C.getColixTranslucent(this.params.colorEncoder.getArgb(v));
+}
+this.jvxlData.contourColors = JU.C.getHexCodes(colors);
+}});
+c$.getColorPhaseIndex = Clazz.defineMethod(c$, "getColorPhaseIndex",
+function(color){
+var colorPhase = -1;
+for (var i = 0; i < J.jvxl.readers.SurfaceReader.colorPhases.length; i++) if (color.equalsIgnoreCase(J.jvxl.readers.SurfaceReader.colorPhases[i])) {
+colorPhase = i;
+break;
+}
+return colorPhase;
+}, "~S");
+Clazz.defineMethod(c$, "getPhase",
+function(pt){
+switch (this.params.colorPhase) {
+case 0:
+case -1:
+case 1:
+return (pt.x > 0 ? 1 : -1);
+case 2:
+return (pt.y > 0 ? 1 : -1);
+case 3:
+return (pt.z > 0 ? 1 : -1);
+case 4:
+return (pt.x * pt.y > 0 ? 1 : -1);
+case 5:
+return (pt.y * pt.z > 0 ? 1 : -1);
+case 6:
+return (pt.x * pt.z > 0 ? 1 : -1);
+case 7:
+return (pt.x * pt.x - pt.y * pt.y > 0 ? 1 : -1);
+case 8:
+return (pt.z * pt.z * 2 - pt.x * pt.x - pt.y * pt.y > 0 ? 1 : -1);
+}
+return 1;
+}, "JU.T3");
+Clazz.defineMethod(c$, "getMinMaxMappedValues",
+function(haveData){
+if (this.minMax != null && this.minMax[0] != 3.4028235E38) return this.minMax;
+if (this.params.colorBySets) return (this.minMax = Clazz.newFloatArray(-1, [0, Math.max(this.meshData.nSets - 1, 0)]));
+var min = 3.4028235E38;
+var max = -3.4028235E38;
+if (this.params.usePropertyForColorRange && this.params.theProperty != null) {
+for (var i = this.params.theProperty.length; --i >= 0; ) {
+if (this.params.rangeSelected && !this.params.bsSelected.get(i)) continue;
+var p = this.params.theProperty[i];
+if (Float.isNaN(p)) continue;
+if (p < min) min = p;
+if (p > max) max = p;
+}
+return (this.minMax = Clazz.newFloatArray(-1, [min, max]));
+}var vertexCount = (this.contourVertexCount > 0 ? this.contourVertexCount : this.meshData.vc);
+var vertexes = this.meshData.vs;
+var useVertexValue = (haveData || this.jvxlDataIs2dContour || this.vertexDataOnly || this.params.colorDensity);
+for (var i = this.meshData.mergeVertexCount0; i < vertexCount; i++) {
+var v;
+if (useVertexValue) v = this.meshData.vvs[i];
+ else v = this.volumeData.lookupInterpolatedVoxelValue(vertexes[i], false);
+if (v < min) min = v;
+if (v > max && v != 3.4028235E38) max = v;
+}
+return (this.minMax = Clazz.newFloatArray(-1, [min, max]));
+}, "~B");
+Clazz.defineMethod(c$, "updateTriangles",
+function(){
+if (this.meshDataServer == null) {
+this.meshData.invalidatePolygons();
+} else {
+this.meshDataServer.invalidateTriangles();
+}});
+Clazz.defineMethod(c$, "updateSurfaceData",
+function(){
+this.meshData.setVertexSets(true);
+this.updateTriangles();
+if (this.params.bsExcluded[1] == null) this.params.bsExcluded[1] = new JU.BS();
+this.meshData.updateInvalidatedVertices(this.params.bsExcluded[1]);
+});
+Clazz.defineMethod(c$, "selectPocket",
+function(doExclude){
+}, "~B");
+Clazz.defineMethod(c$, "excludeMinimumSet",
+function(){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshData.getSurfaceSet();
+var bs;
+for (var i = this.meshData.nSets; --i >= 0; ) if ((bs = this.meshData.surfaceSet[i]) != null && bs.cardinality() < this.params.minSet) this.meshData.invalidateSurfaceSet(i);
+
+this.updateSurfaceData();
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 3, null);
+});
+Clazz.defineMethod(c$, "excludeMaximumSet",
+function(){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshData.getSurfaceSet();
+var bs;
+for (var i = this.meshData.nSets; --i >= 0; ) if ((bs = this.meshData.surfaceSet[i]) != null && bs.cardinality() > this.params.maxSet) this.meshData.invalidateSurfaceSet(i);
+
+this.updateSurfaceData();
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 3, null);
+});
+Clazz.defineMethod(c$, "slabIsosurface",
+function(slabInfo){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.meshData.slabPolygonsList(slabInfo, true);
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 4, null);
+}, "JU.Lst");
+Clazz.defineMethod(c$, "setVertexAnisotropy",
+function(pt){
+pt.x *= this.anisotropy[0];
+pt.y *= this.anisotropy[1];
+pt.z *= this.anisotropy[2];
+pt.add(this.center);
+}, "JU.T3");
+Clazz.defineMethod(c$, "setVectorAnisotropy",
+function(v){
+this.haveSetAnisotropy = true;
+v.x *= this.anisotropy[0];
+v.y *= this.anisotropy[1];
+v.z *= this.anisotropy[2];
+}, "JU.T3");
+Clazz.defineMethod(c$, "setVolumetricAnisotropy",
+function(){
+if (this.haveSetAnisotropy) return;
+this.setVolumetricOriginAnisotropy();
+this.setVectorAnisotropy(this.volumetricVectors[0]);
+this.setVectorAnisotropy(this.volumetricVectors[1]);
+this.setVectorAnisotropy(this.volumetricVectors[2]);
+});
+Clazz.defineMethod(c$, "setVolumetricOriginAnisotropy",
+function(){
+this.volumetricOrigin.setT(this.center);
+});
+Clazz.defineMethod(c$, "setBBoxAll",
+function(){
+if (this.meshDataServer != null) this.meshDataServer.fillMeshData(this.meshData, 1, null);
+this.xyzMin = new JU.P3();
+this.xyzMax = new JU.P3();
+this.meshData.setBox(this.xyzMin, this.xyzMax);
+});
+Clazz.defineMethod(c$, "setBBox",
+function(pt, margin){
+if (this.xyzMin == null) {
+this.xyzMin = JU.P3.new3(3.4028235E38, 3.4028235E38, 3.4028235E38);
+this.xyzMax = JU.P3.new3(-3.4028235E38, -3.4028235E38, -3.4028235E38);
+}JU.BoxInfo.addPoint(pt, this.xyzMin, this.xyzMax, margin);
+}, "JU.T3,~N");
+Clazz.defineMethod(c$, "getValueAtPoint",
+function(pt, getSource){
+return 0;
+}, "JU.T3,~B");
+Clazz.defineMethod(c$, "initializeMapping",
+function(){
+});
+Clazz.defineMethod(c$, "finalizeMapping",
+function(){
+});
+Clazz.defineMethod(c$, "getSurfaceAtomIndex",
+function(){
+return -1;
+});
+c$.colorPhases = Clazz.newArray(-1, ["_orb", "x", "y", "z", "xy", "yz", "xz", "x2-y2", "z2"]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/UhbdReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/UhbdReader.js
new file mode 100755
index 000000000000..1566603341d4
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/UhbdReader.js
@@ -0,0 +1,53 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.UhbdReader", ["JU.SB"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.planeCount = 0;
+this.voxelCount = 0;
+this.pt = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "UhbdReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.UhbdReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.isAngstroms = true;
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.rd();
+this.jvxlFileHeaderBuffer = JU.SB.newS(this.line);
+this.jvxlFileHeaderBuffer.append("UHBD format ").append(this.line).append("\n");
+this.jvxlFileHeaderBuffer.append("see http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec4b78a9/tree/src/mg/vgrid.c\n");
+this.rd();
+this.rd();
+this.voxelCounts[0] = this.parseIntStr(this.line.substring(0, 7));
+this.voxelCounts[1] = this.parseIntStr(this.line.substring(7, 14));
+this.voxelCounts[2] = this.parseIntStr(this.line.substring(14, 21));
+var dx = this.parseFloatStr(this.line.substring(21, 33));
+this.volumetricOrigin.set(this.parseFloatStr(this.line.substring(33, 45)), this.parseFloatStr(this.line.substring(45, 57)), this.parseFloatStr(this.line.substring(57, 69)));
+this.volumetricVectors[0].set(0, 0, dx);
+this.volumetricVectors[1].set(0, dx, 0);
+this.volumetricVectors[2].set(dx, 0, 0);
+this.planeCount = this.voxelCounts[0] * this.voxelCounts[1];
+this.rd();
+this.rd();
+});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+if (this.voxelCount % this.planeCount == 0) {
+this.rd();
+this.pt = 0;
+}if (this.pt % 78 == 0) {
+this.rd();
+this.pt = 0;
+}this.voxelCount++;
+var voxelValue = this.parseFloatStr(this.line.substring(this.pt, this.pt + 13));
+this.pt += 13;
+return voxelValue;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VaspChgcarReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VaspChgcarReader.js
new file mode 100755
index 000000000000..9163233819d7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VaspChgcarReader.js
@@ -0,0 +1,74 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.PeriodicVolumeFileReader"], "J.jvxl.readers.VaspChgcarReader", ["JU.PT", "$.SB", "JU.Logger", "$.SimpleUnitCell"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.volume = 0;
+this.pt = 0;
+this.nPerLine = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "VaspChgcarReader", J.jvxl.readers.PeriodicVolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.VaspChgcarReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+this.isAngstroms = true;
+this.isPeriodic = true;
+this.isProgressive = false;
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("Vasp CHGCAR format\n\n\n");
+this.rd();
+var scale = this.parseFloatStr(this.rd());
+var data = Clazz.newFloatArray (15, 0);
+data[0] = -1;
+for (var i = 0, pt = 6; i < 3; ++i) this.volumetricVectors[i].set(data[pt++] = this.parseFloatStr(this.rd()) * scale, data[pt++] = this.parseFloat() * scale, data[pt++] = this.parseFloat() * scale);
+
+this.volume = JU.SimpleUnitCell.newA(data).volume;
+while (this.rd().length > 2) {
+}
+this.rd();
+var counts = this.getTokens();
+for (var i = 0; i < 3; ++i) {
+this.volumetricVectors[i].scale(1 / ((this.voxelCounts[i] = this.parseIntStr(counts[i]) + 1) - 1));
+if (this.isAnisotropic) this.setVectorAnisotropy(this.volumetricVectors[i]);
+}
+this.swapXZ();
+this.volumetricOrigin.set(0, 0, 0);
+if (this.params.thePlane == null && (this.params.cutoffAutomatic || !Float.isNaN(this.params.sigma))) {
+this.params.cutoff = 0.5;
+JU.Logger.info("Cutoff set to " + this.params.cutoff);
+}});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+if (this.pt++ % this.nPerLine == 0 && this.nData > 0) {
+this.rd();
+this.next[0] = 0;
+}return this.parseFloat() / this.volume;
+});
+Clazz.overrideMethod(c$, "getPeriodicVoxels",
+function(){
+var ni = this.voxelCounts[0] - 1;
+var nj = this.voxelCounts[1] - 1;
+var nk = this.voxelCounts[2] - 1;
+var downSampling = (this.nSkipX > 0);
+this.nPerLine = JU.PT.countTokens(this.rd(), 0);
+for (var i = 0; i < ni; i++) {
+for (var j = 0; j < nj; j++) {
+for (var k = 0; k < nk; k++) {
+this.voxelData[i][j][k] = this.recordData(this.nextVoxel());
+if (downSampling) for (var m = this.nSkipX; --m >= 0; ) this.nextVoxel();
+
+}
+if (downSampling) for (var m = this.nSkipY; --m >= 0; ) this.nextVoxel();
+
+}
+if (downSampling) for (var m = this.nSkipZ; --m >= 0; ) this.nextVoxel();
+
+}
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeDataReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeDataReader.js
new file mode 100755
index 000000000000..d8f53bcbe70f
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeDataReader.js
@@ -0,0 +1,181 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.SurfaceReader"], "J.jvxl.readers.VolumeDataReader", ["JU.AU", "$.SB", "J.jvxl.data.JvxlCoder", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.dataType = 0;
+this.precalculateVoxelData = false;
+this.allowMapData = false;
+this.point = null;
+this.ptsPerAngstrom = 0;
+this.maxGrid = 0;
+this.useOriginStepsPoints = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "VolumeDataReader", J.jvxl.readers.SurfaceReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.VolumeDataReader, []);
+});
+Clazz.overrideMethod(c$, "init",
+function(sg){
+this.initVDR(sg);
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "initVDR",
+function(sg){
+this.initSR(sg);
+this.useOriginStepsPoints = (this.params.origin != null && this.params.points != null && this.params.steps != null);
+this.dataType = this.params.dataType;
+this.precalculateVoxelData = true;
+this.allowMapData = true;
+}, "J.jvxl.readers.SurfaceGenerator");
+Clazz.defineMethod(c$, "setup",
+function(isMapData){
+this.jvxlFileHeaderBuffer = new JU.SB().append("volume data read from file\n\n");
+J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData, this.jvxlFileHeaderBuffer);
+}, "~B");
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.setup(isMapData);
+this.initializeVolumetricData();
+return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readVolumeData",
+function(isMapData){
+try {
+this.readSurfaceData(isMapData);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.out.println(e.toString());
+{
+}return false;
+} else {
+throw e;
+}
+}
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "readVoxelDataIndividually",
+function(isMapData){
+if (isMapData && !this.allowMapData) return;
+if (!isMapData || this.volumeData.sr != null) {
+this.volumeData.setVoxelDataAsArray(this.voxelData = null);
+return;
+}this.newVoxelDataCube();
+for (var x = 0; x < this.nPointsX; ++x) {
+var plane = JU.AU.newFloat2(this.nPointsY);
+this.voxelData[x] = plane;
+var ptyz = 0;
+for (var y = 0; y < this.nPointsY; ++y) {
+var strip = plane[y] = Clazz.newFloatArray (this.nPointsZ, 0);
+for (var z = 0; z < this.nPointsZ; ++z, ++ptyz) {
+strip[z] = this.getValue(x, y, z, ptyz);
+}
+}
+}
+}, "~B");
+Clazz.defineMethod(c$, "setVolumeData",
+function(){
+});
+Clazz.defineMethod(c$, "setVolumeDataParams",
+function(){
+if (this.params.volumeData != null) {
+this.setVolumeDataV(this.params.volumeData);
+return true;
+}if (!this.useOriginStepsPoints) {
+return false;
+}this.volumetricOrigin.setT(this.params.origin);
+this.volumetricVectors[0].set(this.params.steps.x, 0, 0);
+this.volumetricVectors[1].set(0, this.params.steps.y, 0);
+this.volumetricVectors[2].set(0, 0, this.params.steps.z);
+this.voxelCounts[0] = Clazz.floatToInt(this.params.points.x);
+this.voxelCounts[1] = Clazz.floatToInt(this.params.points.y);
+this.voxelCounts[2] = Clazz.floatToInt(this.params.points.z);
+if (this.voxelCounts[0] < 1 || this.voxelCounts[1] < 1 || this.voxelCounts[2] < 1) return false;
+this.showGridInfo();
+return true;
+});
+Clazz.defineMethod(c$, "showGridInfo",
+function(){
+JU.Logger.info("grid origin = " + this.params.origin);
+JU.Logger.info("grid steps = " + this.params.steps);
+JU.Logger.info("grid points = " + this.params.points);
+this.ptTemp.x = this.params.steps.x * this.params.points.x;
+this.ptTemp.y = this.params.steps.y * this.params.points.y;
+this.ptTemp.z = this.params.steps.z * this.params.points.z;
+JU.Logger.info("grid lengths = " + this.ptTemp);
+this.ptTemp.add(this.params.origin);
+JU.Logger.info("grid max xyz = " + this.ptTemp);
+});
+Clazz.defineMethod(c$, "setVoxelRange",
+function(index, min, max, ptsPerAngstrom, gridMax, minPointsPerAngstrom){
+var nGrid;
+var d;
+if (min - max >= -1.0E-4) {
+min = -10;
+max = 10;
+}var range = max - min;
+var resolution = this.params.resolution;
+if (resolution != 3.4028235E38) {
+ptsPerAngstrom = resolution;
+minPointsPerAngstrom = 0;
+}nGrid = Clazz.doubleToInt(Math.floor(range * ptsPerAngstrom)) + 1;
+if (nGrid > gridMax) {
+if ((this.dataType & 256) > 0) {
+if (resolution == 3.4028235E38) {
+if (!this.isQuiet) JU.Logger.info("Maximum number of voxels for index=" + index + " exceeded (" + nGrid + ") -- set to " + gridMax);
+nGrid = gridMax;
+} else {
+if (!this.isQuiet) JU.Logger.info("Warning -- high number of grid points: " + nGrid);
+}} else if (resolution == 3.4028235E38) {
+nGrid = gridMax;
+}}if (nGrid == 1) nGrid = 2;
+ptsPerAngstrom = (nGrid - 1) / range;
+if (ptsPerAngstrom < minPointsPerAngstrom) {
+ptsPerAngstrom = minPointsPerAngstrom;
+nGrid = Clazz.doubleToInt(Math.floor(ptsPerAngstrom * range + 1));
+ptsPerAngstrom = (nGrid - 1) / range;
+}d = this.volumeData.volumetricVectorLengths[index] = 1 / ptsPerAngstrom;
+this.voxelCounts[index] = nGrid;
+if (this.params.sbOut != null) this.params.sbOut.append("isosurface resolution for axis " + (index + 1) + " set to " + ptsPerAngstrom + " points/Angstrom; " + this.voxelCounts[index] + " voxels\n");
+switch (index) {
+case 0:
+this.volumetricVectors[0].set(d, 0, 0);
+this.volumetricOrigin.x = min;
+break;
+case 1:
+this.volumetricVectors[1].set(0, d, 0);
+this.volumetricOrigin.y = min;
+break;
+case 2:
+this.volumetricVectors[2].set(0, 0, d);
+this.volumetricOrigin.z = min;
+if (this.isEccentric) this.eccentricityMatrix.rotate(this.volumetricOrigin);
+if (this.center != null && !Float.isNaN(this.center.x)) this.volumetricOrigin.add(this.center);
+if (this.params.sbOut != null) this.params.sbOut.append((this.voxelCounts[0] * this.voxelCounts[1] * this.voxelCounts[2]) + " voxels total\n");
+}
+if (this.isEccentric) this.eccentricityMatrix.rotate(this.volumetricVectors[index]);
+return this.voxelCounts[index];
+}, "~N,~N,~N,~N,~N,~N");
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+this.readSurfaceDataVDR(isMapData);
+}, "~B");
+Clazz.defineMethod(c$, "readSurfaceDataVDR",
+function(isMapData){
+if (this.isProgressive && !isMapData) {
+this.nDataPoints = this.volumeData.setVoxelCounts(this.nPointsX, this.nPointsY, this.nPointsZ);
+this.voxelData = null;
+return;
+}if (this.precalculateVoxelData) this.generateCube();
+ else this.readVoxelDataIndividually(isMapData);
+}, "~B");
+Clazz.defineMethod(c$, "generateCube",
+function(){
+JU.Logger.info("data type: user volumeData");
+JU.Logger.info("voxel grid origin:" + this.volumetricOrigin);
+for (var i = 0; i < 3; ++i) JU.Logger.info("voxel grid vector:" + this.volumetricVectors[i]);
+
+JU.Logger.info("Read " + this.nPointsX + " x " + this.nPointsY + " x " + this.nPointsZ + " data points");
+});
+Clazz.overrideMethod(c$, "closeReader",
+function(){
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeFileReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeFileReader.js
new file mode 100755
index 000000000000..aa72e126c55e
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/VolumeFileReader.js
@@ -0,0 +1,411 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.SurfaceFileReader"], "J.jvxl.readers.VolumeFileReader", ["JU.AU", "$.PT", "$.SB", "J.api.Interface", "J.atomdata.AtomData", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.endOfData = false;
+this.negativeAtomCount = false;
+this.ac = 0;
+this.nSurfaces = 0;
+this.isAngstroms = false;
+this.canDownsample = false;
+this.downsampleRemainders = null;
+this.getNCIPlanes = false;
+this.nData = 0;
+this.readerClosed = false;
+this.downsampleFactor = 0;
+this.nSkipX = 0;
+this.nSkipY = 0;
+this.nSkipZ = 0;
+this.yzPlanesRaw = null;
+this.iPlaneNCI = 0;
+this.boundingBox = null;
+this.isScaledAlready = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "VolumeFileReader", J.jvxl.readers.SurfaceFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.VolumeFileReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "init2VFR",
+function(sg, br){
+this.init2SFR(sg, br);
+this.canDownsample = this.isProgressive = this.isXLowToHigh = true;
+this.jvxlData.wasCubic = true;
+this.boundingBox = this.params.boundingBox;
+if (this.params.qmOrbitalType == 4) {
+this.hasColorData = (this.params.parameters == null || this.params.parameters[1] >= 0);
+this.getNCIPlanes = true;
+this.params.insideOut = !this.params.insideOut;
+}}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.defineMethod(c$, "recordData",
+function(value){
+if (Float.isNaN(value)) return value;
+if (value < this.dataMin) this.dataMin = value;
+if (value > this.dataMax) this.dataMax = value;
+this.dataMean += value;
+this.nData++;
+return value;
+}, "~N");
+Clazz.overrideMethod(c$, "closeReader",
+function(){
+if (this.readerClosed) return;
+this.readerClosed = true;
+this.closeReaderSFR();
+if (this.nData == 0 || this.dataMax == -3.4028235E38) return;
+this.dataMean /= this.nData;
+JU.Logger.info("VolumeFileReader closing file: " + this.nData + " points read \ndata min/max/mean = " + this.dataMin + "/" + this.dataMax + "/" + this.dataMean);
+});
+Clazz.overrideMethod(c$, "readVolumeParameters",
+function(isMapData){
+this.endOfData = false;
+this.nSurfaces = this.readVolumetricHeader();
+if (this.nSurfaces == 0) return false;
+if (this.nSurfaces < this.params.fileIndex) {
+JU.Logger.warn("not enough surfaces in file -- resetting params.fileIndex to " + this.nSurfaces);
+this.params.fileIndex = this.nSurfaces;
+}return true;
+}, "~B");
+Clazz.overrideMethod(c$, "readVolumeData",
+function(isMapData){
+return this.readVolumeDataVFR(isMapData);
+}, "~B");
+Clazz.defineMethod(c$, "readVolumeDataVFR",
+function(isMapData){
+if (!this.gotoAndReadVoxelData(isMapData)) return false;
+if (!this.vertexDataOnly) JU.Logger.info("JVXL read: " + this.nPointsX + " x " + this.nPointsY + " x " + this.nPointsZ + " data points");
+return true;
+}, "~B");
+Clazz.defineMethod(c$, "readVolumetricHeader",
+function(){
+try {
+this.readParameters();
+if (this.ac == -2147483648) return 0;
+if (!this.vertexDataOnly) JU.Logger.info("voxel grid origin:" + this.volumetricOrigin);
+var downsampleFactor = this.params.downsampleFactor;
+var downsampling = (this.canDownsample && downsampleFactor > 1);
+if (downsampleFactor > 1 && !this.canDownsample) this.jvxlData.msg += "\ncannot downsample this file type";
+if (downsampling) {
+this.downsampleRemainders = Clazz.newIntArray (3, 0);
+JU.Logger.info("downsample factor = " + downsampleFactor);
+for (var i = 0; i < 3; ++i) {
+var n = this.voxelCounts[i];
+this.downsampleRemainders[i] = n % downsampleFactor;
+this.voxelCounts[i] /= downsampleFactor;
+if (this.isPeriodic) {
+this.voxelCounts[i]++;
+this.downsampleRemainders[i]--;
+}this.volumetricVectors[i].scale(downsampleFactor);
+JU.Logger.info("downsampling axis " + (i + 1) + " from " + n + " to " + this.voxelCounts[i]);
+}
+}if (!this.vertexDataOnly) for (var i = 0; i < 3; ++i) {
+if (!this.isAngstroms) this.volumetricVectors[i].scale(0.5291772);
+this.line = this.voxelCounts[i] + " " + this.volumetricVectors[i].x + " " + this.volumetricVectors[i].y + " " + this.volumetricVectors[i].z;
+JU.Logger.info("voxel grid count/vector:" + this.line);
+}
+this.scaleIsosurface(this.params.scale);
+this.volumeData.setVolumetricXml();
+return this.nSurfaces;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error(e.toString());
+return 0;
+} else {
+throw e;
+}
+}
+});
+Clazz.defineMethod(c$, "skipComments",
+function(allowBlankLines){
+var sb = new JU.SB();
+while (this.rd() != null && (allowBlankLines && this.line.length == 0 || this.line.indexOf("#") == 0)) sb.append(this.line).appendC('\n');
+
+return sb.toString();
+}, "~B");
+Clazz.defineMethod(c$, "readVoxelVector",
+function(voxelVectorIndex){
+this.rd();
+var voxelVector = this.volumetricVectors[voxelVectorIndex];
+if ((this.voxelCounts[voxelVectorIndex] = this.parseIntStr(this.line)) == -2147483648) this.next[0] = this.line.indexOf(" ");
+voxelVector.set(this.parseFloat(), this.parseFloat(), this.parseFloat());
+if (this.isAnisotropic) this.setVectorAnisotropy(voxelVector);
+}, "~N");
+Clazz.defineMethod(c$, "initializeSurfaceData",
+function(){
+this.downsampleFactor = this.params.downsampleFactor;
+this.nSkipX = 0;
+this.nSkipY = 0;
+this.nSkipZ = 0;
+if (this.canDownsample && this.downsampleFactor > 0) {
+this.nSkipX = this.downsampleFactor - 1;
+this.nSkipY = this.downsampleRemainders[2] + (this.downsampleFactor - 1) * (this.nSkipZ = ((this.nPointsZ - (this.isPeriodic ? 1 : 0)) * this.downsampleFactor + this.downsampleRemainders[2]));
+this.nSkipZ = this.downsampleRemainders[1] * this.nSkipZ + (this.downsampleFactor - 1) * this.nSkipZ * ((this.nPointsY - (this.isPeriodic ? 1 : 0)) * this.downsampleFactor + this.downsampleRemainders[1]);
+}if (this.params.thePlane != null) {
+this.params.cutoff = 0;
+} else if (this.isJvxl) {
+this.params.cutoff = (this.params.isBicolorMap || this.params.colorBySign ? 0.01 : this.getJVXLCutoff());
+}this.nDataPoints = 0;
+this.next[0] = 0;
+this.line = "";
+this.jvxlNSurfaceInts = 0;
+});
+Clazz.defineMethod(c$, "getJVXLCutoff",
+function(){
+return 0.5;
+});
+Clazz.overrideMethod(c$, "readSurfaceData",
+function(isMapData){
+this.readSurfaceDataVFR(isMapData);
+}, "~B");
+Clazz.defineMethod(c$, "readSurfaceDataVFR",
+function(isMapData){
+this.initializeSurfaceData();
+if (this.isProgressive && !isMapData || this.isJvxl) {
+this.nDataPoints = this.volumeData.setVoxelCounts(this.nPointsX, this.nPointsY, this.nPointsZ);
+this.voxelData = null;
+if (this.isJvxl) this.jvxlVoxelBitSet = this.getVoxelBitSet(this.nDataPoints);
+} else if (isMapData && this.volumeData.hasPlane()) {
+this.volumeData.setVoxelMap();
+var f = this.volumeData.getToPlaneParameter();
+for (var x = 0; x < this.nPointsX; ++x) {
+for (var y = 0; y < this.nPointsY; ++y) {
+for (var z = 0; z < this.nPointsZ; ++z) {
+var v = this.recordData(this.getNextVoxelValue());
+if (this.volumeData.isNearPlane(x, y, z, f)) this.volumeData.setVoxelMapValue(x, y, z, v);
+if (this.nSkipX != 0) this.skipVoxels(this.nSkipX);
+}
+if (this.nSkipY != 0) this.skipVoxels(this.nSkipY);
+}
+if (this.nSkipZ != 0) this.skipVoxels(this.nSkipZ);
+}
+} else {
+this.voxelData = JU.AU.newFloat3(this.nPointsX, -1);
+for (var x = 0; x < this.nPointsX; ++x) {
+var plane = JU.AU.newFloat2(this.nPointsY);
+this.voxelData[x] = plane;
+for (var y = 0; y < this.nPointsY; ++y) {
+var strip = Clazz.newFloatArray (this.nPointsZ, 0);
+plane[y] = strip;
+for (var z = 0; z < this.nPointsZ; ++z) {
+strip[z] = this.recordData(this.getNextVoxelValue());
+if (this.nSkipX != 0) this.skipVoxels(this.nSkipX);
+}
+if (this.nSkipY != 0) this.skipVoxels(this.nSkipY);
+}
+if (this.nSkipZ != 0) this.skipVoxels(this.nSkipZ);
+}
+}this.volumeData.setVoxelDataAsArray(this.voxelData);
+}, "~B");
+Clazz.overrideMethod(c$, "getPlane",
+function(x){
+if (x == 0) this.initPlanes();
+if (this.getNCIPlanes) return this.getPlaneNCI(x);
+var plane = this.getPlaneSR(x);
+if (this.qpc == null) this.getPlaneVFR(plane, true);
+return plane;
+}, "~N");
+Clazz.defineMethod(c$, "getPlaneNCI",
+function(x){
+var plane;
+if (this.iPlaneNCI == 0) {
+this.qpc = J.api.Interface.getOption("quantum.NciCalculation", this.sg.atomDataServer, null);
+var atomData = new J.atomdata.AtomData();
+atomData.modelIndex = -1;
+atomData.bsSelected = this.params.bsSelected;
+this.sg.fillAtomData(atomData, 1);
+(this.qpc).setupCalculation(this.volumeData, this.sg.params.bsSelected, null, null, atomData.atoms, -1, true, null, this.params.parameters, this.params.testFlags);
+this.iPlaneNCI = 1;
+this.qpc.setPlanes(this.yzPlanesRaw = Clazz.newFloatArray (4, this.yzCount, 0));
+if (this.hasColorData) {
+this.getPlaneVFR(this.yzPlanesRaw[0], false);
+this.getPlaneVFR(this.yzPlanesRaw[1], false);
+plane = this.yzPlanes[0];
+for (var i = 0; i < this.yzCount; i++) plane[i] = NaN;
+
+return plane;
+}this.iPlaneNCI = -1;
+}var nan = this.qpc.getNoValue();
+var x1 = this.nPointsX - 1;
+switch (this.iPlaneNCI) {
+case -1:
+plane = this.yzPlanes[x % 2];
+x1++;
+break;
+case 3:
+plane = this.yzPlanesRaw[0];
+this.yzPlanesRaw[0] = this.yzPlanesRaw[1];
+this.yzPlanesRaw[1] = this.yzPlanesRaw[2];
+this.yzPlanesRaw[2] = this.yzPlanesRaw[3];
+this.yzPlanesRaw[3] = plane;
+plane = this.yzPlanesRaw[this.iPlaneNCI];
+break;
+default:
+this.iPlaneNCI++;
+plane = this.yzPlanesRaw[this.iPlaneNCI];
+}
+if (x < x1) {
+this.getPlaneVFR(plane, false);
+this.qpc.calcPlane(x, plane = this.yzPlanes[x % 2]);
+for (var i = 0; i < this.yzCount; i++) if (plane[i] != nan) this.recordData(plane[i]);
+
+} else {
+for (var i = 0; i < this.yzCount; i++) plane[i] = NaN;
+
+}return plane;
+}, "~N");
+Clazz.defineMethod(c$, "getPlaneVFR",
+function(plane, doRecord){
+try {
+for (var y = 0, ptyz = 0; y < this.nPointsY; ++y) {
+for (var z = 0; z < this.nPointsZ; ++z) {
+var v = this.getNextVoxelValue();
+if (doRecord) this.recordData(v);
+plane[ptyz++] = v;
+if (this.nSkipX != 0) this.skipVoxels(this.nSkipX);
+}
+if (this.nSkipY != 0) this.skipVoxels(this.nSkipY);
+}
+if (this.nSkipZ != 0) this.skipVoxels(this.nSkipZ);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+} else {
+throw e;
+}
+}
+}, "~A,~B");
+Clazz.overrideMethod(c$, "getValue",
+function(x, y, z, ptyz){
+if (this.boundingBox != null) {
+this.volumeData.voxelPtToXYZ(x, y, z, this.ptTemp);
+if (this.ptTemp.x < this.boundingBox[0].x || this.ptTemp.x > this.boundingBox[1].x || this.ptTemp.y < this.boundingBox[0].y || this.ptTemp.y > this.boundingBox[1].y || this.ptTemp.z < this.boundingBox[0].z || this.ptTemp.z > this.boundingBox[1].z) return NaN;
+}return this.getValue2(x, y, z, ptyz);
+}, "~N,~N,~N,~N");
+Clazz.defineMethod(c$, "skipVoxels",
+function(n){
+for (var i = n; --i >= 0; ) this.getNextVoxelValue();
+
+}, "~N");
+Clazz.defineMethod(c$, "getVoxelBitSet",
+function(nPoints){
+return null;
+}, "~N");
+Clazz.defineMethod(c$, "getNextVoxelValue",
+function(){
+var voxelValue = 0;
+if (this.nSurfaces > 1 && !this.params.blockCubeData) {
+for (var i = 1; i < this.params.fileIndex; i++) this.nextVoxel();
+
+voxelValue = this.nextVoxel();
+for (var i = this.params.fileIndex; i < this.nSurfaces; i++) this.nextVoxel();
+
+} else {
+voxelValue = this.nextVoxel();
+}return voxelValue;
+});
+Clazz.defineMethod(c$, "nextVoxel",
+function(){
+var voxelValue = this.parseFloat();
+if (Float.isNaN(voxelValue)) {
+while (this.rd() != null && Float.isNaN(voxelValue = this.parseFloatStr(this.line))) {
+}
+if (this.line == null) {
+if (!this.endOfData) JU.Logger.warn("end of file reading cube voxel data? nBytes=" + this.nBytes + " nDataPoints=" + this.nDataPoints + " (line):" + this.line);
+this.endOfData = true;
+this.line = "0 0 0 0 0 0 0 0 0 0";
+}}return voxelValue;
+});
+Clazz.overrideMethod(c$, "gotoData",
+function(n, nPoints){
+if (!this.params.blockCubeData) return;
+if (n > 0) JU.Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
+for (var i = 0; i < n; i++) this.skipData(nPoints);
+
+}, "~N,~N");
+Clazz.defineMethod(c$, "skipData",
+function(nPoints){
+this.skipDataVFR(nPoints);
+}, "~N");
+Clazz.defineMethod(c$, "skipDataVFR",
+function(nPoints){
+var iV = 0;
+while (iV < nPoints) iV += this.countData(this.rd());
+
+}, "~N");
+Clazz.defineMethod(c$, "countData",
+function(str){
+var count = 0;
+var ich = 0;
+var ichMax = str.length;
+var ch;
+while (ich < ichMax) {
+while (ich < ichMax && ((ch = str.charAt(ich)) == ' ' || ch == '\t')) ++ich;
+
+if (ich < ichMax) ++count;
+while (ich < ichMax && ((ch = str.charAt(ich)) != ' ' && ch != '\t')) ++ich;
+
+}
+return count;
+}, "~S");
+c$.checkAtomLine = Clazz.defineMethod(c$, "checkAtomLine",
+function(isXLowToHigh, isAngstroms, strAtomCount, atomLine, bs){
+if (atomLine.indexOf("ANGSTROMS") >= 0) isAngstroms = true;
+var ac = (strAtomCount == null ? 2147483647 : JU.PT.parseInt(strAtomCount));
+switch (ac) {
+case -2147483648:
+ac = 0;
+atomLine = " " + atomLine.substring(atomLine.indexOf(" ") + 1);
+break;
+case 2147483647:
+ac = -2147483648;
+break;
+default:
+var s = "" + ac;
+atomLine = atomLine.substring(atomLine.indexOf(s) + s.length);
+}
+if (isAngstroms) {
+if (atomLine.indexOf("ANGSTROM") < 0) atomLine += " ANGSTROMS";
+} else {
+if (atomLine.indexOf("BOHR") < 0) atomLine += " BOHR";
+}atomLine = (ac == -2147483648 ? "" : (isXLowToHigh ? "+" : "-") + Math.abs(ac)) + atomLine + "\n";
+bs.append(atomLine);
+return isAngstroms;
+}, "~B,~B,~S,~S,JU.SB");
+Clazz.overrideMethod(c$, "getSurfacePointAndFraction",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+return this.getSPFv(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.defineMethod(c$, "getSPFv",
+function(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn){
+var zero = this.getSPF(cutoff, isCutoffAbsolute, valueA, valueB, pointA, edgeVector, x, y, z, vA, vB, fReturn, ptReturn);
+if (this.qpc == null || Float.isNaN(zero) || !this.hasColorData) return zero;
+vA = this.marchingCubes.getLinearOffset(x, y, z, vA);
+vB = this.marchingCubes.getLinearOffset(x, y, z, vB);
+return this.qpc.process(vA, vB, fReturn[0]);
+}, "~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");
+Clazz.defineMethod(c$, "scaleIsosurface",
+function(scale){
+if (this.isScaledAlready) return;
+this.isScaledAlready = true;
+if (this.isAnisotropic) this.setVolumetricAnisotropy();
+if (Float.isNaN(scale)) return;
+JU.Logger.info("applying scaling factor of " + scale);
+this.volumetricOrigin.scaleAdd2((1 - scale) / 2, this.volumetricVectors[0], this.volumetricOrigin);
+this.volumetricOrigin.scaleAdd2((1 - scale) / 2, this.volumetricVectors[1], this.volumetricOrigin);
+this.volumetricOrigin.scaleAdd2((1 - scale) / 2, this.volumetricVectors[2], this.volumetricOrigin);
+this.volumetricVectors[0].scale(scale);
+this.volumetricVectors[1].scale(scale);
+this.volumetricVectors[2].scale(scale);
+}, "~N");
+Clazz.defineMethod(c$, "swapXZ",
+function(){
+var v = this.volumetricVectors[0];
+this.volumetricVectors[0] = this.volumetricVectors[2];
+this.volumetricVectors[2] = v;
+var n = this.voxelCounts[0];
+this.voxelCounts[0] = this.voxelCounts[2];
+this.voxelCounts[2] = n;
+this.params.insideOut = !this.params.insideOut;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XmlReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XmlReader.js
new file mode 100755
index 000000000000..422a9f20d733
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XmlReader.js
@@ -0,0 +1,132 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(null, "J.jvxl.readers.XmlReader", ["JU.P3", "$.PT", "$.SB", "JU.Escape"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.br = null;
+this.line = null;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "XmlReader", null);
+Clazz.makeConstructor(c$,
+function(br){
+this.br = br;
+}, "java.io.BufferedReader");
+Clazz.defineMethod(c$, "getLine",
+function(){
+return this.line;
+});
+Clazz.defineMethod(c$, "toTag",
+function(name){
+this.skipTo("<" + name);
+if (this.line == null) return "";
+var i = this.line.indexOf("<" + name) + name.length + 1;
+if (i == this.line.length) return this.line;
+if (this.line.charAt(i) == ' ' || this.line.charAt(i) == '>') return this.line;
+this.line = null;
+return this.toTag(name);
+}, "~S");
+Clazz.defineMethod(c$, "skipTag",
+function(name){
+this.skipTo("");
+}, "~S");
+Clazz.defineMethod(c$, "getXmlData",
+function(name, data, withTag, allowSelfCloseOption){
+return this.getXmlDataLF(name, data, withTag, allowSelfCloseOption, false);
+}, "~S,~S,~B,~B");
+Clazz.defineMethod(c$, "getXmlDataLF",
+function(name, data, withTag, allowSelfCloseOption, addLF){
+var closer = "";
+var tag = "<" + name;
+if (data == null) {
+var sb = new JU.SB();
+try {
+if (this.line == null) this.line = this.br.readLine();
+while (this.line.indexOf(tag) < 0) {
+this.line = this.br.readLine();
+}
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return null;
+} else {
+throw e;
+}
+}
+sb.append(this.line);
+if (addLF) sb.append("\n");
+var selfClosed = false;
+var pt = this.line.indexOf("/>");
+var pt1 = this.line.indexOf(">");
+if (pt1 < 0 || pt == pt1 - 1) selfClosed = allowSelfCloseOption;
+while (this.line.indexOf(closer) < 0 && (!selfClosed || this.line.indexOf("/>") < 0)) {
+sb.append(this.line = this.br.readLine());
+if (addLF) sb.append("\n");
+}
+data = sb.toString();
+}return J.jvxl.readers.XmlReader.extractTag(data, tag, closer, withTag);
+}, "~S,~S,~B,~B,~B");
+c$.extractTagOnly = Clazz.defineMethod(c$, "extractTagOnly",
+function(data, tag){
+return J.jvxl.readers.XmlReader.extractTag(data, "<" + tag + ">", "", false);
+}, "~S,~S");
+c$.extractTag = Clazz.defineMethod(c$, "extractTag",
+function(data, tag, closer, withTag){
+var pt1 = data.indexOf(tag);
+if (pt1 < 0) return "";
+var pt2 = data.indexOf(closer, pt1);
+if (pt2 < 0) {
+pt2 = data.indexOf("/>", pt1);
+closer = "/>";
+}if (pt2 < 0) return "";
+if (withTag) {
+pt2 += closer.length;
+return data.substring(pt1, pt2);
+}var quoted = false;
+for (; pt1 < pt2; pt1++) {
+var ch;
+if ((ch = data.charAt(pt1)) == '"') quoted = !quoted;
+ else if (quoted && ch == '\\') pt1++;
+ else if (!quoted && (ch == '>' || ch == '/')) break;
+}
+if (pt1 >= pt2) return "";
+while (JU.PT.isWhitespace(data.charAt(++pt1))) {
+}
+return J.jvxl.readers.XmlReader.unwrapCdata(data.substring(pt1, pt2));
+}, "~S,~S,~S,~B");
+c$.unwrapCdata = Clazz.defineMethod(c$, "unwrapCdata",
+function(s){
+return (s.startsWith("") ? JU.PT.rep(s.substring(9, s.length - 3), "]]]]>", "]]>") : s);
+}, "~S");
+c$.getXmlAttrib = Clazz.defineMethod(c$, "getXmlAttrib",
+function(data, what){
+var nexta = Clazz.newIntArray (1, 0);
+var pt = J.jvxl.readers.XmlReader.setNext(data, what, nexta, 1);
+if (pt < 2 || (pt = J.jvxl.readers.XmlReader.setNext(data, "\"", nexta, 0)) < 2) return "";
+var pt1 = J.jvxl.readers.XmlReader.setNext(data, "\"", nexta, -1);
+return (pt1 <= 0 ? "" : data.substring(pt, pt1));
+}, "~S,~S");
+Clazz.defineMethod(c$, "getXmlPoint",
+function(data, key){
+var spt = J.jvxl.readers.XmlReader.getXmlAttrib(data, key).$replace('(', '{').$replace(')', '}');
+var value = JU.Escape.uP(spt);
+if (Clazz.instanceOf(value,"JU.P3")) return value;
+return new JU.P3();
+}, "~S,~S");
+c$.setNext = Clazz.defineMethod(c$, "setNext",
+function(data, what, next, offset){
+var ipt = next[0];
+if (ipt < 0 || (ipt = data.indexOf(what, next[0])) < 0) return -1;
+ipt += what.length;
+next[0] = ipt + offset;
+if (offset > 0 && ipt < data.length && data.charAt(ipt) != '=') return J.jvxl.readers.XmlReader.setNext(data, what, next, offset);
+return next[0];
+}, "~S,~S,~A,~N");
+Clazz.defineMethod(c$, "skipTo",
+function(key){
+if (this.line == null) this.line = this.br.readLine();
+while (this.line != null && this.line.indexOf(key) < 0) this.line = this.br.readLine();
+
+}, "~S");
+Clazz.defineMethod(c$, "isNext",
+function(name){
+if (this.line == null || this.line.indexOf("= 0 && this.line.indexOf("= 0);
+}, "~S");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XplorReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XplorReader.js
new file mode 100755
index 000000000000..aa48fde51b1d
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XplorReader.js
@@ -0,0 +1,72 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.MapFileReader"], "J.jvxl.readers.XplorReader", ["JU.SB", "JU.Logger", "JV.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.nBlock = 0;
+this.linePt = 2147483647;
+this.nRead = 0;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "XplorReader", J.jvxl.readers.MapFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.XplorReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2MFR(sg, br);
+if (this.params.thePlane == null) this.params.insideOut = !this.params.insideOut;
+this.nSurfaces = 1;
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.jvxlFileHeaderBuffer = new JU.SB();
+var nLines = this.parseIntStr(this.getLine());
+for (var i = nLines; --i >= 0; ) {
+this.line = this.br.readLine().trim();
+JU.Logger.info("XplorReader: " + this.line);
+this.jvxlFileHeaderBuffer.append("# ").append(this.line).appendC('\n');
+}
+this.jvxlFileHeaderBuffer.append("Xplor data\nJmol " + JV.Viewer.getJmolVersion() + '\n');
+this.na = this.parseIntStr(this.getLine());
+this.xyzStart[0] = this.parseInt();
+this.n0 = Clazz.floatToInt(this.parseInt() - this.xyzStart[0] + 1);
+this.nb = this.parseInt();
+this.xyzStart[1] = this.parseInt();
+this.n1 = Clazz.floatToInt(this.parseInt() - this.xyzStart[1] + 1);
+this.nc = this.parseInt();
+this.xyzStart[2] = this.parseInt();
+this.n2 = Clazz.floatToInt(this.parseInt() - this.xyzStart[2] + 1);
+this.a = this.parseFloatStr(this.getLine());
+this.b = this.parseFloat();
+this.c = this.parseFloat();
+this.alpha = this.parseFloat();
+this.beta = this.parseFloat();
+this.gamma = this.parseFloat();
+this.getLine();
+this.maps = 3;
+this.mapr = 2;
+this.mapc = 1;
+this.getVectorsAndOrigin();
+this.setCutoffAutomatic();
+this.nBlock = this.voxelCounts[2] * this.voxelCounts[1];
+});
+Clazz.defineMethod(c$, "getLine",
+function(){
+this.rd();
+while (this.line != null && (this.line.length == 0 || this.line.indexOf("REMARKS") >= 0 || this.line.indexOf("XPLOR:") >= 0)) this.rd();
+
+return this.line;
+});
+Clazz.overrideMethod(c$, "nextVoxel",
+function(){
+if (this.linePt >= this.line.length) {
+this.rd();
+this.linePt = 0;
+if ((this.nRead % this.nBlock) == 0) {
+this.rd();
+}}if (this.line == null) return 0;
+var val = this.parseFloatRange(this.line, this.linePt, this.linePt + 12);
+this.linePt += 12;
+this.nRead++;
+return val;
+});
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XsfReader.js b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XsfReader.js
new file mode 100755
index 000000000000..1d3a1a84a6b7
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/jvxl/readers/XsfReader.js
@@ -0,0 +1,62 @@
+Clazz.declarePackage("J.jvxl.readers");
+Clazz.load(["J.jvxl.readers.VolumeFileReader"], "J.jvxl.readers.XsfReader", ["JU.SB", "JU.Logger"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.isBXSF = false;
+Clazz.instantialize(this, arguments);}, J.jvxl.readers, "XsfReader", J.jvxl.readers.VolumeFileReader);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.jvxl.readers.XsfReader, []);
+});
+Clazz.overrideMethod(c$, "init2",
+function(sg, br){
+this.init2VFR(sg, br);
+}, "J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
+Clazz.overrideMethod(c$, "readParameters",
+function(){
+this.isAngstroms = false;
+this.params.blockCubeData = true;
+this.jvxlFileHeaderBuffer = new JU.SB();
+this.jvxlFileHeaderBuffer.append("XsfReader file\n");
+var needCutoff = this.params.cutoffAutomatic;
+this.isAngstroms = true;
+var beginKey = "BEGIN_DATAGRID_3D";
+this.nSurfaces = 1;
+while (this.rd() != null && this.line.indexOf(beginKey) < 0) {
+JU.Logger.info(this.line);
+if (this.line.indexOf("Fermi Energy:") >= 0) {
+this.isBXSF = true;
+beginKey = "BEGIN_BANDGRID_3D";
+if (needCutoff) {
+this.params.cutoff = this.parseFloatStr(this.getTokens()[2]);
+needCutoff = false;
+}}continue;
+}
+if (needCutoff) this.params.cutoff = 0.05;
+if (this.isBXSF) this.nSurfaces = this.parseIntStr(this.rd());
+this.voxelCounts[0] = this.parseIntStr(this.rd());
+this.voxelCounts[1] = this.parseInt();
+this.voxelCounts[2] = this.parseInt();
+this.volumetricOrigin.set(this.parseFloatStr(this.rd()), this.parseFloat(), this.parseFloat());
+for (var i = 0; i < 3; ++i) {
+this.volumetricVectors[i].set(this.parseFloatStr(this.rd()), this.parseFloat(), this.parseFloat());
+this.volumetricVectors[i].scale(1.0 / (this.voxelCounts[i] - 1));
+}
+if (this.isBXSF) {
+} else {
+this.swapXZ();
+}});
+Clazz.overrideMethod(c$, "gotoData",
+function(n, nPoints){
+if (!this.params.blockCubeData) return;
+if (n > 0) JU.Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
+if (this.isBXSF) JU.Logger.info(this.rd());
+for (var i = 0; i < n; i++) this.skipData(nPoints);
+
+}, "~N,~N");
+Clazz.overrideMethod(c$, "skipData",
+function(nPoints){
+this.skipDataVFR(nPoints);
+if (this.isBXSF) JU.Logger.info(this.rd());
+}, "~N");
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKit.js b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKit.js
new file mode 100755
index 000000000000..aca6f14deec3
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKit.js
@@ -0,0 +1,2797 @@
+Clazz.declarePackage("J.modelkit");
+Clazz.load(["JU.Vibration", "JU.BS", "$.P3", "J.i18n.GT"], "J.modelkit.ModelKit", ["java.util.Arrays", "$.Hashtable", "JU.AU", "$.Lst", "$.M4", "$.Measure", "$.PT", "$.Quat", "$.SB", "$.V3", "JS.SV", "JU.BSUtil", "$.Edge", "$.Elements", "$.Logger", "$.SimpleUnitCell", "JV.JC", "$.Viewer"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.vwr = null;
+this.menu = null;
+this.state = 0;
+this.atomHoverLabel = "C";
+this.bondHoverLabel = J.i18n.GT.$("increase order");
+this.allOperators = null;
+this.currentModelIndex = -1;
+this.lastModelSet = null;
+this.lastElementType = "C";
+this.bsHighlight = null;
+this.bondIndex = -1;
+this.bondAtomIndex1 = -1;
+this.bondAtomIndex2 = -1;
+this.bsRotateBranch = null;
+this.branchAtomIndex = 0;
+this.screenXY = null;
+this.$isPickAtomAssignCharge = false;
+this.isRotateBond = false;
+this.showSymopInfo = true;
+this.hasUnitCell = false;
+this.alertedNoEdit = false;
+this.$wasRotating = false;
+this.addHydrogens = true;
+this.clickToSetElement = true;
+this.autoBond = false;
+this.centerPoint = null;
+this.pickAtomAssignType = "C";
+this.pickBondAssignType = 'p';
+this.viewOffset = null;
+this.centerDistance = 0;
+this.symop = null;
+this.centerAtomIndex = -1;
+this.secondAtomIndex = -1;
+this.drawData = null;
+this.drawScript = null;
+this.iatom0 = 0;
+this.lastCenter = "0 0 0";
+this.lastOffset = "0 0 0";
+this.a0 = null;
+this.a3 = null;
+this.constraint = null;
+this.atomConstraints = null;
+this.minBasisAtoms = null;
+this.modelSyms = null;
+this.minBasis = null;
+this.minBasisFixed = null;
+this.minBasisModelAtoms = null;
+this.minBasisModel = 0;
+this.minSelectionSaved = null;
+this.minTempFixed = null;
+this.minTempModelAtoms = null;
+this.$setElementKeys = false;
+this.bsElementKeyModels = null;
+this.bsElementKeyModelsOFF = null;
+this.haveElementKeys = false;
+if (!Clazz.isClassDefined("J.modelkit.ModelKit.DrawAtomSet")) {
+J.modelkit.ModelKit.$ModelKit$DrawAtomSet$ ();
+}
+this.drawAtomSymmetry = null;
+Clazz.instantialize(this, arguments);}, J.modelkit, "ModelKit", null);
+Clazz.prepareFields (c$, function(){
+this.bsHighlight = new JU.BS();
+this.screenXY = Clazz.newIntArray (2, 0);
+this.bsElementKeyModels = new JU.BS();
+this.bsElementKeyModelsOFF = new JU.BS();
+});
+Clazz.makeConstructor(c$,
+function(){
+});
+c$.getText = Clazz.defineMethod(c$, "getText",
+function(key){
+switch (("invSter delAtom dragBon dragAto dragMin dragMol dragMMo incChar decChar rotBond bondTo0 bondTo1 bondTo2 bondTo3 incBond decBond").indexOf(key.substring(0, 7))) {
+case 0:
+return J.i18n.GT.$("invert ring stereochemistry");
+case 8:
+return J.i18n.GT.$("delete atom");
+case 16:
+return J.i18n.GT.$("drag to bond");
+case 24:
+return J.i18n.GT.$("drag atom");
+case 32:
+return J.i18n.GT.$("drag atom (and minimize)");
+case 40:
+return J.i18n.GT.$("drag molecule (ALT to rotate)");
+case 48:
+return J.i18n.GT.$("drag and minimize molecule (docking)");
+case 56:
+return J.i18n.GT.$("increase charge");
+case 64:
+return J.i18n.GT.$("decrease charge");
+case 72:
+return J.i18n.GT.$("rotate bond");
+case 80:
+return J.i18n.GT.$("delete bond");
+case 88:
+return J.i18n.GT.$("single");
+case 96:
+return J.i18n.GT.$("double");
+case 104:
+return J.i18n.GT.$("triple");
+case 112:
+return J.i18n.GT.$("increase order");
+case 120:
+return J.i18n.GT.$("decrease order");
+}
+return key;
+}, "~S");
+c$.getTransform = Clazz.defineMethod(c$, "getTransform",
+function(sym, a, b){
+var fa = JU.P3.newP(a);
+sym.toFractional(fa, false);
+var fb = JU.P3.newP(b);
+sym.toFractional(fb, false);
+return sym.getTransform(fa, fb, true);
+}, "J.api.SymmetryInterface,JM.Atom,JM.Atom");
+c$.getElementKey = Clazz.defineMethod(c$, "getElementKey",
+function(modelIndex){
+return "_!_elkey_" + (modelIndex < 0 ? "" : modelIndex + "_");
+}, "~N");
+c$.isTrue = Clazz.defineMethod(c$, "isTrue",
+function(value){
+return (Boolean.$valueOf(value.toString()) === Boolean.TRUE);
+}, "~O");
+c$.keyToElement = Clazz.defineMethod(c$, "keyToElement",
+function(key){
+var ch1 = (key & 0xFF);
+var ch2 = (key >> 8) & 0xFF;
+var element = "" + String.fromCharCode(ch1) + (ch2 == 0 ? "" : ("" + String.fromCharCode(ch2)).toLowerCase());
+var n = JU.Elements.elementNumberFromSymbol(element, true);
+return (n == 0 ? null : element);
+}, "~N");
+c$.notImplemented = Clazz.defineMethod(c$, "notImplemented",
+function(action){
+System.err.println("ModelKit.notImplemented(" + action + ")");
+}, "~S");
+c$.pointFromTriad = Clazz.defineMethod(c$, "pointFromTriad",
+function(pos){
+var a = JU.PT.parseFloatArray(JU.PT.replaceAllCharacters(pos, "{,}", " "));
+return (a.length == 3 && !Float.isNaN(a[2]) ? JU.P3.new3(a[0], a[1], a[2]) : null);
+}, "~S");
+Clazz.defineMethod(c$, "actionRotateBond",
+function(deltaX, deltaY, x, y, forceFull){
+if (this.bondIndex < 0) return;
+var bsBranch = this.bsRotateBranch;
+var atomFix;
+var atomMove;
+var ms = this.vwr.ms;
+var b = ms.bo[this.bondIndex];
+if (forceFull) {
+bsBranch = null;
+this.branchAtomIndex = -1;
+}if (bsBranch == null) {
+atomMove = (this.branchAtomIndex == b.atom1.i ? b.atom1 : b.atom2);
+atomFix = (atomMove === b.atom1 ? b.atom2 : b.atom1);
+this.vwr.undoMoveActionClear(atomFix.i, 2, true);
+if (this.branchAtomIndex >= 0) bsBranch = this.vwr.getBranchBitSet(atomMove.i, atomFix.i, true);
+if (bsBranch != null) for (var n = 0, i = atomFix.bonds.length; --i >= 0; ) {
+if (bsBranch.get(atomFix.getBondedAtomIndex(i)) && ++n == 2) {
+bsBranch = null;
+break;
+}}
+if (bsBranch == null) {
+bsBranch = ms.getMoleculeBitSetForAtom(atomFix.i);
+forceFull = true;
+}this.bsRotateBranch = bsBranch;
+this.bondAtomIndex1 = atomFix.i;
+this.bondAtomIndex2 = atomMove.i;
+} else {
+atomFix = ms.at[this.bondAtomIndex1];
+atomMove = ms.at[this.bondAtomIndex2];
+}if (forceFull) this.bsRotateBranch = null;
+var v1 = JU.V3.new3(atomMove.sX - atomFix.sX, atomMove.sY - atomFix.sY, 0);
+v1.scale(1 / v1.length());
+var v2 = JU.V3.new3(deltaX, deltaY, 0);
+v1.cross(v1, v2);
+var f = (v1.z > 0 ? 1 : -1);
+var degrees = f * (Clazz.doubleToInt(Clazz.floatToInt(v2.length()) / 2) + 1);
+if (!forceFull && this.a0 != null) {
+var ang0 = JU.Measure.computeTorsion(this.a0, b.atom1, b.atom2, this.a3, true);
+var ang1 = Math.round(ang0 + degrees);
+degrees = ang1 - ang0;
+}var bs = JU.BSUtil.copy(bsBranch);
+bs.andNot(this.vwr.slm.getMotionFixedAtoms());
+this.vwr.rotateAboutPointsInternal(null, atomFix, atomMove, 0, degrees, false, bs, null, null, null, null, true);
+}, "~N,~N,~N,~N,~B");
+Clazz.defineMethod(c$, "addLockedAtoms",
+function(sg, bsLocked){
+if (this.vwr.am.cmi < 0 || bsLocked.cardinality() == 0) return;
+var bsm = this.vwr.getThisModelAtoms();
+var i0 = bsLocked.nextSetBit(0);
+if (sg == null && (sg = this.getSym(i0)) == null) return;
+for (var i = bsm.nextSetBit(0); i >= 0; i = bsm.nextSetBit(i + 1)) {
+if (this.setConstraint(sg, i, J.modelkit.ModelKit.GET_CREATE).type == 6) {
+bsLocked.set(i);
+}}
+}, "J.api.SymmetryInterface,JU.BS");
+Clazz.defineMethod(c$, "checkMovedAtoms",
+function(bsFixed, bsAtoms, apos0){
+var i0 = bsAtoms.nextSetBit(0);
+var n = bsAtoms.cardinality();
+var apos = new Array(n);
+try {
+var atoms = this.vwr.ms.at;
+for (var ip = 0, i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+apos[ip++] = JU.P3.newP(atoms[i]);
+atoms[i].setT(apos0[i]);
+}
+var maxSite = 0;
+for (var i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var s = this.vwr.ms.at[i].getAtomSite();
+if (s > maxSite) maxSite = s;
+}
+var sites = Clazz.newIntArray (maxSite, 0);
+var p1 = new JU.P3();
+var bsModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.ms.at[i0].mi);
+var bsMoved = new JU.BS();
+for (var ip = 0, i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1), ip++) {
+p1.setT(apos[ip]);
+var s = this.vwr.ms.at[i].getAtomSite() - 1;
+if (sites[s] == 0) {
+sites[s] = i + 1;
+bsMoved = this.moveConstrained(i, bsFixed, bsModelAtoms, p1, true, false, bsMoved);
+if (bsMoved == null) {
+n = 0;
+break;
+}}}
+return (n != 0 && this.checkAtomPositions(apos0, apos, bsAtoms) ? n : 0);
+} finally {
+if (n == 0) {
+this.vwr.ms.restoreAtomPositions(apos0);
+bsAtoms.clearAll();
+} else {
+this.updateDrawAtomSymmetry("atomsMoved", bsAtoms);
+}}
+}, "JU.BS,JU.BS,~A");
+Clazz.defineMethod(c$, "checkOption",
+function(type, key){
+var check = null;
+switch ((type).charCodeAt(0)) {
+case 77:
+check = ";view;edit;molecular;";
+break;
+case 83:
+check = ";none;applylocal;retainlocal;applyfull;";
+break;
+case 85:
+check = ";packed;extend;";
+break;
+case 66:
+check = ";key;elementkey;autobond;hidden;showsymopinfo;clicktosetelement;addhydrogen;addhydrogens;";
+break;
+}
+return (check != null && JU.PT.isOneOf(key.toLowerCase(), check));
+}, "~S,~S");
+Clazz.defineMethod(c$, "clearAtomConstraints",
+function(){
+this.modelSyms = null;
+this.minBasisAtoms = null;
+if (this.atomConstraints != null) {
+for (var i = this.atomConstraints.length; --i >= 0; ) this.atomConstraints[i] = null;
+
+}});
+Clazz.defineMethod(c$, "clickAssignAtom",
+function(atomIndex, element, ptNew){
+var n = this.addAtomType(element, Clazz.newArray(-1, [(ptNew == null ? null : ptNew)]), JU.BSUtil.newAndSetBit(atomIndex), "", null, "click");
+if (n > 0) this.vwr.setPickingMode("dragAtom", 0);
+}, "~N,~S,JU.P3");
+Clazz.defineMethod(c$, "cmdAssignAddAtoms",
+function(type, pts, bsAtoms, packing, cmd){
+if (type.startsWith("_")) type = type.substring(1);
+return Math.abs(this.addAtomType(type, pts, bsAtoms, packing, null, cmd));
+}, "~S,~A,JU.BS,~S,~S");
+Clazz.defineMethod(c$, "cmdAssignAtom",
+function(bs, pt, type, cmd){
+if (pt != null && bs != null && bs.cardinality() > 1) bs = JU.BSUtil.newAndSetBit(bs.nextSetBit(0));
+if (type.startsWith("_")) type = type.substring(1);
+this.assignAtomNoAddedSymmetry(pt, -1, bs, type, (pt != null), cmd, 0);
+}, "JU.BS,JU.P3,~S,~S");
+Clazz.defineMethod(c$, "cmdAssignBond",
+function(bondIndex, type, cmd){
+this.assignBondAndType(bondIndex, this.getBondOrder(type, this.vwr.ms.bo[bondIndex]), type, cmd);
+}, "~N,~S,~S");
+Clazz.defineMethod(c$, "cmdAssignConnect",
+function(index, index2, type, cmd){
+var atoms = this.vwr.ms.at;
+var a;
+var b;
+if (index < 0 || index2 < 0 || index >= atoms.length || index2 >= atoms.length || (a = atoms[index]) == null || (b = atoms[index2]) == null) return;
+var state = this.getMKState();
+try {
+var bond = null;
+if (type != '1') {
+var bs = new JU.BS();
+bs.set(index);
+bs.set(index2);
+bs = this.vwr.getBondsForSelectedAtoms(bs);
+bond = this.vwr.ms.bo[bs.nextSetBit(0)];
+}var bondOrder = this.getBondOrder(type, bond);
+var bs1 = this.vwr.ms.getSymmetryEquivAtoms(JU.BSUtil.newAndSetBit(index), null, null);
+var bs2 = this.vwr.ms.getSymmetryEquivAtoms(JU.BSUtil.newAndSetBit(index2), null, null);
+this.connectAtoms(a.distance(b), bondOrder, bs1, bs2);
+if (this.vwr.getOperativeSymmetry() == null) {
+bond = a.getBond(b);
+if (bond != null) {
+bs1.or(bs2);
+this.assignBond(bond.index, 1, bs1);
+}}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+} finally {
+this.setMKState(state);
+}
+}, "~N,~N,~S,~S");
+Clazz.defineMethod(c$, "cmdAssignDeleteAtoms",
+function(bs){
+this.clearAtomConstraints();
+bs.and(this.vwr.getThisModelAtoms());
+bs = this.vwr.ms.getSymmetryEquivAtoms(bs, null, null);
+if (!bs.isEmpty()) {
+this.vwr.deleteAtoms(bs, false);
+}return bs.cardinality();
+}, "JU.BS");
+Clazz.defineMethod(c$, "cmdAssignMoveAtoms",
+function(bsSelected, iatom, p, pts, allowProjection, isMolecule){
+var sym = this.getSym(iatom);
+var n;
+if (sym != null) {
+if (this.addHydrogens) this.vwr.ms.addConnectedHAtoms(this.vwr.ms.at[iatom], bsSelected);
+n = this.assignMoveAtoms(sym, bsSelected, null, null, iatom, p, pts, allowProjection, isMolecule);
+} else {
+n = this.vwr.moveAtomWithHydrogens(iatom, this.addHydrogens ? 1 : 0, 0, 0, p, null);
+}if (n == 0) this.vwr.showString("could not move atoms!", false);
+return n;
+}, "JU.BS,~N,JU.P3,~A,~B,~B");
+Clazz.defineMethod(c$, "cmdAssignSpaceGroup",
+function(bs, name, paramsOrUC, isPacked, doDraw, cmd){
+var sym0 = this.vwr.getCurrentUnitCell();
+var sym = this.vwr.getOperativeSymmetry();
+if (sym0 != null && sym !== sym0) sym.getUnitCell(sym0.getV0abc(null, null), false, "modelkit");
+var sb = new JU.SB();
+var ret = this.assignSpaceGroup(sym, null, bs, paramsOrUC, JU.PT.split(name, ">"), 0, null, null, sb);
+if (ret.endsWith("!")) return ret;
+if (isPacked) {
+var n;
+if (doDraw) {
+n = this.cmdAssignAddAtoms("N:G", null, null, "packed", cmd);
+} else {
+var transform = ret;
+var bsModelAtoms = this.vwr.getThisModelAtoms();
+n = this.cmdAssignSpaceGroupPacked(bsModelAtoms, transform, cmd);
+}sb.append("\n").append(J.i18n.GT.i(J.i18n.GT.$("{0} atoms added"), n));
+}var msg = sb.toString();
+var isError = msg.endsWith("!");
+if (doDraw && !isError) {
+var s = this.drawSymmetry("sym", false, -1, null, 2147483647, null, null, null, 0, -2, 0, null, true);
+this.appRunScript(s);
+}return msg;
+}, "JU.BS,~S,~O,~B,~B,~S");
+Clazz.defineMethod(c$, "cmdAssignSpaceGroupPacked",
+function(bsAtoms, transform, cmd){
+var sym = this.vwr.getOperativeSymmetry();
+if (sym == null) return 0;
+var opsCtr = sym.getSpaceGroupInfoObj("opsCtr", transform, false, false);
+var n0 = bsAtoms.cardinality();
+this.addAtoms(null, null, bsAtoms, "packed", opsCtr, cmd);
+bsAtoms = this.vwr.getThisModelAtoms();
+this.vwr.ms.setSpaceGroup(this.vwr.am.cmi, sym, new JU.BS());
+return bsAtoms.cardinality() - n0;
+}, "JU.BS,~S,~S");
+Clazz.defineMethod(c$, "cmdMinimize",
+function(eval, bsBasis, steps, crit, rangeFixed, flags){
+var wasAppend = this.vwr.getBoolean(603979792);
+try {
+this.vwr.setBooleanProperty("appendNew", true);
+this.minimizeXtal(eval, bsBasis, steps, crit, rangeFixed, flags);
+} finally {
+this.vwr.setBooleanProperty("appendNew", wasAppend);
+}
+}, "J.api.JmolScriptEvaluator,JU.BS,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "cmdRotateAtoms",
+function(bsAtoms, points, endDegrees){
+return this.rotateAtoms(bsAtoms, points, endDegrees);
+}, "JU.BS,~A,~N");
+Clazz.defineMethod(c$, "dispose",
+function(){
+this.menu.jpiDispose();
+this.menu.modelkit = null;
+this.menu = null;
+this.vwr = null;
+});
+Clazz.defineMethod(c$, "getActiveMenu",
+function(){
+return this.menu.activeMenu;
+});
+Clazz.defineMethod(c$, "getDefaultModel",
+function(){
+return (this.addHydrogens ? "5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63" : "1\n\nC 0 0 0\n");
+});
+Clazz.defineMethod(c$, "getProperty",
+function(name){
+name = name.toLowerCase().intern();
+if (name === "exists") return Boolean.TRUE;
+if (name === "constraint") {
+return this.constraint;
+}if (name === "ismolecular") {
+return Boolean.$valueOf(this.getMKState() == 0);
+}if (name === "key" || name === "elementkey") {
+return Boolean.$valueOf(this.isElementKeyOn(this.vwr.am.cmi));
+}if (name === "minimizing") return Boolean.$valueOf(this.minBasis != null);
+if (name === "alloperators") {
+return this.allOperators;
+}if (name === "data") {
+return this.getinfo();
+}return this.setProperty(name, null);
+}, "~S");
+Clazz.defineMethod(c$, "getRotateBondIndex",
+function(){
+return (this.getMKState() == 0 && this.isRotateBond ? this.bondIndex : -1);
+});
+Clazz.defineMethod(c$, "getSym",
+function(iatom){
+var modelIndex = this.vwr.ms.at[iatom].mi;
+if (this.modelSyms == null || modelIndex >= this.modelSyms.length) {
+this.modelSyms = new Array(this.vwr.ms.mc);
+for (var imodel = this.modelSyms.length; --imodel >= 0; ) {
+var sym = this.vwr.ms.getUnitCell(imodel);
+if (sym == null || sym.getSymmetryOperations() != null) this.modelSyms[imodel] = sym;
+}
+}return (iatom < 0 ? null : this.modelSyms[modelIndex]);
+}, "~N");
+Clazz.defineMethod(c$, "handleAssignNew",
+function(pressed, dragged, mp, dragAtomIndex, key){
+var inRange = pressed.inRange(10, dragged.x, dragged.y);
+if (mp != null && this.handleAtomDragging(mp.countPlusIndices)) return true;
+var atomType = (key < 0 ? this.pickAtomAssignType : J.modelkit.ModelKit.keyToElement(key));
+if (atomType == null) return false;
+var x = (inRange ? pressed.x : dragged.x);
+var y = (inRange ? pressed.y : dragged.y);
+if (this.vwr.antialiased) {
+x <<= 1;
+y <<= 1;
+}return this.handleAtomOrBondPicked(x, y, mp, dragAtomIndex, atomType, inRange);
+}, "JV.MouseState,JV.MouseState,JM.MeasurementPending,~N,~N");
+Clazz.defineMethod(c$, "hasConstraint",
+function(iatom, ignoreGeneral, addNew){
+var c = this.setConstraint(this.getSym(iatom), iatom, addNew ? J.modelkit.ModelKit.GET_CREATE : J.modelkit.ModelKit.GET);
+return (c != null && (!ignoreGeneral || c.type != 7));
+}, "~N,~B,~B");
+Clazz.defineMethod(c$, "initializeForModel",
+function(isZap){
+this.resetBondFields();
+this.allOperators = null;
+this.currentModelIndex = -999;
+this.iatom0 = 0;
+this.centerAtomIndex = this.secondAtomIndex = -1;
+this.centerPoint = null;
+this.symop = null;
+this.setDefaultState(0);
+if (isZap) {
+if (this.$setElementKeys) {
+this.updateModelElementKey(this.vwr.am.cmi, true);
+}this.bsElementKeyModels.clearAll();
+this.bsElementKeyModelsOFF.clearAll();
+}}, "~B");
+Clazz.defineMethod(c$, "isHidden",
+function(){
+return this.menu.hidden;
+});
+Clazz.defineMethod(c$, "isPickAtomAssignCharge",
+function(){
+return this.$isPickAtomAssignCharge;
+});
+Clazz.defineMethod(c$, "minimizeEnd",
+function(bsBasis2, isEnd){
+this.minimizeXtalEnd(bsBasis2, isEnd);
+this.vwr.refresh(1, "modelkit minimize");
+}, "JU.BS,~B");
+Clazz.defineMethod(c$, "moveMinConstrained",
+function(iatom, p, bsAtoms){
+var bsMoved = this.moveConstrained(iatom, null, bsAtoms, p, true, true, null);
+return (bsMoved == null ? 0 : bsMoved.cardinality());
+}, "~N,JU.P3,JU.BS");
+Clazz.defineMethod(c$, "setBondMeasure",
+function(bi, mp){
+if (this.branchAtomIndex < 0) return null;
+var b = this.vwr.ms.bo[bi];
+var a1 = b.atom1;
+var a2 = b.atom2;
+this.a0 = this.a3 = null;
+if (a1.getCovalentBondCount() == 1 || a2.getCovalentBondCount() == 1) return null;
+mp.addPoint((this.a0 = J.modelkit.ModelKit.getNearestBondedAtom(a1, a2)).i, null, true);
+mp.addPoint(a1.i, null, true);
+mp.addPoint(a2.i, null, true);
+mp.addPoint((this.a3 = J.modelkit.ModelKit.getNearestBondedAtom(a2, a1)).i, null, true);
+mp.mad = 50;
+mp.inFront = true;
+return mp;
+}, "~N,JM.MeasurementPending");
+Clazz.defineMethod(c$, "setMenu",
+function(menu){
+this.menu = menu;
+this.vwr = menu.vwr;
+menu.modelkit = this;
+this.initializeForModel(false);
+}, "J.modelkit.ModelKitPopup");
+Clazz.defineMethod(c$, "setProperty",
+function(key, value){
+try {
+if (this.vwr == null) return null;
+key = key.toLowerCase().intern();
+if (key === "hoverlabel") {
+return this.getHoverLabel((value).intValue());
+}if (key === "initializemodel") {
+this.initializeForModel(true);
+return null;
+}if (key === "atomset") {
+this.addAtomSet(value);
+return null;
+}if (key === "atomsMoved") {
+if (this.drawAtomSymmetry != null) {
+this.updateDrawAtomSymmetry(key, (value)[0]);
+}return null;
+}if (key === "updatemodelkeys") {
+if (this.haveElementKeys) this.updateModelElementKeys(value == null ? null : (value)[1], true);
+if (this.drawAtomSymmetry != null && value != null) {
+this.updateDrawAtomSymmetry("atomsDeleted", (value)[0]);
+}return null;
+}if (key === "updatekeysfromstate") {
+this.updateElementKeyFromStateScript();
+return null;
+}if (key === "updateatomkeys") {
+var bsAtoms = value;
+this.updateElementKey(bsAtoms);
+return null;
+}if (key === "setelementkey") {
+this.setElementKeys(J.modelkit.ModelKit.isTrue(value));
+return null;
+}if (key === "frameresized") {
+this.clearElementKey(-2);
+this.updateModelElementKeys(null, true);
+return null;
+}if (key === "key" || key === "elementkey") {
+var mi = this.vwr.am.cmi;
+var isOn = J.modelkit.ModelKit.isTrue(value);
+this.bsElementKeyModelsOFF.setBitTo(mi, !isOn);
+this.bsElementKeyModels.setBitTo(mi, false);
+this.setElementKey(mi, isOn);
+return isOn ? "true" : "false";
+}if (key === "branchatomclicked") {
+if (this.isRotateBond && !this.vwr.acm.isHoverable()) this.setBranchAtom((value).intValue(), true);
+return null;
+}if (key === "branchatomdragged") {
+if (this.isRotateBond) this.setBranchAtom((value).intValue(), true);
+return null;
+}if (key === "hidemenu") {
+this.menu.hidePopup();
+return null;
+}if (key === "constraint") {
+this.constraint = null;
+this.clearAtomConstraints();
+var o = value;
+if (o != null) {
+var v1 = o[0];
+var v2 = o[1];
+var plane = o[2];
+if (v1 != null && v2 != null) {
+this.constraint = new J.modelkit.ModelKit.Constraint(null, 4, Clazz.newArray(-1, [v1, v2]));
+} else if (plane != null) {
+this.constraint = new J.modelkit.ModelKit.Constraint(null, 5, Clazz.newArray(-1, [plane]));
+} else if (v1 != null) this.constraint = new J.modelkit.ModelKit.Constraint(null, 6, null);
+}return null;
+}if (key === "reset") {
+return null;
+}if (key === "atompickingmode") {
+if (JU.PT.isOneOf(value, ";identify;off;")) {
+this.exitBondRotation(null);
+this.vwr.setBooleanProperty("bondPicking", false);
+this.vwr.acm.exitMeasurementMode("modelkit");
+}if ("dragatom".equals(value)) {
+this.setHoverLabel("atomMenu", J.modelkit.ModelKit.getText("dragAtom"));
+}return null;
+}if (key === "bondpickingmode") {
+if (value.equals("deletebond")) {
+this.exitBondRotation(J.modelkit.ModelKit.getText("bondTo0"));
+} else if (value.equals("identifybond")) {
+this.exitBondRotation("");
+}return null;
+}if (key === "rotateBond") {
+var i = (value).intValue();
+if (i != this.bondAtomIndex2) this.bondAtomIndex1 = i;
+this.bsRotateBranch = null;
+return null;
+}if (key === "bondindex") {
+if (value != null) {
+this.setBondIndex((value).intValue(), false);
+}return (this.bondIndex < 0 ? null : Integer.$valueOf(this.bondIndex));
+}if (key === "rotatebondindex") {
+if (value != null) {
+this.setBondIndex((value).intValue(), true);
+}return (this.bondIndex < 0 ? null : Integer.$valueOf(this.bondIndex));
+}if (key === "highlight") {
+this.bsHighlight.clearAll();
+if (value != null) this.bsHighlight.or(value);
+return null;
+}if (key === "mode") {
+var isEdit = ("edit".equals(value));
+this.setMKState("view".equals(value) ? 1 : isEdit ? 2 : 0);
+if (isEdit) this.addHydrogens = false;
+return null;
+}if (key === "symmetry") {
+this.setDefaultState(2);
+key = (value).toLowerCase().intern();
+this.setSymEdit(key === "applylocal" ? 32 : key === "retainlocal" ? 64 : key === "applyfull" ? 128 : 0);
+this.showXtalSymmetry();
+return null;
+}if (key === "unitcell") {
+var isPacked = "packed".equals(value);
+this.setUnitCell(isPacked ? 0 : 256);
+this.viewOffset = (isPacked ? J.modelkit.ModelKit.Pt000 : null);
+return null;
+}if (key === "center") {
+this.setDefaultState(1);
+this.centerPoint = value;
+this.lastCenter = this.centerPoint.x + " " + this.centerPoint.y + " " + this.centerPoint.z;
+this.centerAtomIndex = (Clazz.instanceOf(this.centerPoint,"JM.Atom") ? (this.centerPoint).i : -1);
+this.secondAtomIndex = -1;
+this.clickProcessAtom(this.centerAtomIndex);
+return null;
+}if (key === "assignBond") {
+this.cmdAssignBond((value).intValue(), this.pickBondAssignType, "click");
+return null;
+}if (key === "addhydrogen" || key === "addhydrogens") {
+if (value != null) this.addHydrogens = J.modelkit.ModelKit.isTrue(value);
+return Boolean.$valueOf(this.addHydrogens);
+}if (key === "autobond") {
+if (value != null) this.autoBond = J.modelkit.ModelKit.isTrue(value);
+return Boolean.$valueOf(this.autoBond);
+}if (key === "clicktosetelement") {
+if (value != null) this.clickToSetElement = J.modelkit.ModelKit.isTrue(value);
+return Boolean.$valueOf(this.clickToSetElement);
+}if (key === "hidden") {
+if (value != null) {
+this.menu.hidden = J.modelkit.ModelKit.isTrue(value);
+if (this.menu.hidden) this.menu.hidePopup();
+this.vwr.setBooleanProperty("modelkitMode", true);
+}return Boolean.$valueOf(this.menu.hidden);
+}if (key === "showsymopinfo") {
+if (value != null) this.showSymopInfo = J.modelkit.ModelKit.isTrue(value);
+return Boolean.$valueOf(this.showSymopInfo);
+}if (key === "symop") {
+this.setDefaultState(1);
+if (value != null) {
+if (key === "hoverlabel") {
+return this.getHoverLabel((value).intValue());
+}this.symop = value;
+this.showSymop(this.symop);
+}return this.symop;
+}if (key === "atomtype") {
+this.$wasRotating = this.isRotateBond;
+this.isRotateBond = false;
+if (value != null) {
+this.pickAtomAssignType = value;
+this.$isPickAtomAssignCharge = (this.pickAtomAssignType.equalsIgnoreCase("pl") || this.pickAtomAssignType.equalsIgnoreCase("mi"));
+if (this.$isPickAtomAssignCharge) {
+this.setHoverLabel("atomMenu", J.modelkit.ModelKit.getText(this.pickAtomAssignType.equalsIgnoreCase("mi") ? "decCharge" : "incCharge"));
+} else if ("X".equals(this.pickAtomAssignType)) {
+this.setHoverLabel("atomMenu", J.modelkit.ModelKit.getText("delAtom"));
+} else if (this.pickAtomAssignType.equals("Xx")) {
+this.setHoverLabel("atomMenu", J.modelkit.ModelKit.getText("dragBond"));
+} else {
+this.setHoverLabel("atomMenu", "Click or click+drag to bond or for a new " + this.pickAtomAssignType);
+this.lastElementType = this.pickAtomAssignType;
+}}return this.pickAtomAssignType;
+}if (key === "bondtype") {
+if (value != null) {
+var s = (value).substring(0, 1).toLowerCase();
+if (" 0123456pm".indexOf(s) > 0) {
+this.pickBondAssignType = s.charAt(0);
+this.setHoverLabel("bondMenu", J.modelkit.ModelKit.getText(this.pickBondAssignType == 'm' ? "decBond" : this.pickBondAssignType == 'p' ? "incBond" : "bondTo" + s));
+}this.isRotateBond = false;
+}return "" + this.pickBondAssignType;
+}if (key === "offset") {
+if (value === "none") {
+this.viewOffset = null;
+} else if (value != null) {
+this.viewOffset = (Clazz.instanceOf(value,"JU.P3") ? value : J.modelkit.ModelKit.pointFromTriad(value.toString()));
+if (this.viewOffset != null) this.setSymViewState(8);
+}this.showXtalSymmetry();
+return this.viewOffset;
+}if (key === "screenxy") {
+if (value != null) {
+this.screenXY = value;
+this.vwr.acm.exitMeasurementMode("modelkit");
+}return this.screenXY;
+}if (key === "invariant") {
+var iatom = (Clazz.instanceOf(value,"JU.BS") ? (value).nextSetBit(0) : -1);
+var atom = this.vwr.ms.getAtom(iatom);
+return (atom == null ? null : this.vwr.getSymmetryInfo(iatom, null, -1, null, atom, atom, 1275068418, null, 0, 0, 0, null));
+}if (key === "distance") {
+this.setDefaultState(2);
+var d = (value == null ? NaN : Clazz.instanceOf(value, Float) ? (value).floatValue() : JU.PT.parseFloat(value));
+if (!Float.isNaN(d)) {
+J.modelkit.ModelKit.notImplemented("setProperty: distance");
+this.centerDistance = d;
+}return Float.$valueOf(this.centerDistance);
+}if (key === "addconstraint") {
+J.modelkit.ModelKit.notImplemented("setProperty: addConstraint");
+return null;
+}if (key === "removeconstraint") {
+J.modelkit.ModelKit.notImplemented("setProperty: removeConstraint");
+return null;
+}if (key === "removeallconstraints") {
+J.modelkit.ModelKit.notImplemented("setProperty: removeAllConstraints");
+return null;
+}if (key === "vibration") {
+J.modelkit.ModelKit.WyckoffModulation.setVibrationMode(this, value);
+return null;
+}System.err.println("ModelKit.setProperty? " + key + " " + value);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+return "?";
+} else {
+throw e;
+}
+}
+return null;
+}, "~S,~O");
+Clazz.defineMethod(c$, "showMenu",
+function(x, y){
+this.menu.jpiShow(x, y);
+}, "~N,~N");
+Clazz.defineMethod(c$, "updateMenu",
+function(){
+this.menu.jpiUpdateComputedMenus();
+});
+Clazz.defineMethod(c$, "wasRotating",
+function(){
+var b = this.$wasRotating;
+this.$wasRotating = false;
+return b;
+});
+Clazz.defineMethod(c$, "checkNewModel",
+function(){
+var isNew = false;
+if (this.vwr.ms !== this.lastModelSet) {
+this.lastModelSet = this.vwr.ms;
+isNew = true;
+}this.currentModelIndex = Math.max(this.vwr.am.cmi, 0);
+this.iatom0 = this.vwr.ms.am[this.currentModelIndex].firstAtomIndex;
+return isNew;
+});
+Clazz.defineMethod(c$, "clickProcessXtal",
+function(id, action){
+if (this.processSymop(id, false)) return;
+action = action.intern();
+if (action.startsWith("mkmode_")) {
+if (!this.alertedNoEdit && action === "mkmode_edit") {
+this.alertedNoEdit = true;
+this.vwr.alert("ModelKit xtal edit has not been implemented");
+return;
+}this.clickProcessMode(action);
+} else if (action.startsWith("mksel_")) {
+this.clickProcessSel(action);
+} else if (action.startsWith("mkselop_")) {
+while (action != null) action = this.clickProcessSelOp(action);
+
+} else if (action.startsWith("mksymmetry_")) {
+this.clickProcessSym(action);
+} else if (action.startsWith("mkunitcell_")) {
+this.clickProcessUC(action);
+} else {
+J.modelkit.ModelKit.notImplemented("XTAL click " + action);
+}this.menu.updateAllXtalMenuOptions();
+}, "~S,~S");
+Clazz.defineMethod(c$, "exitBondRotation",
+function(text){
+this.$wasRotating = this.isRotateBond;
+this.isRotateBond = false;
+if (text != null) this.bondHoverLabel = text;
+this.vwr.highlight(null);
+}, "~S");
+Clazz.defineMethod(c$, "getAllOperators",
+function(){
+if (this.allOperators != null) return this.allOperators;
+var data = this.runScriptBuffered("show symop");
+this.allOperators = JU.PT.split(data.trim().$replace('\t', ' '), "\n");
+return this.allOperators;
+});
+Clazz.defineMethod(c$, "getBasisAtom",
+function(iatom){
+if (this.minBasisAtoms == null) {
+this.minBasisAtoms = new Array(this.vwr.ms.ac + 10);
+}if (this.minBasisAtoms.length < iatom + 10) {
+var a = new Array(this.vwr.ms.ac + 10);
+System.arraycopy(this.minBasisAtoms, 0, a, 0, this.minBasisAtoms.length);
+this.minBasisAtoms = a;
+}var b = this.minBasisAtoms[iatom];
+return (b == null ? (this.minBasisAtoms[iatom] = this.vwr.ms.getBasisAtom(iatom, false)) : b);
+}, "~N");
+Clazz.defineMethod(c$, "getCenterText",
+function(){
+return (this.centerAtomIndex < 0 && this.centerPoint == null ? null : this.centerAtomIndex >= 0 ? this.vwr.getAtomInfo(this.centerAtomIndex) : this.centerPoint.toString());
+});
+Clazz.defineMethod(c$, "getElementFromUser",
+function(){
+var element = this.promptUser(J.i18n.GT.$("Element?"), "");
+return (element == null || JU.Elements.elementNumberFromSymbol(element, true) == 0 ? null : element);
+});
+Clazz.defineMethod(c$, "getMKState",
+function(){
+return this.state & 3;
+});
+Clazz.defineMethod(c$, "getSymEditState",
+function(){
+return this.state & 224;
+});
+Clazz.defineMethod(c$, "getSymopText",
+function(){
+return (this.symop == null || this.allOperators == null ? null : Clazz.instanceOf(this.symop, Integer) ? this.allOperators[(this.symop).intValue() - 1] : this.symop.toString());
+});
+Clazz.defineMethod(c$, "getSymViewState",
+function(){
+return this.state & 28;
+});
+Clazz.defineMethod(c$, "getUnitCellState",
+function(){
+return this.state & 1792;
+});
+Clazz.defineMethod(c$, "isXtalState",
+function(){
+return ((this.state & 3) != 0);
+});
+Clazz.defineMethod(c$, "processMKPropertyItem",
+function(name, TF){
+name = name.substring(2);
+var pt = name.indexOf("_");
+if (pt > 0) {
+this.setProperty(name.substring(0, pt), name.substring(pt + 1));
+} else {
+this.setProperty(name, Boolean.$valueOf(TF));
+}}, "~S,~B");
+Clazz.defineMethod(c$, "processSymop",
+function(id, isFocus){
+var pt = id.indexOf(".mkop_");
+if (pt >= 0) {
+var op = this.symop;
+this.symop = Integer.$valueOf(id.substring(pt + 6));
+this.showSymop(this.symop);
+if (isFocus) this.symop = op;
+return true;
+}return false;
+}, "~S,~B");
+Clazz.defineMethod(c$, "resetAtomPickType",
+function(){
+this.setProperty("atomtype", this.lastElementType);
+});
+Clazz.defineMethod(c$, "setConstraint",
+function(sym, ia, mode){
+if (ia < 0) return null;
+var a = this.getBasisAtom(ia);
+var iatom = a.i;
+var ac = (this.atomConstraints != null && iatom < this.atomConstraints.length ? this.atomConstraints[iatom] : null);
+if (ac != null || mode != J.modelkit.ModelKit.GET_CREATE) {
+if (ac != null && mode == J.modelkit.ModelKit.GET_DELETE) {
+this.atomConstraints[iatom] = null;
+}return ac;
+}if (sym == null) return this.addConstraint(iatom, new J.modelkit.ModelKit.Constraint(a, 0, null));
+var ops = sym.getInvariantSymops(a, null);
+if (JU.Logger.debugging) System.out.println("MK.getConstraint atomIndex=" + iatom + " symops=" + java.util.Arrays.toString(ops));
+if (ops.length == 0) return this.addConstraint(iatom, new J.modelkit.ModelKit.Constraint(a, 7, null));
+var plane1 = null;
+var line1 = null;
+for (var i = ops.length; --i >= 0; ) {
+var line2 = null;
+var c = sym.getSymmetryInfoAtom(this.vwr.ms, iatom, null, ops[i], null, a, null, "invariant", 1275068418, 0, -1, 0, null);
+if ((typeof(c)=='string')) {
+continue;
+} else if (Clazz.instanceOf(c,"JU.P4")) {
+var plane = c;
+if (plane1 == null) {
+plane1 = plane;
+continue;
+}var line = JU.Measure.getIntersectionPP(plane1, plane);
+if (line == null || line.size() == 0) {
+return J.modelkit.ModelKit.locked;
+}line2 = Clazz.newArray(-1, [line.get(0), line.get(1)]);
+} else if (Clazz.instanceOf(c,"JU.P3")) {
+return J.modelkit.ModelKit.locked;
+} else {
+line2 = c;
+}if (line2 != null) {
+if (line1 == null) {
+line1 = line2;
+} else {
+var v1 = line1[1];
+if (Math.abs(v1.dot(line2[1])) < 0.999) return J.modelkit.ModelKit.locked;
+}if (plane1 != null) {
+if (Math.abs(plane1.dot(line2[1])) > 0.001) return J.modelkit.ModelKit.locked;
+}}}
+if (line1 != null) {
+line1[0] = JU.P3.newP(a);
+}return this.addConstraint(iatom, line1 != null ? new J.modelkit.ModelKit.Constraint(a, 4, line1) : plane1 != null ? new J.modelkit.ModelKit.Constraint(a, 5, Clazz.newArray(-1, [plane1])) : new J.modelkit.ModelKit.Constraint(a, 7, null));
+}, "J.api.SymmetryInterface,~N,~N");
+Clazz.defineMethod(c$, "setHasUnitCell",
+function(){
+return this.hasUnitCell = (this.vwr.getOperativeSymmetry() != null);
+});
+Clazz.defineMethod(c$, "setHoverLabel",
+function(mode, text){
+if (text == null) return;
+if (mode === "bondMenu") {
+this.bondHoverLabel = text;
+} else if (mode === "atomMenu") {
+this.atomHoverLabel = text;
+} else if (mode === "xtalMenu") {
+this.atomHoverLabel = text;
+}}, "~S,~S");
+Clazz.defineMethod(c$, "setMKState",
+function(bits){
+this.state = (this.state & -4) | (this.hasUnitCell ? bits : 0);
+}, "~N");
+Clazz.defineMethod(c$, "addAtomType",
+function(type, pts, bsAtoms, packing, opsCtr, cmd){
+var sym = this.vwr.getOperativeSymmetry();
+var ipt = type.indexOf(":");
+var wyckoff = (ipt > 0 && ipt == type.length - 2 ? type.substring(ipt + 1) : null);
+if (wyckoff != null) {
+type = type.substring(0, ipt);
+if (sym != null) {
+var o = sym.getWyckoffPosition(this.vwr, null, wyckoff);
+if (!(Clazz.instanceOf(o,"JU.P3"))) return 0;
+pts = Clazz.newArray(-1, [o]);
+}}return this.addAtoms(type, pts, bsAtoms, packing, opsCtr, cmd);
+}, "~S,~A,JU.BS,~S,~A,~S");
+Clazz.defineMethod(c$, "addAtoms",
+function(type, pts, bsAtoms, packing, opsCtr, cmd){
+try {
+this.vwr.pushHoldRepaintWhy("modelkit");
+var sym = this.vwr.getOperativeSymmetry();
+if (type != null) {
+var ipt = type.indexOf(":");
+var wyckoff = (ipt > 0 && ipt == type.length - 2 ? type.substring(ipt + 1) : null);
+if (wyckoff != null) {
+type = type.substring(0, ipt);
+if (sym != null) {
+var o = sym.getWyckoffPosition(this.vwr, null, wyckoff);
+if (!(Clazz.instanceOf(o,"JU.P3"))) return 0;
+pts = Clazz.newArray(-1, [o]);
+}}}var isPoint = (bsAtoms == null);
+var atomIndex = (isPoint ? -1 : bsAtoms.nextSetBit(0));
+if (!isPoint && atomIndex < 0 || sym == null && type == null) return 0;
+var n = 0;
+if (sym == null) {
+if (isPoint) {
+for (var i = 0; i < pts.length; i++) this.assignAtomNoAddedSymmetry(pts[i], -1, null, type, true, cmd, -1);
+
+n = -pts.length;
+} else {
+this.assignAtomNoAddedSymmetry(pts[0], atomIndex, null, type, true, cmd, -1);
+n = -1;
+}} else {
+n = this.addAtomsWithSymmetry(sym, bsAtoms, type, atomIndex, isPoint, pts, packing, opsCtr);
+}return n;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+return 0;
+} else {
+throw e;
+}
+} finally {
+this.vwr.popHoldRepaint("modelkit");
+}
+}, "~S,~A,JU.BS,~S,~A,~S");
+Clazz.defineMethod(c$, "addAtomsWithSymmetry",
+function(sym, bsAtoms, type, atomIndex, isPoint, pts, packing, opsCtr){
+var bsM = this.vwr.getThisModelAtoms();
+var n = bsM.cardinality();
+if (n == 0) packing = "zapped;" + packing;
+var stype = "" + type;
+var points = new JU.Lst();
+var site = 0;
+var pf = null;
+if (pts != null && pts.length == 1 && pts[0] != null) {
+pf = JU.P3.newP(pts[0]);
+sym.toFractional(pf, false);
+isPoint = true;
+}for (var i = bsM.nextSetBit(0); i >= 0; i = bsM.nextSetBit(i + 1)) {
+var p = JU.P3.newP(this.vwr.ms.at[i]);
+sym.toFractional(p, false);
+if (pf != null && pf.distanceSquared(p) < 1.96E-6) {
+site = this.vwr.ms.at[i].getAtomSite();
+if (type == null || pts == null) type = this.vwr.ms.at[i].getElementSymbolIso(true);
+}points.addLast(p);
+}
+var nInitial = points.size();
+packing = "fromfractional;tocartesian;" + packing;
+if (isPoint) {
+var bsEquiv = (bsAtoms == null ? null : this.vwr.ms.getSymmetryEquivAtoms(bsAtoms, null, null));
+for (var i = 0; i < pts.length; i++) {
+this.assignAtoms(JU.P3.newP(pts[i]), atomIndex, bsEquiv, stype, true, null, false, site, sym, points, packing, null);
+}
+} else {
+var sites = new JU.BS();
+for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var a = this.vwr.ms.at[i];
+site = a.getAtomSite();
+if (sites.get(site)) continue;
+sites.set(site);
+stype = (type == null ? a.getElementSymbolIso(true) : stype);
+this.assignAtoms(JU.P3.newP(a), -1, null, stype, false, null, false, site, sym, points, packing, opsCtr);
+if (opsCtr == null) {
+for (var j = points.size(); --j >= nInitial; ) points.removeItemAt(j);
+
+} else {
+for (var j = points.size(); --j >= nInitial; ) {
+var p = points.get(j);
+sym.toFractional(p, false);
+}
+nInitial = points.size();
+}}
+}return this.vwr.getThisModelAtoms().cardinality() - n;
+}, "J.api.SymmetryInterface,JU.BS,~S,~N,~B,~A,~S,~A");
+Clazz.defineMethod(c$, "addConstraint",
+function(iatom, c){
+if (c == null) {
+if (this.atomConstraints != null && this.atomConstraints.length > iatom) {
+this.atomConstraints[iatom] = null;
+}return null;
+}if (this.atomConstraints == null) {
+this.atomConstraints = new Array(this.vwr.ms.ac + 10);
+}if (this.atomConstraints.length < iatom + 10) {
+var a = new Array(this.vwr.ms.ac + 10);
+System.arraycopy(this.atomConstraints, 0, a, 0, this.atomConstraints.length);
+this.atomConstraints = a;
+}return this.atomConstraints[iatom] = c;
+}, "~N,J.modelkit.ModelKit.Constraint");
+Clazz.defineMethod(c$, "addInfo",
+function(info, key, value){
+if (value != null) info.put(key, value);
+}, "java.util.Map,~S,~O");
+Clazz.defineMethod(c$, "addOccupiedAtomsToBitset",
+function(bsSelected){
+var bs = new JU.BS();
+for (var iatom = bsSelected.nextSetBit(0); iatom >= 0; iatom = bsSelected.nextSetBit(iatom + 1)) {
+var a = this.vwr.ms.at[iatom];
+if (this.vwr.ms.getOccupancyFloat(a.i) == 100) {
+bsSelected.set(a.i);
+} else {
+bs.clearAll();
+this.vwr.ms.getAtomsWithin(0.0001, a, bs, a.mi);
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (this.vwr.ms.getOccupancyFloat(i) == 100) {
+bs.clear(i);
+bsSelected.clear(i);
+}}
+bsSelected.or(bs);
+}}
+}, "JU.BS");
+Clazz.defineMethod(c$, "appRunScript",
+function(script){
+this.vwr.runScript(script);
+}, "~S");
+Clazz.defineMethod(c$, "assignAtomNoAddedSymmetry",
+function(pt, atomIndex, bs, type, newPoint, cmd, site){
+this.assignAtoms(pt, atomIndex, bs, type, newPoint, cmd, false, site, null, null, null, null);
+}, "JU.P3,~N,JU.BS,~S,~B,~S,~N");
+Clazz.defineMethod(c$, "assignAtoms",
+function(pt, atomIndex, bs, type, newPoint, cmd, isClick, site, sym, points, packing, opsCtr){
+if (sym == null) sym = this.vwr.getOperativeSymmetry();
+var haveAtomByIndex = (atomIndex >= 0);
+var isMultipleAtoms = (bs != null && bs.cardinality() > 1);
+var nIgnored = 0;
+var np = 0;
+if (!haveAtomByIndex) atomIndex = (bs == null ? -1 : bs.nextSetBit(0));
+var atom = (atomIndex < 0 ? null : this.vwr.ms.at[atomIndex]);
+var bd = (pt != null && atom != null ? pt.distance(atom) : -1);
+if (points != null) {
+np = nIgnored = points.size();
+sym.toFractional(pt, false);
+points.addLast(pt);
+if (newPoint && haveAtomByIndex) nIgnored++;
+sym.getEquivPointList(points, nIgnored, packing + (newPoint && atomIndex < 0 ? "newpt" : ""), opsCtr);
+}var bsEquiv = (atom == null ? null : sym != null ? this.vwr.ms.getSymmetryEquivAtoms(bs, sym, null) : bs == null || bs.cardinality() == 0 ? JU.BSUtil.newAndSetBit(atomIndex) : bs);
+var bs0 = (bsEquiv == null ? null : sym == null ? JU.BSUtil.newAndSetBit(atomIndex) : JU.BSUtil.copy(bsEquiv));
+var mi = (atom == null ? this.vwr.am.cmi : atom.mi);
+var ac = this.vwr.ms.ac;
+var state = this.getMKState();
+var isDelete = type.equals("X");
+try {
+if (isDelete) {
+if (isClick) {
+this.setProperty("rotatebondindex", Integer.$valueOf(-1));
+}this.setConstraint(null, atomIndex, J.modelkit.ModelKit.GET_DELETE);
+}if (pt == null && points == null) {
+if (atom == null) return;
+this.vwr.sm.setStatusStructureModified(atomIndex, mi, 1, cmd, 1, bsEquiv);
+for (var i = bsEquiv.nextSetBit(0); i >= 0; i = bsEquiv.nextSetBit(i + 1)) {
+this.assignAtom(i, type, this.autoBond, sym == null, isClick);
+}
+if (!JU.PT.isOneOf(type, ";Mi;Pl;X;")) this.vwr.ms.setAtomNamesAndNumbers(atomIndex, -ac, null, true);
+this.vwr.sm.setStatusStructureModified(atomIndex, mi, -1, "OK", 1, bsEquiv);
+this.vwr.refresh(3, "assignAtom");
+this.updateElementKey(null);
+return;
+}this.setMKState(0);
+var pts;
+if (points == null) {
+pts = Clazz.newArray(-1, [pt]);
+} else {
+pts = new Array(Math.max(0, points.size() - np));
+for (var i = pts.length; --i >= 0; ) {
+pts[i] = points.get(np + i);
+}
+}var vConnections = new JU.Lst();
+var isConnected = false;
+if (site == 0) {
+if (atom != null) {
+if (!isMultipleAtoms) {
+vConnections.addLast(atom);
+isConnected = true;
+} else if (sym != null) {
+var p = JU.P3.newP(atom);
+sym.toFractional(p, false);
+bs.or(bsEquiv);
+var list = sym.getEquivPoints(null, p, packing);
+for (var j = 0, n = list.size(); j < n; j++) {
+for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
+if (this.vwr.ms.at[i].distanceSquared(list.get(j)) < 0.001) {
+vConnections.addLast(this.vwr.ms.at[i]);
+bs.clear(i);
+}}
+}
+}isConnected = (vConnections.size() == pts.length);
+if (isConnected) {
+var d = 3.4028235E38;
+for (var i = pts.length; --i >= 0; ) {
+var d1 = vConnections.get(i).distance(pts[i]);
+if (d == 3.4028235E38) d1 = d;
+ else if (Math.abs(d1 - d) > 0.001) {
+isConnected = false;
+break;
+}}
+}if (!isConnected) {
+vConnections.clear();
+}this.vwr.sm.setStatusStructureModified(atomIndex, mi, 3, cmd, 1, null);
+}if (pt != null || points != null) {
+var bsM = this.vwr.getThisModelAtoms();
+for (var i = bsM.nextSetBit(0); i >= 0; i = bsM.nextSetBit(i + 1)) {
+var as = this.vwr.ms.at[i].getAtomSite();
+if (as > site) site = as;
+}
+site++;
+}}var pickingMode = this.vwr.acm.getAtomPickingMode();
+var wasHidden = this.menu.hidden;
+var isMK = this.vwr.getBoolean(603983903);
+if (!isMK && sym == null) {
+this.vwr.setBooleanProperty("modelkitmode", true);
+this.menu.hidden = true;
+this.menu.allowPopup = false;
+}var htParams = new java.util.Hashtable();
+if (site > 0) htParams.put("fixedSite", Integer.$valueOf(site));
+htParams.put("element", type);
+bs = this.vwr.addHydrogensInline(bs, vConnections, pts, htParams);
+if (bd > 0 && !isConnected && vConnections.isEmpty()) {
+this.connectAtoms(bd, 1, bs0, bs);
+}if (!isMK) {
+this.vwr.setBooleanProperty("modelkitmode", false);
+this.menu.hidden = wasHidden;
+this.menu.allowPopup = true;
+this.vwr.acm.setPickingMode(pickingMode);
+this.menu.hidePopup();
+}var atomIndexNew = bs.nextSetBit(0);
+if (points == null) {
+this.assignAtom(atomIndexNew, type, false, atomIndex >= 0 && sym == null, true);
+if (atomIndex >= 0) {
+var doAutobond = (sym == null && !"H".equals(type));
+this.assignAtom(atomIndex, ".", false, doAutobond, isClick);
+}this.vwr.ms.setAtomNamesAndNumbers(atomIndexNew, -ac, null, true);
+this.vwr.sm.setStatusStructureModified(atomIndexNew, mi, -3, "OK", 1, bs);
+return;
+}if (atomIndexNew >= 0) {
+for (var i = atomIndexNew; i >= 0; i = bs.nextSetBit(i + 1)) {
+this.assignAtom(i, type, false, false, true);
+this.vwr.ms.setSite(this.vwr.ms.at[i], -1, false);
+this.vwr.ms.setSite(this.vwr.ms.at[i], site, true);
+}
+this.vwr.ms.updateBasisFromSite(mi);
+}var firstAtom = this.vwr.ms.am[mi].firstAtomIndex;
+this.vwr.ms.setAtomNamesAndNumbers(firstAtom, -ac, null, true);
+this.vwr.sm.setStatusStructureModified(-1, mi, -3, "OK", 1, bs);
+this.updateModelElementKey(mi, true);
+} catch (ex) {
+if (Clazz.exceptionOf(ex, Exception)){
+ex.printStackTrace();
+} else {
+throw ex;
+}
+} finally {
+this.setMKState(state);
+}
+}, "JU.P3,~N,JU.BS,~S,~B,~S,~B,~N,J.api.SymmetryInterface,JU.Lst,~S,~A");
+Clazz.defineMethod(c$, "assignAtom",
+function(atomIndex, type, autoBond, addHsAndBond, isClick){
+if (isClick) {
+if (this.vwr.isModelkitPickingRotateBond()) {
+this.bondAtomIndex1 = atomIndex;
+return -1;
+}if (this.clickProcessAtom(atomIndex) || !this.clickToSetElement && this.vwr.ms.getAtom(atomIndex).getElementNumber() != 1) return -1;
+}var atom = this.vwr.ms.at[atomIndex];
+if (atom == null) return -1;
+this.vwr.ms.clearDB(atomIndex);
+if (type == null) type = "C";
+var bs = new JU.BS();
+var wasH = (atom.getElementNumber() == 1);
+var atomicNumber = ("PPlMiX".indexOf(type) > 0 ? -1 : type.equals("Xx") ? 0 : JU.PT.isUpperCase(type.charAt(0)) ? JU.Elements.elementNumberFromSymbol(type, true) : -1);
+var isDelete = false;
+if (atomicNumber >= 0) {
+var doTaint = (atomicNumber > 1 || !addHsAndBond);
+this.vwr.ms.setElement(atom, atomicNumber, doTaint);
+this.vwr.shm.setShapeSizeBs(0, 0, this.vwr.rd, JU.BSUtil.newAndSetBit(atomIndex));
+this.vwr.ms.setAtomName(atomIndex, type + atom.getAtomNumber(), doTaint);
+if (this.vwr.getBoolean(603983903)) this.vwr.ms.am[atom.mi].isModelKit = true;
+if (!this.vwr.ms.am[atom.mi].isModelKit || atomicNumber > 1) this.vwr.ms.taintAtom(atomIndex, 0);
+} else if (type.toLowerCase().equals("pl")) {
+atom.setFormalCharge(atom.getFormalCharge() + 1);
+} else if (type.toLowerCase().equals("mi")) {
+atom.setFormalCharge(atom.getFormalCharge() - 1);
+} else if (type.equals("X")) {
+isDelete = true;
+} else if (!type.equals(".") || !this.addHydrogens) {
+return -1;
+}if (!addHsAndBond && !isDelete) return atomicNumber;
+if (!wasH) this.vwr.ms.removeUnnecessaryBonds(atom, isDelete);
+var dx = 0;
+if (atom.getCovalentBondCount() == 1) {
+if (atomicNumber == 1) {
+dx = 1.0;
+} else {
+dx = 1.5;
+}}if (dx != 0) {
+var v = JU.V3.newVsub(atom, this.vwr.ms.at[atom.getBondedAtomIndex(0)]);
+var d = v.length();
+v.normalize();
+v.scale(dx - d);
+this.vwr.ms.setAtomCoordRelative(atomIndex, v.x, v.y, v.z);
+}var bsA = JU.BSUtil.newAndSetBit(atomIndex);
+if (isDelete) {
+this.vwr.deleteAtoms(bsA, false);
+}if (atomicNumber != 1 && autoBond) {
+this.vwr.ms.validateBspf(false);
+bs = this.vwr.ms.getAtomsWithinRadius(1.0, bsA, false, null, null);
+bs.andNot(bsA);
+if (bs.nextSetBit(0) >= 0) this.vwr.deleteAtoms(bs, false);
+bs = this.vwr.getModelUndeletedAtomsBitSet(atom.mi);
+bs.andNot(this.vwr.ms.getAtomBitsMDa(1612709900, null, new JU.BS()));
+this.vwr.ms.makeConnections2(0.1, 1.8, 1, 1073741904, bsA, bs, null, false, false, 0, null);
+}if (this.addHydrogens) this.vwr.addHydrogens(bsA, 1);
+return atomicNumber;
+}, "~N,~S,~B,~B,~B");
+Clazz.defineMethod(c$, "assignBond",
+function(bondIndex, bondOrder, bsAtoms){
+var bond = this.vwr.ms.bo[bondIndex];
+this.vwr.ms.clearDB(bond.atom1.i);
+if (bondOrder < 0) return false;
+try {
+var a1H = (bond.atom1.getElementNumber() == 1);
+var isH = (a1H || bond.atom2.getElementNumber() == 1);
+if (isH && bondOrder > 1) {
+this.vwr.deleteAtoms(JU.BSUtil.newAndSetBit(a1H ? bond.atom1.i : bond.atom2.i), false);
+return true;
+}if (bondOrder == 0) {
+this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(bond.index));
+} else {
+bond.setOrder(bondOrder | 131072);
+if (!isH) {
+this.vwr.ms.removeUnnecessaryBonds(bond.atom1, false);
+this.vwr.ms.removeUnnecessaryBonds(bond.atom2, false);
+}}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+JU.Logger.error("Exception in seBondOrder: " + e.toString());
+} else {
+throw e;
+}
+}
+if (bondOrder != 0 && this.addHydrogens) this.vwr.addHydrogens(bsAtoms, 1);
+return true;
+}, "~N,~N,JU.BS");
+Clazz.defineMethod(c$, "assignBondAndType",
+function(bondIndex, bondOrder, type, cmd){
+var modelIndex = -1;
+var state = this.getMKState();
+try {
+this.setMKState(0);
+var a1 = this.vwr.ms.bo[bondIndex].atom1;
+modelIndex = a1.mi;
+var ac = this.vwr.ms.ac;
+var bsAtoms = JU.BSUtil.newAndSetBit(a1.i);
+bsAtoms.set(this.vwr.ms.bo[bondIndex].atom2.i);
+this.vwr.sm.setStatusStructureModified(bondIndex, modelIndex, 6, cmd, 1, bsAtoms);
+this.assignBond(bondIndex, bondOrder, bsAtoms);
+this.vwr.ms.setAtomNamesAndNumbers(a1.i, -ac, null, true);
+this.vwr.refresh(3, "setBondOrder");
+this.vwr.sm.setStatusStructureModified(bondIndex, modelIndex, -6, "" + type, 1, bsAtoms);
+} catch (ex) {
+if (Clazz.exceptionOf(ex, Exception)){
+JU.Logger.error("assignBond failed");
+this.vwr.sm.setStatusStructureModified(bondIndex, modelIndex, -6, "ERROR " + ex, 1, null);
+} else {
+throw ex;
+}
+} finally {
+this.setMKState(state);
+}
+}, "~N,~N,~S,~S");
+Clazz.defineMethod(c$, "assignMoveAtom",
+function(iatom, pt, bsFixed, bsModelAtoms, bsMoved){
+if (Float.isNaN(pt.x) || iatom < 0) return 0;
+var bs = JU.BSUtil.newAndSetBit(iatom);
+if (bsModelAtoms == null) bsModelAtoms = this.vwr.getThisModelAtoms();
+bs.and(bsModelAtoms);
+if (bs.isEmpty()) return 0;
+var state = this.getMKState();
+this.setMKState(0);
+var n = 0;
+try {
+var sym = this.getSym(iatom);
+var bseq = new JU.BS();
+this.vwr.ms.getSymmetryEquivAtomsForAtom(iatom, null, bsModelAtoms, bseq);
+if (this.setConstraint(sym, bseq.nextSetBit(0), J.modelkit.ModelKit.GET_CREATE).type == 6) {
+return 0;
+}if (bsFixed != null && !bsFixed.isEmpty()) bseq.andNot(bsFixed);
+n = bseq.cardinality();
+if (n == 0) {
+return 0;
+}var a = this.vwr.ms.at[iatom];
+var v0 = sym.getInvariantSymops(a, null);
+var v1 = sym.getInvariantSymops(pt, v0);
+if ((v1 == null) != (v0 == null) || !java.util.Arrays.equals(v0, v1)) return 0;
+var points = new Array(n);
+var ia0 = bseq.nextSetBit(0);
+if (!this.fillPointsForMove(sym, bseq, ia0, a, pt, points)) {
+return 0;
+}bsMoved.or(bseq);
+var mi = this.vwr.ms.at[ia0].mi;
+this.vwr.sm.setStatusStructureModified(ia0, mi, 3, "dragatom", n, bseq);
+for (var k = 0, ia = bseq.nextSetBit(0); ia >= 0; ia = bseq.nextSetBit(ia + 1)) {
+var p = points[k++];
+this.vwr.ms.setAtomCoord(ia, p.x, p.y, p.z);
+}
+this.vwr.sm.setStatusStructureModified(ia0, mi, -3, "dragatom", n, bseq);
+return n;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+System.err.println("Modelkit err" + e);
+return 0;
+} else {
+throw e;
+}
+} finally {
+this.setMKState(state);
+if (n > 0) {
+this.updateDrawAtomSymmetry("atomsMoved", bsMoved);
+}}
+}, "~N,JU.P3,JU.BS,JU.BS,JU.BS");
+Clazz.defineMethod(c$, "assignMoveAtoms",
+function(sym, bsSelected, bsFixed, bsModelAtoms, iatom, p, pts, allowProjection, isMolecule){
+if (sym == null) sym = this.getSym(iatom);
+var npts = bsSelected.cardinality();
+if (npts == 0) return 0;
+var n = 0;
+var i0 = bsSelected.nextSetBit(0);
+if (bsFixed == null) bsFixed = this.vwr.getMotionFixedAtoms(sym, null);
+if (bsModelAtoms == null) bsModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.ms.at[i0].mi);
+if (pts != null) {
+if (npts != pts.length) return 0;
+var bs = new JU.BS();
+for (var ip = 0, i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1)) {
+bs.clearAll();
+bs.set(i);
+n += this.assignMoveAtoms(sym, bs, bsFixed, bsModelAtoms, i, pts[ip++], null, true, isMolecule);
+}
+return n;
+}var nAtoms = bsSelected.cardinality();
+if (bsSelected.intersects(bsFixed)) {
+p.x = NaN;
+return 0;
+}this.addOccupiedAtomsToBitset(bsSelected);
+nAtoms = bsSelected.cardinality();
+if (nAtoms == 1 && !isMolecule) {
+var bsMoved = this.moveConstrained(iatom, bsFixed, bsModelAtoms, p, true, allowProjection, null);
+return (bsMoved == null ? 0 : bsMoved.cardinality());
+}var p1 = JU.P3.newP(p);
+p.x = NaN;
+if (this.moveConstrained(iatom, bsFixed, bsModelAtoms, p1, false, true, null) == null) {
+return 0;
+}var vrel = JU.V3.newV(p1);
+vrel.sub(this.vwr.ms.at[iatom]);
+var apos0 = this.vwr.ms.saveAtomPositions();
+var bsAll = JU.BSUtil.copy(bsSelected);
+if (isMolecule) {
+var bsTest = JU.BSUtil.copy(bsModelAtoms);
+bsTest.andNot(bsSelected);
+var bsSites = new JU.BS();
+for (var i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1)) {
+bsSites.set(this.vwr.ms.at[i].getAtomSite());
+}
+for (var i = bsTest.nextSetBit(0); i >= 0; i = bsTest.nextSetBit(i + 1)) {
+if (bsSites.get(this.vwr.ms.at[i].getAtomSite())) {
+var bs = this.vwr.ms.getMoleculeBitSetForAtom(i);
+n = bs.cardinality();
+if (n > nAtoms) {
+nAtoms = n;
+bsTest.andNot(bs);
+bsAll = bs;
+}}}
+if (!bsAll.equals(bsSelected)) this.vwr.select(bsAll, false, 0, true);
+}var apos = new Array(bsAll.cardinality());
+var maxSite = 0;
+for (var i = bsAll.nextSetBit(0); i >= 0; i = bsAll.nextSetBit(i + 1)) {
+var s = this.vwr.ms.at[i].getAtomSite();
+if (s > maxSite) maxSite = s;
+}
+var sites = Clazz.newIntArray (maxSite, 0);
+pts = new Array(maxSite);
+var bsMoved = new JU.BS();
+for (var ip = 0, i = bsAll.nextSetBit(0); i >= 0; i = bsAll.nextSetBit(i + 1), ip++) {
+p1.setT(this.vwr.ms.at[i]);
+p1.add(vrel);
+apos[ip] = JU.P3.newP(p1);
+var s = this.vwr.ms.at[i].getAtomSite() - 1;
+if (sites[s] == 0) {
+if (this.moveConstrained(i, bsFixed, bsModelAtoms, p1, false, true, bsMoved) == null) {
+return 0;
+}p1.sub(this.vwr.ms.at[i]);
+p1.sub(vrel);
+pts[s] = JU.P3.newP(p1);
+sites[s] = i + 1;
+}}
+bsMoved.clearAll();
+for (var i = sites.length; --i >= 0; ) {
+var ia = sites[i] - 1;
+if (ia >= 0) {
+p1.setT(this.vwr.ms.at[ia]);
+p1.add(vrel);
+if (this.moveConstrained(ia, bsFixed, bsModelAtoms, p1, true, true, bsMoved) == null) {
+bsMoved = null;
+break;
+}}}
+n = (bsMoved == null ? 0 : bsMoved.cardinality());
+if (n == 0) {
+this.vwr.ms.restoreAtomPositions(apos0);
+return 0;
+}return (this.checkAtomPositions(apos0, apos, bsAll) ? n : 0);
+}, "J.api.SymmetryInterface,JU.BS,JU.BS,JU.BS,~N,JU.P3,~A,~B,~B");
+Clazz.defineMethod(c$, "assignSpaceGroup",
+function(sym00, ita00, bs, paramsOrUC, tokens, index, trm, prevNode, sb){
+if (index >= tokens.length) return "invalid CLEG expression!";
+var haveUCParams = (paramsOrUC != null);
+if (tokens.length > 1 && haveUCParams) {
+return "invalid syntax - can't mix transformations and UNITCELL option!";
+}var token = tokens[index].trim();
+var isSubgroupCalc = token.length == 0 || token.equals("sub") || token.equals("super");
+var calcNext = (isSubgroupCalc ? token : null);
+if (isSubgroupCalc) {
+token = tokens[++index].trim();
+}var isFinal = (index == tokens.length - 1);
+var pt = token.lastIndexOf(":");
+var haveUnitCell = (sym00 != null);
+var isUnknown = false;
+var haveTransform = (token.length == 0 || token.indexOf(',') > 0 || "!r!h".indexOf(token) >= 0);
+var haveJmolSetting = (!haveTransform && pt > 0 && pt < token.length - 1);
+var isTransformOnly = (haveTransform && pt < 0);
+var transform = (haveTransform ? token.substring(pt + 1) : null);
+var trTemp = new JU.M4();
+var restarted = false;
+var sym = this.vwr.getSymTemp();
+if (prevNode == null) {
+if (!J.modelkit.ModelKit.ClegNode.checkSyntax(tokens, sym)) return "invalid CLEG expression!";
+if (!haveUnitCell && !haveUCParams && (haveTransform || (pt = token.indexOf('.')) > 0)) {
+var ita = token.substring(0, pt);
+var err = this.assignSpaceGroup(null, null, null, null, Clazz.newArray(-1, [ita]), 0, null, null, sb);
+if (err.endsWith("!")) return err;
+sym00 = this.vwr.getOperativeSymmetry();
+if (sym00 == null) return "modelkit spacegroup initialization error!";
+haveUnitCell = true;
+restarted = true;
+}var ita0 = (haveUnitCell ? sym00.getIntTableNumber() : null);
+var trm0 = null;
+if (haveUnitCell) {
+if (ita0 == null || ita0.equals("0")) ita0 = sym00.getClegId();
+ else trm0 = sym00.getSpaceGroupInfoObj("itaTransform", null, false, false);
+}trm = new JU.M4();
+trm.setIdentity();
+prevNode = new J.modelkit.ModelKit.ClegNode(-1, ita0, trm0);
+if (!prevNode.update(this.vwr, null, trm, trTemp, sym)) return prevNode.errString;
+}if (isSubgroupCalc) {
+prevNode.calcNext = calcNext;
+}if (transform != null) {
+switch (transform) {
+case "r":
+case "!h":
+transform = "2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c";
+break;
+case "h":
+case "!r":
+transform = "!2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c";
+break;
+default:
+if (haveJmolSetting) {
+pt = 0;
+haveTransform = false;
+transform = null;
+}}
+if (pt > 0) token = token.substring(0, pt);
+}if (isTransformOnly) {
+if (isFinal) {
+isUnknown = true;
+return "CLEG pathway is incomplete!";
+}if (transform == null || transform.length == 0) transform = "a,b,c";
+sym.convertTransform(transform, trTemp);
+if (trm == null) trm = trTemp;
+ else trm.mul(trTemp);
+if (token.length != 0) {
+prevNode.addTransform(trTemp);
+System.out.println("ModelKit.assignSpaceGroup index=" + index + " trm=" + trm);
+}return this.assignSpaceGroup(sym00, ita00, bs, null, tokens, ++index, trm, prevNode, sb);
+}var node = new J.modelkit.ModelKit.ClegNode(index, token, transform);
+if (!node.update(this.vwr, prevNode, trm, trTemp, sym)) return node.errString;
+node.updateTokens(tokens, index);
+if (!isFinal) return this.assignSpaceGroup(sym00, ita00, bs, null, tokens, ++index, trm, node, sb);
+var params = null;
+var oabc = null;
+var origin = null;
+params = (!haveUCParams || !JU.AU.isAD(paramsOrUC) ? null : paramsOrUC);
+if (!haveUnitCell) {
+sym.setUnitCellFromParams(params == null ? Clazz.newFloatArray(-1, [10, 10, 10, 90, 90, 90]) : params, false, NaN);
+paramsOrUC = null;
+haveUCParams = false;
+}if (haveUCParams) {
+if (JU.AU.isAD(paramsOrUC)) {
+params = paramsOrUC;
+} else {
+oabc = paramsOrUC;
+origin = oabc[0];
+}} else if (haveUnitCell) {
+sym = sym00;
+if (trm == null) {
+trm = new JU.M4();
+trm.setIdentity();
+}oabc = sym.getV0abc( Clazz.newArray(-1, [trm]), null);
+origin = oabc[0];
+}if (oabc != null) {
+params = sym.getUnitCell(oabc, false, "assign").getUnitCellParams();
+if (origin == null) origin = oabc[0];
+}var isP1 = (token.equalsIgnoreCase("P1") || token.equals("ITA/1.1"));
+this.clearAtomConstraints();
+try {
+if (bs != null && bs.isEmpty()) return "no atoms specified!";
+var bsAtoms = this.vwr.getThisModelAtoms();
+var bsCell = (isP1 ? bsAtoms : JS.SV.getBitSet(this.vwr.evaluateExpressionAsVariable("{within(unitcell)}"), true));
+if (bs == null) {
+bs = bsAtoms;
+}if (bs != null) {
+bsAtoms.and(bs);
+if (!isP1) bsAtoms.and(bsCell);
+}var noAtoms = bsAtoms.isEmpty();
+var mi = (noAtoms && this.vwr.am.cmi < 0 ? 0 : noAtoms ? this.vwr.am.cmi : this.vwr.ms.at[bsAtoms.nextSetBit(0)].getModelIndex());
+this.vwr.ms.getModelAuxiliaryInfo(mi).remove("spaceGroupInfo");
+if (haveUnitCell) {
+sym.replaceTransformMatrix(trm);
+}if (params == null) params = sym.getUnitCellMultiplied().getUnitCellParams();
+var sgInfo = (noAtoms && isUnknown ? null : this.vwr.findSpaceGroup(sym, isUnknown ? bsAtoms : null, isUnknown ? null : node.name, params, origin, oabc, 2 | (haveUnitCell ? 0 : 4)));
+if (sgInfo == null) {
+return "Space group " + node.name + " is unknown or not compatible!";
+}if (oabc == null || !haveUnitCell) oabc = sgInfo.get("unitcell");
+token = sgInfo.get("name");
+var jmolId = sgInfo.get("jmolId");
+var basis = sgInfo.get("basis");
+var sg = sgInfo.remove("sg");
+sym.getUnitCell(oabc, false, null);
+sym.setSpaceGroupTo(sg == null ? jmolId : sg);
+sym.setSpaceGroupName(token);
+if (basis == null) {
+basis = sym.removeDuplicates(this.vwr.ms, bsAtoms, true);
+}this.vwr.ms.setSpaceGroup(mi, sym, basis);
+if (!haveUnitCell || restarted) {
+this.appRunScript("unitcell on; center unitcell;axes unitcell; axes 0.1; axes on;set perspectivedepth false;moveto 0 axis c1;draw delete;show spacegroup");
+}transform = sym.staticGetTransformABC(trm, false);
+var msg = transform + "\n" + JU.PT.join(tokens, '>', 0) + (basis.isEmpty() ? "" : "\n basis=" + basis);
+System.out.println("ModelKit trm=" + msg);
+sb.append(msg).append("\n");
+return transform;
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+if (!JV.Viewer.isJS) e.printStackTrace();
+return e.getMessage() + "!";
+} else {
+throw e;
+}
+}
+}, "J.api.SymmetryInterface,~S,JU.BS,~O,~A,~N,JU.M4,J.modelkit.ModelKit.ClegNode,JU.SB");
+c$.addSGTransform = Clazz.defineMethod(c$, "addSGTransform",
+function(sym, tr, trm0, temp){
+if (trm0 == null) {
+trm0 = new JU.M4();
+trm0.setIdentity();
+}if (tr != null) {
+sym.convertTransform(tr, temp);
+trm0.mul(temp);
+}return trm0;
+}, "J.api.SymmetryInterface,~S,JU.M4,JU.M4");
+Clazz.defineMethod(c$, "checkAtomPositions",
+function(apos0, apos, bs){
+var ok = true;
+for (var ip = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1), ip++) {
+if (this.vwr.ms.at[i].distanceSquared(apos[ip]) > 0.00000001) {
+ok = false;
+break;
+}}
+if (ok) return true;
+this.vwr.ms.restoreAtomPositions(apos0);
+return false;
+}, "~A,~A,JU.BS");
+Clazz.defineMethod(c$, "clearElementKey",
+function(modelIndex){
+if (!this.haveElementKeys) return;
+var key = J.modelkit.ModelKit.getElementKey(modelIndex) + "*";
+var val = Clazz.newArray(-1, [ Clazz.newArray(-1, ["thisID", key]), Clazz.newArray(-1, ["delete", null])]);
+this.vwr.shm.setShapeProperties(22, val);
+this.vwr.shm.setShapeProperties(31, val);
+switch (modelIndex) {
+case -2:
+break;
+case -1:
+this.bsElementKeyModels.clearAll();
+break;
+default:
+this.bsElementKeyModels.clear(modelIndex);
+break;
+}
+this.haveElementKeys = !this.bsElementKeyModels.isEmpty();
+}, "~N");
+Clazz.defineMethod(c$, "clickProcessAtom",
+function(atomIndex){
+switch (this.getMKState()) {
+case 0:
+return this.vwr.isModelkitPickingRotateBond();
+case 1:
+this.centerAtomIndex = atomIndex;
+if (this.getSymViewState() == 0) this.setSymViewState(8);
+this.showXtalSymmetry();
+return true;
+case 2:
+if (atomIndex == this.centerAtomIndex) return true;
+J.modelkit.ModelKit.notImplemented("edit click");
+return false;
+}
+J.modelkit.ModelKit.notImplemented("atom click unknown XTAL state");
+return false;
+}, "~N");
+Clazz.defineMethod(c$, "clickProcessMode",
+function(action){
+this.processMKPropertyItem(action, false);
+}, "~S");
+Clazz.defineMethod(c$, "clickProcessSel",
+function(action){
+if (action === "mksel_atom") {
+this.centerPoint = null;
+this.centerAtomIndex = -1;
+this.secondAtomIndex = -1;
+} else if (action === "mksel_position") {
+var pos = this.promptUser("Enter three fractional coordinates", this.lastCenter);
+if (pos == null) return;
+this.lastCenter = pos;
+var p = J.modelkit.ModelKit.pointFromTriad(pos);
+if (p == null) {
+this.clickProcessSel(action);
+return;
+}this.centerAtomIndex = -2147483647;
+this.centerPoint = p;
+this.showXtalSymmetry();
+}}, "~S");
+Clazz.defineMethod(c$, "clickProcessSelOp",
+function(action){
+this.secondAtomIndex = -1;
+if (action === "mkselop_addoffset") {
+var pos = this.promptUser("Enter i j k for an offset for viewing the operator - leave blank to clear", this.lastOffset);
+if (pos == null) return null;
+this.lastOffset = pos;
+if (pos.length == 0 || pos === "none") {
+this.setProperty("offset", "none");
+return null;
+}var p = J.modelkit.ModelKit.pointFromTriad(pos);
+if (p == null) {
+return action;
+}this.setProperty("offset", p);
+} else if (action === "mkselop_atom2") {
+J.modelkit.ModelKit.notImplemented(action);
+}return null;
+}, "~S");
+Clazz.defineMethod(c$, "clickProcessSym",
+function(action){
+if (action === "mksymmetry_none") {
+this.setSymEdit(0);
+} else {
+this.processMKPropertyItem(action, false);
+}}, "~S");
+Clazz.defineMethod(c$, "clickProcessUC",
+function(action){
+this.processMKPropertyItem(action, false);
+this.showXtalSymmetry();
+}, "~S");
+Clazz.defineMethod(c$, "connectAtoms",
+function(bd, bondOrder, bs1, bs2){
+this.vwr.makeConnections((bd - 0.01), (bd + 0.01), bondOrder, 1073742026, bs1, bs2, new JU.BS(), false, false, 0);
+}, "~N,~N,JU.BS,JU.BS");
+Clazz.defineMethod(c$, "fillPointsForMove",
+function(sg, bseq, i0, a, pt, points){
+var d = a.distance(pt);
+var fa = JU.P3.newP(a);
+var fb = JU.P3.newP(pt);
+sg.toFractional(fa, false);
+sg.toFractional(fb, false);
+for (var k = 0, i = i0; i >= 0; i = bseq.nextSetBit(i + 1)) {
+var p = JU.P3.newP(this.vwr.ms.at[i]);
+var p0 = JU.P3.newP(p);
+sg.toFractional(p, false);
+var m = sg.getTransform(fa, p, false);
+if (m == null) {
+return false;
+}var p2 = JU.P3.newP(fb);
+m.rotTrans(p2);
+sg.toCartesian(p2, false);
+if (Math.abs(d - p0.distance(p2)) > 0.001) return false;
+points[k++] = p2;
+}
+fa.setT(points[0]);
+sg.toFractional(fa, false);
+for (var k = points.length; --k >= 0; ) {
+fb.setT(points[k]);
+sg.toFractional(fb, false);
+var m = sg.getTransform(fa, fb, false);
+if (m == null) {
+return false;
+}for (var i = points.length; --i > k; ) {
+if (points[i].distance(points[k]) < 0.1) return false;
+}
+}
+return true;
+}, "J.api.SymmetryInterface,JU.BS,~N,JU.P3,JU.P3,~A");
+Clazz.defineMethod(c$, "getBondLabel",
+function(atoms){
+return atoms[Math.min(this.bondAtomIndex1, this.bondAtomIndex2)].getAtomName() + "-" + atoms[Math.max(this.bondAtomIndex1, this.bondAtomIndex2)].getAtomName();
+}, "~A");
+Clazz.defineMethod(c$, "getBondOrder",
+function(type, bond){
+if (type == '-') type = this.pickBondAssignType;
+var bondOrder = type.charCodeAt(0) - 48;
+switch ((type).charCodeAt(0)) {
+case 48:
+case 49:
+case 50:
+case 51:
+case 52:
+case 53:
+break;
+case 112:
+case 109:
+bondOrder = (JU.Edge.getBondOrderNumberFromOrder(bond.getCovalentOrder()).charAt(0)).charCodeAt(0) - 48 + (type == 'p' ? 1 : -1);
+if (bondOrder > 3) bondOrder = 1;
+ else if (bondOrder < 0) bondOrder = 3;
+break;
+default:
+return -1;
+}
+return bondOrder;
+}, "~S,JM.Bond");
+Clazz.defineMethod(c$, "getHoverLabel",
+function(atomIndex){
+var state = this.getMKState();
+var msg = null;
+switch (state) {
+case 1:
+if (this.symop == null) this.symop = Integer.$valueOf(1);
+msg = "view symop " + this.symop + " for " + this.vwr.getAtomInfo(atomIndex);
+break;
+case 2:
+msg = "start editing for " + this.vwr.getAtomInfo(atomIndex);
+break;
+case 0:
+var atoms = this.vwr.ms.at;
+if (this.isRotateBond) {
+this.setBranchAtom(atomIndex, false);
+msg = (this.branchAtomIndex >= 0 ? "rotate branch " + atoms[atomIndex].getAtomName() : "rotate bond for " + this.getBondLabel(atoms));
+}if (this.bondIndex < 0) {
+if (this.atomHoverLabel.length <= 2) {
+msg = this.atomHoverLabel = "Click to change to " + this.atomHoverLabel + " or drag to add " + this.atomHoverLabel;
+} else {
+msg = atoms[atomIndex].getAtomName() + ": " + this.atomHoverLabel;
+this.vwr.highlight(JU.BSUtil.newAndSetBit(atomIndex));
+}} else {
+if (msg == null) {
+switch (this.isRotateBond ? this.bsHighlight.cardinality() : atomIndex >= 0 ? 1 : -1) {
+case 0:
+this.vwr.highlight(JU.BSUtil.newAndSetBit(atomIndex));
+case 1:
+case 2:
+var a = this.vwr.ms.at[atomIndex];
+if (!this.isRotateBond) {
+this.menu.setActiveMenu("atomMenu");
+if (this.vwr.acm.getAtomPickingMode() == 1) return null;
+}if (this.atomHoverLabel.indexOf("charge") >= 0) {
+var ch = a.getFormalCharge();
+ch += (this.atomHoverLabel.indexOf("increase") >= 0 ? 1 : -1);
+msg = this.atomHoverLabel + " to " + (ch > 0 ? "+" : "") + ch;
+} else {
+msg = this.atomHoverLabel;
+}msg = atoms[atomIndex].getAtomName() + ": " + msg;
+break;
+case -1:
+msg = (this.bondHoverLabel.length == 0 ? "" : this.bondHoverLabel + " for ") + this.getBondLabel(atoms);
+break;
+}
+}}break;
+}
+return msg;
+}, "~N");
+Clazz.defineMethod(c$, "getinfo",
+function(){
+var info = new java.util.Hashtable();
+this.addInfo(info, "addHydrogens", Boolean.$valueOf(this.addHydrogens));
+this.addInfo(info, "autobond", Boolean.$valueOf(this.autoBond));
+this.addInfo(info, "clickToSetElement", Boolean.$valueOf(this.clickToSetElement));
+this.addInfo(info, "hidden", Boolean.$valueOf(this.menu.hidden));
+this.addInfo(info, "showSymopInfo", Boolean.$valueOf(this.showSymopInfo));
+this.addInfo(info, "centerPoint", this.centerPoint);
+this.addInfo(info, "centerAtomIndex", Integer.$valueOf(this.centerAtomIndex));
+this.addInfo(info, "secondAtomIndex", Integer.$valueOf(this.secondAtomIndex));
+this.addInfo(info, "symop", this.symop);
+this.addInfo(info, "offset", this.viewOffset);
+this.addInfo(info, "drawData", this.drawData);
+this.addInfo(info, "drawScript", this.drawScript);
+this.addInfo(info, "isMolecular", Boolean.$valueOf(this.getMKState() == 0));
+return info;
+});
+c$.getNearestBondedAtom = Clazz.defineMethod(c$, "getNearestBondedAtom",
+function(a1, butNotThis){
+var b = a1.bonds;
+var a2;
+var ret = null;
+var zmin = 2147483647;
+for (var i = a1.getBondCount(); --i >= 0; ) {
+if (b[i] != null && b[i].isCovalent() && (a2 = b[i].getOtherAtom(a1)) !== butNotThis && a2.sZ < zmin) {
+zmin = a2.sZ;
+ret = a2;
+}}
+return ret;
+}, "JM.Atom,JM.Atom");
+Clazz.defineMethod(c$, "handleAtomDragging",
+function(countPlusIndices){
+switch (this.getMKState()) {
+case 0:
+return false;
+case 2:
+if (countPlusIndices[0] > 2) return true;
+J.modelkit.ModelKit.notImplemented("drag atom for XTAL edit");
+break;
+case 1:
+if (this.getSymViewState() == 0) this.setSymViewState(8);
+switch (countPlusIndices[0]) {
+case 1:
+this.centerAtomIndex = countPlusIndices[1];
+this.secondAtomIndex = -1;
+break;
+case 2:
+this.centerAtomIndex = countPlusIndices[1];
+this.secondAtomIndex = countPlusIndices[2];
+break;
+}
+this.showXtalSymmetry();
+return true;
+}
+return true;
+}, "~A");
+Clazz.defineMethod(c$, "handleAtomOrBondPicked",
+function(x, y, mp, dragAtomIndex, atomType, inRange){
+var isCharge = this.$isPickAtomAssignCharge;
+if (mp != null && mp.count == 2) {
+this.vwr.undoMoveActionClear(-1, 4146, true);
+var a = mp.getAtom(1);
+var b = mp.getAtom(2);
+var bond = a.getBond(b);
+if (bond == null) {
+this.cmdAssignConnect(a.i, b.i, '1', "click");
+} else {
+this.cmdAssignBond(bond.index, 'p', "click");
+}} else {
+if (atomType.equals("Xx")) {
+atomType = this.lastElementType;
+}if (inRange) {
+this.vwr.undoMoveActionClear(dragAtomIndex, 4, true);
+} else {
+this.vwr.undoMoveActionClear(-1, 4146, true);
+}var a = this.vwr.ms.at[dragAtomIndex];
+var wasH = (a != null && a.getElementNumber() == 1);
+this.clickAssignAtom(dragAtomIndex, atomType, null);
+if (isCharge) {
+this.appRunScript("{atomindex=" + dragAtomIndex + "}.label='%C'");
+} else {
+this.vwr.undoMoveActionClear(-1, 4146, true);
+if (a == null || inRange) return false;
+if (wasH) {
+this.clickAssignAtom(dragAtomIndex, "X", null);
+} else {
+var ptNew = JU.P3.new3(x, y, a.sZ);
+this.vwr.tm.unTransformPoint(ptNew, ptNew);
+this.clickAssignAtom(dragAtomIndex, atomType, ptNew);
+}}}return true;
+}, "~N,~N,JM.MeasurementPending,~N,~S,~B");
+Clazz.defineMethod(c$, "minimizeXtal",
+function(eval, bsBasis, steps, crit, rangeFixed, flags){
+this.minBasisModel = this.vwr.am.cmi;
+this.minSelectionSaved = this.vwr.bsA();
+this.vwr.am.setFrame(this.minBasisModel);
+this.minBasis = bsBasis;
+this.minBasisFixed = this.vwr.getMotionFixedAtoms(null, null);
+this.minBasisModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.minBasisModel);
+var cif = this.vwr.getModelExtract(bsBasis, false, false, "cif");
+var tempModelIndex = this.vwr.ms.mc;
+var htParams = new java.util.Hashtable();
+htParams.put("eval", eval);
+htParams.put("lattice", JU.P3.new3(444, 666, 1));
+htParams.put("fileData", cif);
+htParams.put("loadScript", new JU.SB());
+if (this.vwr.loadModelFromFile(null, "", null, null, true, htParams, null, null, 0, " ") != null) return;
+var bsBasis2 = JU.BSUtil.copy(this.vwr.ms.am[tempModelIndex].bsAsymmetricUnit);
+this.minTempModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(tempModelIndex);
+this.vwr.am.setFrame(tempModelIndex);
+this.minTempFixed = JU.BSUtil.copy(this.minTempModelAtoms);
+this.minTempFixed.andNot(bsBasis2);
+this.vwr.getMotionFixedAtoms(null, this.minTempFixed);
+this.vwr.minimize(eval, steps, crit, JU.BSUtil.copy(bsBasis2), this.minTempFixed, this.minTempModelAtoms, rangeFixed, flags & -257);
+}, "J.api.JmolScriptEvaluator,JU.BS,~N,~N,~N,~N");
+Clazz.defineMethod(c$, "minimizeXtalEnd",
+function(bsBasis2, isEnd){
+if (this.minBasis == null) return;
+if (bsBasis2 != null) {
+var pts = new Array(bsBasis2.cardinality());
+for (var p = 0, j = this.minBasis.nextSetBit(0), i = bsBasis2.nextSetBit(0); i >= 0; i = bsBasis2.nextSetBit(i + 1), j = this.minBasis.nextSetBit(j + 1)) {
+pts[p++] = JU.P3.newP(this.vwr.ms.at[i].getXYZ());
+}
+var bs = JU.BSUtil.copy(this.minBasis);
+bs.andNot(this.minBasisFixed);
+this.assignMoveAtoms(null, bs, this.minBasisFixed, this.minBasisModelAtoms, this.minBasis.nextSetBit(0), null, pts, true, false);
+}if (isEnd) {
+this.minSelectionSaved = null;
+this.minBasis = null;
+this.minBasisFixed = null;
+this.minTempFixed = null;
+this.minTempModelAtoms = null;
+this.minBasisModelAtoms = null;
+this.minBasisAtoms = null;
+this.modelSyms = null;
+this.vwr.deleteModels(this.vwr.ms.mc - 1, null);
+this.vwr.setSelectionSet(this.minSelectionSaved);
+this.vwr.setCurrentModelIndex(this.minBasisModel);
+}}, "JU.BS,~B");
+Clazz.defineMethod(c$, "moveConstrained",
+function(iatom, bsFixed, bsModelAtoms, ptNew, doAssign, allowProjection, bsMoved){
+var sym = this.getSym(iatom);
+if (sym == null) {
+return null;
+}if (bsMoved == null) bsMoved = JU.BSUtil.newAndSetBit(iatom);
+var a = this.vwr.ms.at[iatom];
+var c = this.constraint;
+var minv = null;
+if (c == null) {
+c = this.setConstraint(sym, iatom, J.modelkit.ModelKit.GET_CREATE);
+if (c.type == 6) {
+iatom = -1;
+} else {
+var b = this.getBasisAtom(iatom);
+if (a !== b) {
+var m = J.modelkit.ModelKit.getTransform(sym, a, b);
+if (m == null) {
+System.err.println("ModelKit - null matrix for " + iatom + " " + a + " to " + b);
+iatom = -1;
+} else {
+if (!doAssign) {
+minv = JU.M4.newM4(m);
+minv.invert();
+}iatom = b.i;
+var p = JU.P3.newP(ptNew);
+sym.toFractional(p, false);
+m.rotTrans(p);
+sym.toCartesian(p, false);
+ptNew.setT(p);
+}}if (iatom >= 0) c.constrain(b, ptNew, allowProjection);
+}} else {
+c.constrain(a, ptNew, allowProjection);
+}if (iatom >= 0 && !Float.isNaN(ptNew.x)) {
+if (!doAssign) {
+if (minv != null) {
+var p = JU.P3.newP(ptNew);
+sym.toFractional(p, false);
+minv.rotTrans(p);
+sym.toCartesian(p, false);
+ptNew.setP(p);
+}return bsMoved;
+}if (this.assignMoveAtom(iatom, ptNew, bsFixed, bsModelAtoms, bsMoved) == 0) bsMoved = null;
+}ptNew.x = NaN;
+return bsMoved;
+}, "~N,JU.BS,JU.BS,JU.P3,~B,~B,JU.BS");
+Clazz.defineMethod(c$, "promptUser",
+function(msg, def){
+return this.vwr.prompt(msg, def, null, false);
+}, "~S,~S");
+Clazz.defineMethod(c$, "resetBondFields",
+function(){
+this.bsRotateBranch = null;
+this.branchAtomIndex = this.bondAtomIndex1 = this.bondAtomIndex2 = -1;
+});
+Clazz.defineMethod(c$, "rotateAtoms",
+function(bsAtoms, points, endDegrees){
+var center = points[0];
+var p = new JU.P3();
+var i0 = bsAtoms.nextSetBit(0);
+var sg = this.getSym(i0);
+var bsAU = new JU.BS();
+var bsToMove = new JU.BS();
+for (var i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var bai = this.getBasisAtom(i).i;
+if (bsAU.get(bai)) {
+continue;
+}if (this.setConstraint(sg, bai, J.modelkit.ModelKit.GET_CREATE).type == 6) {
+return 0;
+}bsAU.set(bai);
+bsToMove.set(i);
+}
+var nAtoms = bsAtoms.cardinality();
+var apos0 = this.vwr.ms.saveAtomPositions();
+var m = JU.Quat.newVA(JU.V3.newVsub(points[1], points[0]), endDegrees).getMatrix();
+var vt = new JU.V3();
+var apos = new Array(nAtoms);
+for (var ip = 0, i = i0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var a = this.vwr.ms.at[i];
+p = apos[ip++] = JU.P3.newP(a);
+vt.sub2(p, center);
+m.rotate(vt);
+p.add2(center, vt);
+this.setConstraint(sg, i, J.modelkit.ModelKit.GET_CREATE).constrain(a, p, false);
+if (Float.isNaN(p.x)) return 0;
+}
+nAtoms = 0;
+var bsFixed = this.vwr.getMotionFixedAtoms(sg, null);
+var bsModelAtoms = this.vwr.getModelUndeletedAtomsBitSet(this.vwr.ms.at[i0].mi);
+var bsMoved = new JU.BS();
+for (var ip = 0, i = i0; i >= 0; i = bsToMove.nextSetBit(i + 1), ip++) {
+nAtoms += this.assignMoveAtom(i, apos[ip], bsFixed, bsModelAtoms, bsMoved);
+}
+var bs = JU.BSUtil.copy(bsAtoms);
+bs.andNot(bsToMove);
+return (this.checkAtomPositions(apos0, apos, bs) ? nAtoms : 0);
+}, "JU.BS,~A,~N");
+Clazz.defineMethod(c$, "runScriptBuffered",
+function(script){
+var sb = new JU.SB();
+try {
+(this.vwr.eval).runBufferedSafely(script, sb);
+} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+}
+return sb.toString();
+}, "~S");
+Clazz.defineMethod(c$, "setBondIndex",
+function(index, isRotate){
+if (!isRotate && this.vwr.isModelkitPickingRotateBond()) {
+this.setProperty("rotatebondindex", Integer.$valueOf(index));
+return;
+}var haveBond = (this.bondIndex >= 0);
+if (!haveBond && index < 0) return;
+if (index < 0) {
+this.resetBondFields();
+return;
+}this.bsRotateBranch = null;
+this.branchAtomIndex = -1;
+this.bondIndex = index;
+this.isRotateBond = isRotate;
+this.bondAtomIndex1 = this.vwr.ms.bo[index].getAtomIndex1();
+this.bondAtomIndex2 = this.vwr.ms.bo[index].getAtomIndex2();
+this.menu.setActiveMenu("bondMenu");
+}, "~N,~B");
+Clazz.defineMethod(c$, "setBranchAtom",
+function(atomIndex, isClick){
+var isBondedAtom = (atomIndex == this.bondAtomIndex1 || atomIndex == this.bondAtomIndex2);
+if (isBondedAtom) {
+this.branchAtomIndex = atomIndex;
+this.bsRotateBranch = null;
+} else {
+this.bsRotateBranch = null;
+this.branchAtomIndex = -1;
+}}, "~N,~B");
+Clazz.defineMethod(c$, "setDefaultState",
+function(mode){
+if (!this.hasUnitCell) mode = 0;
+if (!this.hasUnitCell || this.isXtalState() != this.hasUnitCell) {
+this.setMKState(mode);
+switch (mode) {
+case 0:
+break;
+case 1:
+if (this.getSymViewState() == 0) this.setSymViewState(8);
+break;
+case 2:
+break;
+}
+}}, "~N");
+Clazz.defineMethod(c$, "isElementKeyOn",
+function(modelIndex){
+var data = Clazz.newArray(-1, [J.modelkit.ModelKit.getElementKey(modelIndex) + "*", null]);
+this.vwr.shm.getShapePropertyData(31, "checkID", data);
+return (data[1] != null);
+}, "~N");
+Clazz.defineMethod(c$, "updateElementKeyFromStateScript",
+function(){
+for (var i = this.vwr.ms.mc; --i >= 0; ) {
+if (this.isElementKeyOn(i)) {
+this.bsElementKeyModels.set(i);
+this.haveElementKeys = true;
+}}
+});
+Clazz.defineMethod(c$, "setElementKey",
+function(modelIndex, isOn){
+if (isOn && (modelIndex >= 0 && this.bsElementKeyModels.get(modelIndex))) return;
+this.clearElementKey(modelIndex);
+if (!isOn || modelIndex < 0) return;
+ new J.modelkit.ModelKit.EKey(this.vwr, modelIndex).draw(this.vwr);
+this.bsElementKeyModels.set(modelIndex);
+this.haveElementKeys = true;
+}, "~N,~B");
+Clazz.defineMethod(c$, "setSymEdit",
+function(bits){
+this.state = (this.state & -225) | bits;
+}, "~N");
+Clazz.defineMethod(c$, "setSymViewState",
+function(bits){
+this.state = (this.state & -29) | bits;
+}, "~N");
+Clazz.defineMethod(c$, "setUnitCell",
+function(bits){
+this.state = (this.state & -1793) | bits;
+}, "~N");
+Clazz.defineMethod(c$, "showSymop",
+function(symop){
+this.secondAtomIndex = -1;
+this.symop = symop;
+this.showXtalSymmetry();
+}, "~O");
+Clazz.defineMethod(c$, "showXtalSymmetry",
+function(){
+var script = null;
+switch (this.getSymViewState()) {
+case 0:
+script = "draw * delete";
+break;
+case 8:
+default:
+var offset = null;
+if (this.secondAtomIndex >= 0) {
+script = "draw ID sym symop " + (this.centerAtomIndex < 0 ? this.centerPoint : " {atomindex=" + this.centerAtomIndex + "}") + " {atomindex=" + this.secondAtomIndex + "}";
+} else {
+offset = this.viewOffset;
+if (this.symop == null) this.symop = Integer.$valueOf(1);
+var iatom = (this.centerAtomIndex >= 0 ? this.centerAtomIndex : this.centerPoint != null ? -1 : this.iatom0);
+script = "draw ID sym symop " + (this.symop == null ? "1" : (typeof(this.symop)=='string') ? "'" + this.symop + "'" : JU.PT.toJSON(null, this.symop)) + (iatom < 0 ? this.centerPoint : " {atomindex=" + iatom + "}") + (offset == null ? "" : " offset " + offset);
+}this.drawData = this.runScriptBuffered(script);
+this.drawScript = script;
+this.drawData = (this.showSymopInfo ? this.drawData.substring(0, this.drawData.indexOf("\n") + 1) : "");
+this.appRunScript(";refresh;set echo top right;echo " + this.drawData.$replace('\t', ' '));
+break;
+}
+});
+Clazz.defineMethod(c$, "updateElementKey",
+function(bsAtoms){
+if (bsAtoms == null) {
+this.updateModelElementKey(this.vwr.am.cmi, true);
+return;
+}if (bsAtoms.cardinality() == 1) {
+this.updateModelElementKey(this.vwr.ms.at[bsAtoms.nextSetBit(0)].mi, true);
+return;
+}for (var i = this.vwr.ms.mc; --i >= 0; ) {
+if (this.vwr.ms.am[i].bsAtoms.intersects(bsAtoms)) {
+this.updateModelElementKey(i, true);
+}}
+}, "JU.BS");
+Clazz.defineMethod(c$, "updateModelElementKeys",
+function(bsModels, forceNew){
+if (bsModels == null) bsModels = JU.BSUtil.newBitSet2(0, this.vwr.ms.mc);
+for (var i = bsModels.nextSetBit(0); i >= 0; i = bsModels.nextSetBit(i + 1)) {
+this.updateModelElementKey(i, forceNew);
+}
+}, "JU.BS,~B");
+Clazz.defineMethod(c$, "updateModelElementKey",
+function(modelIndex, forceNew){
+if (this.doUpdateElementKey(modelIndex)) {
+if (forceNew) this.clearElementKey(modelIndex);
+this.setElementKey(modelIndex, true);
+}}, "~N,~B");
+Clazz.defineMethod(c$, "doUpdateElementKey",
+function(modelIndex){
+return modelIndex >= 0 && !this.vwr.ms.isJmolDataFrameForModel(modelIndex) && !this.bsElementKeyModelsOFF.get(modelIndex) && (this.$setElementKeys || this.bsElementKeyModels.get(modelIndex) || this.isElementKeyOn(modelIndex));
+}, "~N");
+Clazz.defineMethod(c$, "setElementKeys",
+function(isOn){
+this.$setElementKeys = isOn;
+if (isOn) {
+this.clearElementKeysOFF();
+}this.clearElementKey(-1);
+if (isOn) {
+this.updateModelElementKeys(null, false);
+}}, "~B");
+Clazz.defineMethod(c$, "clearElementKeysOFF",
+function(){
+this.bsElementKeyModelsOFF.clearAll();
+});
+Clazz.defineMethod(c$, "transformAtomsToUnitCell",
+function(sym, oabc, ucname){
+var bsAtoms = this.vwr.getThisModelAtoms();
+var n = bsAtoms.cardinality();
+var isReset = (sym == null || n == 0);
+if (!isReset) {
+var a = this.vwr.ms.at;
+var fxyz = this.getFractionalCoordinates(sym, bsAtoms);
+this.vwr.ms.setModelCagePts(-1, oabc, ucname);
+sym = this.vwr.getCurrentUnitCell();
+for (var j = bsAtoms.nextSetBit(0), k = 0; j >= 0; j = bsAtoms.nextSetBit(j + 1), k++) {
+a[j].setT(fxyz[k]);
+this.vwr.toCartesianUC(sym, a[j], false);
+}
+this.vwr.ms.setTaintedAtoms(bsAtoms, 2);
+}return isReset;
+}, "J.api.SymmetryInterface,~A,~S");
+Clazz.defineMethod(c$, "getFractionalCoordinates",
+function(sym, bsAtoms){
+var n = bsAtoms.cardinality();
+var a = this.vwr.ms.at;
+var fxyz = new Array(n);
+for (var j = bsAtoms.nextSetBit(0), k = 0; j >= 0; j = bsAtoms.nextSetBit(j + 1), k++) {
+fxyz[k] = JU.P3.newP(a[j]);
+this.vwr.toFractionalUC(sym, fxyz[k], false);
+}
+return fxyz;
+}, "J.api.SymmetryInterface,JU.BS");
+Clazz.defineMethod(c$, "updateDrawAtomSymmetry",
+function(mode, atoms){
+if (this.drawAtomSymmetry == null) return;
+var cmd = "";
+for (var i = this.drawAtomSymmetry.size(); --i >= 0; ) {
+var a = this.drawAtomSymmetry.get(i);
+if (mode === "deleteModelAtoms" ? atoms.get(a.bsAtoms.nextSetBit(0)) : atoms.intersects(a.bsAtoms)) {
+switch (mode) {
+case "deleteModelAtoms":
+case "atomsDeleted":
+System.out.println("remove deleteatoms " + atoms + " " + a.bsAtoms + a.id);
+this.drawAtomSymmetry.removeItemAt(i);
+break;
+case "atomsMoved":
+try {
+if (!this.checkDrawID(a.id)) {
+this.drawAtomSymmetry.removeItemAt(i);
+} else {
+cmd += a.cmd + "#quiet" + "\n";
+}} catch (e) {
+if (Clazz.exceptionOf(e, Exception)){
+e.printStackTrace();
+} else {
+throw e;
+}
+}
+break;
+}
+if (this.drawAtomSymmetry.size() == 0) this.drawAtomSymmetry = null;
+}if (cmd.length > 0) this.vwr.evalStringGUI(cmd);
+}
+}, "~S,JU.BS");
+Clazz.defineMethod(c$, "checkDrawID",
+function(id){
+var o = Clazz.newArray(-1, [id + "*", null]);
+var exists = this.vwr.shm.getShapePropertyData(22, "checkID", o);
+return (exists && o[1] != null);
+}, "~S");
+Clazz.defineMethod(c$, "drawSymop",
+function(a1, a2){
+var s = "({" + a1 + "}) ({" + a2 + "}) ";
+var cmd = "draw ID 'sym' symop " + s;
+this.vwr.evalStringGUI(cmd);
+}, "~N,~N");
+Clazz.defineMethod(c$, "addAtomSet",
+function(data){
+var tokens = JU.PT.split(data, "|");
+var id = tokens[0];
+this.clearAtomSets(id);
+var a1 = JU.PT.parseInt(tokens[1]);
+var a2 = JU.PT.parseInt(tokens[2]);
+var cmd = tokens[3];
+var bs = JU.BSUtil.newAndSetBit(a1);
+bs.set(a2);
+if (this.drawAtomSymmetry == null) {
+this.drawAtomSymmetry = new JU.Lst();
+}this.drawAtomSymmetry.addLast(Clazz.innerTypeInstance(J.modelkit.ModelKit.DrawAtomSet, this, null, bs, id, cmd));
+}, "~S");
+Clazz.defineMethod(c$, "clearAtomSets",
+function(id){
+if (this.drawAtomSymmetry == null) return;
+for (var i = this.drawAtomSymmetry.size(); --i >= 0; ) {
+var a = this.drawAtomSymmetry.get(i);
+if (a.id.equals(id)) {
+this.drawAtomSymmetry.remove(i);
+return;
+}}
+}, "~S");
+Clazz.defineMethod(c$, "drawUnitCell",
+function(id, ucLattice, swidth){
+var sym = this.vwr.getOperativeSymmetry();
+if (sym == null) return;
+var uc = this.vwr.getSymTemp().getUnitCell(sym.getUnitCellVectors(), false, "draw");
+uc.setOffsetPt(ucLattice);
+var cellRange = Clazz.newArray(-1, [ new JU.P3(), new JU.P3()]);
+var s = "";
+if (id == null) id = "uclat";
+var val = Clazz.newArray(-1, [ Clazz.newArray(-1, ["thisID", id + "*"]), Clazz.newArray(-1, ["delete", null])]);
+this.vwr.shm.setShapeProperties(22, val);
+JU.SimpleUnitCell.getCellRange(ucLattice, cellRange);
+for (var p = 1, x = Clazz.floatToInt(cellRange[0].x); x < cellRange[1].x; x++) {
+for (var y = Clazz.floatToInt(cellRange[0].y); y < cellRange[1].y; y++) {
+for (var z = Clazz.floatToInt(cellRange[0].z); z < cellRange[1].z; z++, p++) {
+s += "\ndraw ID " + JU.PT.esc(id + "_" + p) + " " + swidth + " unitcell \"a,b,c;" + x + "," + y + "," + z + "\"";
+}
+}
+}
+s += this.getDrawAxes(id, swidth);
+this.appRunScript(s);
+}, "~S,JU.T3,~S");
+Clazz.defineMethod(c$, "drawAxes",
+function(id, swidth){
+var s = this.getDrawAxes(id, swidth);
+if (s.length > 0) this.appRunScript(s);
+}, "~S,~S");
+Clazz.defineMethod(c$, "getDrawAxes",
+function(id, swidth){
+if (this.vwr.g.axesMode != 603979808 || this.vwr.shm.getShapePropertyIndex(34, "axesTypeXY", 0) === Boolean.TRUE) return "";
+if (id == null) id = "uca";
+if (swidth.indexOf(".") > 0) swidth += "05";
+var origin = this.vwr.shm.getShapePropertyIndex(34, "originPoint", 0);
+var axisPoints = this.vwr.shm.getShapePropertyIndex(34, "axisPoints", 0);
+var s = "";
+var colors = Clazz.newArray(-1, ["red", "green", "blue"]);
+for (var i = 0, a = 6; i < 3; i++, a++) {
+s += "\ndraw ID " + JU.PT.esc(id + "_axis_" + JV.JC.axisLabels[a]) + " " + swidth + " line " + origin + " " + axisPoints[i] + " color " + colors[i];
+}
+return s;
+}, "~S,~S");
+Clazz.defineMethod(c$, "drawSymmetry",
+function(thisId, isSymop, iatom, xyz, iSym, trans, center, target, intScale, nth, options, opList, isModelkit){
+var s = null;
+if (options != 0) {
+var o = this.vwr.getSymmetryInfo(iatom, xyz, iSym, trans, center, target, 134217751, null, intScale / 100, nth, options, opList);
+if (Clazz.instanceOf(o,"JU.P3")) target = o;
+ else s = "";
+}if (thisId == null) thisId = (isSymop ? "sym" : "sg");
+if (s == null) s = this.vwr.getSymmetryInfo(iatom, xyz, iSym, trans, center, target, 135176, thisId, Clazz.doubleToInt(intScale / 100), nth, options, opList);
+if (s != null) {
+s = "draw ID " + (isSymop ? "sg" : "sym") + "* delete;" + s;
+s = "draw ID " + thisId + "* delete;" + s;
+}if (isModelkit) s += ";draw ID sg_xes axes 0.05;";
+return s;
+}, "~S,~B,~N,~S,~N,JU.P3,JU.P3,JU.P3,~N,~N,~N,~A,~B");
+c$.$ModelKit$DrawAtomSet$ = function(){
+/*if4*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+Clazz.prepareCallback(this, arguments);
+this.bsAtoms = null;
+this.cmd = null;
+this.id = null;
+Clazz.instantialize(this, arguments);}, J.modelkit.ModelKit, "DrawAtomSet", null);
+Clazz.makeConstructor(c$,
+function(bs, id, cmd){
+this.bsAtoms = bs;
+this.cmd = cmd;
+this.id = id;
+}, "JU.BS,~S,~S");
+/*eoif4*/})();
+};
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.name = null;
+this.setting = null;
+this.myTrm = null;
+this.myIta = null;
+this.isITA = false;
+this.isHM = false;
+this.hallSymbol = null;
+this.errString = null;
+this.trLink = null;
+this.index = 0;
+this.calcNext = null;
+this.calculated = null;
+Clazz.instantialize(this, arguments);}, J.modelkit.ModelKit, "ClegNode", null);
+Clazz.makeConstructor(c$,
+function(index, name, setting){
+if (name == null) return;
+this.index = index;
+this.setting = (setting == null ? "a,b,c" : setting);
+var pt;
+this.isITA = name.startsWith("ITA/");
+if (this.isITA) {
+name = name.substring(4);
+}this.isHM = false;
+this.hallSymbol = null;
+if (name.charAt(0) == '[') {
+pt = name.indexOf(']');
+if (pt < 0) {
+this.errString = "invalid Hall symbol: " + name + "!";
+return;
+}this.hallSymbol = name.substring(1, pt);
+name = "Hall:" + this.hallSymbol;
+} else if (name.startsWith("HM:")) {
+this.isHM = true;
+} else if (name.length <= 3) {
+this.isITA = true;
+for (var i = name.length; --i >= 0; ) {
+if (!JU.PT.isDigit(name.charAt(i))) {
+this.isITA = false;
+break;
+}}
+if (this.isITA) {
+name += ".1";
+}}if (!this.isITA && this.hallSymbol == null && !this.isHM) {
+pt = (JU.PT.isDigit(name.charAt(0)) ? name.indexOf(" ") : -1);
+if (pt > 0) name = name.substring(0, pt);
+if (name.indexOf('.') > 0 && !Float.isNaN(JU.PT.parseFloat(name))) {
+this.isITA = true;
+if (!name.endsWith(".1") && setting != null) {
+this.errString = "Space group ITA/" + name + " n.m syntax cannot be used with a setting!";
+return;
+}}}this.name = name;
+}, "~N,~S,~S");
+Clazz.defineMethod(c$, "addTransform",
+function(trm){
+if (this.trLink == null) {
+this.trLink = new JU.M4();
+this.trLink.setIdentity();
+}this.trLink.mul(trm);
+}, "JU.M4");
+Clazz.defineMethod(c$, "update",
+function(vwr, prevNode, trm, trTemp, sym){
+if (this.errString != null) return false;
+if (this.name == null) return true;
+if (this.isITA) {
+this.myTrm = (this.name.endsWith(".1") ? "a,b,c" : sym.getITASettingValue(vwr, this.name, "trm"));
+if (this.myTrm == null) {
+this.errString = "Unknown ITA setting: " + this.name + "!";
+return false;
+}var tokens = JU.PT.split(this.name, ".");
+this.myIta = tokens[0];
+this.name = "ITA/" + this.myIta + ":" + (this.myTrm == null || this.myTrm.equals("a,b,c") ? this.setting : this.myTrm);
+} else if (this.hallSymbol != null) {
+if (sym.getSpaceGroupInfoObj("nameToXYZList", "Hall:" + this.hallSymbol, false, false) == null) {
+this.errString = "Invalid Hall notation: " + this.hallSymbol;
+return false;
+}var pt = this.hallSymbol.indexOf("(");
+if (pt > 0) {
+var vabc = JU.PT.split(this.hallSymbol.substring(pt + 1, this.hallSymbol.length - 1), " ");
+this.hallSymbol = this.hallSymbol.substring(0, pt).trim();
+var v = JU.P3.new3(-JU.PT.parseFloat(vabc[0]) / 12, -JU.PT.parseFloat(vabc[1]) / 12, -JU.PT.parseFloat(vabc[2]) / 12);
+this.setting = "a,b,c;" + sym.staticToRationalXYZ(v, ",");
+}this.name = "[" + this.hallSymbol + "]" + (this.setting.equals("a,b,c") ? "" : ":" + this.setting);
+} else {
+this.myTrm = sym.getSpaceGroupInfoObj("itaTransform", this.name, false, false);
+this.myIta = sym.getSpaceGroupInfoObj("itaNumber", this.name, false, false);
+}var trm0 = null;
+var haveCalc = false;
+var haveReferenceCell = (prevNode != null && this.trLink == null && (this.hallSymbol != null || this.myIta != null && (this.myIta.equals(prevNode.myIta) || prevNode.calcNext != null)));
+if (haveReferenceCell) {
+trm0 = JU.M4.newM4(trm);
+if (prevNode != null && prevNode.myTrm != null) {
+J.modelkit.ModelKit.addSGTransform(sym, "!" + prevNode.setting, trm, trTemp);
+J.modelkit.ModelKit.addSGTransform(sym, "!" + prevNode.myTrm, trm, trTemp);
+}var trCalc = null;
+if (prevNode.calcNext != null) {
+var isSub = true;
+var isImplicit = false;
+switch (prevNode.calcNext) {
+case "super":
+isSub = false;
+break;
+case "sub":
+break;
+case "":
+case "set":
+prevNode.calcNext = "set";
+isImplicit = true;
+break;
+}
+var ita1 = JU.PT.parseInt(prevNode.myIta);
+var ita2 = JU.PT.parseInt(this.myIta);
+var isSetting = (isImplicit && ita1 == ita2);
+if (!isSetting) {
+trCalc = sym.getSubgroupJSON(vwr, (isSub ? ita1 : ita2), (isSub ? ita2 : ita1), 0, 1);
+haveCalc = (trCalc != null);
+if (haveCalc && !isSub) trCalc = "!" + trCalc;
+var calc = prevNode.myIta + ">" + trCalc + ">" + this.myIta;
+if (!haveCalc) throw new RuntimeException(calc);
+System.out.println("sub := " + calc);
+J.modelkit.ModelKit.addSGTransform(sym, trCalc, trm, trTemp);
+}}J.modelkit.ModelKit.addSGTransform(sym, this.myTrm, trm, trTemp);
+J.modelkit.ModelKit.addSGTransform(sym, this.setting, trm, trTemp);
+System.out.println("ClegNode " + this + "\n" + trm);
+if (haveCalc) {
+trm0.invert();
+var trm1 = JU.M4.newM4(trm);
+trm1.mul(trm0);
+this.calculated = sym.convertTransform(null, trm1);
+}}return true;
+}, "JV.Viewer,J.modelkit.ModelKit.ClegNode,JU.M4,JU.M4,J.api.SymmetryInterface");
+Clazz.overrideMethod(c$, "toString",
+function(){
+return "[ClegNode #" + this.index + " " + this.name + " " + this.myIta + ":" + this.setting + " " + this.myTrm + "]";
+});
+c$.checkSyntax = Clazz.defineMethod(c$, "checkSyntax",
+function(tokens, sym){
+for (var i = 0; i < tokens.length; i++) {
+var s = tokens[i].trim();
+if (s.length == 0) continue;
+var pt = s.indexOf(":");
+var transform;
+if (pt > 0) {
+transform = s.substring(pt + 1);
+s = s.substring(0, pt);
+} else if (s.indexOf(",") >= 0) {
+transform = s;
+s = null;
+} else {
+transform = "";
+}if (s != null) {
+var itno = JU.PT.parseFloatStrict(s);
+if (itno < 1 || itno >= 231) return false;
+if (Float.isNaN(itno)) transform = s;
+}switch (transform) {
+case "":
+case "sub":
+case "r":
+case "h":
+case "!r":
+case "!h":
+break;
+default:
+if (transform.indexOf(",") >= 0) {
+if ((sym.convertTransform(transform, null)).determinant3() == 0) return false;
+}break;
+}
+}
+return true;
+}, "~A,J.api.SymmetryInterface");
+Clazz.defineMethod(c$, "updateTokens",
+function(tokens, i){
+if (this.myIta != null && this.myTrm != null) tokens[i] = this.myIta + (this.myTrm.equals("a,b,c") ? "" : ":" + this.myTrm);
+if (this.calculated != null) tokens[i - 1] = this.calculated;
+}, "~A,~N");
+/*eoif3*/})();
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.type = 0;
+this.pt = null;
+this.offset = null;
+this.plane = null;
+this.unitVector = null;
+Clazz.instantialize(this, arguments);}, J.modelkit.ModelKit, "Constraint", null);
+Clazz.makeConstructor(c$,
+function(pt, type, params){
+this.pt = pt;
+this.type = type;
+switch (type) {
+case 0:
+case 7:
+case 6:
+break;
+case 4:
+this.offset = params[0];
+this.unitVector = JU.V3.newV(params[1]);
+this.unitVector.normalize();
+break;
+case 5:
+this.plane = params[0];
+break;
+default:
+throw new IllegalArgumentException();
+}
+}, "JU.P3,~N,~A");
+Clazz.defineMethod(c$, "constrain",
+function(ptOld, ptNew, allowProjection){
+var v = new JU.V3();
+var p = JU.P3.newP(ptOld);
+var d = 0;
+switch (this.type) {
+case 0:
+return;
+case 7:
+return;
+case 6:
+ptNew.x = NaN;
+return;
+case 4:
+if (this.pt == null) {
+d = JU.Measure.projectOntoAxis(p, this.offset, this.unitVector, v);
+if (d * d >= 1.96E-6) {
+ptNew.x = NaN;
+break;
+}}d = JU.Measure.projectOntoAxis(ptNew, this.offset, this.unitVector, v);
+break;
+case 5:
+if (this.pt == null) {
+if (Math.abs(JU.Measure.getPlaneProjection(p, this.plane, v, v)) > 0.01) {
+ptNew.x = NaN;
+break;
+}}d = JU.Measure.getPlaneProjection(ptNew, this.plane, v, v);
+ptNew.setT(v);
+break;
+}
+if (!allowProjection && Math.abs(d) > 1e-10) {
+ptNew.x = NaN;
+}}, "JU.P3,JU.P3,~B");
+/*eoif3*/})();
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.bsElements = null;
+this.nAtoms = 0;
+this.elementStrings = null;
+this.colors = null;
+this.isotopeCounts = null;
+this.modelIndex = 0;
+Clazz.instantialize(this, arguments);}, J.modelkit.ModelKit, "EKey", null);
+Clazz.prepareFields (c$, function(){
+this.bsElements = new JU.BS();
+this.elementStrings = Clazz.newArray(120, 10, null);
+this.colors = Clazz.newIntArray (120, 10, 0);
+this.isotopeCounts = Clazz.newIntArray (120, 0);
+});
+Clazz.makeConstructor(c$,
+function(vwr, modelIndex){
+var bsAtoms = vwr.getModelUndeletedAtomsBitSet(modelIndex);
+this.nAtoms = (bsAtoms == null ? 0 : bsAtoms.cardinality());
+this.modelIndex = modelIndex;
+if (this.nAtoms == 0) return;
+var a = vwr.ms.at;
+for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var elem = a[i].getElementSymbol();
+var elemno = a[i].getElementNumber();
+var color = a[i].atomPropertyInt(1765808134);
+var j = 0;
+var niso = this.isotopeCounts[elemno];
+for (; j < niso; j++) {
+if (this.elementStrings[elemno][j].equals(elem)) {
+if (this.colors[elemno][j] != color) {
+this.nAtoms = 0;
+return;
+}break;
+}}
+if (j < niso) {
+continue;
+}this.bsElements.set(elemno);
+this.isotopeCounts[elemno]++;
+this.elementStrings[elemno][j] = elem;
+this.colors[elemno][j] = color;
+}
+}, "JV.Viewer,~N");
+Clazz.defineMethod(c$, "draw",
+function(vwr){
+if (this.nAtoms == 0) return;
+var key = J.modelkit.ModelKit.getElementKey(this.modelIndex);
+var h = vwr.getScreenHeight();
+var font = vwr.getFont3D("SansSerif", "Bold", Clazz.doubleToInt(h * 20 / 400));
+for (var y = 90, elemno = this.bsElements.nextSetBit(0); elemno >= 0; elemno = this.bsElements.nextSetBit(elemno + 1)) {
+var n = this.isotopeCounts[elemno];
+if (n == 0) continue;
+var elem = this.elementStrings[elemno];
+for (var j = 0; j < n; j++) {
+var label = elem[j];
+var color = this.colors[elemno][j];
+vwr.shm.setShapeProperties(22, [ Clazz.newArray(-1, ["init", "elementKey"]), Clazz.newArray(-1, ["thisID", key + "d_" + label]), Clazz.newArray(-1, ["diameter", Float.$valueOf(2)]), Clazz.newArray(-1, ["modelIndex", Integer.$valueOf(this.modelIndex)]), Clazz.newArray(-1, ["points", Integer.$valueOf(0)]), Clazz.newArray(-1, ["coord", JU.P3.new3(90, y, -3.4028235E38)]), Clazz.newArray(-1, ["set", null]), Clazz.newArray(-1, ["color", Integer.$valueOf(color)]), Clazz.newArray(-1, ["thisID", null])]);
+vwr.shm.setShapeProperties(31, [ Clazz.newArray(-1, ["thisID", null]), Clazz.newArray(-1, ["target", key + "e_" + label]), Clazz.newArray(-1, ["model", Integer.$valueOf(this.modelIndex)]), Clazz.newArray(-1, ["xypos", JU.P3.new3(91, y - 2, -3.4028235E38)]), Clazz.newArray(-1, ["text", label]), Clazz.newArray(-1, ["font", font]), Clazz.newArray(-1, ["color", Integer.$valueOf(-74566)]), Clazz.newArray(-1, ["thisID", null])]);
+y -= 5;
+}
+}
+var bs = vwr.getVisibleFramesBitSet();
+vwr.shm.getShape(22).setModelVisibilityFlags(bs);
+vwr.shm.getShape(31).setModelVisibilityFlags(bs);
+}, "JV.Viewer");
+/*eoif3*/})();
+/*if3*/;(function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.oldVib = null;
+this.atom = null;
+this.t = 0;
+this.baseAtom = null;
+this.pt0 = null;
+this.ptf = null;
+this.sym = null;
+this.c = null;
+Clazz.instantialize(this, arguments);}, J.modelkit.ModelKit, "WyckoffModulation", JU.Vibration);
+Clazz.prepareFields (c$, function(){
+this.pt0 = new JU.P3();
+this.ptf = new JU.P3();
+});
+Clazz.makeConstructor(c$,
+function(sym, c, atom, baseAtom){
+Clazz.superConstructor (this, J.modelkit.ModelKit.WyckoffModulation, []);
+this.setType(-3);
+this.sym = sym;
+this.c = c;
+this.atom = atom;
+this.baseAtom = baseAtom;
+this.x = 1;
+}, "J.api.SymmetryInterface,J.modelkit.ModelKit.Constraint,JM.Atom,JM.Atom");
+c$.setVibrationMode = Clazz.defineMethod(c$, "setVibrationMode",
+function(mk, value){
+var atoms = mk.vwr.ms.at;
+var bsAtoms = mk.vwr.getThisModelAtoms();
+if (("off").equals(value)) {
+for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var v = atoms[i].getVibrationVector();
+if (v != null && v.modDim != -3) continue;
+mk.vwr.ms.setVibrationVector(i, (v).oldVib);
+}
+} else if (("wyckoff").equals(value)) {
+for (var i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
+var v = atoms[i].getVibrationVector();
+if (v != null && v.modDim != -3) continue;
+var sym = mk.getSym(i);
+var wv = null;
+if (sym != null) {
+var c = mk.setConstraint(sym, i, J.modelkit.ModelKit.GET_CREATE);
+if (c.type != 6) wv = new J.modelkit.ModelKit.WyckoffModulation(sym, c, atoms[i], mk.getBasisAtom(i));
+}mk.vwr.ms.setVibrationVector(i, wv);
+}
+}mk.vwr.setVibrationPeriod(NaN);
+}, "J.modelkit.ModelKit,~O");
+Clazz.overrideMethod(c$, "setCalcPoint",
+function(pt, t456, scale, modulationScale){
+var v = this.baseAtom.getVibrationVector();
+if (v == null || v.modDim != -3) return pt;
+var wv = (v);
+if (this.sym == null) return pt;
+var m = null;
+if (wv.atom !== this.atom) {
+m = J.modelkit.ModelKit.getTransform(this.sym, wv.atom, this.atom);
+if (m == null) return pt;
+}if (wv.t != t456.x && (Clazz.floatToInt(t456.x * 10)) % 2 == 0) {
+if (this.c.type != 6) {
+wv.setPos(this.sym, this.c, scale);
+}wv.t = t456.x;
+}if (m == null) pt.setT(wv.ptf);
+ else m.rotTrans2(wv.ptf, pt);
+this.sym.toCartesian(pt, false);
+return pt;
+}, "JU.T3,JU.T3,~N,~N");
+Clazz.defineMethod(c$, "setPos",
+function(sym, c, scale){
+this.x = (Math.random() - 0.5) / 10 * scale;
+this.y = (Math.random() - 0.5) / 10 * scale;
+this.z = (Math.random() - 0.5) / 10 * scale;
+this.pt0.setT(this.atom);
+this.ptf.setT(this.pt0);
+this.ptf.add(this);
+c.constrain(this.pt0, this.ptf, true);
+sym.toFractional(this.ptf, false);
+}, "J.api.SymmetryInterface,J.modelkit.ModelKit.Constraint,~N");
+/*eoif3*/})();
+c$.locked = new J.modelkit.ModelKit.Constraint(null, 6, null);
+c$.none = new J.modelkit.ModelKit.Constraint(null, 0, null);
+c$.Pt000 = new JU.P3();
+c$.GET = 0;
+c$.GET_CREATE = 1;
+c$.GET_DELETE = 2;
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopup.js b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopup.js
new file mode 100755
index 000000000000..908b47844458
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopup.js
@@ -0,0 +1,221 @@
+Clazz.declarePackage("J.modelkit");
+Clazz.load(["J.popup.JmolGenericPopup", "J.modelkit.ModelKitPopupResourceBundle"], "J.modelkit.ModelKitPopup", ["J.i18n.GT"], function(){
+var c$ = Clazz.decorateAsClass(function(){
+this.modelkit = null;
+this.hidden = false;
+this.allowPopup = true;
+this.activeMenu = null;
+this.bondRotationCheckBox = null;
+this.prevBondCheckBox = null;
+this.bondRotationName = ".modelkitMenu.bondMenu.rotateBondP!RD";
+this.haveOperators = false;
+Clazz.instantialize(this, arguments);}, J.modelkit, "ModelKitPopup", J.popup.JmolGenericPopup);
+Clazz.makeConstructor(c$,
+function(){
+Clazz.superConstructor (this, J.modelkit.ModelKitPopup, []);
+});
+Clazz.overrideMethod(c$, "getBundle",
+function(menu){
+return J.modelkit.ModelKitPopup.bundle;
+}, "~S");
+Clazz.defineMethod(c$, "jpiShow",
+function(x, y){
+if (!this.hidden) {
+this.updateCheckBoxesForModelKit(null);
+Clazz.superCall(this, J.modelkit.ModelKitPopup, "jpiShow", [x, y]);
+}}, "~N,~N");
+Clazz.overrideMethod(c$, "jpiUpdateComputedMenus",
+function(){
+this.htMenus.get("xtalMenu").setEnabled(this.modelkit.setHasUnitCell());
+if (this.modelkit.checkNewModel()) {
+this.haveOperators = false;
+this.updateOperatorMenu();
+}this.updateAllXtalMenuOptions();
+});
+Clazz.overrideMethod(c$, "appUpdateForShow",
+function(){
+this.jpiUpdateComputedMenus();
+});
+Clazz.defineMethod(c$, "hidePopup",
+function(){
+this.menuHidePopup(this.popupMenu);
+});
+Clazz.defineMethod(c$, "clearLastModelSet",
+function(){
+this.modelkit.lastModelSet = null;
+});
+Clazz.defineMethod(c$, "updateOperatorMenu",
+function(){
+if (this.haveOperators) return;
+this.haveOperators = true;
+var menu = this.htMenus.get("xtalOp!PersistMenu");
+if (menu != null) this.addAllCheckboxItems(menu, this.modelkit.getAllOperators());
+});
+Clazz.defineMethod(c$, "addAllCheckboxItems",
+function(menu, labels){
+this.menuRemoveAll(menu, 0);
+var subMenu = menu;
+var pt = (labels.length > 32 ? 0 : -2147483648);
+for (var i = 0; i < labels.length; i++) {
+if (pt >= 0 && (pt++ % 32) == 0) {
+var id = "mtsymop" + pt + "Menu";
+subMenu = this.menuNewSubMenu((i + 1) + "..." + Math.min(i + 32, labels.length), this.menuGetId(menu) + "." + id);
+this.menuAddSubMenu(menu, subMenu);
+this.htMenus.put(id, subMenu);
+pt = 1;
+}if (i == 0) this.menuEnable(this.menuCreateItem(subMenu, J.i18n.GT.$("none"), "draw sym_* delete", null), true);
+var sym = labels[i];
+this.menuEnable(this.menuCreateItem(subMenu, sym, sym, subMenu.getName() + "." + "mkop_" + (i + 1)), true);
+}
+}, "J.api.SC,~A");
+Clazz.defineMethod(c$, "updateAllXtalMenuOptions",
+function(){
+var text = "";
+switch (this.modelkit.getMKState()) {
+case 0:
+text = " (not enabled)";
+break;
+case 1:
+text = " (view)";
+break;
+case 2:
+text = " (edit)";
+break;
+}
+this.setLabel("xtalModePersistMenu", "Crystal Mode: " + text);
+text = this.modelkit.getCenterText();
+this.setLabel("xtalSelPersistMenu", "Center: " + (text == null ? "(not selected)" : text));
+text = this.modelkit.getSymopText();
+this.setLabel("operator", text == null ? "(no operator selected)" : text);
+switch (this.modelkit.getSymEditState()) {
+case 0:
+text = "do not apply symmetry";
+break;
+case 64:
+text = "retain local symmetry";
+break;
+case 32:
+text = "apply local symmetry";
+break;
+case 128:
+text = "apply full symmetry";
+break;
+}
+this.setLabel("xtalEditOptPersistMenu", "Edit option: " + text);
+switch (this.modelkit.getUnitCellState()) {
+case 0:
+text = "packed";
+break;
+case 256:
+text = "unpacked" + (this.modelkit.viewOffset == null ? "(no view offset)" : "(view offset=" + this.modelkit.viewOffset + ")");
+break;
+}
+this.setLabel("xtalPackingPersistMenu", "Packing: " + text);
+});
+Clazz.defineMethod(c$, "setLabel",
+function(key, label){
+this.menuSetLabel(this.htMenus.get(key), label);
+}, "~S,~S");
+Clazz.defineMethod(c$, "setActiveMenu",
+function(name){
+var active = (name.indexOf("xtalMenu") >= 0 ? "xtalMenu" : name.indexOf("atomMenu") >= 0 ? "atomMenu" : name.indexOf("bondMenu") >= 0 ? "bondMenu" : null);
+if (active != null) {
+this.activeMenu = active;
+if ((active === "xtalMenu") == (this.modelkit.getMKState() == 0)) this.modelkit.setMKState(active === "xtalMenu" ? 1 : 0);
+this.vwr.refresh(1, "modelkit");
+if (active === "bondMenu" && this.prevBondCheckBox == null) this.prevBondCheckBox = this.htMenus.get("assignBond_pP!RD");
+} else if (name.indexOf("optionsMenu") >= 0) {
+this.htMenus.get("undo").setEnabled(this.vwr.undoMoveAction(4165, 1275068425) > 0);
+this.htMenus.get("redo").setEnabled(this.vwr.undoMoveAction(4140, 1275068425) > 0);
+}return active;
+}, "~S");
+Clazz.overrideMethod(c$, "appUpdateSpecialCheckBoxValue",
+function(source, actionCommand, selected){
+if (source == null || !selected) return;
+var name = source.getName();
+var mode;
+if (!this.updatingForShow && (mode = this.setActiveMenu(name)) != null) {
+var text = source.getText();
+if (mode === "bondMenu") {
+if (name.equals(this.bondRotationName)) {
+this.bondRotationCheckBox = source;
+} else {
+this.prevBondCheckBox = source;
+}}this.modelkit.setHoverLabel(this.activeMenu, text);
+}}, "J.api.SC,~S,~B");
+Clazz.defineMethod(c$, "exitBondRotation",
+function(){
+this.modelkit.exitBondRotation(this.prevBondCheckBox == null ? null : this.prevBondCheckBox.getText());
+this.vwr.setPickingMode(null, 33);
+if (this.bondRotationCheckBox != null) this.bondRotationCheckBox.setSelected(false);
+if (this.prevBondCheckBox != null) this.prevBondCheckBox.setSelected(true);
+});
+Clazz.overrideMethod(c$, "appGetBooleanProperty",
+function(name){
+if (name.startsWith("mk")) {
+return (this.modelkit.getProperty(name.substring(2))).booleanValue();
+}return this.vwr.getBooleanProperty(name);
+}, "~S");
+Clazz.overrideMethod(c$, "getUnknownCheckBoxScriptToRun",
+function(item, name, what, TF){
+if (name.startsWith("mk")) {
+this.modelkit.processMKPropertyItem(name, TF);
+return null;
+}var element = this.modelkit.getElementFromUser();
+if (element == null) return null;
+this.menuSetLabel(item, element);
+item.setActionCommand("assignAtom_" + element + "P!:??");
+return "set picking assignAtom_" + element;
+}, "J.api.SC,~S,~S,~B");
+Clazz.overrideMethod(c$, "menuFocusCallback",
+function(name, actionCommand, gained){
+if (gained && !this.modelkit.processSymop(name, true)) {
+this.setActiveMenu(name);
+}}, "~S,~S,~B");
+Clazz.overrideMethod(c$, "menuClickCallback",
+function(source, script){
+if (this.modelkit.processSymop(source.getName(), false)) return;
+if (script.equals("clearQPersist")) {
+for (var item, $item = this.htCheckbox.values().iterator (); $item.hasNext()&& ((item = $item.next ()) || true);) {
+if (item.getActionCommand().indexOf(":??") < 0) continue;
+this.menuSetLabel(item, "??");
+item.setActionCommand("_??P!:");
+}
+this.appRunScript("set picking assignAtom_C");
+return;
+}this.doMenuClickCallback(source, script);
+}, "J.api.SC,~S");
+Clazz.overrideMethod(c$, "getScriptForCallback",
+function(source, id, script){
+if (script.startsWith("mk")) {
+this.modelkit.clickProcessXtal(id, script);
+script = null;
+}return script;
+}, "J.api.SC,~S,~S");
+Clazz.defineMethod(c$, "appRunSpecialCheckBox",
+function(item, basename, script, TF){
+if (basename.indexOf("assignAtom_Xx") == 0) {
+this.modelkit.resetAtomPickType();
+}if (TF && !this.updatingForShow && basename.indexOf("Bond") < 0) {
+this.updatingForShow = true;
+this.exitBondRotation();
+this.updatingForShow = false;
+}return Clazz.superCall(this, J.modelkit.ModelKitPopup, "appRunSpecialCheckBox", [item, basename, script, TF]);
+}, "J.api.SC,~S,~S,~B");
+Clazz.defineMethod(c$, "updateCheckBoxesForModelKit",
+function(menuName){
+var thisAtomType = "assignAtom_" + this.modelkit.pickAtomAssignType + "P";
+var thisBondType = "assignBond_" + this.modelkit.pickBondAssignType;
+for (var entry, $entry = this.htCheckbox.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
+var item = entry.getValue();
+var key = item.getActionCommand();
+if (key.startsWith(thisBondType) || key.startsWith(thisAtomType)) {
+this.updatingForShow = true;
+item.setSelected(false);
+item.setSelected(true);
+this.updatingForShow = false;
+}}
+}, "~S");
+c$.bundle = new J.modelkit.ModelKitPopupResourceBundle(null, null);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopupResourceBundle.js b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopupResourceBundle.js
new file mode 100755
index 000000000000..bafd5306ea53
--- /dev/null
+++ b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/ModelKitPopupResourceBundle.js
@@ -0,0 +1,28 @@
+Clazz.declarePackage("J.modelkit");
+Clazz.load(["J.popup.PopupResource"], "J.modelkit.ModelKitPopupResourceBundle", ["J.i18n.GT", "J.modelkit.ModelKit"], function(){
+var c$ = Clazz.declareType(J.modelkit, "ModelKitPopupResourceBundle", J.popup.PopupResource);
+Clazz.overrideMethod(c$, "getMenuName",
+function(){
+return "modelkitMenu";
+});
+Clazz.overrideMethod(c$, "buildStructure",
+function(menuStructure){
+this.addItems(J.modelkit.ModelKitPopupResourceBundle.menuContents);
+this.addItems(J.modelkit.ModelKitPopupResourceBundle.structureContents);
+if (menuStructure != null) this.setStructure(menuStructure, new J.i18n.GT());
+}, "~S");
+Clazz.overrideMethod(c$, "getWordContents",
+function(){
+var wasTranslating = J.i18n.GT.setDoTranslate(true);
+var words = Clazz.newArray(-1, ["atomMenu", "", "moreAtomMenu", "", "bondMenu", "", "optionsMenu", "", "operator", "(no operator selected)", "xtalMenu", "", "xtalModePersistMenu", "mode", "xtalSelPersistMenu", "select atom or position", "xtalSelOpPersistMenu", "select operator", "xtalOp!PersistMenu", "from list...", "xtalEditOptPersistMenu", "edit options", "xtalOptionsPersistMenu", "more options...", "xtalPackingPersistMenu", "packing", "mkshowSymopInfoCB", "show symmetry operator info", "mkaddHydrogensCB", "add hydrogens on new atoms", "mkclicktosetelementCB", "allow clicking to set atom element", "mkselop_byop", "from list", "mkselop_addOffset", "add/remove lattice offset", "mkselop_atom2", "to second atom", "mksel_atom", "select atom", "mksel_position", "select position", "mkmode_molecular", J.i18n.GT.$("disabled"), "mkmode_view", J.i18n.GT.$("View"), "mkmode_edit", J.i18n.GT.$("Edit"), "mksymmetry_none", J.i18n.GT.$("do not apply"), "mksymmetry_retainLocal", J.i18n.GT.$("retain local"), "mksymmetry_applyLocal", J.i18n.GT.$("apply local"), "mksymmetry_applyFull", J.i18n.GT.$("apply full"), "mkunitcell_extend", J.i18n.GT.$("this operator"), "mkunitcell_packed", J.i18n.GT.$("add translation"), "mkasymmetricUnit", J.i18n.GT.$("asymmetric unit"), "mkallAtoms", J.i18n.GT.$("all atoms"), "new", J.i18n.GT.$("new"), "undo", J.i18n.GT.$("undo (CTRL-Z)"), "redo", J.i18n.GT.$("redo (CTRL-Y)"), "center", J.i18n.GT.$("center"), "ekey", J.i18n.GT.$("element key"), "addh", J.i18n.GT.$("add hydrogens"), "minimize", J.i18n.GT.$("minimize"), "hmin", J.i18n.GT.$("fix hydrogens and minimize"), "clearQPersist", J.i18n.GT.$("clear"), "SIGNEDsaveFile", J.i18n.GT.$("save file"), "SIGNEDsaveState", J.i18n.GT.$("save state"), "invertStereoP!RD", J.modelkit.ModelKit.getText("invStereo"), "assignAtom_XP!RD", J.modelkit.ModelKit.getText("delAtom"), "assignAtom_XxP!RD", J.modelkit.ModelKit.getText("dragBond"), "dragAtomP!RD", J.modelkit.ModelKit.getText("dragAtom"), "dragMinimizeP!RD", J.modelkit.ModelKit.getText("dragMinimize"), "dragMoleculeP!RD", J.modelkit.ModelKit.getText("dragMolecule"), "dragMinimizeMoleculeP!RD", J.modelkit.ModelKit.getText("dragMMol"), "assignAtom_CP!RD", "C", "assignAtom_HP!RD", "H", "assignAtom_NP!RD", "N", "assignAtom_OP!RD", "O", "assignAtom_FP!RD", "F", "assignAtom_ClP!RD", "Cl", "assignAtom_BrP!RD", "Br", "_??P!RD", "??", "assignAtom_plP!RD", J.modelkit.ModelKit.getText("incCharge"), "assignAtom_miP!RD", J.modelkit.ModelKit.getText("decCharge"), "assignBond_0P!RD", J.modelkit.ModelKit.getText("bondTo0"), "assignBond_1P!RD", J.modelkit.ModelKit.getText("bondTo1"), "assignBond_2P!RD", J.modelkit.ModelKit.getText("bondTo2"), "assignBond_3P!RD", J.modelkit.ModelKit.getText("bondTo3"), "assignBond_pP!RD", J.modelkit.ModelKit.getText("incBond"), "assignBond_mP!RD", J.modelkit.ModelKit.getText("decBond"), "rotateBondP!RD", J.modelkit.ModelKit.getText("rotBond"), "exit!Persist", J.i18n.GT.$("exit modelkit mode")]);
+J.i18n.GT.setDoTranslate(wasTranslating);
+return words;
+});
+Clazz.overrideMethod(c$, "getMenuAsText",
+function(title){
+return this.getStuctureAsText(title, J.modelkit.ModelKitPopupResourceBundle.menuContents, J.modelkit.ModelKitPopupResourceBundle.structureContents);
+}, "~S");
+c$.menuContents = Clazz.newArray(-1, [ Clazz.newArray(-1, ["modelkitMenu", "atomMenu bondMenu xtalMenu optionsMenu"]), Clazz.newArray(-1, ["optionsMenu", "new ekey center addh minimize hmin - undo redo - SIGNEDsaveFile SIGNEDsaveState exit!Persist"]), Clazz.newArray(-1, ["atomMenu", "assignAtom_XxP!RD dragAtomP!RD dragMinimizeP!RD dragMoleculeP!RD dragMinimizeMoleculeP!RD invertStereoP!RD - assignAtom_XP!RD assignAtom_CP!RD assignAtom_HP!RD assignAtom_NP!RD assignAtom_OP!RD assignAtom_FP!RD assignAtom_ClP!RD assignAtom_BrP!RD _??P!RD _??P!RD _??P!RD moreAtomMenu assignAtom_plP!RD assignAtom_miP!RD"]), Clazz.newArray(-1, ["moreAtomMenu", "clearQPersist , _??P!RD _??P!RD _??P!RD _??P!RD _??P!RD _??P!RD "]), Clazz.newArray(-1, ["bondMenu", "assignBond_0P!RD assignBond_1P!RD assignBond_2P!RD assignBond_3P!RD assignBond_pP!RD assignBond_mP!RD rotateBondP!RD"]), Clazz.newArray(-1, ["xtalMenu", "xtalSelOpPersistMenu operator "]), Clazz.newArray(-1, ["xtalModePersistMenu", "mkmode_molecular mkmode_view mkmode_edit"]), Clazz.newArray(-1, ["xtalSelPersistMenu", "mksel_atom mksel_position"]), Clazz.newArray(-1, ["xtalSelOpPersistMenu", "xtalOp!PersistMenu "]), Clazz.newArray(-1, ["xtalEditOptPersistMenu", "mksymmetry_none mksymmetry_retainLocal mksymmetry_applyLocal mksymmetry_applyFull"]), Clazz.newArray(-1, ["xtalPackingPersistMenu", "mkunitcell_packed mkunitcell_extend"]), Clazz.newArray(-1, ["xtalOptionsPersistMenu", "mkshowSymopInfoCB mkclicktosetelementCB mkaddHydrogensCB"])]);
+c$.structureContents = Clazz.newArray(-1, [ Clazz.newArray(-1, ["new", "zap"]), Clazz.newArray(-1, ["ekey", "set elementkey= @{!elementkey}"]), Clazz.newArray(-1, ["center", "zoomto 0 {visible} 0/1.5"]), Clazz.newArray(-1, ["addh", "calculate hydrogens {model=_lastframe}"]), Clazz.newArray(-1, ["minimize", "minimize"]), Clazz.newArray(-1, ["hmin", "delete hydrogens and model=_lastframe; minimize addhydrogens"]), Clazz.newArray(-1, ["SIGNEDsaveFile", "select visible;write COORD '?jmol.mol'"]), Clazz.newArray(-1, ["SIGNEDsaveState", "write '?jmol.jpg'"]), Clazz.newArray(-1, ["clearQ", "clearQ"]), Clazz.newArray(-1, ["undo", "!undoMove"]), Clazz.newArray(-1, ["redo", "!redoMove"]), Clazz.newArray(-1, ["operator", ""]), Clazz.newArray(-1, ["exit!Persist", "set modelkitMode false"])]);
+});
+;//5.0.1-v2 Fri Jun 07 15:32:46 BST 2024
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/modelkit/images/atoms.png b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/images/atoms.png
new file mode 100755
index 0000000000000000000000000000000000000000..12bb8e0b80b351a494451fbc4ad4bc61aeb1e208
GIT binary patch
literal 1408
zcmeHG`%BXS5I_5#wtSE>F)cGe6KgalQrHY+>QK?GxlJm6FsJF#EH!67kTj8++VWA&
zS(eWCV_UXDK|xboW6H#!(3GJ)W;01l@R2C?wf`dO;6C@@;NbJQE8}s)9c&NV0)Rtg
zL>Qlp&U;QFNbJAxBbW?U+5GSj&`h{5k_C!c92UUKO1o{5HCcNmMesQQ1wH`9r2t!G
ztJngN!vOf60KilL9LlWkk2wcG054j|CIgXzAUz7+kQY5*eo5{cvrQVRxxon~5tpIw!na*#Y
z_hv>S!&pLJLDFWWHG{`y_@ABNDC|<4N26<1D(_sk1M#<|j4%fClu;kSiW{XdUFnu3
zM{4W!M(>QeYL8K4~>CAlDql9kN}wf<6*7;2>Q?<{0x
zYqczE(@04@C)8_%IQsFDtJ8x%;@6lVzN+k?A^hs6a8ceqcqQ`?4^xj&_bxY*%?;Cp
HB$WIHz;zvG
literal 0
HcmV?d00001
diff --git a/config/plugins/visualizations/jmol/static/j2s/J/modelkit/images/bonds.png b/config/plugins/visualizations/jmol/static/j2s/J/modelkit/images/bonds.png
new file mode 100755
index 0000000000000000000000000000000000000000..3053ba4d1d9b1fd5844d6e75a0a9e3dde17decfb
GIT binary patch
literal 1378
zcmeAS@N?(olHy`uVBq!ia0vp^A|TAc3?z4jzqJQajKx9jP7LeL$-D$|SkfJR9T^xl
z_H+M9WCijSl0AZa85pY67#JE_7#My5g&JNkFq9fFFuY1&V6d9Oz#v{QXIG#N0|PTd
zfKP}kPyr*O3?rkgjEsz|tSkeA3Q!dTgB=5dy^M^WnwpxWrKP>SJtLzBBcmrHqYopa
zFC(KLGjlWpL#&L9i>$1htZWc7a|#nvDl>B-GjkCWQ!x`$2@_K(3kwjH>FRnpIy$<#
zy1Kc!1qKF&hK9z(#5g~3$+|8ReZ{4~DboMA14FSqS;6jJJKQIe0lmz(&
z{~y_aA^1DHDlkMPN?apKg7ec#$`gxH83GbB^GfvmTtgJfjP;DoRz80OQnSR<#W6%9
zcx}LOu_glnmc=)!of)~6l)lCN|G)j1h>wWnuJ$KyQ_8(eRHl3r|L`nm7Q1zX>zsRb
zz0MB%98-#`{Ik5icCD<*;5fhL^4eDc3%+YU)zJxeILv0mSAFLUr+5_486){kuQiu{
z4tsBQJ85g0r}yI0*Ds16?MrmAJFMMUuXQnR_VFC0Yx=HL{VPAFGwiUQ+7Vp&(dATS
i&L{I{&odsK-_H;d>lvz_^Xrp*(7D42QlWGr9{*~xdd!P28fK>8-rB3`*riv~pohOZ?o`F|9LK+!hy_W;Ui?#3G#;WuyO2hvM1;;R1OuXrhoqJuXh70;+tVzs5r`0!0Jz~WXECEQ
zp;E{UOYDLhgxw0m4(m{pi<~SCsk4=B^FR{;o7hb7y?3p
zQVNSnxKY><7$JxNlu}p>!fl1^hao}KLMg)XE_5$hDJ&xBqSc1qfFw|>l)@sCE}}Lf
z20{V>r3i~C6yUnBZ5RfGfa3M!Ew1ZyR4&TQ?$|04=5WJePG?4CLZ*-y#$REXf5IF(
z7A>8+N>!#TQ7Xd12Av$O4D|$6K{-sRYcCe^bk=D()EB8{DVw{({>K7~gcV_7YinzB
zb8~fdb!BB`etv#>dfGJ2;o;$AG8vD@qtR$zUtc5=>F(|hg+gs@ZGk|bv9YnPuCBVe
zn!ocSBcqz8?L2mR$L)ld-sIKsUlnCQ8BTk<-jDF%V%0eIRW-=ZuFZ)&-fo9emG|!)
zQom%&w5#U_zqxix^O+-B;@DcvGqwS8ObYK@`K2j0?NibY?qw^TsRnElvswiDp6v`P^o}pPzWkhfdDd<$c~C1ffN{$
z@AQ4ly>~~#1#3&1?Q^>OboV*m`OcYRGt(QE^u4>Ur>AGhrj1iu@$Z%N=ki|s-Fxo-
zTk+3wZ{1GsX45v9)mYb(8l%vox3+87z#<7INc-(ea_u
zk_|hTLHSZ|>vXy2|LDKs&a3BPV{y~ei=$e+ij;#|MFLFJovRw{6Xb@_5R#5
z_&IT+chluPCmw(Okpn{f-GiT6y62j2jyXT*`QGL1>d#))`zK3IKmNw!XC8j^|*
zL+?EI$BRb)@c1{*ocZcgPc6Rw=+p20i_*yHv#-6jcf4sDO=&tc2bG;w#>HW%C
zwtDS7)5fFE*0;X!#<@>0_e)FP^Szf}5SP6^{gwAT@$AitTy8vZcGKj_ttC97*G6q
z$4AazvwQX1-*wNql^=ilr+@wLubh79M?dVHz2oq!H{LdI*SlWq`RSG&fA-HuPrhy*
zKKZNT$5$UcI(@)B?iKcqKFcc)UH0Ou%YM=`Vc1U!wS4D>#@l9AZycK0xM7?1>Zez%
zdUDGL{^_NY_dYhi@`f9(dvwcJpD+H^iGP^r{qj>cuK2;vo_+sKd)YUZEoX~o@44oa
zH~qKS{Q13x(Nq?nJNubex8L{fkAD8rzx?2n=AQiG(|4Xfb!68!pS8rkQ?C0mdf9J2?
zEcN{I`!64T@%Qh25l+>!Y2EbH@in&{?aL0xA13{Fomt_U#x+(}UET2*iCEvYzEF6I
z$Jrcr1$pg-TzpkuU$tSW(zEvo?(NVm&2E-y?)C3uhp?FA@+x;-uI@0bdg_c8@9_P
zSpV*p4BXt_{!mu9h-~NrvWBI5DmRP^h;d-1m=&E{-VAqD{KJN&jU>?YYPBJFC>R@-
z$AUmOTx}SN%RINi(}SUUp|C(=H@VA(ac#Jr*fQ%{j&0G_qoD*Am+OkATQycy3=!?o
z8K04B<)gI@l0NrGhgS8?r(SivZt%{V2Ky_9VK+k;@;yi-_fs5)TiP^lCQgb`gL^Zs
z-D4SFu#ia+%l@@v71=yv>T|=@1>tWpa?qKl9;iEzq$Q4cFk|2|7l{WI+fmkd^Vs
zs@HJ&ln_qB^kDM#sU2(*M+^6>+HfQqpeyLy=e5$Md|Re;m#d!b;{Md}?CnTggBqX9
zR_uz$g(t66svBgp?V5_m`s<$Oi1BQ;il-DAR~40v?bfmgR*TfKE7ot?ye{KtmE`oz
zdQGu@(;|jc66wWMz1mq!n6&XW*GLGe#_p3ACrZtALHWbu~%<@x4G
z<5%N?aH0vJRae%yH>6Ea79{&_n>Db2Su=kXcsxI!E1`z4t-%kIKL(F
z#z{@nB|Imfz@K}wGN-J^^LrgXBYRBUBIldZ0m4DZgx(2}Zt4dmm09cR2nWgz6g0Vf
zH=VM_9l=;W7aht(!0A8$+F^}i;lEUz!v|sW#=r-+@R;ACv`8!fvG|FpxZWfn1xHq+_@$6x*#Qcs
zfoy*!+wv46<5;!Z?>Nv6pd>;z7Lsu^bvWy)X839dX{@;W7Om3ddOs;+Zx+$d4
zG~UiAt^y$BZUS^A>IbNyST%ziN`)J&f5rC6&D++o72Bpa&6cH8#WhvRh=P2Tvwp&g
z1sYoL&TnZs%~e2rUArj|poFF}-^DkS%iuL&n7P7Tu$vUO+6N(4x(IzF?oUARLN#1J
z?!E)YiTxoIKB4i^I4%Tg5}$cXNA-{}gwc>`y~{c0v?lAP;FRXc97Y+D2c*h3K}0SS
zDVX*gN&#}TL`2GT>e|Gd1cyg@;AKe#M4pU0)7J2mHX^gLv&^YZx11`1oa)&GGwDrX
z2ceOOB{c;{BGshj7_1_alNPlwF{DUgz$h4$7DfbyM(k>pE&w5tCX)-um
zVka7RWtvACF?4u;_cZTyP4g;3(zdONA~@G-usN}IC^c+#e?UQl*CvbO((V(hz{qyj
zB@G4a+U-8e#ctf|E)y4CQb;^a+Fw_6OU2m)&=OET$CJiriU*+sNP+XS{==&nKIu2yssch6C)n_xS~w|X7a*-_Tb|Gla+V*C
z9S4FsqBZ4=bV~p~;_x1?2YE_CaoA2qJI<*)!qznfbSt@KOhiz6AtA+A;;lRLQ0!>B
ze}@!RQLsfC6#z=&0wM`6NCh#WDlB@rxbQ-I0&!D`m0R4cwFv~-#%;6(`s$!fWc5jGg48`@%VpY$6kmt>ftucUnhHjVrZ{#zLYe
z{Z|83XotC)P))b0cI5I@iTiv=7j_Uj`*|v=IwE8lhr3=I_iTH0dZKukT}023MQ1VG
z?DmH6^lIDW3ibp$K>#L?MI?(7B>`9**ker7p9@c?q+z7y$5xj4J{g@R7xfgbU`QzB
zpl#&eI{I`;d%%6k{X)8g`;1EZI4uVC2x##ISut87c&~cm;^IpP@XGWfC*(2<#7Q+A
zM{nTELqJ6|R5G?$w3#*{*G8yO6sOJ_uyi_br5j5RX*?fF
z0i{5t&IENZfXAH!fV7rxb3Iai)&K{};
z1RKjo-8f%XLE)b!5_h<40-dmxju9}UL}Zg%SU70hQ}i@;3m|r-EgdyEQH~=}
zWyzk5CPCGFC<1Av+1;vnC0)&v&&ZCE<-v6-DcFxofGeuo>8
z9W{o*I9!f=1+oM98jPVDh&Z}!G9n0ckRp8NVNuddYWTki7F*hFfI-WyW?*YB6ESJx
z`5rP$&8r8To)tR*Dy1TP+SJw3%n-sO&xW<2d4^M05Go8zA6HPL9`n(x}l_0cEy
zF#$!GVg&uA#G-*Orc+orjC6@hP4T-x7!<(C9eo*0)nhDePOr%54N_&S3~Va8Oev@a
zJUd}n6U|r&6|#0mG$!{ssBs5$GQzimwrvJgX2P*)9N!7ll10lwiUUTi>;*ldTZr)_
z`a?b*u#73)~0aGs$d)c0tF9{OMr#p-4Iz%SYvryszj>7Ob(!QsLYk
z5Q)v5l8&En@;O~J6k{vp(Kwk?k!W4T*B|oNs!->=Vz(F?=Afs79U3g)i<>cYW{Yfa
zI8z)Q8!F~U*9{hF_jz_`I8(}xvf)f&q&SSVhjSyt^XytSM;wFW3&H$oDKlCsjz}=1
zmL8JvA>epntW+u$Ss{}zjE$B`WB63e6^iofA4aV@ggbFod^yB&EYGkPcsG6z|6FVl
z7&4X{&5aC=`qMF)R>?7(GF(71S_MrT+okUjB~xep0ftNN5m-SR9%6L7!7&_lu$YG>
znUN9<8XL|G6~YBCdaSo(ku-^bhboK|ei0z~4+wjtA|+2y$DP19*=eO;cCn$@Z@0!p
z>(NCdq0|Lci00w*u22!5qe=KobBL9u`{ZRAa=_fA3y07aff^-vs-mZD&!5uC6bqJ&
zzPe_plF?41bQFDq8We7^z+x=*wKv@f4XsBdAfALOo*AXhniM?11_
zUQXr^pB8c~pBFbbI~yy*e{U@8yliZD3^rb$%GCcUt2fOB}Bh@8k}`_c@oWMTuzZT&2jm+P?EFbQzyl*DKI6Ok$n+^H};C`
z!EXZNUk;|vzd{-8OZrz1H0`a|RZhHij=Ve9Kf&`!OLR^gz`UnTs}Q|
zO=;2d)m2v8$gbP8-Os6)R|{#ZyOmFtc3t{x+~$r=QvFNhjIRtb15nBU^is(-*`GO+
z{+A$I9*W@^jnbA(8yZ0!TGohayh_f0=2Ov@454z5{eKxL04Re}SeogdCI6=tB{*?P
zqz?A8NfyrdFPgn;<$Jh_3;#*F<%FO|2xJySdgnwiKnN}siH027|4BYOLH_^h1iC{*
z+PzA+)#vNjDYN7B%hlvP+}HxgbWPTq&Im!I?B@uvlWZQY$@Ba?ch3Eo&$Trg3XG;p
z3dysgBOG#sT-A+N!V5VbDs%Xp+%^LDF%3anotMGc8(9a+-flxHsLCDtyZs{+BLpp;
zHlLr)vpJ?L%=3L`Yaw>PdestzAy3d`u|1&;*X$yj|7QO=1IT|6v&QQov3z!CU;no`
z8F`(}?`W{MC*F2H`6GJhK0~-f>w5U`(b3TFrJwM7XUyIZjV&4Ve-2Y9|I>;pszwar
zF0#{n8M|e7XCC%8pZV=4FGUPuJLvv91D6)V+rV+SRmW-v4!A5l6GYn9f+br;`ICL4
zlP7GozxOdl-44-YVdk#Q`}Hv-$x-u>cf{}ij(tsD#m%a3oY+OWy^fYptfLk9=ybgF
zm0_@>^CoM5c(k^rYS_>I8MG0mrxMc}KW5ATZD-GfUsqtnvZNzawpm!)arpB>HT^@+
zdL;cZj%Hqy=)(HutLc9MGEkD+^_=Wy8|5)Ew$$u7SFq13EjL80&v_9$zq_f!uR6w`
zLg-kXadmKlP+724tFcSIxc&D#T-wj&E>8|;%V#f@5JqSW#oOc?B)a+;jNu
zj%%5l0v^wcYTKIjX#QV!&uf3WeBUlEo-^PXDusW|Uf(BeW7+<`yEyPoon=<^iHlWK
z-!wHfC0X_MGU>ybet1~{J1#)fU~v*iwfj0rI_qMg
z*=*gHJ9)f%(c$rP;OHiiG^sKu{l5gM{eAFmTiPWcd^%mHx0iSn62rIu`%9^kBco@4
ze2=twSf%ii&Q(vUHK`qg(LcJmg_1HXQ|Q)?36mwZuh;YYf8bKnCs#Vi2-7r|&(N6_
zNfGNc6^>Es4`R723hJF-nwatVIdHVn-(t)F{l7lbv;5I!qpRsl4W05#6klyO+ubD|APr)CYMh^2cx7>L`51}y
zx~$BLk?Jcp=d;yj67nRv^1No;F+On0*0#NYP38+&II}zD9w)q+`@Lb04-{d%impNUvLt!X(LO*U5wY?Bl6^LjaKlLHB@Yrj2@&3YkJ
z37MYLhHqgsp_$`_U!gSPHj!_5^8wGGUvx?q8BvVafg%bUV#BN}N?XByvvcd~
z+OU5Kvm1+)-c>Uyciwvo8ra;-{qI_&VL1ObkfGjoU~y*1M{s-o)GEtUwXtf_@Pc>h
z7(xC6M(o{dYMj}9>dE&prt2aHrfbOvQuhjp|2ioryb3X=v2jbE4^x}#pezDCfeP*|
zH>}?hozyXW+xxbY{pV0Rr{%Y}odkU}ZJzqSxqf>&+$f8S^VCyW|2wemH6~UqP`=V)
zmE?!B?3>NX>iX^U&*gbcJ()}?@C>{#1AQ!)cb*1xjZWF^#BrdB{HrO9q~Qu-1oP{U
zjPhrM?PqR3Gm-{|H=Vn9#(_yMu
zNT%$DNFCQBPq_PusT15h2S6rr_&vLW7iLhvRwQl=#Y}DpBgWxlUj8$lR
zAG5Nwlqka;){;pUC(=^gI|NedAAp_I^Pel59{v{qBW!P&EhNxnhgVoIoTonCxuq6O
zJ2cUu@7{nT{X(pFvlj6%w)R2{S8j#1Ub@0xSty+YnK@Vb{BK+07{S0vjo0mg&=OvO
zjJCFRUzc>m!juu-?aU|{Y;buupgWk~kO!Bai%bBcv~!I+BDVhZFiLw`F8FkIoqa1U
z{T_kO){=ESjI{L$SSe3e*^HIc2uw4Oks^QsCJNeRvBsQnoZc{))Zy&iiJ4&+3y;O;
zoNd^L3;hEbEOdt(MvOS7R|eVGlDT(BVdMGvDScsj@o8H@G=Br^Ce5=)W*s*mHTBy5
zWRMeby9M!@P6svyFcDflPC$ZyP3OaskcC9!uRl-M?+KlG#^6?w7*YIZzr7G497BO3
zfrMlo9BJJim14n!9D~y)bvG|*O1|g`FyJV5U}w0CHn4ELOjI85iIAzPG$4mk0*M`bVI*Tm@M6ofbi?>PQ^hiCuo
zb6+mO;^mKo$$KGQhT{>NBS!Y;_wuTsE@;i&!B}-QHLKD}b#-;^`k_}-;nj_ow}Z;Q
zDPale9K(;D)!Q-K0ExeNP}6bMY?mpJwze=;k>9#Ii(XM-5!6b`e^vDZEs^DnwJ*0B
z>b3iL_yDomZE{ME^-r+sAP8Gi5(;@pZC5NdwTMo!onuHG2VfnK9g~u77B|>6@lS1}
zH#7e70Az)!dkt4ep5I=CRzUO0=wm7HYjXJmul$9=f=JF>H+MG_Ljlsi9_9_K;eIxQ
zx`KDU$<>8$t#O~UKDT5Kl2OmVTiP6FRs;Ih{Jf^2bIR%1Q{eO$z9An?Svi;~rZW8Irxopk*EDiO(PJuCs4%(mP*nTbp)zAyUiet*DZ~
ze=(9#<(K$;j5@c>5#@7%J6j$pcwqX7V-PdBsq2CQ_}7^rf0Ve?Ut*zy2@?Kj|MOE
z?+>~I3%2t1UTz4hh*XW&d`!V}
zgOdD4bXd_~STH;oPb+ekIAI_5D25}+X^_Pilq&8OMfH`+H+eXGCt+&akZ`_jJ+e9u
z8mm*l)>zATCO0~U6TzDoBmI8m2J>!DBj+L))|y98Cf^YX{J@N_ILIJy;fhXA8Y0CL
z!ng)vk%0u{%S{5o`vMoYlO%ec4^GEgj&^S+6N-k!t4uV3HfA`BMLyg_RM<$p3=nLXwY1-LLo6app=M@uk1=g%Cfxv^@DIe{?fMAf1RwzIce*u;z($kh8?xrr@Q8cc`Nt#BRPh|`W_G6P}z3`@UiW^
z#1eIR;-n^Hbyn&ENTgE!ZZTtQa0yLoQ|a)$)z}SbPnaegk3_(-i4F%zG1V%qtcpSH
zEwj&fj%DMPj54G9p_@OI$o>A>Mb8aw;55MT4Z^mKcYPvue~?Sw4E@+40dQkxj9^02
z*?Q*a=vFOda$!H%p*pHeKla;?F)`o|fx(tlR04eb3b${gmdVWBocf&4#`V?oDJphxY5i&G!qBF86>q!3WULPhwF}
zsZx%}Qc;``;@pxED&bqB&3qK6l_||?a%qg`5Ennc>rpp8Pqz5et~vkX;vW~wpF8`z
zal(^9$$N3)u3}AY@XWkfN(?By(lbeEcH&Y7!QaT$F2!WAEvlNAreMcmf_J_WUa30W
zEvTjGK#yMaE*kh$Esd@ur6wj#3HeW5z#0#ru6;XydZ@3d8H_Ei4IO4MTZu3aOXXOmnpfMR)ei+KREv{^
z30y3N5Gb`ctcXyTs(_%2TuLn6=wt#?4SLsb`QEk{3=N1VAh!t(b@
zvK+)pyqw<79RrY5s@pF3B4uTXd)w$kDxqDjkWNHJ>;nZL?+PMFpps3fY!SOfjep)y
zltt1t)dApmqZ&PQ+@0a!P8x`c0oV(?jhGU0MmJR|`Cnh%H#*3mjYQGbwrTKh&w2?s
z&Xy_G^(9i&Mm;BiF5UcP<`kz_QU3&*NKCJU%kcdP5w(_)3bloD4f
z6LPYkPJ8=?lp!8}TT@ea&OPNaSkO1LE?94ZUp`c>9gU$J%#GWSOnOEYPM#xtUhUvB
z0r=oy`e}|zJ{81-9ctv_UrXiUw9s(I6e3^3hGij>0T1;NjUotqVOqvm?I(;WLEqy9
zZs5To4qJBP`AkpXBk_Jz75=K~pPH35!t)nU_sNf@rdd_dWOXRzcIVTSb$}6Z&1Fe_@4MBAy@ZiS
z(#-}Vvi5s%UYF6}Vlq-t2KQ*IS@yS5Yw_=eN7$|JmGZ?Q%3+OgtD
zdl6u*D>aiHP}XYE0$~Nj85IA)RB=R2CmJU#_|dUrvk^+dc2mHQDOw6!-6wxAlz`@F
z@hyh=M`Io+?L>@YFJ@tf<;YFq##*Jhyt#xNWm^jwj9CNP?>MMqEaLX)UmGXn5y1!J
z*>IypFc)3_{Ks9uw1j%pyv)z`5I@_)Hj_BRyhgZSJaG#Uxo4{0ltjb}FtdosZZLA|
z!qe@*(rb6f?)aBP6hpMH&wdz~^I6AH^4>w$}`AR5YkvZC8>54Tj8;6<3X0w4tgSeVU$LDc5o*PJ;F%
zU9Pa7g*gR5I6jBI5^x#PP|(LOypWAx$1-6+6~gZT#9cNjasj$G#3N8cpk25KXtT)w
zsKr~glPY|>jvw>d-#_Qub#9dhb#$3$D#C<6Mjg9k3l2YP563Csl7FU9x0r$bSJG6Z
zUY!)~K<%>>*JPGQ>%Kf{U1)rZ$iCKpKeNpK%;s)aT6W#4y$`xAF8^oda^l?66Q)QUEnW|P8wR7`ayh?Tdt!asc^s8BOW
zSYh~4)3zxA0rKMj%Qeh^cFeFw4^^Dm9E>v*74UlU(7S%x&}g={QDi@eAJ4|rMLGTl
zr1N$$o6MhUZg31#>d6#UH$`4d?7(+*{~n>wy225%c3y0n5!##eO~Z?T3rG8*b3Vzw
zlX)zHvz6us(I=j)vX)sWVZQ!;y;<+DXA%1Q6N&IjK{y*N)-$g;80qI37Jg6Rm$Dd-
zDz9jhZKj#Le{Y8(@xt)Kq(nXRxM*HQ+_wMEjkDrOMwP7Ay91qd!
z{9Pqg+IB*q15_0Cj>#B>=P?plwpTQ_=kPTla%d=!YC!{_JMOC-{g8Od`G@~-Pjr=~
zIosArvtjCG?%rO$Cc6S1Wu2i!^AXSjp2rO90Nne_Uy5iI8?qn}-A~_U%AI@V|Fp3n
zRPy<>@_k&p9|Q&xOGtKTX3EQy*5UO5TOTMJA<$UF1Rvu(8ME
zcK}0P58fX2?Y{Jm5}iA&c!y?*;Xh&FO#F*^j3V=q+Ox|QN}lsW#2;9n1WvQpwc^A!
zocUqGxf9G+oDVy2F_j(&myKODYJK>MmJ4pf2pqwiB^C!Ko0Sa@bKPBU?PEW*9An>3
zm#}S+L;cpueScx2&+moGp3G-Hu=mNkxaMfbi+~F*Qc`mnSlDi3y~5!fkCTC_n9MD7
zf81;`A7n{JDLTN>OV%xavr
z6LHNLd+hG7$aD;g}C+*rT$(vv1Ts-_C&}tph`0+GOzuGNnDA8?_CAgtVk!IlSI*Wg&
zX6qQ&a^M#l!Mh#vzH;SMGIb-=DpawT=`amj=?A-D~nGVNFY1-;r$EY=>TR
zY@xwoYJw7|@Vu4iZT**q_-$zgU4%cvtcb=@=_GNFIV^TguEQ{Gph#<+jmI3}FD(AzMcbq~N{
zSO(9{xXK0+@#S#p#X!)Jfa`*#(95zyV5^hZ22t+|x&-@*7V!y?r00zZs
zGUl|+;#xv_EIc34m3e(QW@wloi0AE3V#0yLkdGt*@JOIie(WQM^sNWxZ>&^%w^>lQ
zCUjc<<9nhCD2JpK6VINTEA|&Is(jRy(uzP*J0@47hw%f6Jd@q+3o9<2xdIpqHApXI
z<8-6n;O_@%%dHltaGm_%y|y7s`u31hyo}NgFM=;k0Ba?06T#}V-a%!8(oRCqk6a0!
zuqS6S^}AFPTw1&575Q@~`58;U;N@5Qx*tF#rE%Q6-mvT?o@b6A9cIOl@QAcHPKybW
zp1mnEDJk9k&Lv~te?PypBu)5Dv!g!x+yv=XzgkadCHQiy+H7GUe{UHMlAJX8g((m$
zhZe;Zmm&4a-Q{M@M1CCA(O{-_HTDc%$HQeSS_O_SX~)}6Bu5D_)=Rtf^?uHNgiLoL
zQ>3#JEq=;6Ry{Ze=Exth2V}c4~uw7@bTM|fK#2WBxc;;fGQL;fS=R4Wv
z!xjeh4FQ!rnmv{LRmwmS{6V2l0*u8n)`KlIkwF53h4D!*kV3NFyJ_NLp1{YcTRq@x
zc6&p&S{dq8jGN{9!O(`{v=BzKG~%)!H5P(ZhH*l)yc@|W5J}IU>Id<3w=U(m8J`-O
zh4}5bc)t;@_a++)HvaLA+I4*6ENqIB1=)AU_-~0bVf|{MhPnS-F$;h65jH;_6q4_|
zC{(iE4Yq8NME*q1F&
zT)Wz(@k{xkKs-2j`2>e+MM>*Zq;WAyf~2RC4DIz26u)xaEaA7QfM1Xb>kEw=M+yv?ja-bMUy$Noy5#!<;~h^YI46V^VIic
z+;{okO|i4L?UY+W!NcC6r%HB1jzjtS;8>*B6QwOvM0^-ttLSDdqBg(FQ;GAUWrWj7dkb5VTYMK&LPAq?VI-~(
zDAV?({HwOdXDeXnaN>o8=;zgmUkZWLF<1s)Vwn|P9+_gP5GVEZB6nNrd1;u0=t_@l
zoKKA}H4Zv6CM-8+9bk!rh*ZIH)S;B>xW$Ra42iDKUp1kMO-*jxCJN{a*OY!;RFob@
zQ~d!B=3nxo&L>K=1COObxhSzC)IXOZ(I+aP>oNKNnHh+hPd+5vASRbfni;@ej+mIT
zpV_k@L}~b@{t2xS&nGG5D&$E^C;(tqrsZ=+>l3N
zEnJv*E{VLNF%`?F-bhaf5hj9-1&6+^umCwWIY(6~r2K8nYtYQ1Z1)%aRAjsG?-8kS
zq6meg2x*p2EZ
z?(kXJE%@S(MEfOnN9YWGIN;Y$C8D(`$^ulBQ6spFD$9jUj@z4VYFKQBky7@YWR@wm
z)|RxtU*%%E$%)3qd;@z?AW|iY8
zo#3?wD?F@)BC#CQ4o$d+wbvT}llk_RtpwoXEoFgAL2k6*9R8uenue2<6-=@fW&))P
zil%PMo){*G;FAcEZa<~CoVDv#3^KPg6r2y|NK?9)0%xTpy_yp4^hW#&Op$MrEzn)wEy5=(dQ>EUI1M%y`W;Xtn44}a?5<8Vfh?@Nce38R+52J
z_Fq&@5PalITY*N9NBJEm@kQy88fa(ZRdZ|
zEMmmh^f>SeYe{7iydh=x>zMB>!$nn!iO$Iq$>Y%g76lBfFGp&D+NouO#S4kowv(Q~
zeqzbIe+R8oS)8ve+V$#+neE%@jf_}2B#5!EACEuNQsy^zQ$Us_tWVP7c5{9>Z0Tb#+oatggiRCq%=vN30Sap9lW>&b2KBM<05rWOR^j`
z3{-20IoqHQxFe(An_HEZO_!#iPv>NBBOEvJB{g7FJFR6|L)|de+SxYIo~qRIf?iPM
z6yue_pF@sJdhMZ`h#19B-ifM~okaL(ns6G|NkyuBo^*fKMT*sAN~3H4@I49qw_drd
zHIeDJT$z!6Z;(Xo7%m1UUcgu|{a3}xS57Wbd#y73Yi0S?$XNC+sqVE+OzrbpdAFJa
z*}ul3#M+0yn5?~xd1dceu05Ra?bXZv
z?Nifbhl`zF*UwM%fwK7JE~eVE5uO3Ni3}I~RX9|4d;}(4j>hyNfxA$+pmdC;T?AjO
zRS!O_2PNP+`;6o_FHnW=^+|$Fp<7W(qOhLcPJE6EKQ%}AH2N*bklPj(3|e}!t+z1b
zuyrrduJ_29T)F&QGPL$*%tM4}c%CBJU=M1E^anzJ)-O>6jbdLt37isqR=9&!ij7e_
zic_?HLi42QGvLA%lyd(MAj=ir60E8a@_2+lSB4Ve||C_S5g1EhZ-UEJnBl4qS1Xw(I26wFR0R
zeQ!=*odP90yYtg_JxtW{rZV7eaO&^|qQbHQ4phP=_|#&
z@3?S^t8)0zW|8l`$mZ6P+*l(ZpB_dC)nxz2->eD$taM%
zR|muFtKh4et_~8V+BZ^~nttFha5?-4=zA4G|E`^uIk{tP2evT64jUND?~aNNjD+m{
zm^>!oEI08YL(L$Q(IQr&a&Fopu#5)~`}S)XqZU@#eR$C1DCqtvHnA~RaWmRTdp-P^
zXC1SM3NYsym~#Z77dOt91a(t3d>4=_x%f*DG9*VZfT!RLlYILI>j3n=K4R#f4gCZ#
z(IrmwE|tyhZNw2pcGx>~dF;ox(AP;wXPX6iOdkkJ;DJQOdlUh+*YN)48BZon@Z*BX
zShh_;SZF|*fXqa^l&9gyRFTTq)5kB{_hvC8M;nNXLVVFE{fx5_XhZ={%U0?4#)lDT
z>RUfxjAYG51m2Vnr(Rs@E%G>Q!-bJ7M)JZYNA1_1Fs>~*iH!G?vP6R}K{8yieEl2!v0>ZR(1~gL@vlq86V63Q8P||Te`dlWfi3DhJK6%8
zB4(b8sm!jeU8bw4xr4rSeidyF9|P;nZ?7HA?>C*Rj-FT5hOBBYLHv$qtH=JXn5<}c
z-pEQoBcG@GFYdfz%fT6RN{U3o61S;5uCABvkvuoL39PVmLqpq3JGLwXK
zye!)exTQuodt#Q?7_0HkA8I3&UsGyP(t=SpXvj>iSbWw`(Q~X$7?Al6xI5P$g^n>L
zSqbIws(Jfzd{vzUVLdYAmiSD0E-2xHGr=)^OChU>#|P|}^JBB~(6qBPCLbQdjRDo7
zC*1<-x>igP?59+&)gA^mO6o|y9^^M03S$IDk-a9rQ2Z&{Ek-j%#%UaYJE)rIg!_T!
z2y@a~gC;LsKOq=WT?AQXpONqG`|v*lGH;r)MZm5j+-3qRULpHvd
zm~|Vj{aw$_FK73+d(_L;>98$30O!&HQv^7%-sOtb5gKL3LYgX{D5*@k?!`0nUBJQb)J!MWunaC(*9$g2V9yox+gK2TCADh*eT=_Rs-kLZU4HA-yE
z#&HfsOYGndPNWa5yG4ms#EmjG==T)fy^r8kIyGy_(bF{IAL6uNRAVU4lIVnFzCS!TjBYY4KhVvUAeiG(kCcr!$+SvZUF)
zHup8c?K&&7m{~7jcUZKjq>f&3MlFTOZ*$w*Q@=;8l%Lu}^LAGnTK8&I=R_KN%jI6<
zJayLh^B-HuRZ390#CIT1%Z4&nRSx%Y)=|KbS52yP67p>H=F$mJYYc_>*_QfyY+hmI
zCcN!u6{dupLY?oYyZZq?r^WRVIO^%D{KE_iV$uxtaQILYBBVs180G$52X(tD@E4y^
zXz^4$v09mKa4saDIuJmIL=Ml+J}hCA)SHy@L?hh3f|^-zqAiC1#Pbe0|#Mi=q9gxZ7m@1f2;(2R!0aGOxcx>VX--3)4
zx+Byar_@0kUyr$9XXU!gr<;uwXRJW-lRseDz}I+ts@~QmWZ?eLXr8=HD<5s(a5I`{
zNmsEsD8NQn1ctz|j=pYTw@Pr}F%O3XW#S;i;V5~C{m$+^5euZPpNlz}r%rWK)5^nE
z8lk7WH;76!7@7Bvh@=;@QzWJ#h&ImpXUFw$R^oMpIqteTmxAF^4u1&Z<|DV
zMc3S(;NQXB`detE*?~bhNYiyj^62qN0cf(C34VEhzYLff({=1f5!BgqU$qzhxQ+|B
zNy>ZMf)j3eIjN}mb3kBFcMz9jcdFkM@G_gH7XH5Z@8hx2(D69_()Wnl+sqh%oll>7Iy%gFr5`6xh;7St(Ph#Q`z~AQye_
zxlpKAusfWEV5pE5gQ}?R)}lH5+;?YX%}(6TzoYf~2-j(Wla4b-pHX>*QhjQF_uPCo
zVPTkFjNZxW#}oe$zNq7}UvWK|E7NatuhMBWd7l~{UlQm^She~^MA4{Mo0|m
zlDZx);+mJ1KSBQom2koA2z&RsiQFO5fVTu`k^;Qf<*lm-QvauiRmX_%Z=|&CpR@}Y
zIW#&s#DtaS2;sLNlgj6iUswydgpTd#|IpdsMqFIyJp;u?1^2NeNwt9~w>d@Ny}`d=
zQ6v+mgYD0GpS-No+humq(b1gO$8};^9Enar=F4>6z=Oq6^
z{)PEv8Tuxl+#Ec-=46kP0exB6M>7Akh~uR8ZT)ASr!?!L80ZC
zR~g*>b?tE%>kG5Fzm@iA*lt&BYs^D9eV&RSP6J*_18yjPA-nvLBcNv%R42Bk8#(4Q
z$~bRN7OIL1_e0OC|47%6=iQYyljT|%Z=}CmxX~SmkwzCD&c1-iYQ$f~Sn%3Z+$mLVb=q!xCHhG|Vs^lJjS`lkb4n*&x^E&DH?_Z&z=z7kckShC@t9nF0O
zr0xs3-`=7BL205_d#v3qlnugNVw>3CS;r3D_lAv5*;$7i!=SRIw;(cOnUNA|6Xlig
zXGMrLA;^Yih-DJn!`8;Zs~AVyKhEF*+f|a{6L`CF9o*0q)15)-8S7*=h)1BD1>DU@
zqsKjN_%N3=@6oK%%2gG-5qqrl%npV>EOyPV>+bwiEbwXSQ9+FV80FOhNwnq(5a6}7Ym^r5{Bn-eG(hs(A+4@
zD58L!vRF;_Ilj%2B4w9QILAyfWr(ioFu*D*(Z0vfR~UhsAdh@4wl}nmDmAvZ;zv;u
zs^uc_yY+7%ADI~hP6!-Yaxu9+zvH?3H8%6GmO`hz`t(U>>&Xmq3|7hSq
zccyFzANsM-(er|g{D=SR>SiHR<9V6txo9edF1{*45l7(wwN9ve-l;cB;1rkF5bVwkbqM0
zq%Xf=>di>RyE!XBUQIuDN)p6^4*nY#kFI$`lUUcIoZy>7QR189>}R99l4P>^vd}DG
zBBv9T3q_?IY%sc8mPVohqq*^yUHiOs5?ga!4o}!AW(VUWi<*@uAh0%cTV=6H%Y56>
z%kBJpt|o(JsOh1;Ko~NC6V96-2AFa;U6L3x)|1eWh98P5(&N;(Eb&Bpdp$D*=M5Y!
zXgBFZ04#{QBPin#pP)(k^N(dW*5m0W2F(&dU0#K0`&0dB=d56as!;kMwiw-JN%fblI$qJo8&;SSfs?tir;kBd7COn@vCa
z6(jNc3!PfBheobFE!od*Tprpi{gRg&|9b`lF-(IKR0lDlDC2d*&r(sj%v?bl|HIo^
zBFaPuS^{r~bdZ0wQc~eT1>)p7(f&(ORBgn2e6l)1(F(**U&Pmf&mGLD<8O(1*%^YU
zLQiB*At}Btf$$6HDI%i$`$x&M>L@Dkr`Q&#p~Y8I0Us_lQgXM3ANz)6Wu^6Z3NPEi
zd2DV>25+G}GM3NJ-Ub=bWc}n2U?>emL2Ov#amb$J!tn?N7Mh!(HIUh5k>S(;cQ8WE*%%P#f6-1LXT(7MvU
z{2fU~DBIQv@t}5!+1$T6kd?uAmc#ub1o#+6ZvIb9%8cRSqebpdZ5+8yv=!|`*H_IA
z=h*N8UP6dPOVF=d)Mm)ir4LsN&ql@Rm7Y_Oqw<09U(5%^q&TQ?7)18s-UAZ>4?f@a
z_Z7L<@3J=E!l8STHo{Z_QA2~cWMw|%LB^a$1=>EhYQmqAo_YDowRo6T#pX4f&>>&v
zcXO+^(4TR>(iGRIJjdTdBg(Qh3dj;F9sUx*kkQ_jCPLi>$!-wx#9n4_l0?>>M4^8p
zbdj#imd^}i7@N1R%*ssdIuX*^h`((=sKxvSxNWe&Tv_Azgf$g`BOMm?N)<9f+D(+K
zk*tjP=6gAut81Jd$hs*!G-MBM&0-)yo@@2q4Il50{^-?weWbvqzC4y0IT$N>k{N;L
zvRim3Z!MsyE}>cxeZGCpEPn``#QC)l)f@7LE??ZF9yGq25~u%n^;23}?Q?SH*dO7C
zr;4&l)(V&UGn&ZrlceuQ(jsVj6znx!AKqv`Qpzv!e~@pFEO
zS_H}J+1Esf(a04@kiRoh#Eiq`z`D{A+$~U_&lHJVZ;_AmsP+
zuYJWLG{AS%J=+x^;dV3fG)7J4tJ=V*;+bBh)AU9|9?F25wb?A*3wzMwl|6S9eMhLc
z;+iU*d(&`x{XLQyt>M+2OKFU3H6Tq%0$w;kHBkd1Ie-*8TUo!zLIRN}+%m9Zw3#63
zW`0?aV_bL7Av=_R8zbCx4`vw{TFo|US<0Cm4F|NgYay$KYVK9nViolpXzQ3|vE^>a
z_SU5TuoV|2fCOaj+RiKqAzC@1RF;lRNjuM=uagE)G<751wJ&%Wqy99(Aw7hg^O4^S
zO4|<8_`3@2xAf3W6aOOxDk;8HaKk@E%NPZB_X{wk?0tVo;g)afznLk>R4YK(Pm$8UsFZqj>)N*j^t{@8$u4ar>hT4rfkSw!jPs2T~Fv09g
zalo{5kj1^7;NJ7l%7#b9R4I*irGc%8LQJ)>*6V-?P&tvJ0uc=p6(mn{HxSl89=K%n
ziepatdE!ljJDR@VxTn}$4QU`W?C39%E}2zv<1k5$#y=|Dab|QY9Qbq(mtEP>3}~U6hE4_&Wf8>p;0;&~fIwl*_QD$;
z%acLX3>M+`IZpIJioKs?32mX{0RT+Mwb_h*0Vj|CJ3X~LXV8}$u89}2*G;f6
zu&1&4^O4p3=f6X0ZMIZSv@pEw(}5CBgCq6-)w-u{r-D~
z!BYi_l+*YEO-<9_oVsOHSPd4Jr+K7lAU2J!}-;JiAH
z@NVvEwp^tIo5&Uz<)uX0uTEi08DA{~hKD~dn5#U91^A!PGMOVr2uJi~vC#fiopFJy
zKN?=`Aj>M#xEAaI0{PGQht0zctS?k=!V25vR1L(%)*l_LtbBxRzGNgkTwpR=>d^F
zKJp>B=d={Cr;gPhxEaL*i@`o_vbP0agk6AaYUtZ*QqwB*lXdBG1kPLdyP-0c=BrP@
zmGUOw?uZg;s1CLe?dx~PRrJ-OR-_Q`x*en)f+zKJT~5d`)VZ=8+H{RqK9fmRHH=x^
zX0{sAPNy{mkW=+0TF9gw-vZu`c%+H@&r>5i!m0*P_&!eG64uJ=NaN#~q8m*109zrN
zzneZmK=|Bl>j8-?&t=(VhZV$c<{p+y`B^EsxuO{CuHb2R-*bJPOxB}zt)-Ak$3GvX
zwRS-xQ;0gysuIw1AAhQv&|lW@YXwK=0HZrCAxnq*6(Gg#LJ5iA(xuh5hSD{5`mzF$
z8y
zXxr%J3%+kX-&D3{%TfXMN)(o#!k&geqACyN3Hu`UEeku``!rJ=!1E*ydoVvq3wW9~
zaqB|kiTL$oG!lklqa;7}S&f$T+Yc3*#sG(R0SwOMAD%@;`7DdrhG>gU9fw`mkRbGe
z$@!B(xQ_S6ny+Gc-EiY#md16g>p1xLkrHsazbTKtPVE1}B#0^)8>FU8UuYjA!QMqv
z*H{Wv;FKXz#n9i^2J$O0SXVrodXraLn0c5xSTf5SDjEK%CLw$~`>LSem@TG@06M=A
z?5Za0&E+hZW+*_Lo$Vq<>>xz+TWUDY%j7hDuGdXR&wMV-z{&(LdXJDemRM0o`?GR3
zI?5p;eIkJFn9?3@W9)Qv%5X%BIMQrVkGi_AhfQ2@qWuqe`ld1bk?)JLUyQy}_-}j_
z(h$}7t#tHHS5w#daL`;m!d>b8-&sJk2@O~CH0V(-(oUT(?nH>Djm9r{oHfCbZZ*&KJMuZZ
zPlMd$1JCz!W}#=1Je0}BNdlwBHjj5_!<+Jz)AGd}b4HzZB1B^3u%BUKmpm4J)4xVC
zEGC3Jx?g&${{5|7PII_!5_VHDeg9r>Vae3>_D-z`QVJKN5i8&(`rz5_RI&1){f2{R
zj}oRCAy!;4{ib4NLCe9&$=R%0G%gkU!fA77QY7^}k@fngn-4t~J#Y0WvpMh5Fu?q+
zLAn}ATCsl&mATvc^pbyZJL4;KG-|Zx{>(dQzVj!}zGV+kC3v#eMjVYinq@!oZ?F(c
zWD6Wlh}OvepzIyH>*~UP;n=p-q`{8a*lw&H+jbgjCuwZ8F&gX`jqS#6Y};(kzMubi
z&N#2m80QnLxz@VooELt;T4hk~Umfh@RbAEOCX&U6)^-xnC;
zfX*Z~|6G-8k*mpR#9_tWdAe&mC1Mu;fHCR0uR6%d?L~yvfpsWkVW_pe3@mk*>pJ>n798K>=-`fi_S;MwlRsR(QR%
zNQs~Rjtq@7czR?g6Br-`i2~#}k~rIWn-*B@O_?~}!CF%(ht-z?bUU*DHsZc;)vpKO
zA7}g@{Q=N`ow$V1BTt(8V8uz)^DGoBtEANED~4Lo7YVwot?ad+_4yDR)