icn3d 3.26.6 → 3.26.8

package/icn3d.js

@@ -6031,6 +6031,21 @@ class ClickMenu {
         thisClass.setLogCmd("export pdb hydrogen", true);
        });
 
+       me.myEventCls.onIds("#" + me.pre + "m1_exportIgstrand", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+       ic.refnumCls.exportRefnum('igstrand');
+       thisClass.setLogCmd("export refnum igstrand", true);
+      });
+
+      me.myEventCls.onIds("#" + me.pre + "m1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+         ic.refnumCls.exportRefnum('kabat');
+         thisClass.setLogCmd("export refnum kabat", true);
+      });
+
+      me.myEventCls.onIds("#" + me.pre + "m1_exportImgt", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+      ic.refnumCls.exportRefnum('imgt');
+      thisClass.setLogCmd("export refnum imgt", true);
+      });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
            thisClass.setLogCmd("export stl file", false);
            //ic.threeDPrintCls.hideStabilizer();
@@ -8603,6 +8618,16 @@ class SetMenu {
             html += this.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
         }
 
+        //!!!
+        /*
+        html += this.getMenuText('m1_exportrefnum', 'Reference Numbers', undefined, undefined, 2);
+        html += "<ul>";
+        html += this.getLink('mn1_exportIgstrand', 'Ig Strand', undefined, 3);
+        html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
+        html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
+        html += "</ul>";
+        */
+
         html += "<li><br/></li>";
 
         html += "</ul>";
@@ -12859,7 +12884,7 @@ class Events {
             if(esmfold_fasta.indexOf('>') != -1) { //FASTA with header
                 let pos = esmfold_fasta.indexOf('\n');
                 ic.esmTitle = esmfold_fasta.substr(1, pos - 1).trim();
-                pdbid = ic.esmTitle.substr(0, ic.esmTitle.indexOf(' '));
+                pdbid = (ic.esmTitle.indexOf(' ') != -1) ? ic.esmTitle.substr(0, ic.esmTitle.indexOf(' ')) : ic.esmTitle;
                 if(pdbid.length < 6) pdbid = pdbid.padEnd(6, '-');
 
                 esmfold_fasta = esmfold_fasta.substr(pos + 1);
@@ -42092,6 +42117,7 @@ class ShowSeq {
                 break;
             }
         }
+
         if(kabat_or_imgt == 1 && !bKabatFound) {
             return {html: '', html3: ''};
         }
@@ -44435,9 +44461,14 @@ class LineGraph {
                     domainAtomsArray.push(currAtoms);
 
                     let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
+
+                    let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(currAtoms);
+                    let atomLast = ic.firstAtomObjCls.getLastAtomObj(currAtoms);
+                    let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+
                     for(let n = 0, nl = residueArray.length; n < nl; ++n) {
                         let resid = residueArray[n];
-                        ic.resid2domainid[resid] = chainid + '-0' + '_' + Object.keys(currAtoms).length; 
+                        ic.resid2domainid[resid] = chainid + '-0' + '_' + resiSum; 
                     }
                 }
                 else {                 
@@ -44457,13 +44488,17 @@ class LineGraph {
 
                         domainAtomsArray.push(domainAtoms);
 
+                        let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
+                        let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtoms);
+                        let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+
                         for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                             let startResi = segArray[m];
                             let endResi = segArray[m+1];
                             for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
                                 let resid = chainid + '_' + pos2resi[n];
                                 //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
-                                ic.resid2domainid[resid] = chainid + '-' + k + '_' + Object.keys(domainAtoms).length; 
+                                ic.resid2domainid[resid] = chainid + '-' + k + '_' + resiSum; 
                             }
                         }
                     }
@@ -44487,7 +44522,7 @@ class LineGraph {
                         pdb_query = header + pdb_query;
 
                         let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]};
-                        let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj, undefined, undefined, undefined, undefined, undefined, true) ;
+                        let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
                         
                         domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
@@ -44503,8 +44538,9 @@ class LineGraph {
             // dataArray2 = await allPromise;
 
             //split arrays into chunks of 100 jobs
-            let n = (me.bNode) ? 16 : 96;
-            for(let i = 0, il = (ajaxArray.length - 1) / n + 1; i < il; ++i) {
+            let n = (me.bNode) ? 96 : 96;
+
+            for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
                 let currAjaxArray = [];
                 if(i == il - 1) { // last one 
                     currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
@@ -44518,7 +44554,6 @@ class LineGraph {
 
                 dataArray2 = dataArray2.concat(currDataArray);
             }
-
         
             let bRound1 = true;
             await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
@@ -44628,7 +44663,7 @@ class LineGraph {
 
             //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
             if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
-                if(!me.bNode) console.log("some of the Ig strands B, C, E, F are missing...");
+                if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
                 continue;
             }
 
@@ -44726,6 +44761,8 @@ class LineGraph {
         if(!ic.resid2refnum) ic.resid2refnum = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};
         if(!ic.chainsMapping) ic.chainsMapping = {};
+
+        if(!ic.refPdbList) ic.refPdbList = [];
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
 
@@ -44734,7 +44771,8 @@ class LineGraph {
             let chainList = this.getTemplateList(chainid);
 
             //if(!me.bNode) console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
-            console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
+            if(!me.bNode) console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
+            ic.refPdbList.push("The reference PDB(s) for chain " + chainid + " are " + chainList);
 
             let prevStrand;
             let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
@@ -44917,9 +44955,121 @@ class LineGraph {
         ic.annotationCls.setAnnoViewAndDisplay('detailed view');
     }
 
-    rmStrandFromRefnumlabel(refnumLabel) {
+    rmStrandFromRefnumlabel(refnumLabel) { let ic = this.icn3d; ic.icn3dui;
         return (!refnumLabel) ? refnumLabel : refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
     }
+
+    exportRefnum(type) { let ic = this.icn3d, me = ic.icn3dui;
+        let refData = '';
+
+        // 1. show IgStrand ref numbers
+        if(type == 'igstrand' || type == 'IgStrand') {
+            // iGStrand reference numbers were adjusted when showing in sequences
+            if(me.bNode) {
+                for(let chnid in ic.chains) {
+                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chnid]);
+                    if(ic.proteins.hasOwnProperty(atom.serial)) {
+                        let giSeq = [];
+                        for(let i = 0; i < ic.chainsSeq[chnid].length; ++i) {
+                            giSeq.push(ic.chainsSeq[chnid][i].name);
+                        }
+                        ic.showSeqCls.showRefNum(giSeq, chnid);
+                    }
+                }
+            }
+    
+            let resid2refnum = {};
+            for(let resid in ic.resid2refnum) {
+                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                if(!atom) continue;
+                
+                let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+        
+                let domainid = ic.resid2domainid[resid];
+                let refnumLabel = ic.resid2refnum[resid];
+        
+                if(refnumLabel) {
+                    let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+                    (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
+                }
+        
+                if(ic.resid2refnum[resid]) {
+                    if(ic.residIgLoop.hasOwnProperty(resid)) { // loop
+                    resid2refnum[resid + '_' + resn] = ic.resid2refnum[resid] + '_loop';
+                    }
+                    else {
+                    resid2refnum[resid + '_' + resn] = ic.resid2refnum[resid];
+                    }
+                }
+            }
+
+            refData += '{"ref PDB" : ' + JSON.stringify(ic.refPdbList) + ",\n";
+    
+            refData += '"data": {\n';
+            for(let chnid in ic.chains) {
+            let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chnid]);
+            if(ic.proteins.hasOwnProperty(atom.serial)) {
+                for(let i = 0; i < ic.chainsSeq[chnid].length; ++i) {
+                const resid = chnid + '_' + ic.chainsSeq[chnid][i].resi + '_' + ic.chainsSeq[chnid][i].name;
+    
+                refData += "'" + resid + "': '" + resid2refnum[resid] + "',\n";
+                }
+            }
+            }
+            refData += '}\n';
+            refData += '}\n';
+        }
+        // 2. show Kabat ref numbers
+        else if(type == 'kabat' || type == 'Kabat') {
+            let resid2kabat = {};
+            for(let resid in ic.resid2refnum) {
+            let domainid = ic.resid2domainid[resid];
+            let refnumStr, refnumLabel = ic.resid2refnum[resid];
+    
+            let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+            let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+    
+            if(refnumLabel) {
+                let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+                refnumStr = (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
+            }
+    
+            resid2kabat[resid + '_' + resn] = refnumStr;
+            }
+            
+            refData += JSON.stringify(resid2kabat);
+        }
+        // 3. show IMGT ref numbers
+        else if(type == 'imgt'|| type == 'IMGT') {
+            let resid2imgt = {};
+            for(let resid in ic.resid2refnum) {
+            let domainid = ic.resid2domainid[resid];
+            let refnumStr, refnumLabel = ic.resid2refnum[resid];
+    
+            let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+            let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+    
+            if(refnumLabel) {
+                let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+                refnumStr = (ic.domainid2ig2imgt[domainid]) ? ic.domainid2ig2imgt[domainid][refnumStr_ori] : undefined;
+            }
+    
+            resid2imgt[resid + '_' + resn] = refnumStr;
+            }
+            
+            refData += JSON.stringify(resid2imgt);
+        }
+
+
+        if(!me.bNode) {
+            let file_pref = Object.keys(me.utilsCls.getHlStructures()).join(',');
+    
+            ic.saveFileCls.saveFile(file_pref + '_refnum_' + type + '.txt', 'text', [refData]);
+        }
+        else {
+            return refData;
+        }
+    }
  }
 
 /**
@@ -57454,6 +57604,11 @@ class ApplyCommand {
       else if(command == 'export pdb hydrogen') {
         await ic.scapCls.exportPdbProfix(true);
       }
+      else if(command.indexOf('export refnum ') != -1) {
+        let type = command.substr(14);
+        
+        ic.refnumCls.exportRefnum(type);
+      }
       else if(command == 'export secondary structure') {
          me.htmlCls.setHtmlCls.exportSecondary();
       }