icn3d 3.26.7 → 3.26.9

package/icn3d.js

@@ -6031,6 +6031,21 @@ class ClickMenu {
         thisClass.setLogCmd("export pdb hydrogen", true);
        });
 
+       me.myEventCls.onIds("#" + me.pre + "mn1_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 + "mn1_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 + "mn1_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; 
                             }
                         }
                     }
@@ -44502,8 +44537,8 @@ class LineGraph {
             // let allPromise = Promise.allSettled(ajaxArray);
             // dataArray2 = await allPromise;
 
-            //split arrays into chunks of 100 jobs
-            let n = (me.bNode) ? 16 : 96;
+            //split arrays into chunks of 96 jobs or me.cfg.maxajax jobs
+            let n = (me.cfg.maxajax) ? me.cfg.maxajax : 96;
 
             for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
                 let currAjaxArray = [];
@@ -44603,6 +44638,8 @@ class LineGraph {
             let refpdbname = domainidpairArray[i].substr(domainidpairArray[i].indexOf('|') + 1);
             //let chainid = domainid.split('-')[0];
 
+            if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
+
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
             // Ig domain may require G (7050). But we'll leave that out for now.
             let bBstrand = false, bCstrand = false, bEstrand = false, bFstrand = false;
@@ -44726,6 +44763,8 @@ 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 +44773,8 @@ 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 +44957,121 @@ 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;
+        }
+    }
  }
 
 /**
@@ -48261,7 +48413,7 @@ class ChainalignParser {
             let chainid = chainidArray[i];
             let pos = chainid.indexOf('_');
             let struct = chainid.substr(0, pos); 
-            if(struct != ic.defaultPdbId) struct = struct.toUpperCase();
+            //if(struct != ic.defaultPdbId) struct = struct.toUpperCase();
 
             if(!struct2cnt.hasOwnProperty(struct)) {
                 struct2cnt[struct] = 1;
@@ -51511,7 +51663,7 @@ class RealignParser {
             let pos = chainidArray[i].indexOf('_');
             let mmdbid = chainidArray[i].substr(0, pos); //.toUpperCase();
 
-            if(!bRealign) mmdbid =  mmdbid.toUpperCase();
+            // if(!bRealign) mmdbid =  mmdbid.toUpperCase();
 
             if(i == 0) {
                 mmdbid_t = mmdbid;
@@ -51690,14 +51842,12 @@ class RealignParser {
         for(let j = 0, jl = resiArray.length; j < jl; ++j) {
             if(resiArray[j].indexOf('-') != -1) {
                 let startEnd = resiArray[j].split('-');
-
                 for(let k = parseInt(startEnd[0]); k <= parseInt(startEnd[1]); ++k) {
                     // from VAST neighbor page, use NCBI residue number
                     //if(me.cfg.usepdbnum === false) k += base - 1;
 
                     //let seqIndex = k - base;
                     let seqIndex = ic.setSeqAlignCls.getPosFromResi(chainid, k);
-
                     // if(ic.bNCBI) {
                     //     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chainid + '_' + k]);
                     //     if(atom && atom.resiNCBI) seqIndex = atom.resiNCBI - 1;
@@ -51714,9 +51864,9 @@ class RealignParser {
                 }            
             }
             else { // one residue
+                
                 //let k = parseInt(resiArray[j]);
                 let k = resiArray[j];
-
                 // from VAST neighbor page, use NCBI residue number
                 //if(me.cfg.usepdbnum === false) k += base - 1;
 
@@ -54640,22 +54790,23 @@ class SetSeqAlign {
     }
 
     getPosFromResi(chainid, resi) { let ic = this.icn3d; ic.icn3dui;
-/*        
-        let pos = undefined; //parseInt(resi);
-
-        for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
-            if(ic.chainsSeq[chainid][i].resi == resi) {
-                pos = i;
-                break;
-            }
-        }
-*/
         let residNCBI = ic.resid2ncbi[chainid + '_' + resi];
         let pos = undefined;
+        
         if(residNCBI) {
             let resiNCBI = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
             pos = resiNCBI - 1;
         }
+        // else {
+        //     //let il = ic.chainsSeq[chainid].length;
+        //     let il = (ic.chainsSeq[chainid]) ? ic.chainsSeq[chainid].length : 0;
+        //     for(let i = 0; i < il; ++i) {
+        //         if(ic.chainsSeq[chainid][i].resi == resi) {
+        //             pos = i;
+        //             break;
+        //         }
+        //     }
+        // }
 
         return pos;
     }
@@ -56114,6 +56265,7 @@ class LoadPDB {
 
                 // different residue
                 //if(residueNum !== prevResidueNum) {
+                    
                 if(oriResidueNum !== prevOriResidueNum) {
                     let residue = me.utilsCls.residueName2Abbr(resn);
                     ic.residueId2Name[residueNum] = residue;
@@ -57454,6 +57606,11 @@ 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();
       }
@@ -67306,6 +67463,26 @@ class SaveFile {
          return html;
     }
 
+    printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt) { let ic = this.icn3d; ic.icn3dui;
+        let ssText = '';
+
+        // print prev
+        if(prevRealSsObj) {
+            if(bHelix) {
+                let helixType = 1;
+                ssText += prevRealSsObj.resn.padStart(5, ' ') + prevRealSsObj.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
+                    + prevRealSsObj.resi.toString().padStart(5, ' ') + '  ' + helixType + ssCnt.toString().padStart(36, ' ') + '\n';
+            }
+            else if(bSheet) {
+                let sense = 0;
+                ssText += prevRealSsObj.resn.padStart(5, ' ') + prevRealSsObj.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
+                    + prevRealSsObj.resi.toString().padStart(4, ' ') + '  ' + sense + '\n';
+            }
+        }
+
+        return ssText;
+    }
+
     //getAtomPDB: function(atomHash, bPqr, bPdb, bNoChem) { let ic = this.icn3d, me = ic.icn3dui;
     getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid) { let ic = this.icn3d, me = ic.icn3dui;
         let pdbStr = '';
@@ -67338,8 +67515,6 @@ class SaveFile {
 
         let calphaHash = me.hashUtilsCls.intHash(atomHash, ic.calphas);
         let helixStr = 'HELIX', sheetStr = 'SHEET';
-        let bHelixBegin = false, bHelixEnd = true;
-        let bSheetBegin = false, bSheetEnd = true;
 
         let stru2header = {};
         for(let stru in ic.structures) {
@@ -67347,48 +67522,82 @@ class SaveFile {
         }
 
 //        if(!bNoSs) {
-            let prevResi, stru, chainid;
+            let prevResi, stru;
+            let ssArray = [];
             for(let i in calphaHash) {
                 let atom = ic.atoms[i];
                 stru = atom.structure;
-                chainid = atom.structure + '_' + atom.chain;
+                atom.structure + '_' + atom.chain;
 
-                if(atom.ssbegin) {
-                    if(atom.ss == 'helix') {
-                        bHelixBegin = true;
-                        if(bHelixEnd) stru2header[stru] += helixStr.padEnd(15, ' ') + atom.resn.padStart(3, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
-                            + atom.resi.toString().padStart(5, ' ');
-                        bHelixEnd = false;
-                        prevResi = atom.resi;
-                    }
-                    else if(atom.ss == 'sheet') {
-                        bSheetBegin = true;
-                        if(bSheetEnd) stru2header[stru] += sheetStr.padEnd(17, ' ') + atom.resn.padStart(3, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
-                            + atom.resi.toString().padStart(4, ' ');
-                        bSheetEnd = false;
-                    }
+                let ssObj = {};
+                ssObj.chain = atom.chain;
+                ssObj.resn = atom.resn;
+                ssObj.resi = atom.resi;
+
+                if(parseInt(atom.resi) > parseInt(prevResi) + 1) {
+                    ssObj.ss = ' ';
+                    ssArray.push(ssObj);
+                }
+
+                if(atom.ss == 'helix') {
+                    ssObj.ss = 'H';
+                    ssArray.push(ssObj);
+                }
+                else if(atom.ss == 'sheet') {
+                    ssObj.ss = 'S';
+                    ssArray.push(ssObj);
                 }
 
                 if(atom.ssend) {
-                    if(atom.ss == 'helix') {
-                        bHelixEnd = true;
-                        let residEnd = ic.resid2ncbi[chainid + '_' + atom.resi];
-                        let residStart = ic.resid2ncbi[chainid + '_' + prevResi];
-                        let helixLen = (residEnd && residStart) ? parseInt(residEnd.substr(residEnd.lastIndexOf('_') + 1)) - parseInt(residStart.substr(residStart.lastIndexOf('_') + 1)) : 0;
-                        let helixType = 1;
-                        if(bHelixBegin) stru2header[stru] += atom.resn.padStart(5, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
-                            + atom.resi.toString().padStart(5, ' ') + '  ' + helixType + helixLen.toString().padStart(36, ' ') + '\n';
-                        bHelixBegin = false;
-                    }
-                    else if(atom.ss == 'sheet') {
-                        bSheetEnd = true;
-                        let sense = 0;
-                        if(bSheetBegin) stru2header[stru] += atom.resn.padStart(5, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
-                            + atom.resi.toString().padStart(4, ' ') + '  ' + sense + '\n';
-                        bSheetBegin = false;
+                    let ssObj2 = me.hashUtilsCls.cloneHash(ssObj);
+                    ssObj2.ss = ' ';
+                    ssArray.push(ssObj2);
+                }
+
+                prevResi = atom.resi;
+            }
+
+            let prevSs, prevRealSsObj, ssCnt = 0, bHelix = false, bSheet = false;
+            for(let i = 0, il = ssArray.length; i < il; ++i) {
+                let ssObj = ssArray[i];
+
+                if(ssObj.ss != prevSs) {
+                    // print prev
+                    stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
+
+                    // print current
+                    ssCnt = 0;
+                    bHelix = false;
+                    bSheet = false;
+                    prevRealSsObj = undefined;
+
+                    if(ssObj.ss != ' ') {
+                        if(ssObj.ss == 'H') {
+                            bHelix = true;
+                            prevRealSsObj = ssObj;
+                            stru2header[stru] += helixStr.padEnd(15, ' ') + ssObj.resn.padStart(3, ' ') + ssObj.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
+                                + ssObj.resi.toString().padStart(5, ' ');
+                        }
+                        else if(ssObj.ss == 'S') {
+                            bSheet = true;
+                            prevRealSsObj = ssObj;
+                            stru2header[stru] += sheetStr.padEnd(17, ' ') + ssObj.resn.padStart(3, ' ') + ssObj.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
+                                + ssObj.resi.toString().padStart(4, ' ');
+                        }
                     }
                 }
+
+                if(ssObj.ss != ' ') {
+                    ++ssCnt;
+                    prevRealSsObj = ssObj;
+                }
+
+                prevSs = ssObj.ss;
             }
+
+            // print prev
+            stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
+
             // add a new line in case the structure is a subset
             stru2header[stru] += '\n';
 //        }
@@ -67819,7 +68028,7 @@ class SaveFile {
             let structureidArray = Object.keys(idHash);
             inputid = structureidArray.join(',');
 
-            text = inputid.toUpperCase();
+            text = (me.cfg.refseqid) ? ic.inputid : inputid.toUpperCase();
 
             //idName = (isNaN(inputid) && inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
             if(bPdb && bAlphaFold) {
@@ -71309,6 +71518,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         }
         else if(me.cfg.resdef !== undefined && me.cfg.matchedchains !== undefined) {
             let stru_t = Object.keys(ic.structures)[0];
+
             let chain_t = stru_t + '_' + me.cfg.masterchain;
             let domainidArray = me.cfg.matchedchains.split(',');
             let chainidArray = [];