icn3d 3.29.6 → 3.29.7

package/icn3d.js

@@ -7633,7 +7633,7 @@ class ClickMenu {
 
         $(document).on("click", "." + me.pre + "mn6_rotate90", function(e) { let ic = me.icn3d; //e.preventDefault();
           let value = $(this).attr('v').toLowerCase();
-          let direction = value.split('-')[0];
+          let direction = value.split(' ')[1];
 
           thisClass.setLogCmd(value, true);
           let axis;
@@ -8674,14 +8674,14 @@ class SetMenu {
         }
 
         //!!!
-
+/*
         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>";
 
@@ -8902,7 +8902,7 @@ class SetMenu {
         html += "</li>";
 
         html += this.getLink('mn2_translate', 'Translate XYZ', undefined, 1);
-        html += this.getLink('mn2_matrix', 'Apply Matrix', undefined, 1);
+        html += this.getLink('mn2_matrix', 'Rotate with Matrix', undefined, 1);
 
         html += this.getMenuText('mn2_camera', 'Camera', undefined, undefined, 1);
         html += "<ul>";
@@ -9525,8 +9525,8 @@ class SetMenu {
             //}
 
             //!!!
-            html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9657,7 +9657,7 @@ class SetMenu {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
             //!!!
-            html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
+            //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9749,13 +9749,13 @@ class SetMenu {
 
             html += "<ul>";
 //!!!
-
+/*
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
             html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
 
             html += this.getMenuSep();
-
+*/
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -11895,7 +11895,7 @@ class SetDialog {
         html += "11: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix11' value='0' size=2> ";
         html += "15: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix15' value='1' size=2><br>";
 
-        html += me.htmlCls.buttonStr + "matrix_pdb'>Apply Matrix</button>";
+        html += me.htmlCls.buttonStr + "matrix_pdb'>Rotate with Matrix</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_igrefTpl' class='" + dialogClass + "'>";
@@ -35212,6 +35212,7 @@ class SetColor {
                 break;
 
             case 'secondary structure green':
+            case 'secondary structure':
                 ic.sheetcolor = 'green';
                 for (let i in atoms) {
                     let atom = ic.atoms[i];
@@ -35224,7 +35225,7 @@ class SetColor {
                 break;
 
             case 'secondary structure yellow':
-            case 'secondary structure':
+            //case 'secondary structure':
                 ic.sheetcolor = 'yellow';
                 for (let i in atoms) {
                     let atom = ic.atoms[i];
@@ -40316,14 +40317,16 @@ class AddTrack {
 
               html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue" ' + tmpStr + '>' + c + '</span>';
 
-              let tmpStrExon = 'style="background-color:' + pos2exonColor[cnt] + '"';
-              htmlExon += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + ', Exon ' + (pos2exonIndex[cnt] + 1) + ': ' + pos2genome[cnt] + '" class="icn3d-residue" ' + tmpStrExon + '>&nbsp;</span>';
+              if(exonArray) {
+                let tmpStrExon = 'style="background-color:' + pos2exonColor[cnt] + '"';
+                htmlExon += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + ', Exon ' + (pos2exonIndex[cnt] + 1) + ': ' + pos2genome[cnt] + '" class="icn3d-residue" ' + tmpStrExon + '>&nbsp;</span>';
 
-              // set atom color
-              for(let serial in ic.residues[chnid + '_' + pos]) {
-                let atom = ic.atoms[serial];
-                atom.color = me.parasCls.thr(pos2exonColor[cnt]);
-                ic.atomPrevColors[serial] = atom.color;
+                // set atom color
+                for(let serial in ic.residues[chnid + '_' + pos]) {
+                    let atom = ic.atoms[serial];
+                    atom.color = me.parasCls.thr(pos2exonColor[cnt]);
+                    ic.atomPrevColors[serial] = atom.color;
+                }
               }
 
               htmlTmp2 += ic.showSeqCls.insertGapOverview(chnid, i);
@@ -43047,6 +43050,8 @@ class ShowSeq {
             giSeq = ic.giSeq[chnid];
         }
 
+        if(!giSeq) return;
+
         // remove null giSeq[i]
         let giSeqTmp = [];
         for(let i = 0, il = giSeq.length; i < il; ++i) {
@@ -46198,12 +46203,12 @@ class LineGraph {
 
         if(bRerunDomain) {
             let atomsAssigned = {};
-            // for(let resid in ic.resid2refnum_ori) {
-            //     atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
-            // }
-            for(let resid in ic.resid2refnum) {
-                if(ic.resid2refnum[resid]) atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            for(let resid in ic.resid2refnum_ori) {
+                atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
             }
+            // for(let resid in ic.resid2refnum) {
+            //     if(ic.resid2refnum[resid]) atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            // }
 
             currAtoms = me.hashUtilsCls.exclHash(currAtoms, atomsAssigned);
 
@@ -46356,12 +46361,14 @@ class LineGraph {
 
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
-            let queryData = dataArray[i].value; //[0];
+            let queryData = (dataArray[i]) ? dataArray[i].value : undefined; //[0];
 
             if(!queryData || queryData.length == 0) {
                 if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
                 continue;
             }
+
+            if(queryData[0].score === undefined) continue;
             
             //let domainid_index = domainidpairArray[i].split(',');
             //let domainid = domainid_index[0];
@@ -46569,7 +46576,7 @@ class LineGraph {
 
         // assign ic.resid2refnum, ic.refnum2residArray, ic.chainsMapping
         if(!ic.resid2refnum) ic.resid2refnum = {};
-        // if(!ic.resid2refnum_ori) ic.resid2refnum_ori = {};
+        if(!ic.resid2refnum_ori) ic.resid2refnum_ori = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};
         if(!ic.chainsMapping) ic.chainsMapping = {};
 
@@ -46598,7 +46605,8 @@ class LineGraph {
             let CAtom, CpAtom, DAtom, EAtom;
             //let chainid = domainid.split(',')[0];
 
-            let cntBtCE = 0;
+            let cntBtwCE;
+            let CpToDResi = [], DToCpResi = [];
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 if(!seg) continue;
@@ -46608,47 +46616,59 @@ class LineGraph {
 
                 if(seg.q_start.indexOf('3550') != -1) {
                     bCstrand = true;
-                    CAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    CAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+
+                    // a chain could have multiple Ig domains
+                    cntBtwCE = 0;
                 }
                 else if(seg.q_start.indexOf('4550') != -1) {
                     bCpstrand = true;
-                    CpAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                    ++cntBtCE;
+                    CpAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+                    ++cntBtwCE;
                 }
                 // else if(seg.q_start.indexOf('5550') != -1) {
                 //     bCppstrand = true;
-                //     CppAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                //     ++cntBtCE;
+                //     CppAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+                //     ++cntBtwCE;
                 // }
                 else if(seg.q_start.indexOf('6550') != -1) {
                     bDstrand = true;
-                    DAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                    ++cntBtCE;
+                    DAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+                    ++cntBtwCE;
                 }
                 else if(seg.q_start.indexOf('7550') != -1) {
                     bEstrand = true;
-                    EAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                }
+                    EAtom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
 
-                if(bCstrand && bCpstrand && bCppstrand && bDstrand && bEstrand) break;
-            }
+                    // check C' and D strands
+                    if(cntBtwCE == 1) {
+                        let distToC = (bCpstrand) ? CpAtom.coord.distanceTo(CAtom.coord) : DAtom.coord.distanceTo(CAtom.coord);
+                        let distToE = (bCpstrand) ? CpAtom.coord.distanceTo(EAtom.coord) : DAtom.coord.distanceTo(EAtom.coord);
+                        distToC = parseInt(distToC);
+                        distToE = parseInt(distToE);
 
-            let CpToDResi, DToCpResi;
-            if(cntBtCE == 1) {
-                let distToC = (bCpstrand) ? CpAtom.coord.distanceTo(CAtom.coord) : DAtom.coord.distanceTo(CAtom.coord);
-                let distToE = (bCpstrand) ? CpAtom.coord.distanceTo(EAtom.coord) : DAtom.coord.distanceTo(EAtom.coord);
+                        let resiDistToC = (bCpstrand) ? parseInt(CpAtom.resi) - parseInt(CAtom.resi) : parseInt(DAtom.resi) - parseInt(CAtom.resi);
+                        let resiDistToE = (bCpstrand) ? parseInt(EAtom.resi) - parseInt(CpAtom.resi) : parseInt(EAtom.resi) - parseInt(DAtom.resi);
 
-                if(bCpstrand && distToC > distToE) { // rename C' to D
-                    CpToDResi = CAtom.resi;
-                }
-                else if(bDstrand && distToC < distToE) { // rename D to C'
-                    DToCpResi = DAtom.resi;
+                        if(bCpstrand) {
+                            if(distToC > distToE || (distToC == distToE && resiDistToC > resiDistToE)) { // rename C' to D
+                                CpToDResi.push(CpAtom.resi);
+                            }
+                        }
+                        else if(bDstrand) {
+                            if(distToC < distToE || (distToC == distToE && resiDistToC < resiDistToE)) { // rename D to C'
+                                DToCpResi.push(DAtom.resi);
+                            }
+                        }
+                    }
                 }
+
+                if(bCstrand && bCpstrand && bCppstrand && bDstrand && bEstrand) break;
             }
-            // adjust C' and D strands ======end
 
-            let prevStrand;
-            let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
+
+            let currStrand;
+            refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 if(!seg) continue;
@@ -46669,21 +46689,33 @@ class LineGraph {
                     //let refnum = qStart + postfix;
                     let refnum = qStart;
 
-                    let prevStrandFinal = prevStrand;
-                    if(prevStrand == "C'" && CpToDResi && parseInt(seg.t_start) < parseInt(CpToDResi) + 10 
-                        && parseInt(seg.t_start) > parseInt(CpToDResi) - 10 ) {
-                        prevStrandFinal = "D";
+                    let refnumLabel = this.getLabelFromRefnum(refnum);
+                    currStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
+
+                    let currStrandFinal = currStrand;
+                    if(currStrand == "C'" && CpToDResi.length > 0) {
+                        for(let j = 0, jl = CpToDResi.length; j < jl; ++j) {
+                            if(parseInt(seg.t_start) < parseInt(CpToDResi[j]) + 10 && parseInt(seg.t_start) > parseInt(CpToDResi[j]) - 10 ) {
+                                currStrandFinal = "D";
+                                break;
+                            }
+                        }
                     }
-                    else if(prevStrand == "D" && DToCpResi && parseInt(seg.t_start) < parseInt(DToCpResi) + 10 
-                        && parseInt(seg.t_start) > parseInt(DToCpResi) - 10 ) {
-                        prevStrandFinal = "C'";
+                    else if(currStrand == "D" && DToCpResi.length > 0) {
+                        for(let j = 0, jl = DToCpResi.length; j < jl; ++j) {
+                            if(parseInt(seg.t_start) < parseInt(DToCpResi[j]) + 10 && parseInt(seg.t_start) > parseInt(DToCpResi[j]) - 10 ) {
+                                currStrandFinal = "C'";
+                                break;
+                            }
+                        }
                     }
 
-                    let refnumLabel = this.getLabelFromRefnum(refnum, prevStrandFinal, bCd19);
-                    prevStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
-
-                    ic.resid2refnum[resid] = refnumLabel;
-                    // ic.resid2refnum_ori[resid] = refnumLabel;
+                    if(currStrand != currStrandFinal) {
+                        refnumLabel = this.getLabelFromRefnum(refnum, currStrandFinal);
+                    }
+                   
+                    ic.resid2refnum[resid] = refnumLabel;                
+                    ic.resid2refnum_ori[resid] = refnumLabel;
 
                     // final reference numbers will be assign in ic.showSeqCls.showRefNum()
 
@@ -46725,7 +46757,7 @@ class LineGraph {
         }
     }
 
-    getLabelFromRefnum(oriRefnum, prevStrand, bCd19) { let ic = this.icn3d; ic.icn3dui;
+    getLabelFromRefnum(oriRefnum, prevStrand) { let ic = this.icn3d; ic.icn3dui;
         let refnum = parseInt(oriRefnum);
 
         //N-terminus = 0999-0001
@@ -46752,28 +46784,34 @@ class LineGraph {
 
         // loops may have numbers such as 1310, 1410
 
-        if(refnum < 1000) return undefined;
-        else if(refnum >= 1200 && refnum < 1290) return "A---" + oriRefnum;
-        else if(refnum >= 1320 && refnum < 1390) return "A--" + oriRefnum;
-        else if(refnum >= 1420 && refnum < 1490) return "A-" + oriRefnum;
-        else if(refnum >= 1520 && refnum < 1590) return "A" + oriRefnum; 
-        else if(refnum >= 1620 && refnum < 1690) return "A+" + oriRefnum; 
-        else if(refnum >= 1820 && refnum < 1890) return "A'" + oriRefnum;
-        else if(refnum >= 2000 && refnum < 2900) return "B" + oriRefnum;
-        else if(refnum >= 3300 && refnum < 3390) return "C--" + oriRefnum;
-        else if(refnum >= 3420 && refnum < 3490) return "C-" + oriRefnum;
-        else if(refnum >= 3520 && refnum < 3590) return "C" + oriRefnum;
-        else if(refnum >= 4000 && refnum < 4900) return "C'" + oriRefnum;
-        else if(refnum >= 5000 && refnum < 5900) return "C''" + oriRefnum;
-        else if(refnum >= 6000 && refnum < 6900) return "D" + oriRefnum;
-        else if(refnum >= 7500 && refnum < 7590) return "E" + oriRefnum; 
-        else if(refnum >= 7620 && refnum < 7900) return "E+" + oriRefnum; 
-        else if(refnum >= 8000 && refnum < 8900) return "F" + oriRefnum;
-        else if(refnum >= 9500 && refnum < 9590) return "G" + oriRefnum;
-        else if(refnum >= 9620 && refnum < 9690) return "G+" + oriRefnum;
-        else if(refnum >= 9720 && refnum < 9790) return "G++" + oriRefnum;
-        else if(refnum > 9900) return undefined;
-        else return " " + oriRefnum;    }
+        let refnumLabel;
+        
+        if(refnum < 1000) refnumLabel = undefined;
+        else if(refnum >= 1200 && refnum < 1290) refnumLabel = "A---" + oriRefnum;
+        else if(refnum >= 1320 && refnum < 1390) refnumLabel = "A--" + oriRefnum;
+        else if(refnum >= 1420 && refnum < 1490) refnumLabel = "A-" + oriRefnum;
+        else if(refnum >= 1520 && refnum < 1590) refnumLabel = "A" + oriRefnum; 
+        else if(refnum >= 1620 && refnum < 1690) refnumLabel = "A+" + oriRefnum; 
+        else if(refnum >= 1820 && refnum < 1890) refnumLabel = "A'" + oriRefnum;
+        else if(refnum >= 2000 && refnum < 2900) refnumLabel = "B" + oriRefnum;
+        else if(refnum >= 3300 && refnum < 3390) refnumLabel = "C--" + oriRefnum;
+        else if(refnum >= 3420 && refnum < 3490) refnumLabel = "C-" + oriRefnum;
+        else if(refnum >= 3520 && refnum < 3590) refnumLabel = "C" + oriRefnum;
+        else if(refnum >= 4000 && refnum < 4900) refnumLabel = "C'" + oriRefnum;
+        else if(refnum >= 5000 && refnum < 5900) refnumLabel = "C''" + oriRefnum;
+        else if(refnum >= 6000 && refnum < 6900) refnumLabel = "D" + oriRefnum;
+        else if(refnum >= 7500 && refnum < 7590) refnumLabel = "E" + oriRefnum; 
+        else if(refnum >= 7620 && refnum < 7900) refnumLabel = "E+" + oriRefnum; 
+        else if(refnum >= 8000 && refnum < 8900) refnumLabel = "F" + oriRefnum;
+        else if(refnum >= 9500 && refnum < 9590) refnumLabel = "G" + oriRefnum;
+        else if(refnum >= 9620 && refnum < 9690) refnumLabel = "G+" + oriRefnum;
+        else if(refnum >= 9720 && refnum < 9790) refnumLabel = "G++" + oriRefnum;
+        else if(refnum > 9900) refnumLabel = undefined;
+        else refnumLabel = " " + oriRefnum;
+        if(prevStrand) refnumLabel = prevStrand + oriRefnum;
+
+        return refnumLabel
+    }
 
     async parseCustomRefFile(data) { let ic = this.icn3d; ic.icn3dui;
         ic.bShowCustomRefnum = true;
@@ -52185,6 +52223,7 @@ class MmcifParser {
     }
 
     async downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d, me = ic.icn3dui;
+      try {
         // https://files.rcsb.org/header/ is not accessible in Node.js and Mac
         // Some header files are in the wrong format. So we use the full mmCIF file
         //let url = (me.bNode || me.utilsCls.isMac()) ? "https://files.rcsb.org/view/" + mmcifid + ".cif" : "https://files.rcsb.org/header/" + mmcifid + ".cif";
@@ -52250,6 +52289,11 @@ class MmcifParser {
         }
 
         ///// if(ic.deferredSymmetry !== undefined) ic.deferredSymmetry.resolve();
+      }
+      catch (err) {
+        if(!me.bNode) console.log("mmcifparser.cgi issues: " + err);
+        return;
+      }
     }
 
     //Atom "data" from mmCIF file was parsed to set up parameters for the 3D viewer by calling the function
@@ -64321,6 +64365,9 @@ class SelectByCommand {
            }
            else {
              chainStr = testStr.substr(periodPos + 1);
+             //replace "A_1" with "A"
+             chainStr = chainStr.replace(/_/g, '');
+
              testStr = testStr.substr(0, periodPos);
            }
 
@@ -74759,7 +74806,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.29.3';
+    this.REVISION = '3.29.4';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -75379,8 +75426,8 @@ iCn3DUI.prototype.getAjaxPostPromise = async function(url, data, beforeSend, ale
                 },
                 error : function() {
                     //if(alertMess) var aaa = 1; //alert(alertMess);
-                    if(alertMess) console.log(alertMess);
-                    if(logMess) console.log(logMess);
+                    if(!me.bNode && alertMess) console.log(alertMess);
+                    if(!me.bNode && logMess) console.log(logMess);
                     
                     // reject('error');
                     // keep running the program