icn3d 3.31.11 → 3.31.13

package/icn3d.js

@@ -16953,7 +16953,7 @@ class Events {
                 //ic.initUI();
                 ic.init();
                 ic.bInputfile = true;
-                ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : data;
+                ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : dataStr;
                 ic.InputfileType = 'mmcif';
                 // await ic.mmcifParserCls.loadMmcifData(data); 
                 await ic.opmParserCls.loadOpmData(dataStr, undefined, undefined, 'mmcif', undefined, bText);
@@ -17608,11 +17608,13 @@ class Events {
             let command;
             if(shape == 'Sphere') {
                 ic.sphereCls.createSphereBase(pos1, color, radius, undefined, undefined, undefined, opacity);
-                command = 'add sphere | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                // command = 'add sphere | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                command = 'add sphere | ' + nameArray + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
             }
             else {
                 ic.boxCls.createBox_base(pos1, radius, color, undefined, undefined, undefined, opacity);
-                command = 'add cube | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                // command = 'add cube | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                command = 'add cube | ' + nameArray + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
             }
 
             thisClass.setLogCmd(command, true);
@@ -28146,14 +28148,14 @@ class Strand {
         // include the whole sheet or helix when highlighting
         let atomsAdjust = {};
 
-        //if( (bHighlight === 1 || bHighlight === 2) && !ic.bAllAtoms) {
-        //if( !ic.bAllAtoms) {
-        if( Object.keys(atoms).length < Object.keys(ic.atoms).length) {
-            atomsAdjust = this.getSSExpandedAtoms(atoms);
-        }
-        else {
-            atomsAdjust = atoms;
-        }
+        // if( Object.keys(atoms).length < Object.keys(ic.atoms).length) {
+        //     atomsAdjust = this.getSSExpandedAtoms(atoms);
+        // }
+        // else {
+        //     atomsAdjust = atoms;
+        // }
+
+        atomsAdjust = atoms;
 
         if(bHighlight === 2) {
             if(fill) {
@@ -28211,9 +28213,16 @@ class Strand {
 
         let maxDist = 6.0;
 
+        //get the last residue
+        let atomArray = Object.keys(atoms);
+        let lastAtomSerial = atomArray[atomArray.length - 1];
+        let lastAtom = atoms[lastAtomSerial];
+        let lastResid = lastAtom.structure + '_' + lastAtom.chain + '_' + lastAtom.resi;
+
         for (let i in atomsAdjust) {
           atom = atomsAdjust[i];
           let chainid = atom.structure + '_' + atom.chain;
+          let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
           if ((atom.name === 'O' || atom.name === 'CA') && !atom.het) {
             // "CA" has to appear before "O"
 
@@ -28250,7 +28259,7 @@ class Strand {
                 if(atom.ssend && atom.ss === 'sheet') {
                     bSheetSegment = true;
                 }
-                else if(atom.ssend && atom.ss === 'helix') {
+                else if( (atom.ssend && atom.ss === 'helix') || resid == lastResid) { // partial sheet will draw as helix
                     bHelixSegment = true;
                 }
 
@@ -28357,7 +28366,7 @@ class Strand {
                 // }
 
                 //if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
-                if ((currentChain !== atom.chain || atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0) {
+                if ((currentChain !== atom.chain || atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs || resid == lastResid) && pnts[0].length > 0) {
                     let atomName = 'CA';
                 
                     let prevone = [], nexttwo = [];
@@ -28500,8 +28509,11 @@ class Strand {
                     bHelixSegment = false;
                 } // end if (atom.ssbegin || atom.ssend)
 
-                // end of a chain
-                if ((currentChain !== atom.chain || ic.ParserUtilsCls.getResiNCBI(atom.structure + '_' + currentChain, currentResi) + 1 !== ic.ParserUtilsCls.getResiNCBI(chainid, atom.resi)) && pnts[0].length > 0) {
+                // end of a chain, or end of selection
+                if ((currentChain !== atom.chain 
+                    || ic.ParserUtilsCls.getResiNCBI(atom.structure + '_' + currentChain, currentResi) + 1 !== ic.ParserUtilsCls.getResiNCBI(chainid, atom.resi)
+                    || resid == lastResid
+                    ) && pnts[0].length > 0) {
                 //if ((currentChain !== atom.chain) && pnts[0].length > 0) {
 
                     let atomName = 'CA';
@@ -40003,6 +40015,9 @@ class AnnoCddSite {
                 // if(type != 'domain') setname += "_" + index + "_" + r; 
                 if(type != 'domain') setname = chnid + "_" + index + "_" + r  + "_" + domain; 
 
+                //remove space in setname
+                setname = setname.replace(/\s+/g, '');
+
                 if(type == 'domain') pssmid2fromArray[pssmid] = fromArray;
                 if(type == 'domain') pssmid2toArray[pssmid] = toArray;
 
@@ -43903,27 +43918,12 @@ class AddTrack {
         });
 
         // Isoform Alignment
-        me.myEventCls.onIds("#" + ic.pre + "addtrack_button2c", "click", async function(e) { let ic = thisClass.icn3d;
+        me.myEventCls.onIds("#" + ic.pre + "addtrack_button2c", "click", async function(e) { thisClass.icn3d;
             e.stopImmediatePropagation();
             //e.preventDefault();
             dialog.dialog( "close" );
 
-            let chainid = $("#" + ic.pre + "track_chainid").val();    
-            let geneid = $("#" + ic.pre + "track_geneid").val();
-            if(!geneid) {
-                var aaa = 1; //alert("Please fill in the Gene ID...");
-                return;
-            }
-
-            let startpos = $("#" + ic.pre + "fasta_startpos2").val();
-            if(!startpos) startpos = 1;
-
-            //let colorseqby = $("#" + ic.pre + "colorseqby2").val();
-            //let type =(colorseqby == 'identity') ? 'identity' : 'custom';
-
-            let type = 'identity';
-    
-            await thisClass.addExonTracks(chainid, geneid, startpos, type);
+            await thisClass.addExonTracksWrap();
         });
 
         // BED file
@@ -45514,6 +45514,25 @@ class AddTrack {
         return acclistTmp;
     }
 
+    async addExonTracksWrap() { let ic = this.icn3d; ic.icn3dui;
+        let chainid = $("#" + ic.pre + "track_chainid").val();    
+        let geneid = $("#" + ic.pre + "track_geneid").val();
+        if(!geneid) {
+            var aaa = 1; //alert("Please fill in the Gene ID...");
+            return;
+        }
+
+        let startpos = $("#" + ic.pre + "fasta_startpos2").val();
+        if(!startpos) startpos = 1;
+
+        //let colorseqby = $("#" + ic.pre + "colorseqby2").val();
+        //let type =(colorseqby == 'identity') ? 'identity' : 'custom';
+
+        let type = 'identity';
+
+        await thisClass.addExonTracks(chainid, geneid, startpos, type);
+    }
+
     async addExonTracks(chainid, geneid, startpos, type) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -47708,11 +47727,12 @@ class HlSeq {
                   ic.bAlignSeq = false;
                   ic.bAnnotations = true;
               }
-
+              
               if(ic.bSelectResidue === false && !ic.bShift && !ic.bCtrl) {
+            //   if(!ic.bShift && !ic.bCtrl) {
                   ic.selectionCls.removeSelection();
               }
-
+              
               // select residues
               $("span.ui-selected", this).each(function() {
                   let id = $(this).attr('id');
@@ -47723,11 +47743,12 @@ class HlSeq {
               });
 
               ic.selectionCls.saveSelectionPrep(true);
-              ic.selectionCls.saveSelection(undefined, undefined, true);
+              //ic.selectionCls.saveSelection(undefined, undefined, true);
+              // do not use selected residues, use ic.hAtoms instead
+              ic.selectionCls.saveSelection(undefined, undefined, false);
 
               //ic.residueLabelsCls.addResidueLabels(ic.hAtoms, false, 0.5);
               ic.hlObjectsCls.addHlObjects();  // render() is called
-
               // get all chainid in the selected residues
               let chainHash = {};
               for(let residueid in ic.selectedResidues) {
@@ -47810,7 +47831,9 @@ class HlSeq {
                    thisClass.selectResidues(id, this);
 
                    ic.selectionCls.saveSelectionPrep(true);
-                   ic.selectionCls.saveSelection(undefined, undefined, true);
+                   //ic.selectionCls.saveSelection(undefined, undefined, true);
+                   // do not use selected residues, use ic.hAtoms instead
+                   ic.selectionCls.saveSelection(undefined, undefined, false);
               }
           //});
 
@@ -48135,9 +48158,10 @@ class HlSeq {
       if(me.bNode) return;
 
       if(ic.bSelectResidue === false && !ic.bShift && !ic.bCtrl) {
+    //   if(!ic.bShift && !ic.bCtrl) {
           ic.selectionCls.removeSelection();
       }
-
+      
       if(id !== undefined && id !== '') {
         // add "align_" in front of id so that full sequence and aligned sequence will not conflict
         //if(id.substr(0, 5) === 'align') id = id.substr(5);
@@ -65168,11 +65192,13 @@ class ApplyCommand {
         ic.drawCls.draw();
       }
       else if(command.indexOf('add sphere') == 0) {
-        this.addShape(command, 'sphere');
+        this.addShape(commandOri, 'sphere');
+        ic.shapeCmdHash[commandOri] = 1;
         //ic.drawCls.draw();
       }
       else if(command.indexOf('add cube') == 0) {
-        this.addShape(command, 'cube');
+        this.addShape(commandOri, 'cube');
+        ic.shapeCmdHash[commandOri] = 1;
         //ic.drawCls.draw();
       }
       else if(command.indexOf('clear shape') == 0) {
@@ -65628,8 +65654,8 @@ class ApplyCommand {
 
         ic.hlUpdateCls.updateHlAll();
 
-        // change graph color
-        ic.getGraphCls.updateGraphColor();
+        // change graph color, was done in color command
+        //ic.getGraphCls.updateGraphColor();
       }
       else if(commandOri.indexOf('remove legend') == 0) {
         $("#" + me.pre + "legend").hide();
@@ -65915,7 +65941,7 @@ class ApplyCommand {
     }
 
     addShape(command, shape) { let ic = this.icn3d, me = ic.icn3dui;
-      ic.shapeCmdHash[command] = 1;
+      // ic.shapeCmdHash[command] = 1;
       
       let paraArray = command.split(' | ');
       let p1Array = paraArray[1].split(' ');
@@ -65926,7 +65952,17 @@ class ApplyCommand {
       colorStr = '#' + colorStr.replace(/\#/g, '');
       let color = me.parasCls.thr(colorStr);
 
-      let pos1 = new THREE.Vector3(parseFloat(p1Array[1]), parseFloat(p1Array[3]), parseFloat(p1Array[5]));
+      let pos1;
+
+      if(p1Array[0] == 'x1') { // input position
+        pos1 = new THREE.Vector3(parseFloat(p1Array[1]), parseFloat(p1Array[3]), parseFloat(p1Array[5]));
+      }
+      else { // input sets
+        let nameArray = paraArray[1].split(',');
+        let atomSet1 = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        let posArray1 = ic.contactCls.getExtent(atomSet1);
+        pos1 = new THREE.Vector3(posArray1[2][0], posArray1[2][1], posArray1[2][2]);
+      }
 
       if(shape == 'sphere') {
         ic.sphereCls.createSphereBase(pos1, color, parseFloat(radius), undefined, undefined, undefined, parseFloat(opacity));
@@ -66906,7 +66942,7 @@ class SelectCollections {
 
     ic.ssbondpnts = {};
 
-    ic.bShowHighlight = false;
+    ic.bShowHighlight = undefined;
     ic.bResetSets = true;
   }
 
@@ -67037,8 +67073,8 @@ class SelectCollections {
             ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
           }
           
-        ic.opts["color"] = "structure";
-        ic.setStyleCls.setAtomStyleByOptions();
+        ic.opts["color"] = (Object.keys(ic.structures).length == 1) ? "chain" : "structure";
+        // ic.setStyleCls.setAtomStyleByOptions();
         ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
 
         ic.transformCls.zoominSelection();
@@ -71063,6 +71099,8 @@ class Dssp {
                     if(bBstrand && bCstrand && bEstrand && bFstrand) break;
                 }
 
+                console.log("### " + bBstrand + bCstrand + bEstrand + bFstrand);
+
                 // if(refpdbname != 'CD19_6al5A_human-n1') { // relax for CD19
                     if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
                     // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
@@ -71076,7 +71114,6 @@ class Dssp {
                         continue;  
                   }
                 // }
-
             }
 
             if(!bRound1) {
@@ -71624,15 +71661,21 @@ class Dssp {
 
                 let resi = refAA[i][j].trim();
                 let refnum = refAA[refI][j].trim();
+
+                if(!ic.chainsMapping.hasOwnProperty(chainid)) {
+                    ic.chainsMapping[chainid] = {};
+                }
+
+                let resid = chainid + '_' + resi;
+
                 if(resi && refnum) {
-                    let resid = chainid + '_' + resi;
                     ic.resid2refnum[resid] = refnum;
 
-                    if(!ic.chainsMapping.hasOwnProperty(chainid)) {
-                        ic.chainsMapping[chainid] = {};
-                    }
                     ic.chainsMapping[chainid][resid] = refnum;
                 }
+                else {
+                    ic.chainsMapping[chainid][resid] = resi;
+                }
             }
         }
 
@@ -71697,6 +71740,7 @@ class Dssp {
 
         // if(bIgDomain) {
             for(let structure in ic.structures) {
+                let bIgDomain = 0;
                 let refDataTmp = '';
                 for(let m = 0, ml = ic.structures[structure].length; ic.bShowRefnum && m < ml; ++m) {
                     let chnid = ic.structures[structure][m]; 
@@ -71726,17 +71770,17 @@ class Dssp {
                             refDataTmp += '],\n';
 
                             refDataTmp += '},\n';
+
+                            bIgDomain = 1;
                         }
 
                         refDataTmp += '}},\n';
                     }
                 }
 
-                let bIgDomain = (refDataTmp) ? 1 : 0;
-
                 refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
 
-                refData += refDataTmp;
+                if(bIgDomain) refData += refDataTmp;
 
                 refData += ']}},\n';
             }
@@ -72107,17 +72151,18 @@ class Dssp {
                 }
                 
                 // assign before removing
-                let resid = chnid + '_' + strandArray[i].startResi;
+                chnid + '_' + strandArray[i].startResi;
 
                 strandArray.splice(i, 1);
 
-                if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
-                    if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
+                // do not remove BCEF strands even though they are short
+                // if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
+                //     if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
                     
-                    let domainid = ic.resid2domainid[resid];
-                    removeDomainidHash[domainid] = 1;
-                    continue;
-                }   
+                //     let domainid = ic.resid2domainid[resid];
+                //     removeDomainidHash[domainid] = 1;
+                //     continue;
+                // }   
             }
         }
 
@@ -72335,7 +72380,7 @@ class Dssp {
 
                 // remove the postfix when comparing interactions
                 //ic.chainsMapping[chnid][residueid] = refnumLabel;
-                ic.chainsMapping[chnid][residueid] = refnumLabelNoPostfix;
+                ic.chainsMapping[chnid][residueid] = (refnumLabelNoPostfix) ? refnumLabelNoPostfix : currResi;
             }
         }
 
@@ -80488,7 +80533,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.3';
+    this.REVISION = '3.31.4';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;