icn3d 3.37.0 → 3.37.2

package/icn3d.js

@@ -11102,9 +11102,9 @@ class ClickMenu {
 
         $("#" + me.pre + "newvs2").on('submit', function() {
             // fill the pdbstr
-            let pdbstr = ic.saveFileCls.getAtomPDB(ic.hAtoms);
+            let bVastSearch = true;
+            let pdbstr = ic.saveFileCls.getAtomPDB(ic.hAtoms, undefined, undefined, undefined, undefined, undefined, undefined, bVastSearch);
             $("#" + me.pre + "pdbstr").val(pdbstr);
-
             return true;
         });
 
@@ -14017,7 +14017,7 @@ class SetDialog {
         html += '<div style="width:550px;">You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.<br>';
         html += '<pre>refnum,11,12,,21,22,,10C,11C,20C<br>';
         html += '1TUP_A,100,101,,,132,,,,<br>';
-        html += '1TUP_B,110,111,,141,142,,,,</pre>';
+        html += '1TUP_B,110,111,,141,142,,,,<br>';
         html += '1TUP_C,,,,,,,200,201,230</pre>';
         html += 'The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.<br><br>';
         html += 'To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#selectb" target="_blank">Specification</a>. For example, "%12"  selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.<br>';
@@ -19269,8 +19269,8 @@ class SetHtml {
         });
     }
 
-    // async loadPng(imageStr, command) { let me = this.icn3dui, ic = me.icn3d;
-    async loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
+    async loadPng(imageStr, command, bRender) { let me = this.icn3dui, ic = me.icn3d;
+    // async loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
        let matchedStr = 'Share Link: ';
        let pos = imageStr.indexOf(matchedStr);
        let matchedStrState = "Start of state file======\n";
@@ -19291,8 +19291,8 @@ class SetHtml {
            let posData = imageStr.indexOf(matchedStrData);
            ic.bInputfile =(posData == -1) ? false : true;
            ic.bInputPNGWithData = ic.bInputfile;
-        //    let commandStr = (command) ? command.replace(/;/g, "\n") : '';
-           let commandStr = '';
+           let commandStr = (command) ? command.replace(/;/g, "\n") : '';
+        //    let commandStr = '';
 
         //    let statefile;
         //    if(ic.bInputfile) {
@@ -19313,31 +19313,37 @@ class SetHtml {
                //statefile = decodeURIComponent(statefile);
                statefile = decodeURIComponent(statefile + "\n" + commandStr);
 
-/*
-                if(type === 'pdb') {
-                    await ic.pdbParserCls.loadPdbData(data);
+               if(bRender) {
+                    if(type === 'pdb') {
+                        await ic.pdbParserCls.loadPdbData(data);
 
-                    ic.commands = [];
-                    ic.optsHistory = [];
-                    //await ic.loadScriptCls.loadScript(statefile, true);
-                }
-                else {
-                    if(type === 'mol2') {
-                        await ic.mol2ParserCls.loadMol2Data(data);
-                    }
-                    else if(type === 'sdf') {
-                        await ic.sdfParserCls.loadSdfData(data);
+                        ic.commands = [];
+                        ic.optsHistory = [];
+                        //await ic.loadScriptCls.loadScript(statefile, true);
                     }
-                    else if(type === 'xyz') {
-                        await ic.xyzParserCls.loadXyzData(data);
-                    }
-                    else if(type === 'mmcif') {
-                        await ic.mmcifParserCls.loadMmcifData(data);
+                    else {
+                        if(type === 'mol2') {
+                            await ic.mol2ParserCls.loadMol2Data(data);
+                        }
+                        else if(type === 'sdf') {
+                            await ic.sdfParserCls.loadSdfData(data);
+                        }
+                        else if(type === 'xyz') {
+                            await ic.xyzParserCls.loadXyzData(data);
+                        }
+                        else if(type === 'mmcif') {
+                            await ic.mmcifParserCls.loadMmcifData(data);
+                        }
+                        ic.commands = [];
+                        ic.optsHistory = [];
+                        //await ic.loadScriptCls.loadScript(statefile, true);
                     }
-                   ic.commands = [];
-                   ic.optsHistory = [];
-                   //await ic.loadScriptCls.loadScript(statefile, true);
-               }
+
+                    await ic.loadScriptCls.loadScript(statefile, true);
+
+                    // me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
+                }
+/*                   
            }
            else { // url length > 4000
                //var matchedStrState = "Start of state file======\n";
@@ -42102,8 +42108,6 @@ class AnnoDomain {
                 }
             }
 
-            if(bNotShowDomain) continue;
-
             // save 3D domain info for node.js script
             if(me.bNode) {
                 let domainName = '3D domain ' +(index+1).toString();
@@ -42118,13 +42122,15 @@ class AnnoDomain {
                         // 0-based
                         let obj = {};
                         // let resi = ic.ParserUtilsCls.getResi(chnid, j);
-                        let resid = ic.ncbi2resid(chnid + '_' + j);
+                        let resid = ic.ncbi2resid[chnid + '_' + j];
                         obj[resid] = domainName;
                         ic.resid2domain[chnid].push(obj);
                     }
                 }
             }
 
+            if(bNotShowDomain) continue;
+
             let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
             let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
             html3 += htmlTmp2 + htmlTmp3 + '<br>';
@@ -49705,7 +49711,7 @@ class LineGraph {
                           }
                           else {                           
                             ++linkedNodeCnt[mappingid];   
-                            linkedNodeInterDiff[mappingid] += link.n; 
+                            linkedNodeInterDiff[mappingid] += link.n;
                             
                             linkedNodeInterDiffBool[mappingid] = (linkedNodeInterDiff[mappingid] / link.n == linkedNodeCnt[mappingid]) ? 0 : 1; 
                           }
@@ -49759,7 +49765,7 @@ class LineGraph {
                           let linkDiff = me.hashUtilsCls.cloneHash(link);
                           linkDiff.source += separatorDiff + ic.chainsMapping[chainid1][resid1];
                           linkDiff.target += separatorDiff + ic.chainsMapping[chainid2][resid2];
-                      
+                          
                           if(linkedNodeCnt[mappingid] == structureArray.length && (bIgRef || linkedNodeInterDiffBool[mappingid] == 0)) {
                               linkArraySplitCommon[index].push(linkCommon);
                           }  
@@ -50452,6 +50458,7 @@ class GetGraph {
                 nodeArray2.push(node);
             }
         }
+
         // sort array
         nodeArray1.sort(function(a,b) {
           return thisClass.compNode(a, b);
@@ -50459,6 +50466,7 @@ class GetGraph {
         nodeArray2.sort(function(a,b) {
           return thisClass.compNode(a, b, bReverseNode);
         });
+
         return {"nodeArray1": nodeArray1, "nodeArray2": nodeArray2, "name2node": name2nodeCommon};
     }
     updateGraphJson(struc, index, nodeArray1, nodeArray2, linkArray) { let ic = this.icn3d, me = ic.icn3dui;
@@ -50763,7 +50771,9 @@ class GetGraph {
         }
 
         for(let linkStr in linkstr2cnt) {
-            hbondStr += ', {' + linkStr + ', "n": ' + linkstr2cnt[linkStr] + '}';
+            // do not differentiate the number of contacts
+            let n = (value == me.htmlCls.contactInsideValue || value == me.htmlCls.contactValue) ? 1 : linkstr2cnt[linkStr];
+            hbondStr += ', {' + linkStr + ', "n": ' + n + '}';
         }
 
         return hbondStr;
@@ -57603,8 +57613,7 @@ class PdbParser {
             await ic.mmcifParserCls.loadMmcifData(data);
         }
         else if(type === 'icn3dpng') {
-            // await me.htmlCls.setHtmlCls.loadPng(data, command);
-            await me.htmlCls.setHtmlCls.loadPng(data);
+            await me.htmlCls.setHtmlCls.loadPng(data, command, true);
         }
         else if(type === 'pae') {
             me.htmlCls.dialogCls.openDlg('dl_alignerrormap', 'Show Predicted Aligned Error (PAE) map');
@@ -57734,7 +57743,7 @@ class PdbParser {
     }
 
     async execStatefile(structure, statefile) {let ic = this.icn3d, me = ic.icn3dui;
-        // if(!statefile) return;
+        if(!statefile) return;
 
         let commandArray = statefile.trim().split('\n');
         commandArray = ['select $' + structure].concat(commandArray);
@@ -63090,7 +63099,8 @@ class LoadPDB {
         this.icn3d = icn3d;
     }
 
-    getStructureId(id, moleculeNum, bMutation) { let ic = this.icn3d; ic.icn3dui;
+    getStructureId(id, moleculeNum, bMutation, bNMR) { let ic = this.icn3d; ic.icn3dui;
+        id = (bNMR && ic.idNMR) ? ic.idNMR : id;
         let structure = id;
     
         if(id == ic.defaultPdbId || bMutation || ic.structures.hasOwnProperty(id)) { // bMutation: side chain prediction
@@ -63157,6 +63167,7 @@ class LoadPDB {
         //let chainMissingResidueArray = {}
 
         let id = (pdbid) ? pdbid : ic.defaultPdbId;
+        let oriId = id;
 
         let structure = id;
 
@@ -63176,6 +63187,7 @@ class LoadPDB {
 
                 ///id = line.substr(62, 4).trim();
                 id = line.substr(62).trim();
+                oriId = id;
 
                 if(id == '') {
                     if(bAppend) {
@@ -63187,7 +63199,7 @@ class LoadPDB {
                     }
                 }
 
-                structure = this.getStructureId(id, moleculeNum, bMutation);
+                structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
 
                 ic.molTitle = '';
                 ic.molTitleHash = {};
@@ -63258,6 +63270,7 @@ class LoadPDB {
                  else if (remarkType == 210) {
                      if((line.substr(11, 32).trim() == 'EXPERIMENT TYPE') && line.substr(45).trim() == 'NMR') {
                         bNMR = true;
+                        ic.idNMR = oriId;
                      }
                  }
                  else if (remarkType == 350 && line.substr(13, 5) == 'BIOMT') {
@@ -63311,7 +63324,7 @@ class LoadPDB {
                 ++moleculeNum;
                 id = ic.defaultPdbId;
 
-                structure = this.getStructureId(id, moleculeNum, bMutation);
+                structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
                 //helices = [];
                 //sheets = [];
                 if(!bNMR) {
@@ -63334,7 +63347,7 @@ class LoadPDB {
                 segId = line.substr(72, 4).trim();
 
                 if(bFirstAtom) {
-                    structure = this.getStructureId(id, moleculeNum, bMutation);
+                    structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
 
                     bFirstAtom = false;
                 }
@@ -63342,7 +63355,7 @@ class LoadPDB {
                     ++moleculeNum;
                     id = ic.defaultPdbId;
     
-                    structure = this.getStructureId(id, moleculeNum, bMutation);
+                    structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
     
                     //helices = [];
                     //sheets = [];
@@ -78497,7 +78510,7 @@ class SaveFile {
     }
 
     //getAtomPDB: function(atomHash, bPqr, bPdb, bNoChem) { let ic = this.icn3d, me = ic.icn3dui;
-    getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid, bMergeIntoOne) { let ic = this.icn3d, me = ic.icn3dui;
+    getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid, bMergeIntoOne, bVastSearch) { let ic = this.icn3d, me = ic.icn3dui;
         let pdbStr = '';
 
         // get all phosphate groups in lipids
@@ -78574,7 +78587,7 @@ class SaveFile {
             for(let i = 0, il = ssArray.length; i < il; ++i) {
                 let ssObj = ssArray[i];
 
-                if(ssObj.ss != prevSs) {
+                if(ssObj.ss != prevSs || ssObj.ssbegin) {
                     // print prev
                     stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
 
@@ -78772,6 +78785,7 @@ class SaveFile {
                 //line +=(atom.chain.length <= 1) ? atom.chain.padStart(1, ' ') : atom.chain.substr(0, 1);
                 if(atom.chain.length >= 2) {
                     let chainTmp = atom.chain.replace(/_/gi, '').substr(0, 2);
+                    if(bVastSearch) chainTmp = ' ' + chainTmp.substr(0,1); // VAST search only support one lettter chain ID
                     line += chainTmp;
                 }
                 else if(atom.chain.length == 1) {
@@ -78850,7 +78864,9 @@ class SaveFile {
             }
             else {
                 line += "1.00".padStart(6, ' ');
-                line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : ' '.padStart(6, ' ');
+                // line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : ' '.padStart(6, ' ');
+                let defaultBFactor = (bVastSearch) ? "1.0" : " ";
+                line +=(atom.b) ? parseFloat(atom.b).toFixed(2).toString().padStart(6, ' ') : defaultBFactor.padStart(6, ' ');
                 line += ' '.padStart(10, ' ');
                 line += atom.elem.padStart(2, ' ');
                 line += ' '.padStart(2, ' ');