icn3d 3.51.3 → 3.52.0

package/icn3d.js

@@ -101152,20 +101152,12 @@ class GetGraph {
        let thickness = me.htmlCls.coilValue;
        let prevChain = '', prevResName = '', prevResi = 0;
        // add chemicals as well
-       let residHash = {};
-       for(let i in atomSet) {
-           let atom = ic.atoms[i];
+       let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(atomSet);
+       for(let resid in residHash) {
+           let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
 
-           if(atom.chain != 'DUM' && (bAnyAtom || atom.het || (atom.name == "CA" && atom.elem == "C") || atom.name == "O3'" || atom.name == "O3*" || atom.name == "P")) {
-           // starting nucleotide have "P"
-           //if(atom.chain != 'DUM' &&(atom.name == "CA" || atom.name == "P")) {
-               let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
-               if(residHash.hasOwnProperty(resid)) {
-                   continue;
-               }
-               else {
-                   residHash[resid] = 1;
-               }
+           //if(atom.chain != 'DUM' && (bAnyAtom || atom.het || (atom.name == "CA" && atom.elem == "C") || atom.name == "O3'" || atom.name == "O3*" || atom.name == "P")) {
+           if(atom.chain != 'DUM') {
                let resName = me.utilsCls.residueName2Abbr(atom.resn) + atom.resi;
                if(labelType == 'chain' || labelType == 'structure') resName += '.' + atom.chain;
                if(labelType == 'structure') resName += '.' + atom.structure;
@@ -108113,12 +108105,15 @@ class OpmParser {
 
     async loadOpmData(data, pdbid, bFull, type, pdbid2, bText) { let ic = this.icn3d, me = ic.icn3dui;
         try {
-             if(!pdbid) pdbid = ic.defaultPdbId;
-            let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
+            if(!pdbid) pdbid = ic.defaultPdbId;
 
-            let opmdata = await me.getAjaxPromise(url, 'jsonp', false);
-    
-            this.setOpmData(opmdata); // set ic.bOpm
+            //if(me.cfg.mmtfid === undefined && me.cfg.bcifid === undefined) { // skip opm for bcif files
+                let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
+
+                let opmdata = await me.getAjaxPromise(url, 'jsonp', false);
+        
+                this.setOpmData(opmdata); // set ic.bOpm
+            //}
 
             await this.parseAtomData(data, pdbid, bFull, type, pdbid2, bText);
         }
@@ -116295,6 +116290,36 @@ class LoadCIF {
         this.icn3d = icn3d;
     }
 
+    // Fast replacements for ic.loadPDBCls.isSecondary(), which does a linear scan
+    // ($.inArray, or a hand-rolled loop with a substr() per comparison for bNMR) over
+    // residArray - and gets called up to 6 times per atom in the main atom loop below.
+    // buildSecondarySet() precomputes, once per model, exactly what isSecondary would
+    // have compared against on every call (the raw resid strings for non-NMR, or the
+    // structure-prefix-stripped "chain_resi" strings for NMR - matching isSecondary's
+    // two branches exactly), so membership becomes an O(1) Set lookup instead of an
+    // O(residArray.length) scan repeated for every atom. isSecondary's 4th parameter
+    // (bNonFull) is intentionally not replicated here: in the actual implementation
+    // it's dead (the only reference to it is commented out), so it has no behavior to
+    // preserve.
+    buildSecondarySet(residArray, bNMR) {
+        let s = new Set();
+        if(!bNMR) {
+            for(let i = 0, il = residArray.length; i < il; ++i) s.add(residArray[i]);
+        }
+        else {
+            for(let i = 0, il = residArray.length; i < il; ++i) {
+                let r = residArray[i];
+                s.add(r.substr(r.indexOf('_') + 1));
+            }
+        }
+        return s;
+    }
+
+    isSecondaryFast(resid, secondarySet, bNMR) {
+        if(!bNMR) return secondarySet.has(resid);
+        return secondarySet.has(resid.substr(resid.indexOf('_') + 1));
+    }
+
     loadCIF(bcifData, bcifid, bText, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
         let hAtoms = {};
 
@@ -116671,7 +116696,10 @@ class LoadCIF {
             // check 3QUM
             let chainArray = atom_site.getColumn("auth_asym_id");
 
-            let resiArray = atom_site.getColumn("label_seq_id");
+            // label_seq_id used to be fetched into "resiArray" here and decoded into
+            // "resi" below, but that value was always immediately overwritten by
+            // auth_seq_id (oriResi) before being used anywhere - decoding it per atom
+            // was pure wasted work, so it is no longer fetched at all.
             let resiOriArray = atom_site.getColumn("auth_seq_id");
             let altArray = atom_site.getColumn("label_alt_id");
 
@@ -116684,6 +116712,14 @@ class LoadCIF {
             let autochainArray = atom_site.getColumn("label_asym_id");
             let modelNumArray = atom_site.getColumn("pdbx_PDB_model_num");
 
+            // built once per model instead of scanned per atom - see isSecondaryFast()
+            let sheetSet = this.buildSecondarySet(sheetArray, bNMR);
+            let sheetStartSet = this.buildSecondarySet(sheetStart, bNMR);
+            let sheetEndSet = this.buildSecondarySet(sheetEnd, bNMR);
+            let helixSet = this.buildSecondarySet(helixArray, bNMR);
+            let helixStartSet = this.buildSecondarySet(helixStart, bNMR);
+            let helixEndSet = this.buildSecondarySet(helixEnd, bNMR);
+
             // get the bond info
             let ligSeqHash = {}, prevAutochain = '';
             let prevResn;
@@ -116710,14 +116746,13 @@ class LoadCIF {
                 let atom = nameArray.getString(i);
                 let entityid = entiyidArray.getString(i);
                 let chain = chainArray.getString(i);
-                let resi = resiArray.getString(i);
                 let oriResi = resiOriArray.getString(i); 
                 let alt = altArray.getString(i);
                 let bFactor = bArray.getString(i);
 
                 let autochain = autochainArray.getString(i);
 
-                resi = oriResi;
+                let resi = oriResi;
 
                 let molecueType;
                 if(atom_hetatm == "ATOM") {
@@ -116872,26 +116907,26 @@ class LoadCIF {
 
                 // Assign secondary structures from the input
                 // if a residue is assigned both sheet and helix, it is assigned as sheet
-                if(ic.loadPDBCls.isSecondary(residueNum, sheetArray, bNMR, !bFull)) {
+                if(this.isSecondaryFast(residueNum, sheetSet, bNMR)) {
                     ic.atoms[serial].ss = 'sheet';
-                    if(ic.loadPDBCls.isSecondary(residueNum, sheetStart, bNMR, !bFull)) {
+                    if(this.isSecondaryFast(residueNum, sheetStartSet, bNMR)) {
                     ic.atoms[serial].ssbegin = true;
                     }
 
                     // do not use else if. Some residues are both start and end of secondary structure
-                    if(ic.loadPDBCls.isSecondary(residueNum, sheetEnd, bNMR, !bFull)) {
+                    if(this.isSecondaryFast(residueNum, sheetEndSet, bNMR)) {
                     ic.atoms[serial].ssend = true;
                     }
                 }
-                else if(ic.loadPDBCls.isSecondary(residueNum, helixArray, bNMR, !bFull)) {
+                else if(this.isSecondaryFast(residueNum, helixSet, bNMR)) {
                     ic.atoms[serial].ss = 'helix';
 
-                    if(ic.loadPDBCls.isSecondary(residueNum, helixStart, bNMR, !bFull)) {
+                    if(this.isSecondaryFast(residueNum, helixStartSet, bNMR)) {
                     ic.atoms[serial].ssbegin = true;
                     }
 
                     // do not use else if. Some residues are both start and end of secondary structure
-                    if(ic.loadPDBCls.isSecondary(residueNum, helixEnd, bNMR, !bFull)) {
+                    if(this.isSecondaryFast(residueNum, helixEndSet, bNMR)) {
                     ic.atoms[serial].ssend = true;
                     }
                 }
@@ -117009,7 +117044,7 @@ class LoadCIF {
 */
 
             // clear memory
-            atom_hetatmArray = resnArray = elemArray = nameArray = chainArray = resiArray = resiOriArray 
+            atom_hetatmArray = resnArray = elemArray = nameArray = chainArray = resiOriArray 
                 = altArray = bArray = xArray = yArray = zArray = autochainArray = [];
 
             let mChainSeq = {};
@@ -117181,7 +117216,6 @@ class LoadCIF {
         // check the bonds between chemicals and all other atoms
         let processedChemicals = {};
         for(let i in ic.chemicals) {
-            console.log(" i = ", i, " processedChemicals = ", processedChemicals);
             if(processedChemicals.hasOwnProperty(i)) continue;
 
             let atom = ic.atoms[i];
@@ -120659,6 +120693,7 @@ class DefinedSets {
                }
            }
        //}
+
        return residuesHash;
     }
     
@@ -122589,6 +122624,8 @@ class Selection {
     selectMainChains() { let ic = this.icn3d, me = ic.icn3dui;
         let currHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
+        ic.opts.pk = 'atom';
+
         ic.hAtoms = ic.applyDisplayCls.selectMainChainSubset(currHAtoms);
 
         ic.hlUpdateCls.showHighlight();
@@ -122598,6 +122635,8 @@ class Selection {
     selectSideChains() { let ic = this.icn3d, me = ic.icn3dui;
         let currHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
+        ic.opts.pk = 'atom';
+
         ic.hAtoms = this.getSideAtoms(currHAtoms);
         ic.hlUpdateCls.showHighlight();
     }
@@ -122619,6 +122658,8 @@ class Selection {
     selectMainSideChains() { let ic = this.icn3d, me = ic.icn3dui;
         let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
 
+        ic.opts.pk = 'residue';
+
         ic.hAtoms = {};
         for(let resid in residHash) {
             ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, ic.residues[resid]);
@@ -122795,8 +122836,9 @@ class Selection {
             description = name;
         }
 
-        if(Object.keys(ic.selectedResidues).length > 0) {
-            if(ic.pk == 1) {
+        //if(Object.keys(ic.selectedResidues).length > 0) {
+            // if(ic.pk == 1) {
+            if(ic.opts.pk == 'atom') {
                 let bAtom = true;
                 this.selectResidueList(ic.hAtoms, name, description, undefined, undefined, bAtom);
                 //ic.hlUpdateCls.updateHlAll();
@@ -122823,7 +122865,7 @@ class Selection {
                     me.htmlCls.clickMenuCls.setLogCmd('select ' + ic.resid2specCls.residueids2spec(Object.keys(ic.selectedResidues)), true);
                 }
             }
-        }
+        //}
     }
 
     saveSelInCommand() { let ic = this.icn3d, me = ic.icn3dui;
@@ -135875,7 +135917,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.51.2';
+    this.REVISION = '3.52.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;