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Pull request #663: Fixed an issue related to previous chain IDs such …
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…as "A_1" (changed to "A1") in previous sharable links.

Merge in STRUC/icn3d from release3361 to master

* commit 'c4d0ae293a85a91fcf9bd2a9153fb29735aec5ba':
  Fixed an issue related to previous chain IDs such as "A_1" (changed to "A1") in previous sharable links.
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@jiywang3
jiywang3 committed Oct 7, 2024
2 parents 8c65e58 + c4d0ae2 commit 072246f
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Showing 28 changed files with 302 additions and 186 deletions.
2 changes: 2 additions & 0 deletions CHANGELOG.md
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@@ -1,4 +1,6 @@
## Change Log
[icn3d-3.36.1](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.36.1.zip) was release on October 7, 2024. Fixed an issue related to previous chain IDs such as "A_1" (changed to "A1") in previous sharable links.

[icn3d-3.36.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.36.0.zip) was release on October 3, 2024. Allowed to load multiple iCn3D PNG images.

[icn3d-3.35.0](https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d-3.35.0.zip) was release on September 12, 2024. Retrieved updated ClinVar annotations directly from NCBI ClinVar database.
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84 changes: 53 additions & 31 deletions build/icn3d.js
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Original file line number Diff line number Diff line change
Expand Up @@ -16363,6 +16363,9 @@ var icn3d = (function (exports) {
if(bPng) {
let result = await me.htmlCls.setHtmlCls.loadPng(dataStr);
dataStr = result.pdb;

if(!dataStr) return; // old iCn3D PNG with sharable link

if(!ic.statefileArray) ic.statefileArray = [];
ic.statefileArray.push(result.statefile);
}
Expand Down Expand Up @@ -20138,11 +20141,11 @@ var icn3d = (function (exports) {
if(pos == -1 && posState == -1) {
alert('Please load a PNG image saved by clicking the menu "File > Save File > iCn3D PNG Image"...');
}
// else if(!bReturn && pos != -1) { // no need to return pdb and state files
// let url = imageStr.substr(pos + matchedStr.length);
// me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
// window.open(url, '_self');
// }
else if(pos != -1) {
let url = imageStr.substr(pos + matchedStr.length);
me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
window.open(url, '_self');
}
else if(posState != -1) {
let matchedStrData = "Start of data file======\n";
let posData = imageStr.indexOf(matchedStrData);
Expand Down Expand Up @@ -56921,9 +56924,9 @@ var icn3d = (function (exports) {
let color =(molid2rescount[i].color === undefined) ? '#CCCCCC' : '#' +( '000000' + molid2rescount[i].color.toString( 16 ) ).slice( - 6 );
let chainName =(molid2rescount[i].chain === undefined) ? '' : molid2rescount[i].chain.trim();
// remove "_" in chain name
if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
// if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
chainName = chainName.replace(/_/g, '');
}
// }

if(chainNameHash[chainName] === undefined) {
chainNameHash[chainName] = 1;
Expand Down Expand Up @@ -57336,7 +57339,7 @@ var icn3d = (function (exports) {

let bFull = (atomSize * 10 > ic.maxatomcnt) ? false : true;

let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray = [];
let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray, modelNumArray;

if(!bNoCoord) {
atom_hetatmArray = atom_site.getColumn("group_PDB");
Expand All @@ -57357,6 +57360,7 @@ var icn3d = (function (exports) {
zArray = atom_site.getColumn("Cartn_z");

autochainArray = atom_site.getColumn("label_asym_id");
modelNumArray = atom_site.getColumn("pdbx_PDB_model_num");

// get the bond info
let ligSeqHash = {}, prevAutochain = '';
Expand Down Expand Up @@ -57530,17 +57534,14 @@ var icn3d = (function (exports) {
text += ", \"atoms\":[\n";
prevResn = "";
serial = 1;

let structure = atom_site.getColumn("pdbx_PDB_model_num").getString(0);

if(structure == "1") {
structure = bcifid;
}
else {
structure = bcifid + structure;
}
let structure = bcifid;

for (let i = 0; i < atomSize; ++i) {
let modelNum = modelNumArray.getString(i);
if(modelNum != "1" && modelNum != "") {
structure = bcifid + modelNum;
}

let atom_hetatm = atom_hetatmArray.getString(i);
let resn = resnArray.getString(i);
let elem = elemArray.getString(i);
Expand Down Expand Up @@ -57739,6 +57740,8 @@ var icn3d = (function (exports) {
// print sequences
text += ", \"sequences\":{";
let bData = false;
// need to consider different models in NMR structures
// But this function is only used for meta data,
for(let chain in sChain) {
let seq;
if(ligSeqHash.hasOwnProperty(chain)) {
Expand Down Expand Up @@ -61672,9 +61675,9 @@ var icn3d = (function (exports) {
let chain = data.moleculeInfor[molid].chain.trim();

// remove "_" in chain name
if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
// if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
chain = chain.replace(/_/g, '');
}
// }

let chainid = pdbidTmp + '_' + chain;

Expand Down Expand Up @@ -61816,9 +61819,9 @@ var icn3d = (function (exports) {
atm.chain = atm.chain.trim(); //.replace(/_/g, '');

// remove "_" in chain name
if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
// if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
atm.chain = atm.chain.replace(/_/g, '');
}
// }

// mmcif has pre-assigned structure in mmcifparser.cgi output
if(type === 'mmdbid' || type === 'align') {
Expand Down Expand Up @@ -64750,13 +64753,13 @@ var icn3d = (function (exports) {
// if(!bMutation && !bAppend) {
if(!bAppend) {
ic.init();
moleculeNum = 1;
moleculeNum = 0; //1;
serial = 0;
}
else {
ic.oriNStru = (ic.structures) ? Object.keys(ic.structures).length : 0;

moleculeNum = ic.oriNStru + 1; //Object.keys(ic.structures).length + 1;
moleculeNum = ic.oriNStru; //ic.oriNStru + 1; //Object.keys(ic.structures).length + 1;
// Concatenation of two pdbs will have several atoms for the same serial
serial = (ic.atoms) ? Object.keys(ic.atoms).length : 0;
}
Expand All @@ -64771,8 +64774,6 @@ var icn3d = (function (exports) {

let structure = id;
let CSerial, prevCSerial, OSerial, prevOSerial;

let bFirstAtom = true;

let cifArray = (bText) ? bcifData.split('ENDMDL\n') : [bcifData];

Expand Down Expand Up @@ -65076,12 +65077,27 @@ var icn3d = (function (exports) {
let zArray = atom_site.getColumn("Cartn_z");

let autochainArray = atom_site.getColumn("label_asym_id");
let modelNumArray = atom_site.getColumn("pdbx_PDB_model_num");

// get the bond info
let ligSeqHash = {}, prevAutochain = '';
let prevResn;
let sChain = {};
let prevModelNum = '';
for (let i = 0; i < atomSize; ++i) {
let modelNum = modelNumArray.getString(i);
if(i > 0 && modelNum != prevModelNum) {
++moleculeNum;

if(modelNum == "1") {
structure = id;
}
else {
structure = id + modelNum;
}
}
prevModelNum = modelNum;

let atom_hetatm = atom_hetatmArray.getString(i);
let resn = resnArray.getString(i);
let elem = elemArray.getString(i);
Expand Down Expand Up @@ -65126,11 +65142,11 @@ var icn3d = (function (exports) {

sChain[chain] = 1;

if(bFirstAtom) {
structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
// if(bFirstAtom) {
// structure = ic.loadPDBCls.getStructureId(id, moleculeNum);

bFirstAtom = false;
}
// bFirstAtom = false;
// }

// "CA" has to appear before "O". Otherwise the cartoon of secondary structure will have breaks
// Concatenation of two pdbs will have several atoms for the same serial
Expand Down Expand Up @@ -68731,6 +68747,12 @@ var icn3d = (function (exports) {
let prevLabel = 'or';

for(let i = 0, il = idArray.length; i < il; ++i) {
// replace 1CD8_A_1 with 1CD8_A1
let tmpArray = idArray[i].split('_');
if(tmpArray.length == 3 && !isNaN(tmpArray[2])) {
idArray[i] = tmpArray[0] + '_' + tmpArray[1] + tmpArray[2];
}

if(idArray[i] === 'or' || idArray[i] === 'and' || idArray[i] === 'not') {
prevLabel = idArray[i];
continue;
Expand Down Expand Up @@ -70260,6 +70282,7 @@ var icn3d = (function (exports) {
}
else {
chainStr = testStr.substr(periodPos + 1);

//replace "A_1" with "A"
chainStr = chainStr.replace(/_/g, '');

Expand Down Expand Up @@ -70387,7 +70410,6 @@ var icn3d = (function (exports) {

for(let l = 0, ll = residArray.length; l < ll; ++l) {
let residueId = residArray[l];

if(i === 0) {
residueHash[residueId] = 1;
}
Expand Down Expand Up @@ -83103,7 +83125,7 @@ var icn3d = (function (exports) {
//even when multiple iCn3D viewers are shown together.
this.pre = this.cfg.divid + "_";

this.REVISION = '3.36.0';
this.REVISION = '3.36.1';

// In nodejs, iCn3D defines "window = {navigator: {}}"
this.bNode = (Object.keys(window).length < 2) ? true : false;
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8 changes: 4 additions & 4 deletions build/icn3d.min.js
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