icn3d 3.45.3 → 3.45.5

package/icn3d.js

@@ -54156,7 +54156,7 @@ class HashUtilsCls {
     //Get the union of two hashes "atoms1" and "atoms2". The returned hash has atom index as key and 1 as value.
     unionHash(atoms1, atoms2) { let me = this.icn3dui;
         // much slower
-        //return me.hashUtilsCls.unionHashNotInPlace(atoms1, atoms2);
+        // return me.hashUtilsCls.unionHashNotInPlace(atoms1, atoms2);
 
         // much faster
         return me.hashUtilsCls.unionHashInPlace(atoms1, atoms2);
@@ -57999,7 +57999,7 @@ class ClickMenu {
            let sigmafofc = parseFloat($("#" + me.pre + "sigmafofc" ).val());
            let type = 'fofc';
            //await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
-           await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
+           await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigmafofc);
            //ic.setOptionCls.setOption('map', 'fofc');
            thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
         });
@@ -59369,7 +59369,7 @@ class SetMenu {
         html += this.getLink('mn1_mmcifid', 'RCSB mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
         //html += this.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
 
-        html += this.getLink('mn1_cid', 'PubChem CID/Name/InchI ' + me.htmlCls.wifiStr, 1, 2);
+        html += this.getLink('mn1_cid', 'PubChem CID/Name/InChI ' + me.htmlCls.wifiStr, 1, 2);
         html += this.getLink('mn1_smiles', 'Chemical SMILES ', undefined, 2);
         
         html += "</ul>";
@@ -59737,9 +59737,9 @@ class SetMenu {
 
         html += this.getMenuText('mn2_rotate90', 'Rotate 90&deg;', undefined, undefined, 2);
         html += "<ul>";
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatex', 'rotate x', undefined, undefined, 2);
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatey', 'rotate y', undefined, undefined, 2);
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatez', 'rotate z', undefined, undefined, 2);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatex', 'rotate x', undefined, undefined, 3);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatey', 'rotate y', undefined, undefined, 3);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatez', 'rotate z', undefined, undefined, 3);
         html += "</ul>";
         html += "</li>";
         html += this.getMenuText('mn2_rotateauto', 'Auto Rotation', undefined, 1, 2);
@@ -61823,7 +61823,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_mmdbafid' class='" + dialogClass + "' style='max-width:600px'>";
         html += this.addNotebookTitle('dl_mmdbafid', 'Please input a list of PDB/AlphaFold IDs');
-        html += "List of PDB, MMDB, or AlphaFold UniProt structures: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30> <br><br>";
+        html += "List of PDB, MMDB, or AlphaFold UniProt structures: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbafid' placeholder='e.g., 1HHO,pdb_00004n7n,P69905,P01942' size=30> <br><br>";
         html += "<div style='display:inline-block; width:20px'></div>" + me.htmlCls.buttonStr + "reload_mmdbaf' style='width:150px'>Load Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdbaf_asym' style='margin-left:30px; width:250px'>Load Asymmetric Unit (All Chains)</button>" + "<br/><br/>";
         html += "<div style='display:inline-block; width:20px'>or</div>" + me.htmlCls.buttonStr + "reload_mmdbaf_append' style='width:150px'>Append Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdbaf_asym_append' style='margin-left:30px; width:250px'>Append Asymmetric Unit (All Chains)</button>" + "<br/><br/>";
 
@@ -61870,7 +61870,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_cid' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_cid', 'Please input a PubChem Compound');
-        html += "PubChem CID/Name/InchI: " + me.htmlCls.inputTextStr + "id='" + me.pre + "cid' value='2244' size=8> ";
+        html += "PubChem CID/Name/InChI: " + me.htmlCls.inputTextStr + "id='" + me.pre + "cid' value='2244' size=8> ";
         html += me.htmlCls.buttonStr + "reload_cid'>Load</button>";
         html += "</div>";
 
@@ -61900,7 +61900,6 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_video' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_video', 'Save canvas changes in a video');
-        html += "State file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "state'><br/>";
         html += me.htmlCls.buttonStr + "video_start' style='margin-top: 6px;'>Video Start</button>";
         html += me.htmlCls.buttonStr + "video_end' style='margin: 6px 0px 0px 30px;'>Video End</button>";
         html += "</div>";
@@ -63434,7 +63433,7 @@ class Events {
             ic.cam.quaternion.setFromUnitVectors(new Vector3$1(0, 0, -1), new Vector3$1(directionArray[0], directionArray[1], directionArray[2]));
             ic.cam.up.set(upvectorArray[0], upvectorArray[1], upvectorArray[2]);
             ic.cam.fov = fov;
-            //ic.container.whratio = aspect;
+            // ic.container.whratio = aspect;
 
             ic.drawCls.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
             ic.drawCls.render();
@@ -64018,7 +64017,7 @@ class Events {
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
-           let alignment = $("#" + me.pre + "chainalignids").val();
+           let alignment = $("#" + me.pre + "chainalignids").val().replace(/\s/g, '');
            let alignment_final = thisClass.convertUniProtInChains(alignment);
 
            thisClass.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
@@ -64030,7 +64029,7 @@ class Events {
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
-            let alignment = $("#" + me.pre + "chainalignids2").val();
+            let alignment = $("#" + me.pre + "chainalignids2").val().replace(/\s/g, '');
             let alignment_final = thisClass.convertUniProtInChains(alignment);
             let resalign = $("#" + me.pre + "resalignids").val();
  
@@ -64043,7 +64042,7 @@ class Events {
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
-            let alignment = $("#" + me.pre + "chainalignids3").val();
+            let alignment = $("#" + me.pre + "chainalignids3").val().replace(/\s/g, '');
             let alignment_final = thisClass.convertUniProtInChains(alignment);
 
             let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, ': ');
@@ -64061,7 +64060,7 @@ class Events {
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
-            let alignment = $("#" + me.pre + "chainalignids4").val();
+            let alignment = $("#" + me.pre + "chainalignids4").val().replace(/\s/g, '');
             let alignment_final = thisClass.convertUniProtInChains(alignment);
 
             let predefinedres = $("#" + me.pre + "predefinedres2").val().trim().replace(/\n/g, ': ');
@@ -64070,7 +64069,8 @@ class Events {
                 return;
             }
 
-            me.cfg.resdef = predefinedres.replace(/:/gi, ';');
+            // me.cfg.resdef = predefinedres.replace(/:/gi, ';');
+            me.cfg.resdef = predefinedres;
 
             let bRealign = true, bPredefined = true;
             let chainidArray = alignment_final.split(',');
@@ -65350,7 +65350,6 @@ class Events {
         });
         me.myEventCls.onIds("#" + me.pre + "applypick_aroundsphere", "click", function(e) { let ic = me.icn3d;
             //e.preventDefault();
-            
             let radius = parseFloat($("#" + me.pre + "radius_aroundsphere").val());
             let nameArray = $("#" + me.pre + "atomsCustomSphere").val();
             let nameArray2 = $("#" + me.pre + "atomsCustomSphere2").val();
@@ -74154,8 +74153,11 @@ class Scene {
 
         ic.fogCls.setFog();
 
-        if(ic.bSetCamera) { // load a URL with trackball transformation, or no info after "|||"
-            ic.cameraCls.setCamera();
+        ic.cameraCls.setCamera();
+        // set the ratio for view point, which was set in ic.transformCls.resetOrientation_base
+        if(!ic.container.whratio) {
+            ic.container.whratio = me.htmlCls.WIDTH / me.htmlCls.HEIGHT; 
+            ic.cam.aspect = ic.container.whratio;
         }
 
         if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
@@ -78611,8 +78613,8 @@ class Tube {
                                 }
                             }
 
-                            // add one more residue if only one residue is available
-                            if(pnts.length == 1 && ic.residues.hasOwnProperty(nextoneResid)) {
+                            // add one more residue if only one residue is available and it's not part of helix/sheet
+                            if(pnts.length == 1 && ic.residues.hasOwnProperty(nextoneResid) && atom.ss == 'coil') {
                                 let nextAtom = ic.firstAtomObjCls.getAtomFromResi(nextoneResid, atomName);
 
                                 if(nextAtom) {
@@ -83392,8 +83394,10 @@ class ApplyCenter {
 
         //ic.container.widthInv  = 1 / (ic.scaleFactor*width);
         //ic.container.heightInv = 1 / (ic.scaleFactor*height);
-
-        ic.container.whratio = width / height;
+        if(ic.cam) {
+            ic.container.whratio = width / height;
+            ic.cam.aspect = ic.container.whratio;
+        }
     }
 }
 
@@ -86465,7 +86469,6 @@ class Alternate {
           this.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
           this.render(bVrAr);
         }
-
         //ic.impostorCls.clearImpostors();
 
         // show membranes
@@ -92728,7 +92731,8 @@ class AnnoSnpClinVar {
 
           let snpResn = snpStr.substr(posSymbol - 1, 1);
           let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chnid + '_' + realResi]);
-          let oneLetterRes = (atom) ? me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)) : '';
+        //   let oneLetterRes = (atom) ? me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)) : ''; // !!!
+          let oneLetterRes = (atom) ? me.utilsCls.residueName2Abbr(atom.resn) : '';
           if(!bFromClinVarDb && ic.chainsSeq[chnid][resi - 1]) {
             oneLetterRes = ic.chainsSeq[chnid][resi - 1].name;
           }
@@ -96858,7 +96862,8 @@ class Annotation {
             
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chainid]);
             if(atom && atom.resn !== undefined) {
-                let oneLetterRes = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                // let oneLetterRes = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                let oneLetterRes = me.utilsCls.residueName2Abbr(atom.resn);
                 $("#" + ic.pre + "anno_" + oneLetterRes).show();
             }
         }
@@ -101062,23 +101067,27 @@ class ShowInter {
             ic.hAtoms[i] = 1;
           }
         }
+
         // do not change the set of displaying atoms
         //ic.dAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
         let commandname, commanddesc, commandname2;
         let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(atomlistTarget);
 
         if(firstAtom !== undefined) {
-            commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
+            // commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
+            commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn).trim() + firstAtom.resi + "-" + radius + "A";
             //sometimes firstAtom.resi changed, thus we add a general name
             commandname2 = "sphere-" + radius + "A";
             if(bInteraction) {
-                commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+                // commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+                commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
                 commandname2 = "interactions-" + $("#" + ic.pre + "contactthreshold").val() + "A";
             }
             commanddesc = commandname;
             ic.selectionCls.addCustomSelection(residueArray, commandname, commanddesc, select, true);
             ic.selectionCls.addCustomSelection(residueArray, commandname2, commanddesc, select, true);
         }
+
         ic.selectionCls.saveSelectionIfSelected();
         ic.drawCls.draw();
     }
@@ -101328,8 +101337,10 @@ class ViewInterPairs {
                     let commandname, commanddesc;
                     let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(residues);
                     if(firstAtom !== undefined) {
-                        commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
-                        if(bInteraction) commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+                        // commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
+                        commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn).trim() + firstAtom.resi + "-" + radius + "A";
+                        // if(bInteraction) commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+                        if(bInteraction) commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
                         commanddesc = commandname;
                         ic.selectionCls.addCustomSelection(residueArray, commandname, commanddesc, select, true);
                     }
@@ -101340,6 +101351,7 @@ class ViewInterPairs {
                 tableHtml += this.exportSpherePairs(true, type, labelType);
            } // same set
        }
+
        ic.hAtoms = me.hashUtilsCls.cloneHash(hAtoms);
        ic.bRender = true;
        //ic.hlUpdateCls.updateHlAll();
@@ -103304,7 +103316,6 @@ class ChainalignParser {
         for(let i = 0, il = dataArray.length; i < il; ++i) {
             let mmdbid_q = struArray[i];
             let index = indexArray[i];
-
             this.transformStructure(mmdbid_q, index, 'query');
         }
 
@@ -103535,7 +103546,8 @@ class ChainalignParser {
 
     transformStructure(mmdbid, index, alignType, bForce) { let ic = this.icn3d, me = ic.icn3dui;
         let chainidArray = ic.structures[mmdbid];
-        
+        if(!chainidArray) return;
+
         for(let i = 0, il = chainidArray.length; i < il; ++i) {
             for(let serial in ic.chains[chainidArray[i]]) {
                 let atm = ic.atoms[serial];
@@ -103670,6 +103682,8 @@ class ChainalignParser {
     addPostfixForStructureids(structArray) { let ic = this.icn3d; ic.icn3dui;
         let struct2cnt = {};
         for(let i = 0, il = structArray.length; i < il; ++i) {
+            if(structArray[i].toLowerCase().toLowerCase().substr(0,8) == 'pdb_0000') structArray[i] = structArray[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
+
             let struct = structArray[i].toUpperCase(); 
 
             if(!struct2cnt.hasOwnProperty(struct)) {
@@ -104054,6 +104068,8 @@ class ChainalignParser {
         }
         else {
             for(let i = 0, il = structArrayTmp.length; i < il; ++i) {
+                if(structArrayTmp[i].toLowerCase().substr(0,8) == 'pdb_0000') structArrayTmp[i] = structArrayTmp[i].substr(8); // temperary support long PDB ID such as pdb_00001tup
+
                 let id = structArrayTmp[i].toUpperCase();
                 if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
             }
@@ -105922,7 +105938,6 @@ class MmdbParser {
 
             hAtoms = ic.loadAtomDataCls.loadAtomDataIn(data, pdbid, 'mmdbid', undefined, type, chainid, chainIndex, bLastQuery, bNoTransformNoSeqalign);
         }
-
         // show ligand-protein interaction
         if(me.cfg.ligand) { // sid123059722
             for(let chainid in ic.chainid2sid) {
@@ -105994,7 +106009,6 @@ class MmdbParser {
                 }
             } // for each domainArray
         } // for each molid
-
         // "asuAtomCount" is defined when: 1) atom count is over the threshold 2) bu=1 3) asu atom count is smaller than biological unit atom count
         ic.bAssemblyUseAsu =(data.asuAtomCount !== undefined) ? true : false;
         if(type !== undefined) {
@@ -106128,7 +106142,6 @@ class MmdbParser {
         //ic.molid2color = molid2color;
         //ic.chain2molid = chain2molid;
         ic.molid2chain = molid2chain;
-
         // small structure with all atoms
         // show surface options
         $("#" + ic.pre + "accordion5").show();
@@ -108366,7 +108379,8 @@ class RealignParser {
                     ic.realignResid[chainid] = [];
                 }
 
-                ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)).substr(0, 1)});
+                // ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3)).substr(0, 1)});
+                 ic.realignResid[chainid].push({'resid': chainid + '_' + atom.resi, 'resn': me.utilsCls.residueName2Abbr(atom.resn).substr(0, 1)});
 
                 struct2chain[atom.structure] = atom.structure + '_' + atom.chain;
 
@@ -108790,7 +108804,9 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
                             let alignAjax;
                             if(me.cfg.aligntool != 'tmalign') {
                                 let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
-            
+console.log("@@@ realign " + struct1 + " " + chainid1 + " and " + struct2 + " " + chainid2);
+console.log("@@@ jsonStr_q " + jsonStr_q);
+console.log("@@@ jsonStr_t " + jsonStr_t);            
                                 let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
                                 alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
                             }
@@ -108924,8 +108940,9 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
         let predefinedResArray, predefinedResPair;
 
         if(bPredefined) {
-            // predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split(': ');
-            predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split('; ');
+            me.cfg.resdef.replace(/; /gi, ': ');
+            predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split(': ');
+            // predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split('; ');
             
             if(predefinedResArray.length != chainidArray.length - 1) {
                var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
@@ -111370,7 +111387,8 @@ class LoadAtomData {
                 atm.coord = new Vector3$1(atm.coord.x, atm.coord.y, atm.coord.z);
             }
 
-            let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn.substr(0, 3));
+            // let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn.substr(0, 3));
+            let oneLetterRes = me.utilsCls.residueName2Abbr(atm.resn);
 
             if((type === 'mmdbid' || type === 'align') && ic.bFullUi ) {
                 // set ic.mmdbMolidResid2mmdbChainResi
@@ -111497,7 +111515,6 @@ class LoadAtomData {
             let residueid = chainid + '_' + atm.resi;
             if(ic.residues[residueid] === undefined) ic.residues[residueid] = {};
             ic.residues[residueid][serial] = 1;
-
             residueNum = chainNum + '_' + atm.resi;
 
             // different residue
@@ -111666,7 +111683,6 @@ class LoadAtomData {
         }
         // remove the reference
         data.atoms = {};
-
         //ic.cnt =(alignType === undefined || alignType === 'target') ? serial : serial - ic.lastTargetSerial;
         ic.cnt = serial;
 
@@ -112343,7 +112359,7 @@ class SetSeqAlign {
                       }
                   }
               }
-            
+
               for(let j = 0; j <= end1 - start1; ++j) {
                   ///if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid2] === undefined) break;
 
@@ -112456,11 +112472,15 @@ class SetSeqAlign {
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let start1, end1;
                 
-                // start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
-                // end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
-
-                start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
-                end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+                //ic.qt_start_end is zero-based
+                if(!bRealign && me.cfg.aligntool != 'tmalign') { // vast alignment
+                    start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
+                    end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
+                }
+                else {
+                    start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
+                    end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+                }
 
                 for(let j = start1; j <= end1; ++j) {
                     let resi, resid;
@@ -112553,7 +112573,6 @@ class SetSeqAlign {
             resObject.color2 = (resid2range_t[resid]) ? '#FF0000' : me.htmlCls.GREYC; // color by conservation
             // resObject.class = (resid2range_t[resid]) ? 'icn3d-align' : 'icn3d-nalign';
             resObject.class = (resid2range_t[resid]) ? 'icn3d-cons' : 'icn3d-nalign';
-    
             ic.alnChainsSeq[chainid1].push(resObject);
 
             if(resid2range_t[resid]) {
@@ -112712,6 +112731,7 @@ class SetSeqAlign {
         for(let j = 0, jl = alignedChainIndice.length - 1; j < jl; ++j) {
             let chainidTmp = chainidArray[alignedChainIndice[j]];
             let gapResObject = this.getResObject(chainidTmp, true);
+            
             //for(let k = 0, kl = len - nGap; k < kl; ++k) {
             for(let k = 0, kl = len; k < kl; ++k) {
                 ic.alnChainsSeq[chainidTmp].splice(pos_t, 0, gapResObject);
@@ -112721,12 +112741,12 @@ class SetSeqAlign {
         //return len - nGap;
     }
 
-    insertNotAlignRes(chainid, start, len, bRealign) { let ic = this.icn3d; ic.icn3dui;
+    insertNotAlignRes(chainid, start, len, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
         // insert non-aligned residues in query seq
         for(let j = 0, jl = len; j < jl; ++j) {
             // let resi2 = ic.ParserUtilsCls.getResi(chainid, start + j);
             // let resn2 = this.getResn(chainid, start + j);
-            let resi2 = start + j;
+            let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start + j : ic.ParserUtilsCls.getResi(chainid, start + j);
             let resn2 = this.getResnFromResi(chainid, resi2);
             let resn1 = '-';
             let bAlign = false;
@@ -112735,16 +112755,21 @@ class SetSeqAlign {
         }
     }
 
-    getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
+    getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
         // let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
         // let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
-        let startResi = start;
-        let endResi = end;
+        if(bRealign && me.cfg.aligntool == 'tmalign') { // vast alignment
+            let startResi = start;
+            let endResi = end;
 
-        let result1 = this.getResiPosInTemplate(chainid1, startResi);
-        let result2 = this.getResiPosInTemplate(chainid1, endResi);
- 
-        return {"pos1": result1.pos, "pos2": result2.pos};
+            let result1 = this.getResiPosInTemplate(chainid1, startResi);
+            let result2 = this.getResiPosInTemplate(chainid1, endResi);
+    
+            return {"pos1": result1.pos, "pos2": result2.pos};
+        }
+        else {
+            return {"pos1": start, "pos2": end};
+        }
     }
 
     mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resid2range_t, start_t, end_t, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -112807,6 +112832,9 @@ class SetSeqAlign {
 
         let result;
 
+        let nGapInTemplate = 0; // number of gaps inserted into the template sequence
+        let startPosInTemplate = 0; // position in the template sequence to start the mapping
+
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos;
             
@@ -112840,6 +112868,8 @@ class SetSeqAlign {
 
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
+                startPosInTemplate = start1Pos;
+
                 //result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
                 result = this.getTemplatePosFromOriResi(chainid1, start_t, start1Pos, bRealign);
                 pos1 = result.pos1;
@@ -112862,7 +112892,6 @@ class SetSeqAlign {
 
                 // insert non-aligned residues in query seq
                 this.insertNotAlignRes(chainid2, prevIndex2+1, notAlnLen2, bRealign);
-
                 if(notAlnLen1 >= notAlnLen2) {
                     // add gaps before the query sequence
                     for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
@@ -112872,6 +112901,7 @@ class SetSeqAlign {
                 else {
                     // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
                     this.addGapAllAlnChains(chainidArray, alignedChainIndice, chainid1, resiStart1, notAlnLen2 - notAlnLen1);
+                    nGapInTemplate += (notAlnLen2 - notAlnLen1);
                 }                           
             }
 
@@ -112880,18 +112910,19 @@ class SetSeqAlign {
             //result = this.getTemplatePosFromOriResi(chainid1, start1Pos, end1Pos, bRealign);
             pos1 = result.pos1;
             pos2 = result.pos2;
-            
+
             let k = 0;    
             if(!ic.chainsMapping[chainid1]) ic.chainsMapping[chainid1] = {};
             if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
+            let resiAdjust = (bRealign && me.cfg.aligntool == 'tmalign') ? 0 : - startPosInTemplate + nGapInTemplate; 
             for(let j = pos1; j <= pos2; ++j) {
                 // inherit the gaps from the template
-                if(ic.alnChainsSeq[chainid1][j].resn == '-') {
+                if(ic.alnChainsSeq[chainid1][j + resiAdjust].resn == '-') {
                     ic.alnChainsSeq[chainid2].push(gapResObject2);
                 }
                 else {                   
-                    let resi1 = (bRealign) ? start1 + k : ic.ParserUtilsCls.getResi(chainid1, start1 + k);
-                    let resi2 = (bRealign) ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
+                    let resi1 = (bRealign && me.cfg.aligntool == 'tmalign') ? start1 + k : ic.ParserUtilsCls.getResi(chainid1, start1 + k);
+                    let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
                     let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
                     let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
 
@@ -112899,7 +112930,7 @@ class SetSeqAlign {
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
                     ic.alnChainsSeq[chainid2].push(resObject);
                     // update color in the template
-                    ic.alnChainsSeq[chainid1][j].color = resObject.color;
+                    ic.alnChainsSeq[chainid1][j + resiAdjust].color = resObject.color;
 
                     ic.chainsMapping[chainid1][chainid1 + '_' + resi1] = resn1 + resi1;
                     ic.chainsMapping[chainid2][chainid2 + '_' + resi2] = resn1 + resi1;  
@@ -114239,7 +114270,8 @@ class LoadPDB {
                   || (ic.nucleotides.hasOwnProperty(serialArray[i]) && (atom.name == "O3'" || atom.name == "O3*")) ) {
                     if(atom.resi == lastResi) continue; // e.g., Alt A and B
 
-                    let resn = (atom.resn.trim().length > 3) ? atom.resn.trim().substr(0, 3) : atom.resn.trim();
+                    // let resn = (atom.resn.trim().length > 3) ? atom.resn.trim().substr(0, 3) : atom.resn.trim();
+                    let resn = atom.resn.trim();
                     if(!me.parasCls.chargeColors.hasOwnProperty(resn)) {
                         continue; // regular residues
                     }
@@ -116961,20 +116993,23 @@ class ApplyCommand {
           || commandOri.indexOf('ligplot interaction pairs') == 0
           ) {
         let paraArray = commandOri.split(' | ');
-        if(paraArray.length >= 3) {
+        if(paraArray.length >= 2) {
             let setNameArray = paraArray[1].split(' ');
 
             if(setNameArray.length == 2) {
                 let nameArray2 = setNameArray[0].split(',');
                 let nameArray = setNameArray[1].split(',');
 
-                let bHbond = paraArray[2].indexOf('hbonds') !== -1;
-                let bSaltbridge = paraArray[2].indexOf('salt bridge') !== -1;
-                let bInteraction = paraArray[2].indexOf('interactions') !== -1;
+                let bHbond = 1, bSaltbridge = 1, bInteraction = 1, bHalogen = 1, bPication = 1, bPistacking = 1;
+                if(paraArray.length >= 3) {
+                    bHbond = paraArray[2].indexOf('hbonds') !== -1;
+                    bSaltbridge = paraArray[2].indexOf('salt bridge') !== -1;
+                    bInteraction = paraArray[2].indexOf('interactions') !== -1;
 
-                let bHalogen = paraArray[2].indexOf('halogen') !== -1;
-                let bPication = paraArray[2].indexOf('pi-cation') !== -1;
-                let bPistacking = paraArray[2].indexOf('pi-stacking') !== -1;
+                    bHalogen = paraArray[2].indexOf('halogen') !== -1;
+                    bPication = paraArray[2].indexOf('pi-cation') !== -1;
+                    bPistacking = paraArray[2].indexOf('pi-stacking') !== -1;
+                }
 
                 let bHbondCalc;
                 if(paraArray.length >= 4) {
@@ -117899,12 +117934,10 @@ class DefinedSets {
     //Set the menu of defined sets with an array of defined names "commandnameArray".
     setAtomMenu(commandnameArray) { let ic = this.icn3d; ic.icn3dui;
       let html = "";
-
       let nameArray1 =(ic.defNames2Residues !== undefined) ? Object.keys(ic.defNames2Residues) : [];
       let nameArray2 =(ic.defNames2Atoms !== undefined) ? Object.keys(ic.defNames2Atoms) : [];
 
       let nameArrayTmp = nameArray1.concat(nameArray2).sort();
-
       let nameArray = [];
         //  $.each(nameArrayTmp, function(i, el){
         //       if($.inArray(el, nameArray) === -1) nameArray.push(el);
@@ -117922,7 +117955,6 @@ class DefinedSets {
         //         }
         //     });
         // });
-
       //for(let i in ic.defNames2Atoms) {
       for(let i = 0, il = nameArray.length; i < il; ++i) {
           let name = nameArray[i];
@@ -117953,7 +117985,6 @@ class DefinedSets {
             html += "<option value='" + name + "' style='color:#" + color + "'>" + name + "</option>";
           }
       }
-
       return html;
     }
 
@@ -117978,17 +118009,18 @@ class DefinedSets {
             }
             else { // chemicals, etc
               let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
-              let resn = atom.resn.substr(0, 3);
+            //   let resn = atom.resn.substr(0, 3);
+              let resn = atom.resn;
 
               if(!nonProtNuclResHash[resn]) {
-                nonProtNuclResHash[resn] = ic.residues[resid];
+                nonProtNuclResHash[resn] = me.hashUtilsCls.cloneHash(ic.residues[resid]);
               }
               else {
                 nonProtNuclResHash[resn] = me.hashUtilsCls.unionHash(nonProtNuclResHash[atom.resn], ic.residues[resid]);
               }
             }
         }
-
+        
         // chemicals etc
         for(let resn in nonProtNuclResHash) {
             ic.defNames2Residues[resn] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(nonProtNuclResHash[resn]));
@@ -117996,7 +118028,7 @@ class DefinedSets {
 
             ic.defNames2Command[resn] = 'select :3' + resn;
         }
-
+        
         // select whole structure
         if(ic.structures && Object.keys(ic.structures) == 1) {
           let structure = Object.keys(ic.structures)[0];
@@ -118089,10 +118121,8 @@ class DefinedSets {
 
         if(ic.bSetChainsAdvancedMenu === undefined || !ic.bSetChainsAdvancedMenu || ic.bResetSets) {
            this.setPredefinedInMenu();
-
            ic.bSetChainsAdvancedMenu = true;
         }
-
         ic.hAtoms = me.hashUtilsCls.cloneHash(prevHAtoms);
         ic.dAtoms = me.hashUtilsCls.cloneHash(prevDAtoms);
 
@@ -121745,14 +121775,22 @@ class Delphi {
           let paraArray = command.split(" | ");
 
           let typeArray = paraArray[0].split(" ");
-          let contourArray = paraArray[1].split(" ");
-          let gsizeArray = paraArray[2].split(" ");
-          let saltArray = paraArray[3].split(" ");
-
           let type = typeArray[2];
-          let contour = contourArray[1]; //parseFloat(contourArray[1]);
-          let gsize = gsizeArray[1]; //parseInt(gsizeArray[1]);
-          let salt = saltArray[1]; //parseFloat(saltArray[1]);
+
+          let contour = 2, gsize = 65, salt = 0.15; // default values for contour, gsize, salt 
+          ic.phisurftype = 22; // default value for surface type
+          ic.phisurfop = 1.0; // default value for surface opacity
+          ic.phisurfwf = "no"; // default value for surface wireframe
+
+          if(paraArray.length == 7) {
+            let contourArray = paraArray[1].split(" ");
+            let gsizeArray = paraArray[2].split(" ");
+            let saltArray = paraArray[3].split(" ");
+
+            contour = contourArray[1]; //parseFloat(contourArray[1]);
+            gsize = gsizeArray[1]; //parseInt(gsizeArray[1]);
+            salt = saltArray[1]; //parseFloat(saltArray[1]);
+          }
 
           // The values should be string
           $("#" + ic.pre + "delphi1gsize").val(gsize);
@@ -121769,12 +121807,12 @@ class Delphi {
               ic.phisurftype = surfaceArray[1];
               ic.phisurfop = opacityArray[1]; //parseFloat(opacityArray[1]);
               ic.phisurfwf = wireframeArray[1];
-
-              $("#" + ic.pre + "delphi" + "surftype").val(ic.phisurftype);
-              $("#" + ic.pre + "delphi" + "surfop").val(ic.phisurfop);
-              $("#" + ic.pre + "delphi" + "surfwf").val(ic.phisurfwf);
           }
 
+            $("#" + ic.pre + "delphi" + "surftype").val(ic.phisurftype);
+            $("#" + ic.pre + "delphi" + "surfop").val(ic.phisurfop);
+            $("#" + ic.pre + "delphi" + "surfwf").val(ic.phisurfwf);
+
           let bSurface =(type == 'surface') ? true : false;
 
           await thisClass.CalcPhi(gsize, salt, contour, bSurface);
@@ -123312,7 +123350,8 @@ class Dssp {
                 let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
                 if(!atom) continue;
 
-                let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                // let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                let resn = me.utilsCls.residueName2Abbr(atom.resn);
 
                 let domainid = ic.resid2domainid[resid];
                 let refnumLabel = ic.resid2refnum[resid];
@@ -123389,7 +123428,8 @@ class Dssp {
 
                 let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
                 if(!atom) continue;
-                let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                // let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                let resn = me.utilsCls.residueName2Abbr(atom.resn);
 
                 if(refnumLabel) {
                     let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
@@ -123412,7 +123452,8 @@ class Dssp {
 
                 let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
                 if(!atom) continue;
-                let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                // let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
+                let resn = me.utilsCls.residueName2Abbr(atom.resn);
 
                 if(refnumLabel) {
                     let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
@@ -127682,7 +127723,8 @@ class Ligplot {
             }
         }
 
-        let oneLetterRes = me.utilsCls.residueName2Abbr(atom2.resn.substr(0, 3));
+        // let oneLetterRes = me.utilsCls.residueName2Abbr(atom2.resn.substr(0, 3));
+        let oneLetterRes = me.utilsCls.residueName2Abbr(atom2.resn);
         let resName2 = oneLetterRes + atom2.resi;
         let textColor2 = (atom2.color) ? atom2.color.getHexString() : '000';
         let lineColor = ic.lineGraphCls.getStrokecolor(undefined, interactionType);
@@ -128060,11 +128102,12 @@ class Transform {
         this.icn3d = icn3d;
     }
 
-    resetOrientation_base(commandTransformation) { let ic = this.icn3d; ic.icn3dui;
+    resetOrientation_base(commandTransformation) { let ic = this.icn3d, me = ic.icn3dui;
         if(commandTransformation.length == 2 && commandTransformation[1].length > 0) {
+            if(commandTransformation[1].substr(0, 4) == 'pos:') ic.bSetCamera = false;
+
             if(ic.bSetCamera) { // |||{"factor"...}
                 let transformation = JSON.parse(commandTransformation[1]);
-
                 ic._zoomFactor = transformation.factor;
 
                 ic.mouseChange.x = transformation.mouseChange.x;
@@ -128095,6 +128138,12 @@ class Transform {
                         }
                     }
                 });
+
+                // set the aspect ratio
+                if(!ic.container.whratio) {
+                    ic.container.whratio = me.htmlCls.WIDTH / me.htmlCls.HEIGHT; 
+                    ic.cam.aspect = ic.container.whratio;
+                }
             }
         }
         else {
@@ -132793,7 +132842,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.45.1';
+    this.REVISION = '3.45.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -133044,18 +133093,21 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         await ic.pdbParserCls.downloadUrl(url, type, me.cfg.command);
     }
     else if(me.cfg.mmtfid !== undefined) {
+        if(me.cfg.mmtfid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.mmtfid = me.cfg.mmtfid.substr(8); // temperary support long PDB ID such as pdb_00001tup
        ic.inputid = me.cfg.mmtfid;
        ic.loadCmd = 'load mmtf ' + me.cfg.mmtfid;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
        await ic.bcifParserCls.downloadBcif(me.cfg.mmtfid);
     }
     else if(me.cfg.bcifid !== undefined) {
+        if(me.cfg.bcifid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.bcifid = me.cfg.bcifid.substr(8); // temperary support long PDB ID such as pdb_00001tup
         ic.inputid = me.cfg.bcifid;
         ic.loadCmd = 'load bcif ' + me.cfg.bcifid;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         await ic.bcifParserCls.downloadBcif(me.cfg.bcifid);
      }
     else if(me.cfg.pdbid !== undefined) {
+        if(me.cfg.pdbid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.pdbid = me.cfg.pdbid.substr(8); // temperary support long PDB ID such as pdb_00001tup
        ic.inputid = me.cfg.pdbid;
        ic.loadCmd = 'load pdb ' + me.cfg.pdbid;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
@@ -133078,6 +133130,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
        await ic.opmParserCls.downloadOpm(me.cfg.opmid);
     }
     else if(me.cfg.mmdbid !== undefined) {
+        if(me.cfg.mmdbid.toLowerCase().substr(0,8) == 'pdb_0000') me.cfg.mmdbid = me.cfg.mmdbid.substr(8); // temperary support long PDB ID such as pdb_00001tup
        ic.inputid = me.cfg.mmdbid;
        // ic.bNCBI = true;
        ic.loadCmd = 'load mmdb ' + me.cfg.mmdbid + ' | parameters ' + me.cfg.inpara;
@@ -133216,6 +133269,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         await ic.sdfParserCls.downloadSmiles(me.cfg.smiles);
     }
     else if(me.cfg.mmcifid !== undefined) {
+        // long PDB ID was supported with mmcifid
         ic.inputid = me.cfg.mmcifid;
         ic.loadCmd = 'load mmcif ' + me.cfg.mmcifid;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);