icn3d 3.37.0 → 3.37.1

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;
         });
 
@@ -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);
+                        ic.commands = [];
+                        ic.optsHistory = [];
+                        //await ic.loadScriptCls.loadScript(statefile, true);
                     }
-                    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);
+                    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>';
@@ -57603,8 +57609,7 @@ 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 +57739,7 @@ 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 +63095,8 @@ 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 +63163,7 @@ class LoadPDB {
         //let chainMissingResidueArray = {}
 
         let id = (pdbid) ? pdbid : ic.defaultPdbId;
+        let oriId = id;
 
         let structure = id;
 
@@ -63176,6 +63183,7 @@ class LoadPDB {
 
                 ///id = line.substr(62, 4).trim();
                 id = line.substr(62).trim();
+                oriId = id;
 
                 if(id == '') {
                     if(bAppend) {
@@ -63187,7 +63195,7 @@ class LoadPDB {
                     }
                 }
 
-                structure = this.getStructureId(id, moleculeNum, bMutation);
+                structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
 
                 ic.molTitle = '';
                 ic.molTitleHash = {};
@@ -63258,6 +63266,7 @@ 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 +63320,7 @@ 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 +63343,7 @@ 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 +63351,7 @@ class LoadPDB {
                     ++moleculeNum;
                     id = ic.defaultPdbId;
     
-                    structure = this.getStructureId(id, moleculeNum, bMutation);
+                    structure = this.getStructureId(id, moleculeNum, bMutation, bNMR);
     
                     //helices = [];
                     //sheets = [];
@@ -78497,7 +78506,7 @@ 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 +78583,7 @@ 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 +78781,7 @@ 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 +78860,9 @@ 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, ' ');