icn3d 3.26.8 → 3.26.9

package/icn3d.js

@@ -6031,17 +6031,17 @@ 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();
+       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 + "m1_exportKabat", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+      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 + "m1_exportImgt", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+      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);
       });
@@ -44537,8 +44537,8 @@ class LineGraph {
             // let allPromise = Promise.allSettled(ajaxArray);
             // dataArray2 = await allPromise;
 
-            //split arrays into chunks of 100 jobs
-            let n = (me.bNode) ? 96 : 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 = [];
@@ -44638,6 +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;
@@ -48411,7 +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;
@@ -51661,7 +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;
@@ -51840,14 +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;
@@ -51864,9 +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;
 
@@ -54790,22 +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;
     }
@@ -56264,6 +56265,7 @@ class LoadPDB {
 
                 // different residue
                 //if(residueNum !== prevResidueNum) {
+                    
                 if(oriResidueNum !== prevOriResidueNum) {
                     let residue = me.utilsCls.residueName2Abbr(resn);
                     ic.residueId2Name[residueNum] = residue;
@@ -67461,6 +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 = '';
@@ -67493,8 +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) {
@@ -67502,48 +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';
 //        }
@@ -67974,7 +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) {
@@ -71464,6 +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 = [];