From 5cf1b98bd20f3a05bb797784755f1df24bc8cd61 Mon Sep 17 00:00:00 2001 From: "Wang, Jiyao" Date: Tue, 5 Nov 2019 11:44:09 -0500 Subject: [PATCH] Display/output salt bridges; color helices and sheets with spectrum in the menu "Color > Secondary > Spectrum". --- CHANGELOG.md | 2 + README.md | 2 +- icn3d.html | 13 +- package.json | 2 +- src/icn3d/display/display_common.js | 68 ++++- src/icn3d/display/display_full.js | 62 +++- src/icn3d/icn3d.js | 2 + src/icn3d/loadpdb.js | 2 - src/icn3d/other.js | 30 ++ src/icn3d/other_full.js | 64 ++++- src/icn3dui/common_full_simple.js | 6 +- src/icn3dui/full_ui.js | 351 ++++++++++++++++------- src/icn3dui/html/set_html.js | 49 +++- src/icn3dui/parsers/mmcif_mmdb_parser.js | 14 +- src/icn3dui/selection/commands.js | 64 ++++- 15 files changed, 574 insertions(+), 157 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 27286541..693d1d72 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,6 @@ ## Change Log +[icn3d-2.8.3](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.3.zip) was release on November 5, 2019. Display/output salt bridges; color helices and sheets with spectrum in the menu "Color > Secondary > Spectrum". + [icn3d-2.8.2](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.2.zip) was release on October 29, 2019. Reduced the size of three.js (version 103) library. Added links to dbSNP in the mouseover texts of SNP annotations. [icn3d-2.8.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.1.zip) was release on October 21, 2019. Fixed the 2D interaction display in structure alignment. The bug was introduced in the last release. diff --git a/README.md b/README.md index bc460f07..f61fdea9 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,7 @@ We provided two types of iCn3D widgets: [basic interface](https://www.ncbi.nlm.n Either of these widgets could be easily added to your own web pages as shown in the section of "Embed iCn3D with iframe or JavaScript libraries" below. -Complete package of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.2.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.2.zip). The "Download ZIP" link in this page does not include third-party libraries. +Complete package of iCn3D including Three.js and jQuery can be downloaded from [https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.3.zip](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-2.8.3.zip). The "Download ZIP" link in this page does not include third-party libraries. ## Usage diff --git a/icn3d.html b/icn3d.html index 98fcdff8..f0f1ee1d 100644 --- a/icn3d.html +++ b/icn3d.html @@ -601,7 +601,7 @@

How to embed iCn3D Structure Viewer in your html page:Embed using iframe

To embed iCn3D Structure Viewer in your own HTML page using iframe, simply add the following to your page: -

<iframe src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup&width=300&height=300&showmenu=0&rotate=0" width="320" height="320" style="border:none"></iframe>

+

<iframe src="https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1tup&width=300&height=300&showcommand=0&mobilemenu=1&showtitle=0" width="320" height="320" style="border:none"></iframe>

  • Embed using Javascript
    @@ -926,10 +926,14 @@

    Menus, Commands, and Methods of the advanced interfaceShow: set chemicalbinding show me.setOption('chemicalbinding', 'show'); Hide: set chemicalbinding hide me.setOption('chemicalbinding', 'hide'); -
    f) View -> H-Bonds to Selection +
    f) View -> H-Bonds Show: hbonds [hbond threshold in angstrom] showHbonds Hide: set hbonds off hideHbonds +
    f) View -> Salt Bridge +Show: salt bridge [salt bridge threshold in angstrom] showSaltbridge +Hide: set salt bridge off hideSaltbridge + g) View -> Interactions Display: select zone cutoff [cutoff in angstrom] pickCustomSphere @@ -954,6 +958,7 @@

    Menus, Commands, and Methods of the advanced interface
    l) View -> Label by Picking Atoms: add label [label text] | x [x] y [y] z [z] | size [label size] | color [FF0000] | background [FFFFFF] addLabel per Selection: add label [label text] | size [label size] | color [FF0000] | background [FFFFFF] addLabel +per Atom: add atom labels addAtomLabels per Residue: add residue labels addResiudeLabels per Chain: add chain labels addLabel N- & C- Termini: add terminal labels addTerminiLabels @@ -1127,6 +1132,7 @@

    Menus, Commands, and Methods of the advanced interfaceColor -> Spectrum: color spectrum setColorByOptions Color -> Secondary (Sheet in Green): color secondary structure setColorByOptions Color -> Secondary (Sheet in Yellow): color secondary structure yellow setColorByOptions +Color -> Secondary (Spectrum): color secondary structure spectrum setColorByOptions Color -> Charge: color charge setColorByOptions Color -> Hydrophobic: color hydrophobic setColorByOptions Color -> Chain: color chain setColorByOptions @@ -1269,6 +1275,7 @@

    Display Options   

    Change Log:back to top

    +icn3d-2.8.3 was release on November 5, 2019. Display/output salt bridges; color helices and sheets with spectrum in the menu "Color > Secondary > Spectrum". + icn3d-2.8.2 was release on October 29, 2019. Reduced the size of three.js (version 103) library. Added links to dbSNP in the mouseover texts of SNP annotations.

    diff --git a/package.json b/package.json index 66360e01..f598aeca 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "icn3d", - "version": "2.8.2", + "version": "2.8.3", "description": "iCn3D Structure Viewer", "main": "index.html", "scripts": { diff --git a/src/icn3d/display/display_common.js b/src/icn3d/display/display_common.js index 42cbddfe..68cebd08 100644 --- a/src/icn3d/display/display_common.js +++ b/src/icn3d/display/display_common.js @@ -90,11 +90,11 @@ iCn3D.prototype.setColorByOptions = function (options, atoms, bUseInputColor) { if(!atom.het) ++cnt; } - var lastTerSerialInv = 1 / cnt; + var lastTerSerialInv = (cnt > 1) ? 1 / (cnt - 1) : 1; for (var i in atoms) { var atom = this.atoms[i]; - atom.color = atom.het ? this.atomColors[atom.elem] || this.defaultAtomColor : new THREE.Color().setHSL(2 / 3 * (1 - idx++ * lastTerSerialInv), 1, 0.45); - //atom.color = this.atomColors[atom.elem] || this.defaultAtomColor; + //atom.color = atom.het ? this.atomColors[atom.elem] || this.defaultAtomColor : new THREE.Color().setHSL(2 / 3 * (1 - idx++ * lastTerSerialInv), 1, 0.45); + atom.color = atom.het ? this.atomColors[atom.elem] || this.defaultAtomColor : new THREE.Color().setHSL(3 / 4 * (1 - idx++ * lastTerSerialInv), 1, 0.45); this.atomPrevColors[i] = atom.color; } @@ -149,6 +149,68 @@ iCn3D.prototype.setColorByOptions = function (options, atoms, bUseInputColor) { break; + case 'secondary structure spectrum': + var idx = 0, cnt = 0; + + var ssArray = [], coilArray = []; + var prevI = -9999, start; + var currSS, prevSS, currResi, prevResi; + for (var i in atoms) { + // only for proteins + if(!this.proteins.hasOwnProperty(i)) continue; + + var atom = this.atoms[i]; + + currSS = atom.ss; + currResi = atom.resi; + + if(prevI == -9999) start = parseInt(i); + + if(prevI != -9999 && (currSS != prevSS || Math.abs(currResi - prevResi) > 1) ) { + if(prevSS == 'coil') { + coilArray.push([start, prevI]); + } + else { + ssArray.push([start, prevI]); + } + start = i; + } + + prevI = parseInt(i); + prevSS = currSS; + prevResi = currResi; + } + + if(prevSS == 'coil') { + coilArray.push([start, prevI]); + } + else { + ssArray.push([start, prevI]); + } + + cnt = ssArray.length; + var lastTerSerialInv = (cnt > 1) ? 1 / (cnt - 1) : 1; + for (var i = 0, il = ssArray.length; i < il; ++i) { + //var color = new THREE.Color().setHSL(2 / 3 * (1 - idx++ * lastTerSerialInv), 1, 0.45); + var color = new THREE.Color().setHSL(3 / 4 * (1 - idx++ * lastTerSerialInv), 1, 0.45); + + for(var serial = ssArray[i][0]; serial <= ssArray[i][1]; ++serial) { + var atom = this.atoms[serial]; + atom.color = color; + this.atomPrevColors[serial] = atom.color; + } + } + + var color = this.ssColors2['coil'] + for (var i = 0, il = coilArray.length; i < il; ++i) { + for(var serial = coilArray[i][0]; serial <= coilArray[i][1]; ++serial) { + var atom = this.atoms[serial]; + atom.color = color; + this.atomPrevColors[serial] = atom.color; + } + } + break; + case 'residue': for (var i in atoms) { var atom = this.atoms[i]; diff --git a/src/icn3d/display/display_full.js b/src/icn3d/display/display_full.js index 0eaaa613..5c4b8ad9 100644 --- a/src/icn3d/display/display_full.js +++ b/src/icn3d/display/display_full.js @@ -69,6 +69,29 @@ iCn3D.prototype.hideHbonds = function () { } }; +iCn3D.prototype.hideSaltbridge = function () { + this.opts["saltbridge"] = "no"; + if(this.lines === undefined) this.lines = {}; + this.lines['saltbridge'] = []; + this.saltbridgepnts = []; + + for(var i in this.atoms) { + this.atoms[i].style2 = 'nothing'; + } + + for(var i in this.sidec) { + if(this.hAtoms.hasOwnProperty(i)) { + this.atoms[i].style2 = this.opts["sidec"]; + } + } + + for(var i in this.water) { + if(this.hAtoms.hasOwnProperty(i)) { + this.atoms[i].style = this.opts["water"]; + } + } +}; + iCn3D.prototype.applySsbondsOptions = function (options) { if(options === undefined) options = this.opts; @@ -477,16 +500,46 @@ iCn3D.prototype.applySurfaceOptions = function (options) { } }; +iCn3D.prototype.setHbondsSaltbridge = function (options, bSaltbridge) { + var hbond_saltbridge = (bSaltbridge !== undefined && bSaltbridge) ? 'saltbridge' : 'hbond'; + var hbonds_saltbridge = (bSaltbridge !== undefined && bSaltbridge) ? 'saltbridge' : 'hbonds'; + + this.lines[hbond_saltbridge] = []; + + if (options[hbonds_saltbridge].toLowerCase() === 'yes') { + var color = '#00FF00'; + var pnts = (bSaltbridge !== undefined && bSaltbridge) ? this.saltbridgepnts : this.hbondpnts; + + for (var i = 0, lim = Math.floor(pnts.length / 2); i < lim; i++) { + var line = {}; + line.position1 = pnts[2 * i].coord; + line.serial1 = pnts[2 * i].serial; + line.position2 = pnts[2 * i + 1].coord; + line.serial2 = pnts[2 * i + 1].serial; + line.color = color; + line.dashed = true; + + // only draw bonds connected with currently displayed atoms + if(line.serial1 !== undefined && line.serial2 !== undefined && !this.dAtoms.hasOwnProperty(line.serial1) && !this.dAtoms.hasOwnProperty(line.serial2)) continue; + + //if(this.lines[hbond_saltbridge] === undefined) this.lines[hbond_saltbridge] = []; + this.lines[hbond_saltbridge].push(line); + } + } +}; + iCn3D.prototype.applyOtherOptions = function (options) { if(options === undefined) options = this.opts; if(this.lines !== undefined) { - this.lines['hbond'] = []; + //this.lines['hbond'] = []; + //this.lines['saltbridge'] = []; //common part options - // lines - //if (options.hbonds.toLowerCase() === 'yes' || options.ncbonds.toLowerCase() === 'yes') { + // hbond lines + this.setHbondsSaltbridge(options); +/* if (options.hbonds.toLowerCase() === 'yes') { var color = '#00FF00'; var pnts = this.hbondpnts; @@ -509,6 +562,9 @@ iCn3D.prototype.applyOtherOptions = function (options) { //this.createLines(this.lines); } +*/ + // salt bridge lines + this.setHbondsSaltbridge(options, true); if (this.pairArray !== undefined && this.pairArray.length > 0) { this.updateStabilizer(); // to update this.stabilizerpnts diff --git a/src/icn3d/icn3d.js b/src/icn3d/icn3d.js index 47cacc6f..cfae3daa 100644 --- a/src/icn3d/icn3d.js +++ b/src/icn3d/icn3d.js @@ -197,6 +197,7 @@ var iCn3D = function (id) { //labels: 'no', //effect: 'none', hbonds: 'no', + saltbridge: 'no', //stabilizer: 'no', ssbonds: 'no', //ncbonds: 'no', @@ -1169,6 +1170,7 @@ iCn3D.prototype = { this.calphas = {}; this.hbondpnts = []; + this.saltbridgepnts = []; this.stabilizerpnts = []; //this.ncbondpnts = []; // non-covalent bonds diff --git a/src/icn3d/loadpdb.js b/src/icn3d/loadpdb.js index 5d371dba..00ad02d8 100644 --- a/src/icn3d/loadpdb.js +++ b/src/icn3d/loadpdb.js @@ -132,8 +132,6 @@ iCn3D.prototype.loadPDB = function (src) { this.ssbondpnts[id].push(resid1); this.ssbondpnts[id].push(resid2); - -console.log("this.ssbondpnts: " + JSON.stringify(this.ssbondpnts)); } else if (record === 'REMARK') { var type = parseInt(line.substr(7, 3)); // from GLMol diff --git a/src/icn3d/other.js b/src/icn3d/other.js index 01c9a66f..33787f70 100644 --- a/src/icn3d/other.js +++ b/src/icn3d/other.js @@ -738,6 +738,36 @@ iCn3D.prototype.addResiudeLabels = function (atoms, bSchematic, alpha) { this.removeHlObjects(); }; +iCn3D.prototype.addAtomLabels = function (atoms) { + var size = 18; + var background = "#CCCCCC"; + + var atomsHash = this.intHash(this.hAtoms, atoms); + + if(this.labels['residue'] === undefined) this.labels['residue'] = []; + + for(var i in atomsHash) { + var atom = this.atoms[i]; + + var label = {}; // Each label contains 'position', 'text', 'color', 'background' + + label.position = atom.coord; + + label.bSchematic = 0; + + label.text = atom.name; + label.size = size; + + var atomColorStr = atom.color.getHexString().toUpperCase(); + label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr; + label.background = background; + + this.labels['residue'].push(label); + } + + this.removeHlObjects(); +}; + iCn3D.prototype.setCenter = function(center) { if(!this.bChainAlign) { this.mdl.position.set(0,0,0); diff --git a/src/icn3d/other_full.js b/src/icn3d/other_full.js index 5fa8d934..b61cbab0 100644 --- a/src/icn3d/other_full.js +++ b/src/icn3d/other_full.js @@ -3,7 +3,7 @@ */ // get hbonds between "molecule" and "chemical" -iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, threshold) { var me = this; +iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, threshold, bSaltbridge) { var me = this; if(Object.keys(startAtoms).length === 0 || Object.keys(targetAtoms).length === 0) return; me.resid2Residhash = {}; @@ -16,8 +16,14 @@ iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, thr for (var i in startAtoms) { var atom = startAtoms[i]; - if(atom.elem === "N" || atom.elem === "O" || atom.elem === "F") { // calculate hydrogen bond - chain_resi_atom = atom.structure + "_" + atom.chain + "_" + atom.resi + "_" + atom.name; + // salt bridge: calculate hydrogen bond between Lys/Arg and Glu/Asp + // hbonds: calculate hydrogen bond + var bAtomCond = (bSaltbridge !== undefined && bSaltbridge) ? ( (atom.resn === 'ARG' || atom.resn === 'LYS') && atom.elem === "N" && atom.name !== "N") + || ( (atom.resn === 'GLU' || atom.resn === 'ASP') && atom.elem === "O" && atom.name !== "O") : atom.elem === "N" || atom.elem === "O" || atom.elem === "F"; + + if(bAtomCond) { + chain_resi = atom.structure + "_" + atom.chain + "_" + atom.resi; + chain_resi_atom = chain_resi + "_" + atom.name; atomHbond[chain_resi_atom] = atom; } @@ -29,17 +35,31 @@ iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, thr for (var i in targetAtoms) { var atom = targetAtoms[i]; + // salt bridge: calculate hydrogen bond between Lys/Arg and Glu/Asp + // hbonds: calculate hydrogen bond + var bAtomCond = (bSaltbridge !== undefined && bSaltbridge) ? ( (atom.resn === 'ARG' || atom.resn === 'LYS') && atom.elem === "N" && atom.name !== "N") + || ( (atom.resn === 'GLU' || atom.resn === 'ASP') && atom.elem === "O" && atom.name !== "O") : atom.elem === "N" || atom.elem === "O" || atom.elem === "F"; + var currResiHash = {}; - if(atom.elem === "N" || atom.elem === "O" || atom.elem === "F") { // calculate hydrogen bond + if(bAtomCond) { chain_resi = atom.structure + "_" + atom.chain + "_" + atom.resi; chain_resi_atom = chain_resi + "_" + atom.name; - var oriResidName = chain_resi + ' ' + atom.resn; + //var oriResidName = atom.resn + ' ' + chain_resi_atom; + var oriResidName = atom.resn + ' $' + atom.structure + '.' + atom.chain + ':' + atom.resi + '@' + atom.name; if(me.resid2Residhash[oriResidName] === undefined) me.resid2Residhash[oriResidName] = {}; for (var j in atomHbond) { + if(bSaltbridge !== undefined && bSaltbridge) { + // skip both positive orboth negative cases + if( ( (atom.resn === 'LYS' || atom.resn === 'ARG') && (atomHbond[j].resn === 'LYS' || atomHbond[j].resn === 'ARG') ) || + ( (atom.resn === 'GLU' || atom.resn === 'ASP') && (atomHbond[j].resn === 'GLU' || atomHbond[j].resn === 'ASP') ) ) { + continue; + } + } + // skip same protein residue - if(chain_resi == j.substr(0, j.lastIndexOf('_')) && this.proteins.hasOwnProperty(atomHbond[j].serial)) continue; + if(chain_resi == j.substr(0, j.lastIndexOf('_') ) && this.proteins.hasOwnProperty(atomHbond[j].serial)) continue; var xdiff = Math.abs(atom.coord.x - atomHbond[j].coord.x); if(xdiff > threshold) continue; @@ -54,16 +74,26 @@ iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, thr if(dist > maxlengthSq) continue; // output hydrogen bonds - this.hbondpnts.push({'serial': atom.serial, 'coord': atom.coord}); - this.hbondpnts.push({'serial': atomHbond[j].serial, 'coord': atomHbond[j].coord}); + if(bSaltbridge !== undefined && bSaltbridge) { + this.saltbridgepnts.push({'serial': atom.serial, 'coord': atom.coord}); + this.saltbridgepnts.push({'serial': atomHbond[j].serial, 'coord': atomHbond[j].coord}); + } + else { + this.hbondpnts.push({'serial': atom.serial, 'coord': atom.coord}); + this.hbondpnts.push({'serial': atomHbond[j].serial, 'coord': atomHbond[j].coord}); + } hbondsAtoms = this.unionHash(hbondsAtoms, this.residues[atom.structure + "_" + atom.chain + "_" + atom.resi]); hbondsAtoms = this.unionHash(hbondsAtoms, this.residues[atomHbond[j].structure + "_" + atomHbond[j].chain + "_" + atomHbond[j].resi]); residueHash[chain_resi] = 1; - var residName = atomHbond[j].structure + "_" + atomHbond[j].chain + "_" + atomHbond[j].resi + " " + atomHbond[j].resn; - me.resid2Residhash[oriResidName][residName] = 1; + //var residName = atomHbond[j].resn + " " + atomHbond[j].structure + "_" + atomHbond[j].chain + "_" + atomHbond[j].resi + '_' + atomHbond[j].name; + var residName = atomHbond[j].resn + ' $' + atomHbond[j].structure + '.' + atomHbond[j].chain + ':' + atomHbond[j].resi + '@' + atomHbond[j].name; + + if(me.resid2Residhash[oriResidName][residName] === undefined || me.resid2Residhash[oriResidName][residName] > dist) { + me.resid2Residhash[oriResidName][residName] = dist.toFixed(1); + } } // end of for (var j in atomHbond) { } } // end of for (var i in targetAtoms) { @@ -75,7 +105,6 @@ iCn3D.prototype.calculateChemicalHbonds = function (startAtoms, targetAtoms, thr for(var j in this.residues[residueArray[i]]) { // all atoms should be shown for hbonds this.atoms[j].style2 = 'stick'; - //this.atoms[j].style2 = 'lines'; } } @@ -148,7 +177,9 @@ iCn3D.prototype.getChainsFromAtoms = function(atomsHash) { var oriResidName; if(bGetPairs) { - oriResidName = oriAtom.structure + '_' + oriAtom.chain + '_' + oriAtom.resi + ' ' + oriAtom.resn; + //oriResidName = oriAtom.structure + '_' + oriAtom.chain + '_' + oriAtom.resi + '_' + oriAtom.name + ' ' + oriAtom.resn; + //oriResidName = oriAtom.structure + '_' + oriAtom.chain + '_' + oriAtom.resi + ' ' + oriAtom.resn; + oriResidName = '$' + oriAtom.structure + '.' + oriAtom.chain + ':' + oriAtom.resi + ' ' + oriAtom.resn; if(me.resid2Residhash[oriResidName] === undefined) me.resid2Residhash[oriResidName] = {}; } @@ -167,8 +198,13 @@ iCn3D.prototype.getChainsFromAtoms = function(atomsHash) { var residName; if(bGetPairs) { - residName = atom.structure + '_' + atom.chain + '_' + atom.resi + ' ' + atom.resn; - me.resid2Residhash[oriResidName][residName] = 1 + //residName = atom.structure + '_' + atom.chain + '_' + atom.resi + '_' + atom.name + ' ' + atom.resn; + //residName = atom.structure + '_' + atom.chain + '_' + atom.resi + ' ' + atom.resn; + residName = '$' + atom.structure + '.' + atom.chain + ':' + atom.resi + ' ' + atom.resn; + var dist = Math.sqrt(atomDistSq).toFixed(1); + if(me.resid2Residhash[oriResidName][residName] === undefined || me.resid2Residhash[oriResidName][residName] > dist) { + me.resid2Residhash[oriResidName][residName] = dist; + } } } } diff --git a/src/icn3dui/common_full_simple.js b/src/icn3dui/common_full_simple.js index 552d7f3b..4fb5e8e0 100644 --- a/src/icn3dui/common_full_simple.js +++ b/src/icn3dui/common_full_simple.js @@ -94,6 +94,8 @@ iCn3DUI.prototype.showTitle = function() { var me = this; if(me.icn3d.molTitle !== undefined && me.icn3d.molTitle !== '') { var title = me.icn3d.molTitle; + var titlelinkColor = (me.opts['background'] == 'white' || me.opts['background'] == 'grey') ? 'black' : me.GREYD; + if(me.inputid === undefined) { if(me.icn3d.molTitle.length > 40) title = me.icn3d.molTitle.substr(0, 40) + "..."; @@ -102,7 +104,7 @@ iCn3DUI.prototype.showTitle = function() { var me = this; else if(me.cfg.cid !== undefined) { var url = me.getLinkToStructureSummary(); - $("#" + me.pre + "title").html("PubChem CID " + me.inputid.toUpperCase() + ": " + title); + $("#" + me.pre + "title").html("PubChem CID " + me.inputid.toUpperCase() + ": " + title); } else if(me.cfg.align !== undefined) { $("#" + me.pre + "title").html(title); @@ -121,7 +123,7 @@ iCn3DUI.prototype.showTitle = function() { var me = this; //var asymmetricStr = (me.bAssemblyUseAsu) ? " (Asymmetric Unit)" : ""; var asymmetricStr = ""; - $("#" + me.pre + "title").html("PDB ID " + me.inputid.toUpperCase() + "" + asymmetricStr + ": " + title); + $("#" + me.pre + "title").html("PDB ID " + me.inputid.toUpperCase() + "" + asymmetricStr + ": " + title); } } else { diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js index 43643fd3..fd0d4932 100644 --- a/src/icn3dui/full_ui.js +++ b/src/icn3dui/full_ui.js @@ -15,7 +15,7 @@ if (!$.ui.dialog.prototype._makeDraggableBase) { var iCn3DUI = function(cfg) { var me = this; - this.REVISION = '2.8.2'; + this.REVISION = '2.8.3'; me.bFullUi = true; @@ -157,6 +157,7 @@ var iCn3DUI = function(cfg) { me.opts['water'] = 'nothing'; //sphere, dot, nothing me.opts['ions'] = 'sphere'; //sphere, dot, nothing me.opts['hbonds'] = 'no'; //yes, no + me.opts['saltbridge'] = 'no'; //yes, no //me.opts['stabilizer'] = 'no'; //yes, no me.opts['ssbonds'] = 'yes'; //yes, no me.opts['rotationcenter'] = 'molecule center'; //molecule center, pick center, display center @@ -668,7 +669,8 @@ iCn3DUI.prototype = { me.loadScript(me.cfg.command); } else { - alert("Please use the \"File\" menu to retrieve a structure of interest or to display a local file."); + //alert("Please use the \"File\" menu to retrieve a structure of interest or to display a local file."); + me.openDialog(me.pre + 'dl_mmdbid', 'Please input MMDB or PDB ID'); } }); @@ -1120,27 +1122,17 @@ iCn3DUI.prototype = { else { if(me.icn3d.defNames2Residues[commandname] !== undefined && me.icn3d.defNames2Residues[commandname].length > 0) { for(var j = 0, jl = me.icn3d.defNames2Residues[commandname].length; j < jl; ++j) { - var serial = me.icn3d.defNames2Residues[commandname][j]; + var resid = me.icn3d.defNames2Residues[commandname][j]; - if(serial !== undefined) { - var atom = me.icn3d.atoms[serial]; - var resid = atom.structure + '_' + atom.chain + '_' + atom.resi; - - residuesHash = me.icn3d.unionHash(residuesHash, me.icn3d.residues[resid]); - } + residuesHash = me.icn3d.unionHash(residuesHash, me.icn3d.residues[resid]); } } if(me.icn3d.defNames2Atoms[commandname] !== undefined && me.icn3d.defNames2Atoms[commandname].length > 0) { for(var j = 0, jl = me.icn3d.defNames2Atoms[commandname].length; j < jl; ++j) { - var serial = me.icn3d.defNames2Atoms[commandname][j]; + var resid = me.icn3d.defNames2Atoms[commandname][j]; - if(serial !== undefined) { - var atom = me.icn3d.atoms[serial]; - var resid = atom.structure + '_' + atom.chain + '_' + atom.resi; - - residuesHash = me.icn3d.unionHash(residuesHash, me.icn3d.residues[resid]); - } + residuesHash = me.icn3d.unionHash(residuesHash, me.icn3d.residues[resid]); } } } @@ -1149,17 +1141,21 @@ iCn3DUI.prototype = { return residuesHash; }, - pickCustomSphere: function (radius, nameArray) { var me = this; // me.icn3d.pAtom is set already + pickCustomSphere: function (radius, nameArray, nameArray2) { var me = this; // me.icn3d.pAtom is set already // me.removeHlMenus(); - var select = "select zone cutoff " + radius + " | sets " + nameArray; + var select = "select zone cutoff " + radius + " | sets " + nameArray + " " + nameArray2; var atomlistTarget = {}, otherAtoms = {}; - for(var i in me.icn3d.hAtoms) { - atomlistTarget[i] = me.icn3d.atoms[i]; + if(nameArray2[0] === 'selected') { + atomlistTarget = me.icn3d.hash2Atoms(me.icn3d.hAtoms); + } + else { + atomlistTarget = me.icn3d.hash2Atoms(me.getAtomsFromSets(nameArray2)); } - if(nameArray.length == 0) { // select all hAtoms + + if(nameArray.length == 0 || nameArray[0] === 'all') { // select all hAtoms otherAtoms = me.icn3d.atoms; } else { @@ -1215,17 +1211,31 @@ iCn3DUI.prototype = { }, // between the highlighted and atoms in nameArray - showHbonds: function (threshold, nameArray) { var me = this; - me.icn3d.opts["hbonds"] = "yes"; - me.icn3d.opts["water"] = "dot"; + showHbonds: function (threshold, nameArray, nameArray2, bSaltbridge) { var me = this; + var hbonds_saltbridge, select; + if(bSaltbridge !== undefined && bSaltbridge) { + hbonds_saltbridge = 'saltbridge'; + select = 'salt bridge ' + threshold + ' | sets ' + nameArray + " " + nameArray2; + } + else { + hbonds_saltbridge = 'hbonds'; + select = 'hbonds ' + threshold + ' | sets ' + nameArray + " " + nameArray2; + } - var select = 'hbonds ' + threshold + ' | sets ' + nameArray; + me.icn3d.opts[hbonds_saltbridge] = "yes"; + me.icn3d.opts["water"] = "dot"; - var complement = {}; + var firstSetAtoms = {}, complement = {}; + if(nameArray2[0] === 'selected') { + firstSetAtoms = me.icn3d.hash2Atoms(me.icn3d.hAtoms); + } + else { + firstSetAtoms = me.icn3d.hash2Atoms(me.getAtomsFromSets(nameArray2)); + } - if(nameArray.length == 0) { + if(nameArray.length == 0 || nameArray[0] === 'all') { for(var i in me.icn3d.atoms) { - if(!me.icn3d.hAtoms.hasOwnProperty(i) && me.icn3d.dAtoms.hasOwnProperty(i)) { + if(!firstSetAtoms.hasOwnProperty(i) && me.icn3d.dAtoms.hasOwnProperty(i)) { complement[i] = me.icn3d.atoms[i]; } } @@ -1234,11 +1244,20 @@ iCn3DUI.prototype = { complement = me.icn3d.hash2Atoms(me.getAtomsFromSets(nameArray)); } - var firstAtom = me.icn3d.getFirstAtomObj(me.icn3d.hAtoms); + var firstAtom = me.icn3d.getFirstAtomObj(firstSetAtoms); - if(Object.keys(complement).length > 0 && Object.keys(me.icn3d.hAtoms).length > 0) { - var selectedAtoms = me.icn3d.calculateChemicalHbonds(complement, me.icn3d.intHash2Atoms(me.icn3d.dAtoms, me.icn3d.hAtoms), parseFloat(threshold) ); - me.resid2ResidhashHbond = me.icn3d.cloneHash(me.icn3d.resid2Residhash); + if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) { + var selectedAtoms = me.icn3d.calculateChemicalHbonds(complement, me.icn3d.intHash2Atoms(me.icn3d.dAtoms, firstSetAtoms), parseFloat(threshold), bSaltbridge ); + + var commanddesc; + if(bSaltbridge !== undefined && bSaltbridge) { + me.resid2ResidhashSaltbridge = me.icn3d.cloneHash(me.icn3d.resid2Residhash); + commanddesc = 'all atoms that have salt bridges with the selected atoms'; + } + else { + me.resid2ResidhashHbond = me.icn3d.cloneHash(me.icn3d.resid2Residhash); + commanddesc = 'all atoms that are hydrogen-bonded with the selected atoms'; + } var residues = {}, atomArray = undefined; @@ -1256,18 +1275,13 @@ iCn3DUI.prototype = { } } - var commandname = 'hbonds_' + firstAtom.serial; - var commanddesc = 'all atoms that are hydrogen-bonded with the selected atoms'; + var commandname = hbonds_saltbridge + '_' + firstAtom.serial; me.addCustomSelection(Object.keys(residues), commandname, commanddesc, select, true); var nameArray = [commandname]; - //me.changeCustomResidues(nameArray); - me.saveSelectionIfSelected(); - //me.setStyle('sidec', 'ball and stick'); - me.icn3d.draw(); } }, @@ -1751,7 +1765,7 @@ iCn3DUI.prototype = { } } - var text = '

    ' + cnt + ' hydrogen bond pairs:

    '; + var text = '

    ' + cnt + ' hydrogen bond pairs:

    Residue ID 1Residue ID 2
    '; text += tmpText; @@ -1761,48 +1775,41 @@ iCn3DUI.prototype = { me.saveFile(file_pref + '_hbond_pairs.html', 'html', text); }, - exportSpherePairs: function() { var me = this; + exportSaltbridgePairs: function() { var me = this; var tmpText = ''; var cnt = 0; - for(var resid1 in me.resid2ResidhashSphere) { // e.g., resid1: 1KQ2_A_6 ASN - var resid1Final = resid1.substr(0, resid1.indexOf(' ')); - - var caSerial1, caSerial2, tmpSerial; - for(var serial in me.icn3d.residues[resid1Final]) { - if(me.icn3d.calphas.hasOwnProperty(serial)) { - caSerial1 = serial; - break; - } - tmpSerial = serial; + for(var resid1 in me.resid2ResidhashSaltbridge) { + for(var resid2 in me.resid2ResidhashSaltbridge[resid1]) { + tmpText += ''; + ++cnt; } - if(caSerial1 === undefined) caSerial1 = tmpSerial; + } - var ca1 = me.icn3d.atoms[caSerial1]; - var caVec1 = new THREE.Vector3(ca1.coord.x, ca1.coord.y, ca1.coord.z); + var text = '

    ' + cnt + ' Salt bridge pairs:

    Atom 1Atom 2
    ' + resid1 + '' + resid2 + '
    '; - for(var resid2 in me.resid2ResidhashSphere[resid1]) { - var resid2Final = resid2.substr(0, resid2.indexOf(' ')); + text += tmpText; - for(var serial in me.icn3d.residues[resid2Final]) { - if(me.icn3d.calphas.hasOwnProperty(serial)) { - caSerial2 = serial; - break; - } - tmpSerial = serial; - } - if(caSerial2 === undefined) caSerial2 = tmpSerial; + text += '
    Atom 1Atom 2

    '; - var ca2 = me.icn3d.atoms[caSerial2]; - var caVec2 = new THREE.Vector3(ca2.coord.x, ca2.coord.y, ca2.coord.z); + var file_pref = (me.inputid) ? me.inputid : "custom"; + me.saveFile(file_pref + '_saltbridge_pairs.html', 'html', text); + }, - var dist = caVec1.distanceTo(caVec2).toFixed(1); + exportSpherePairs: function() { var me = this; + var tmpText = ''; + var cnt = 0; + for(var resid1 in me.resid2ResidhashSphere) { // e.g., resid1: 1KQ2_A_6_C ASN + for(var resid2 in me.resid2ResidhashSphere[resid1]) { + var dist = me.resid2ResidhashSphere[resid1][resid2]; tmpText += '' + resid1 + '' + resid2 + '' + dist + ''; ++cnt; } } - var text = '

    ' + cnt + ' residue pairs in sphere:

    '; + var text = '

    ' + cnt + + ' residue pairs in sphere:

    Residue ID 1Residue ID 2Cα-Cα Dist (Å)
    ' + + ''; text += tmpText; @@ -2226,7 +2233,7 @@ iCn3DUI.prototype = { clkMn1_mmdbid: function() { var me = this; $("#" + me.pre + "mn1_mmdbid").click(function(e) { - me.openDialog(me.pre + 'dl_mmdbid', 'Please input MMDB ID'); + me.openDialog(me.pre + 'dl_mmdbid', 'Please input MMDB or PDB ID'); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -2851,13 +2858,17 @@ iCn3DUI.prototype = { var definedAtomsHtml = me.setAtomMenu(['protein']); if($("#" + me.pre + "atomsCustomSphere").length) { - $("#" + me.pre + "atomsCustomSphere").html(definedAtomsHtml); + $("#" + me.pre + "atomsCustomSphere").html(" " + definedAtomsHtml); + } + if($("#" + me.pre + "atomsCustomSphere2").length) { + $("#" + me.pre + "atomsCustomSphere2").html(" " + definedAtomsHtml); } - me.openDialog(me.pre + 'dl_aroundsphere', 'Select a sphere around current selection'); + me.openDialog(me.pre + 'dl_aroundsphere', 'Select a sphere around a set of residues'); me.bSphereCalc = false; $("#" + me.pre + "atomsCustomSphere").resizable(); + $("#" + me.pre + "atomsCustomSphere2").resizable(); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -3259,6 +3270,13 @@ iCn3DUI.prototype = { }); }, + clkMn4_clrSSSpectrum: function() { var me = this; + $("#" + me.pre + "mn4_clrSSSpectrum").click(function(e) { + me.setOption('color', 'secondary structure spectrum'); + me.setLogCmd('color secondary structure spectrum', true); + }); + }, + clkMn4_clrResidue: function() { var me = this; $("#" + me.pre + "mn4_clrResidue").click(function(e) { me.setOption('color', 'residue'); @@ -3836,17 +3854,23 @@ iCn3DUI.prototype = { }); }, + clkMn6_addlabelAtoms: function() { var me = this; + $("#" + me.pre + "mn6_addlabelAtoms").click(function(e) { + me.icn3d.addAtomLabels(me.icn3d.hAtoms); + + me.saveSelectionIfSelected(); + me.setLogCmd('add atom labels', true); + me.icn3d.draw(); + }); + }, + clkMn6_addlabelResidues: function() { var me = this; $("#" + me.pre + "mn6_addlabelResidues").click(function(e) { - //me.setLogCmd('add residue labels', true); - me.icn3d.addResiudeLabels(me.icn3d.hAtoms); me.saveSelectionIfSelected(); me.setLogCmd('add residue labels', true); me.icn3d.draw(); - - //$( ".icn3d-accordion" ).accordion(me.closeAc); }); }, @@ -3888,7 +3912,7 @@ iCn3DUI.prototype = { clkMn6_addlabelSelection: function() { var me = this; $("#" + me.pre + "mn6_addlabelSelection").click(function(e) { - me.openDialog(me.pre + 'dl_addlabelselection', 'Add custom labels by the current selection'); + me.openDialog(me.pre + 'dl_addlabelselection', 'Add custom labels by the selected'); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -3896,7 +3920,7 @@ iCn3DUI.prototype = { clkMn2_saveselection: function() { var me = this; $("#" + me.pre + "mn2_saveselection").click(function(e) { - me.openDialog(me.pre + 'dl_saveselection', 'Save the current selection'); + me.openDialog(me.pre + 'dl_saveselection', 'Save the selected'); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4193,6 +4217,7 @@ iCn3DUI.prototype = { me.setLogCmd('set background black', true); $("#" + me.pre + "title").css("color", me.GREYD); + $("#" + me.pre + "titlelink").css("color", me.GREYD); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4204,6 +4229,7 @@ iCn3DUI.prototype = { me.setLogCmd('set background grey', true); $("#" + me.pre + "title").css("color", "black"); + $("#" + me.pre + "titlelink").css("color", "black"); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4215,6 +4241,7 @@ iCn3DUI.prototype = { me.setLogCmd('set background white', true); $("#" + me.pre + "title").css("color", "black"); + $("#" + me.pre + "titlelink").css("color", "black"); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4226,6 +4253,7 @@ iCn3DUI.prototype = { me.setLogCmd('set background transparent', true); $("#" + me.pre + "title").css("color", me.GREYD); + $("#" + me.pre + "titlelink").css("color", me.GREYD); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4302,13 +4330,17 @@ iCn3DUI.prototype = { var definedAtomsHtml = me.setAtomMenu(['protein']); if($("#" + me.pre + "atomsCustomHbond").length) { - $("#" + me.pre + "atomsCustomHbond").html(definedAtomsHtml); + $("#" + me.pre + "atomsCustomHbond").html(" " + definedAtomsHtml); + } + if($("#" + me.pre + "atomsCustomHbond2").length) { + $("#" + me.pre + "atomsCustomHbond2").html(" " + definedAtomsHtml); } - me.openDialog(me.pre + 'dl_hbonds', 'Hydrogen bonds to selection'); + me.openDialog(me.pre + 'dl_hbonds', 'Hydrogen bonds between two sets'); me.bHbondCalc = false; $("#" + me.pre + "atomsCustomHbond").resizable(); + $("#" + me.pre + "atomsCustomHbond2").resizable(); //$( ".icn3d-accordion" ).accordion(me.closeAc); }); @@ -4326,6 +4358,41 @@ iCn3DUI.prototype = { }); }, + clkMn6_saltbridgeYes: function() { var me = this; + $("#" + me.pre + "mn6_saltbridgeYes").click(function(e) { + if(me.bSetChainsAdvancedMenu === undefined || !me.bSetChainsAdvancedMenu) { + me.setPredefinedInMenu(); + + me.bSetChainsAdvancedMenu = true; + } + + var definedAtomsHtml = me.setAtomMenu(['protein']); + + if($("#" + me.pre + "atomsCustomSaltbridge").length) { + $("#" + me.pre + "atomsCustomSaltbridge").html(" " + definedAtomsHtml); + } + if($("#" + me.pre + "atomsCustomSaltbridge2").length) { + $("#" + me.pre + "atomsCustomSaltbridge2").html(" " + definedAtomsHtml); + } + + me.openDialog(me.pre + 'dl_saltbridge', 'Salt bridge between two sets'); + me.bSaltbridgeCalc = false; + + $("#" + me.pre + "atomsCustomSaltbridge").resizable(); + $("#" + me.pre + "atomsCustomSaltbridge2").resizable(); + }); + }, + + clkMn6_saltbridgeNo: function() { var me = this; + $("#" + me.pre + "mn6_saltbridgeNo").click(function(e) { + var select = "set salt bridge off"; + me.setLogCmd(select, true); + + me.icn3d.hideSaltbridge(); + me.icn3d.draw(); + }); + }, + clkmn1_stabilizerYes: function() { var me = this; $("#" + me.pre + "mn1_stabilizerYes").click(function(e) { //me.openDialog(me.pre + 'dl_stabilizer', 'Hydrogen bonds inside selection'); @@ -5314,78 +5381,145 @@ iCn3DUI.prototype = { }, clickApplypick_aroundsphere: function() { var me = this; + $("#" + me.pre + "atomsCustomSphere2").add("#" + me.pre + "atomsCustomSphere").change(function(e) { + me.bSphereCalc = false; + }); + $("#" + me.pre + "applypick_aroundsphere").click(function(e) { //e.preventDefault(); //dialog.dialog( "close" ); var radius = parseFloat($("#" + me.pre + "radius_aroundsphere").val()); var nameArray = $("#" + me.pre + "atomsCustomSphere").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomSphere2").val(); - var select = "select zone cutoff " + radius + " | sets " + nameArray; - //me.setLogCmd(select, true); - - if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray); - me.bSphereCalc = true; + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + var select = "select zone cutoff " + radius + " | sets " + nameArray + " " + nameArray2; - me.updateHlAll(); + if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray, nameArray2); + me.bSphereCalc = true; - me.setLogCmd(select, true); + me.updateHlAll(); - //$( ".icn3d-accordion" ).accordion(me.closeAc); + me.setLogCmd(select, true); + } }); $("#" + me.pre + "sphereExport").click(function(e) { e.preventDefault(); - dialog.dialog( "close" ); + //dialog.dialog( "close" ); var radius = parseFloat($("#" + me.pre + "radius_aroundsphere").val()); var nameArray = $("#" + me.pre + "atomsCustomSphere").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomSphere2").val(); - if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray); - me.bSphereCalc = true; - - me.exportSpherePairs(); + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray, nameArray2); + me.bSphereCalc = true; - me.setLogCmd("export pairs in the sphere", false); + me.exportSpherePairs(); - //$( ".icn3d-accordion" ).accordion(me.closeAc); + me.setLogCmd("export pairs in the sphere", false); + } }); }, clickApplyhbonds: function() { var me = this; + $("#" + me.pre + "atomsCustomHbond2").add("#" + me.pre + "atomsCustomHbond").change(function(e) { + me.bHbondCalc = false; + }); + $("#" + me.pre + "applyhbonds").click(function(e) { //e.preventDefault(); //dialog.dialog( "close" ); var threshold = parseFloat($("#" + me.pre + "hbondthreshold" ).val()); var nameArray = $("#" + me.pre + "atomsCustomHbond").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomHbond2").val(); - var select = "hbonds " + threshold + " | sets " + nameArray; - //me.setLogCmd(select, true); + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + var select = "hbonds " + threshold + " | sets " + nameArray + " " + nameArray2; - if(!me.bHbondCalc) me.showHbonds(threshold, nameArray); - me.bHbondCalc = true; + if(!me.bHbondCalc) me.showHbonds(threshold, nameArray, nameArray2); + me.bHbondCalc = true; - me.setLogCmd(select, true); - - //$( ".icn3d-accordion" ).accordion(me.closeAc); + me.setLogCmd(select, true); + } }); $("#" + me.pre + "hbondExport").click(function(e) { e.preventDefault(); - dialog.dialog( "close" ); + //dialog.dialog( "close" ); var threshold = parseFloat($("#" + me.pre + "hbondthreshold" ).val()); var nameArray = $("#" + me.pre + "atomsCustomHbond").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomHbond2").val(); - if(!me.bHbondCalc) me.showHbonds(threshold, nameArray); - me.bHbondCalc = true; + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + if(!me.bHbondCalc) me.showHbonds(threshold, nameArray, nameArray2); + me.bHbondCalc = true; - me.exportHbondPairs(); + me.exportHbondPairs(); - me.setLogCmd("export hbond pairs", false); + me.setLogCmd("export hbond pairs", false); + } + }); + }, - //$( ".icn3d-accordion" ).accordion(me.closeAc); + clickApplysaltbridge: function() { var me = this; + $("#" + me.pre + "atomsCustomSaltbridge2").add("#" + me.pre + "atomsCustomSaltbridge").change(function(e) { + me.bSaltbridgeCalc = false; + }); + + $("#" + me.pre + "applysaltbridge").click(function(e) { + var threshold = parseFloat($("#" + me.pre + "saltbridgethreshold" ).val()); + var nameArray = $("#" + me.pre + "atomsCustomSaltbridge").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomSaltbridge2").val(); + + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + var select = "salt bridge " + threshold + " | sets " + nameArray + " " + nameArray2; + + if(!me.bSaltbridgeCalc) me.showHbonds(threshold, nameArray, nameArray2, true); + me.bSaltbridgeCalc = true; + + me.setLogCmd(select, true); + } + }); + + $("#" + me.pre + "saltbridgeExport").click(function(e) { + e.preventDefault(); + //dialog.dialog( "close" ); + + var threshold = parseFloat($("#" + me.pre + "saltbridgethreshold" ).val()); + var nameArray = $("#" + me.pre + "atomsCustomSaltbridge").val(); + var nameArray2 = $("#" + me.pre + "atomsCustomSaltbridge2").val(); + + if(nameArray2.length == 0) { + alert("Please select the first set at step #1"); + } + else { + if(!me.bSaltbridgeCalc) me.showHbonds(threshold, nameArray, nameArray2, true); + me.bSaltbridgeCalc = true; + + me.exportSaltbridgePairs(); + + me.setLogCmd("export salt bridge pairs", false); + } }); }, @@ -6014,6 +6148,7 @@ iCn3DUI.prototype = { me.clkMn4_clrChain(); me.clkMn4_clrSSGreen(); me.clkMn4_clrSSYellow(); + me.clkMn4_clrSSSpectrum(); me.clkMn4_clrResidue(); me.clkMn4_clrCharge(); me.clkMn4_clrHydrophobic(); @@ -6072,6 +6207,7 @@ iCn3DUI.prototype = { me.clkMn6_assemblyYes(); me.clkMn6_assemblyNo(); me.clkMn6_addlabelResidues(); + me.clkMn6_addlabelAtoms(); me.clkMn6_addlabelChains(); me.clkMn6_addlabelTermini(); me.clkMn6_addlabelYes(); @@ -6121,6 +6257,8 @@ iCn3DUI.prototype = { me.clkMn6_showaxisNo(); me.clkMn6_hbondsYes(); me.clkMn6_hbondsNo(); + me.clkMn6_saltbridgeYes(); + me.clkMn6_saltbridgeNo(); me.clkmn1_stabilizerYes(); me.clkmn1_stabilizerNo(); me.clkMn6_ssbondsYes(); @@ -6161,6 +6299,7 @@ iCn3DUI.prototype = { me.clickApplycustomcolor(); me.clickApplypick_aroundsphere(); me.clickApplyhbonds(); + me.clickApplysaltbridge(); me.clickApplymap2fofc(); me.clickApplymapfofc(); // me.clickApplystabilizer(); diff --git a/src/icn3dui/html/set_html.js b/src/icn3dui/html/set_html.js index 9132dd7e..35cd9383 100644 --- a/src/icn3dui/html/set_html.js +++ b/src/icn3dui/html/set_html.js @@ -522,13 +522,20 @@ iCn3DUI.prototype.setMenu2b_base = function() { var me = this; html += " "; html += " "; - html += "
  • H-Bonds to
    Selection"; + html += "
  • H-Bonds"; html += "
      "; html += me.getRadio('mn6_hbonds', 'mn6_hbondsYes', 'Show'); html += me.getRadio('mn6_hbonds', 'mn6_hbondsNo', 'Hide', true); html += "
    "; html += "
    • "; + html += "
  • Salt Bridge"; + html += "
      "; + html += me.getRadio('mn6_saltbridge', 'mn6_saltbridgeYes', 'Show'); + html += me.getRadio('mn6_saltbridge', 'mn6_saltbridgeNo', 'Hide', true); + html += "
    "; + html += "
    • "; + html += me.getLink('mn2_aroundsphere2', 'Interactions'); html += "
  • Disulfide Bonds"; @@ -569,6 +576,7 @@ iCn3DUI.prototype.setMenu2b_base = function() { var me = this; html += "
      "; html += me.getRadio('mn6_addlabel', 'mn6_addlabelYes', 'by Picking Atoms'); html += me.getRadio('mn6_addlabel', 'mn6_addlabelSelection', 'per Selection'); + html += me.getRadio('mn6_addlabel', 'mn6_addlabelAtoms', 'per Atom'); if(me.cfg.cid === undefined) { html += me.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue'); html += me.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain'); @@ -920,6 +928,7 @@ iCn3DUI.prototype.setMenu4_base = function() { var me = this; html += "
        "; html += me.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green'); html += me.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow'); + html += me.getRadio('mn4_clr', 'mn4_clrSSSpectrum', 'Spectrum'); html += "
      "; html += me.getRadio('mn4_clr', 'mn4_clrCharge', 'Charge'); @@ -1279,7 +1288,7 @@ iCn3DUI.prototype.setDialogs = function() { var me = this; html += ""; html += "
      "; - html += "MMDB ID: "; + html += "MMDB or PDB ID: "; html += ""; html += "
      "; @@ -1364,7 +1373,9 @@ iCn3DUI.prototype.setDialogs = function() { var me = this; html += ""; html += "
      "; - html += "
      1. Make a selection in 3D, 2D or 1D whenever this window is open

      "; + html += "
      1. Select the first set:
      "; + html += "

      "; html += "
      2. Threshold of H-bonds: Å

      "; - html += "
      3. Select sets to apply the H-bonds:
      "; + html += "
      3. Select the second set to apply the H-bonds:
      "; html += "

      "; @@ -1385,6 +1396,30 @@ iCn3DUI.prototype.setDialogs = function() { var me = this; html += "
      H-bond pairs in a file
      "; html += "
      "; + html += "
      "; + html += "
      1. Select the first set:
      "; + html += "

      "; + html += "
      2. Threshold of salt bridge: Å

      "; + + html += "
      3. Select the second set to apply the salt bridges:
      "; + html += "

      "; + + html += "
      4. salt bridges between current selection and the selected set

      "; + html += "
      salt bridge pairs in a file
      "; + html += "
      "; + html += "
      "; html += " Contour at: "; + html += "

      "; html += "
      2. Sphere with a radius: Å

      "; - html += "
      3. Select sets to apply the sphere:
      "; + html += "
      3. Select the second set to apply the sphere:
      "; html += "

      "; diff --git a/src/icn3dui/parsers/mmcif_mmdb_parser.js b/src/icn3dui/parsers/mmcif_mmdb_parser.js index 6ba589b5..e43d8121 100644 --- a/src/icn3dui/parsers/mmcif_mmdb_parser.js +++ b/src/icn3dui/parsers/mmcif_mmdb_parser.js @@ -309,8 +309,10 @@ iCn3DUI.prototype.parseMmdbData = function (data, type) { var me = this; var index = 1; var chainNameHash = {}; for(var i in molid2rescount) { - var color = '#' + ( '000000' + molid2rescount[i].color.toString( 16 ) ).slice( - 6 ); - var chainName = molid2rescount[i].chain.trim(); + if(Object.keys(molid2rescount[i]).length === 0) continue; + + var color = (molid2rescount[i].color === undefined) ? '#CCCCCC' : '#' + ( '000000' + molid2rescount[i].color.toString( 16 ) ).slice( - 6 ); + var chainName = (molid2rescount[i].chain === undefined) ? '' : molid2rescount[i].chain.trim(); if(chainNameHash[chainName] === undefined) { chainNameHash[chainName] = 1; } @@ -320,7 +322,6 @@ iCn3DUI.prototype.parseMmdbData = function (data, type) { var me = this; var chainNameFinal = (chainNameHash[chainName] === 1) ? chainName : chainName + chainNameHash[chainName].toString(); var chain = id + '_' + chainNameFinal; - //html += "
    • "; molid2color[i] = color; chain2molid[chain] = i; @@ -328,7 +329,10 @@ iCn3DUI.prototype.parseMmdbData = function (data, type) { var me = this; me.icn3d.chainsColor[chain] = (type !== undefined) ? new THREE.Color(me.GREY8) : new THREE.Color(color); - me.icn3d.chainsGene[chain] = {'geneId': molid2rescount[i].geneId, 'geneSymbol': molid2rescount[i].geneSymbol, 'geneDesc': molid2rescount[i].geneDesc}; + var geneId = (molid2rescount[i].geneId === undefined) ? '' : molid2rescount[i].geneId; + var geneSymbol = (molid2rescount[i].geneSymbol === undefined) ? '' : molid2rescount[i].geneSymbol; + var geneDesc = (molid2rescount[i].geneDesc === undefined) ? '' : molid2rescount[i].geneDesc; + me.icn3d.chainsGene[chain] = {'geneId': geneId, 'geneSymbol': geneSymbol, 'geneDesc': geneDesc}; ++index; } @@ -702,6 +706,8 @@ iCn3DUI.prototype.loadAtomDataIn = function (data, id, type, seqalign, alignType var molidCnt = 1; for(var molid in data.moleculeInfor) { + if(Object.keys(data.moleculeInfor[molid]).length === 0) continue; + var chain = data.moleculeInfor[molid].chain.trim(); var chainid = pdbidTmp + '_' + chain; diff --git a/src/icn3dui/selection/commands.js b/src/icn3dui/selection/commands.js index b9482030..06f3990f 100644 --- a/src/icn3dui/selection/commands.js +++ b/src/icn3dui/selection/commands.js @@ -773,6 +773,10 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; me.icn3d.hideHbonds(); me.icn3d.draw(); } + else if(command == 'set salt bridge off') { + me.icn3d.hideSaltbridge(); + me.icn3d.draw(); + } else if(command == 'hydrogens') { me.showHydrogens(); @@ -916,6 +920,11 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; me.icn3d.draw(); } + else if(command == 'add atom labels') { + me.icn3d.addAtomLabels(me.icn3d.hAtoms); + + me.icn3d.draw(); + } else if(command == 'add chain labels') { me.addChainLabels(me.icn3d.hAtoms); @@ -1136,16 +1145,19 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; var paraArray = commandOri.split(' | '); // | sets a,b,c var radius = parseFloat(paraArray[0].substr(paraArray[0].lastIndexOf(' ') + 1)); - var nameArray = []; - if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c - var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); - nameArray = nameStr.split(","); + var nameArray = [], nameArray2 = []; + if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c e,f,g + //var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); + //nameArray = nameStr.split(","); + var setsArray = paraArray[1].split(" "); + if(setsArray.length > 1) nameArray = setsArray[1].split(","); + if(setsArray.length > 2) nameArray2 = setsArray[2].split(","); } - if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray); + if(!me.bSphereCalc) me.pickCustomSphere(radius, nameArray, nameArray2); me.bSphereCalc = true; - me.updateHlAll(); + //me.updateHlAll(); } else if(command.indexOf('set surface opacity') == 0) { var value = command.substr(command.lastIndexOf(' ') + 1); @@ -1180,9 +1192,11 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; if(value == 'white' || value == 'grey') { $("#" + me.pre + "title").css("color", "black"); + $("#" + me.pre + "titlelink").css("color", "black"); } else { $("#" + me.pre + "title").css("color", me.GREYD); + $("#" + me.pre + "titlelink").css("color", me.GREYD); } } else if(commandOri.indexOf('set thickness') == 0) { @@ -1336,23 +1350,47 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; me.icn3d.showPicking(me.icn3d.pAtom); } - else if(command.indexOf('hbonds') == 0) { + else if(commandOri.indexOf('hbonds') == 0) { if(me.bSetChainsAdvancedMenu === undefined || !me.bSetChainsAdvancedMenu) { me.setPredefinedInMenu(); me.bSetChainsAdvancedMenu = true; } - var paraArray = command.split(' | '); + var paraArray = commandOri.split(' | '); + + var threshold = parseFloat(paraArray[0].substr(paraArray[0].indexOf(' ') + 1)); + var nameArray = [], nameArray2 = []; + if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c e,f,g + //var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); + //nameArray = nameStr.split(","); + var setsArray = paraArray[1].split(" "); + if(setsArray.length > 1) nameArray = setsArray[1].split(","); + if(setsArray.length > 2) nameArray2 = setsArray[2].split(","); + } + + if(!isNaN(threshold)) me.showHbonds(threshold, nameArray, nameArray2); + } + else if(commandOri.indexOf('salt bridge') == 0) { + if(me.bSetChainsAdvancedMenu === undefined || !me.bSetChainsAdvancedMenu) { + me.setPredefinedInMenu(); + + me.bSetChainsAdvancedMenu = true; + } + + var paraArray = commandOri.split(' | '); var threshold = parseFloat(paraArray[0].substr(paraArray[0].indexOf(' ') + 1)); - var nameArray = []; - if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c - var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); - nameArray = nameStr.split(","); + var nameArray = [], nameArray2 = []; + if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c e,f,g + //var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); + //nameArray = nameStr.split(","); + var setsArray = paraArray[1].split(" "); + if(setsArray.length > 1) nameArray = setsArray[1].split(","); + if(setsArray.length > 2) nameArray2 = setsArray[2].split(","); } - if(!isNaN(threshold)) me.showHbonds(threshold, nameArray); + if(!isNaN(threshold)) me.showHbonds(threshold, nameArray, nameArray2, true); } else if(command.indexOf('color') == 0) { var color = command.substr(command.indexOf(' ') + 1);
    Residue 1Residue 2Min Distance (Å)
    " + index + "" + chainNameFinal + "" + molid2rescount[i].resCount + "