icn3d 3.33.1 → 3.33.2

package/icn3d.module.js

@@ -11301,8 +11301,8 @@ class ClickMenu {
            //if(!me.cfg.notebook) dialog.dialog( "close" );
            let sigma2fofc = parseFloat($("#" + me.pre + "sigma2fofc" ).val());
            let type = '2fofc';
-           await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
-           //ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
+           //await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
+           await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
 
            //ic.setOptionCls.setOption('map', '2fofc');
            thisClass.setLogCmd('set map 2fofc sigma ' + sigma2fofc, true);
@@ -11314,7 +11314,8 @@ class ClickMenu {
            //if(!me.cfg.notebook) dialog.dialog( "close" );
            let sigmafofc = parseFloat($("#" + me.pre + "sigmafofc" ).val());
            let type = 'fofc';
-           await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
+           //await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
+           await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma2fofc);
            //ic.setOptionCls.setOption('map', 'fofc');
            thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
         });
@@ -11863,6 +11864,18 @@ class ClickMenu {
             me.htmlCls.dialogCls.openDlg('dl_contact', 'Set contact map');
         });
 
+        me.myEventCls.onIds(["#" + me.pre + "mn6_DSSP"], "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+         thisClass.setLogCmd('set dssp sse', true);
+         await ic.pdbParserCls.applyCommandDssp();
+         ic.bResetAnno = true;
+
+         if(ic.bAnnoShown) {
+             await ic.showAnnoCls.showAnnotations();
+ 
+             ic.annotationCls.resetAnnoTabAll();
+         }
+        });
+
 
         me.myEventCls.onIds("#" + me.pre + "mn6_hbondsNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
            ic.showInterCls.hideHbondsContacts();
@@ -13783,6 +13796,8 @@ class SetMenu {
             html += "</ul>";
             html += "</li>";
 
+            html += this.getLink('mn6_DSSP', 'DSSP Secondary', undefined, 1);
+
             let bOnePdb = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.mmdbafid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
 
             if(bOnePdb) {
@@ -15083,14 +15098,14 @@ class SetDialog {
 
         html += "<span style='white-space:nowrap;font-weight:bold;'>2fofc contour at default threshold or at: " 
           + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigma2fofc' value='' size=8> &sigma;</span><br/>";
-        //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'> " + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button><br><br><br/>";
-        html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
+        //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6file2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
+        html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6file2fofc'><br>" + me.htmlCls.buttonStr + "reload_ccp4file2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfile2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfile2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
 
         html += "<span style='white-space:nowrap;font-weight:bold;'>fofc contour at default threshold or at: "
           + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmafofc' value='' size=8> &sigma;</span><br/>";
 
-        //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'> " + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button><br><br><br>";
-        html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
+        //html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_dsn6filefofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
+        html += me.htmlCls.inputFileStr + "id='" + me.pre + "dsn6filefofc'><br>" + me.htmlCls.buttonStr + "reload_ccp4filefofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfilefofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfilefofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
 
 
         html += me.htmlCls.buttonStr + "elecmapNo4'>Remove Map</button><br>";
@@ -15104,12 +15119,16 @@ class SetDialog {
         html += "<span style='white-space:nowrap;font-weight:bold;'>2fofc contour at default threshold or at: "
           + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmaurl2fofc' value='' size=8> &sigma;</span><br/>";
 
-        html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurl2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
+        //html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurl2fofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
+
+        html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurl2fofc' size=20><br>" + me.htmlCls.buttonStr + "reload_ccp4fileurl2fofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>" + me.htmlCls.buttonStr + "reload_mtzfileurl2fofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>" + me.htmlCls.buttonStr + "reload_rcsbmtzfileurl2fofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br/>";
 
         html += "<span style='white-space:nowrap;font-weight:bold;'>fofc contour at default threshold or at: "
         + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6sigmaurlfofc' value='' size=8> &sigma;</span><br/>";
 
-        html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurlfofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
+        //html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_dsn6fileurlfofc' style='margin: 6px 20px 0 0;'>Load DSN6</button>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
+
+        html += "URL in the same host: " + me.htmlCls.inputTextStr + "id='" + me.pre + "dsn6fileurlfofc' size=20><br>" + me.htmlCls.buttonStr + "reload_ccp4fileurlfofc' style='margin: 6px 20px 0 0;'>Load CCP4</button>"  + me.htmlCls.buttonStr + "reload_mtzfileurlfofc' style='margin: 6px 20px 0 0;'>Load MTZ</button>"  + me.htmlCls.buttonStr + "reload_rcsbmtzfileurlfofc' style='margin-top: 6px;'>Load RCSB MTZ</button><br><br><br>";
 
         html += me.htmlCls.buttonStr + "elecmapNo5'>Remove Map</button><br>";
 
@@ -15658,8 +15677,9 @@ class SetDialog {
         html += "</div>";
 
 
-        html += me.htmlCls.divStr + "dl_anglemanysets' class='" + dialogClass + "'>";
+        html += me.htmlCls.divStr + "dl_anglemanysets' class='" + dialogClass + "' style='max-width:500px'>";
         html += this.addNotebookTitle('dl_anglemanysets', 'Measure angles among many sets');
+        html += me.htmlCls.spanNowrapStr + "Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated.<br/><br/>";
         html += me.htmlCls.spanNowrapStr + "1. Select sets for pairwise angles</span><br/>";
         html += "<table border=0 width=400 cellspacing=10><tr><td>";
 
@@ -15981,8 +16001,8 @@ class SetDialog {
         html += "Z: " + me.htmlCls.inputTextStr + "id='" + me.pre + "v2Z' value='' size=6><br>";
         html += "<br>";
         
-        html += me.htmlCls.buttonStr + "measure_angle'>Measure Angle</button>";
-        html += "The angle is: " + me.htmlCls.inputTextStr + "id='" + me.pre + "angle_value' value='' size=6> degree.";
+        html += me.htmlCls.buttonStr + "measure_angle'>Measure Angle</button><br><br>";
+        html += "The angle is: " + me.htmlCls.inputTextStr + "id='" + me.pre + "angle_value' value='' size=6> degree.<br><br>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_matrix' class='" + dialogClass + "'>";
@@ -45427,7 +45447,7 @@ class AddTrack {
 
     }
 
-    showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray, seqStartLen, exonArray) {  let ic = this.icn3d, me = ic.icn3dui;
+    showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray, seqStartLen, exonArray, offsetArray) {  let ic = this.icn3d, me = ic.icn3dui;
         //if(ic.customTracks[chnid] === undefined) {
         //    ic.customTracks[chnid] = {}
         //}
@@ -45645,14 +45665,16 @@ class AddTrack {
 
         if(fromArray !== undefined) {
             htmlTmp2 = '';
-            let fromArray2 = [], toArray2 = [];
+            let fromArray2 = [], toArray2 = [], offsetArray2 = [];
             for(let i = 0, il = fromArray.length; i < il; ++i) {
                 fromArray2.push(fromArray[i]);
+                offsetArray2.push(offsetArray[i]);
 
                 for(let j = parseInt(fromArray[i]); j <= parseInt(toArray[i]); ++j) {
                     if(ic.targetGapHash !== undefined && ic.targetGapHash.hasOwnProperty(j)) {
                         toArray2.push(j - 1);
                         fromArray2.push(j);
+                        offsetArray2.push(offsetArray[i]);
                     }
                 }
 
@@ -45686,6 +45708,7 @@ class AddTrack {
                     // determine how this range sits in the exon ranges in exonArray
                     let startExon, endExon;
                     
+                    let offset = offsetArray2[i];
                     cnt = toArray[i] - fromArray[i] + 1;
                     let from = prevCntTotal, to = prevCntTotal + cnt - 1;
 
@@ -45714,26 +45737,26 @@ class AddTrack {
                         endColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, to);
 
                         colorGradient = startColorStr + ' 0%, #FFF 50%, ' + endColorStr + ' 100%';
-                        htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, endExon.to, startExon.genomeRange, chnid, simpTitle);
+                        htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, endExon.to, startExon.genomeRange, chnid, simpTitle, offset);
                     }
                     else {
                         if(startExon) {
                             startColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, from);
 
                             colorGradient = startColorStr + ' 0%, #FFF 50%, #00F 100%';
-                            htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, startExon.rangeEnd, startExon.genomeRange, chnid, simpTitle);
+                            htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, startExon.rangeEnd, startExon.genomeRange, chnid, simpTitle, offset);
                         }
 
                         if(startExon && endExon) {
                             for(let j = startExon.exonIndex + 1; j < endExon.exonIndex; ++j) {
                                 colorGradient = '#F00 0%, #FFF 50%, #00F 100%';
-                                htmlTmp2 += this.getExonHtml(j, colorGradient, exonArray[j].resStart, exonArray[j].resEnd, exonArray[j].genomeRange, chnid, simpTitle);
+                                htmlTmp2 += this.getExonHtml(j, colorGradient, exonArray[j].resStart, exonArray[j].resEnd, exonArray[j].genomeRange, chnid, simpTitle, offset);
                             }
 
                             endColorStr = this.getExonColor(endExon.rangeStart, endExon.rangeEnd, to);
 
                             colorGradient = '#F00 0%, #FFF 50%, ' + endColorStr + ' 100%';
-                            htmlTmp2 += this.getExonHtml(endExon.exonIndex, colorGradient, endExon.rangeStart, endExon.to, endExon.genomeRange, chnid, simpTitle);
+                            htmlTmp2 += this.getExonHtml(endExon.exonIndex, colorGradient, endExon.rangeStart, endExon.to, endExon.genomeRange, chnid, simpTitle, offset);
                         }
                     }
 
@@ -45767,8 +45790,8 @@ class AddTrack {
         }
     }
 
-    getExonHtml(exonIndex, colorGradient, from, to, genomeRange, chainid, simpTitle) { let ic = this.icn3d; ic.icn3dui;
-        return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + from + '" to="' + to + '" setname="' + simpTitle + ', ' + (exonIndex + 1) + '" title="Exon: ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+    getExonHtml(exonIndex, colorGradient, from, to, genomeRange, chainid, simpTitle, offset) { let ic = this.icn3d; ic.icn3dui;
+        return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" domain="' + (exonIndex + 1) + '" from="' + (from + offset) + '" to="' + (to + offset) + '" setname="' + simpTitle + ', ' + (exonIndex + 1) + '" title="Exon: ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
     }
 
     getExonColor(start, end, pos) { let ic = this.icn3d; ic.icn3dui;
@@ -46715,6 +46738,7 @@ class AddTrack {
             let fromArray = [], toArray = [];
             let bFound = false;
             let seqStartLen = 0;
+            let offset = 0, offsetArray = [];
             //    for(let k = seqStart; k <= seqEnd; ++k) {
             for(let k = 0; k < seqLength; ++k) {
                 //if(seqFirst[k] == '-') continue;
@@ -46723,19 +46747,29 @@ class AddTrack {
 
                 resn = trackSeqArray[j][k];
 
+                if(resn != '-') {
+                    if(!bFound) {
+                        seqStartLen = k;
+                        bFound = true;
+                        
+                        offset = ic.startposGiSeq - ic.seqStartLen[chainid] + seqStartLen;
+                    }
+                }
+
                 if(prevResn == '-' && resn != '-') {
                     fromArray.push(k);
+                    offsetArray.push(offset);
                 }
 
                 if(prevResn != '-' && resn == '-') {
                     toArray.push(k - 1);
                 }
 
-                if(resn != '-') {
-                    if(!bFound) {
-                        seqStartLen = k;
-                        bFound = true;
-                    }
+                // use "offset" to adjut the residue numbers, e.g., P20138
+                // some isoforms starts residues before the first residue in the template sequence
+                if(k >= ic.seqStartLen[chainid]) {
+                    if(seqFirst[k] == '-') offset--;
+                    if(resn == '-') offset++;
                 }
 
                 text += resn; //ic.giSeq[chainid][i];
@@ -46756,7 +46790,7 @@ class AddTrack {
             let title =(trackTitleArray[j].length < 20) ? trackTitleArray[j] : trackTitleArray[j].substr(0, 20) + '...';
             let bMsa = true;
             let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
-            this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray);
+            this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray, offsetArray);
         }
 
         // update exon color
@@ -53564,8 +53598,10 @@ class ChainalignParser {
             //$.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 await ic.pdbParserCls.applyCommandDssp(true);
 
+                // original version =============
                 // align PDB chains
                 for(let index in ic.pdbChainIndexHash) {
+                    //ic.pdbChainIndexHash[index] = mmdbid_q_tmp + "_" + ic.chain_q + "_" + ic.mmdbid_t + "_" + ic.chain_t;
                     let idArray = ic.pdbChainIndexHash[index].split('_');
                     mmdbid_q = idArray[0];
                     idArray[1];
@@ -53580,25 +53616,49 @@ class ChainalignParser {
                 let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
                 let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
+                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
+
                 for(let index in ic.afChainIndexHash) {
                     let idArray = ic.afChainIndexHash[index].split('_');
                     mmdbid_q = idArray[0];
                     let chain_q = idArray[1];
+                    let chainid_q = mmdbid_q + '_' + chain_q;
+
                     mmdbid_t = idArray[2];
                     let chain_t = idArray[3];
+                    let chainid_t = mmdbid_t + '_' + chain_t;
+
+                    let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainid_t).hAtoms : ic.chains[chainid_t];
+                    let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainid_q).hAtoms : ic.chains[chainid_q];
+                // end of original version =============
+                
+/*
+                // new version to be done for VASTsrv ==============
+                // dynamically align pairs in all chainids
+                let ajaxArray = [], indexArray = [], struArray = [];
+                let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
+                let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
+
+                // dynamically align pairs in all chainids
+                let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainidArray[0]).hAtoms : ic.chains[chainidArray[0]];
+                for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
+                    let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainidArray[index]).hAtoms : ic.chains[chainidArray[index]];
+                // end of new version to be done for VASTsrv ==============
+*/
 
                     let alignAjax;
                     if(me.cfg.aligntool != 'tmalign') {
-                        let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_q + '_' + chain_q]);
-                        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_t + '_' + chain_t]);
+                        let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(atomSet_q);
+                        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(atomSet_t);
                             
                         let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
                         alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
                     }
                     else {
-                        let pdb_query = ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_q + '_' + chain_q]);
-                
-                        let pdb_target= ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_t + '_' + chain_t]);
+                        let pdb_query = ic.saveFileCls.getAtomPDB(atomSet_q);
+                        let pdb_target= ic.saveFileCls.getAtomPDB(atomSet_t);
 
                         let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target};
                         alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);                
@@ -54001,7 +54061,7 @@ class ChainalignParser {
         return chainidArray;
     }
 
-    async downloadChainalignment(chainalign, resnum, resdef) { let ic = this.icn3d, me = ic.icn3dui;
+    async downloadChainalignment(chainalign) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         ic.opts['proteins'] = 'c alpha trace';
@@ -54278,7 +54338,7 @@ class ChainalignParser {
     async loadOpmDataForChainalign(data1, data2, chainidArray, mmdbidArray) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        if(me.cfg.resnum || me.cfg.resdef) {
+        if(me.cfg.resnum || me.cfg.resdef || me.cfg.resrange) {
             if(!ic.bCommandLoad) ic.init(); // remove all previously loaded data
             await this.downloadChainalignmentPart2(data1, data2, undefined, chainidArray);
 
@@ -59155,6 +59215,7 @@ class DensityCifParser {
 
        //https://www.ebi.ac.uk/pdbe/densities/doc.html
        if(type == '2fofc' || type == 'fofc') {
+           detail = 0;
            url = "https://www.ebi.ac.uk/pdbe/densities/x-ray/" + pdbid.toLowerCase() + "/cell?detail=" + detail;
        }
        else if(type == 'em') {
@@ -59195,6 +59256,39 @@ class DensityCifParser {
         }
     }
 
+    async densityCifParserBase(url, type, sigma, location, bInputSigma) { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
+        //https://stackoverflow.com/questions/33902299/using-jquery-ajax-to-download-a-binary-file
+        if(type == '2fofc' && ic.bAjax2fofc) {
+            ic.mapData.sigma2 = sigma;
+            ic.setOptionCls.setOption('map', type);
+        }
+        else if(type == 'fofc' && ic.bAjaxfofc) {
+            ic.mapData.sigma = sigma;
+            ic.setOptionCls.setOption('map', type);
+        }
+        else {
+            let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', type);
+            
+            thisClass.parseChannels(arrayBuffer, type, sigma);
+
+            if(type == '2fofc' || type == 'fofc') {
+                ic.bAjax2fofc = true;
+                ic.bAjaxfofc = true;
+
+                ic.setOptionCls.setOption('map', type);
+            }
+            else if(type == 'em') {
+                ic.bAjaxEm = true;
+
+                ic.setOptionCls.setOption('emmap', type);
+            }
+        }
+
+        // return sigma;
+    }
+
     parseChannels(densitydata, type, sigma) { let ic = this.icn3d; ic.icn3dui;
         let cif = this.BinaryParse(densitydata);
 
@@ -64187,7 +64281,7 @@ class LoadCIF {
         
         let bFirstAtom = true;
 
-        let cifArray = bcifData.split('ENDMDL\n');
+        let cifArray = (bText) ? bcifData.split('ENDMDL\n') : [bcifData];
 
         for(let index = 0, indexl = cifArray.length; index  < indexl; ++index) {
             ++moleculeNum;
@@ -67178,6 +67272,16 @@ class ApplyCommand {
         ic.transformCls.rotateCoord(ic.hAtoms, mArrayFloat);
         ic.drawCls.draw();
       }
+      else if(command.indexOf('set dssp sse') == 0) {
+        await ic.pdbParserCls.applyCommandDssp();
+        ic.bResetAnno = true;
+
+        if(ic.bAnnoShown) {
+            await ic.showAnnoCls.showAnnotations();
+
+            ic.annotationCls.resetAnnoTabAll();
+        }
+      }
 
     // special, select ==========
 
@@ -69160,20 +69264,23 @@ class LoadScript {
           }
         }
         else if(command.indexOf('load chainalignment') !== -1) {
-          //load chainalignment [id] | resnum [resnum] | resdef [resnum] | aligntool [aligntool] | parameters [inpara]
+          //load chainalignment [id] | resnum [resnum] | resdef [resdef] | aligntool [aligntool] | parameters [inpara] | resrange [resrange] 
           let urlArray = command.split(" | ");
           if(urlArray.length > 1 && urlArray[1].indexOf('resnum') != -1) {
                 me.cfg.resnum = urlArray[1].substr(urlArray[1].indexOf('resnum') + 7);
           }
           if(urlArray.length > 2 && urlArray[2].indexOf('resdef') != -1) {
-                me.cfg.resdef = urlArray[2].substr(urlArray[1].indexOf('resdef') + 7);
+                me.cfg.resdef = urlArray[2].substr(urlArray[2].indexOf('resdef') + 7);
           }
           if(urlArray.length > 3 && urlArray[3].indexOf('aligntool') != -1) {
-                me.cfg.aligntool = urlArray[3].substr(urlArray[1].indexOf('aligntool') + 10);
+                me.cfg.aligntool = urlArray[3].substr(urlArray[3].indexOf('aligntool') + 10);
+          }
+          if(urlArray.length > 5 && urlArray[5].indexOf('resrange') != -1) {
+            me.cfg.resrange = urlArray[5].substr(urlArray[5].indexOf('resrange') + 9);
           }
 
           me.cfg.chainalign = id;
-          await ic.chainalignParserCls.downloadChainalignment(id, me.cfg.resnum, me.cfg.resdef);
+          await ic.chainalignParserCls.downloadChainalignment(id);
         }
         else if(command.indexOf('load url') !== -1) {
             let typeStr = load_parameters[1]; // type pdb
@@ -69222,7 +69329,8 @@ class LoadScript {
               if(urlArray.length == 2) {
                 let bInputSigma = true;
                 if(fileType == 'dsn6') {
-                  await ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
+                  // await ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
+                  await ic.densityCifParserCls.densityCifParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
                 }
                 else if(fileType == 'ccp4') {
                   await ic.ccp4ParserCls.ccp4ParserBase(urlArray[1], type, sigma, 'url', bInputSigma);
@@ -69235,7 +69343,8 @@ class LoadScript {
                 }
               }
               else {
-                await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
+                // await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
+                await ic.densityCifParserCls.densityCifParser(ic.inputid, type, sigma);
               }
           }
     //   }); // end of me.deferred = $.Deferred(function() {
@@ -82037,7 +82146,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.33.2';
+    this.REVISION = '3.33.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -82480,9 +82589,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
 
         ic.bChainAlign = true;
         ic.inputid = me.cfg.chainalign;
-        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara;
+        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara + ' | resrange ' + me.cfg.resrange;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
-        await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign, me.cfg.resnum, me.cfg.resdef);
+        await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
     }
     else if(me.cfg.mmdbafid !== undefined) {
         // ic.bNCBI = true;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.33.1",
+  "version": "3.33.2",
   "main": "./icn3d.js",
   "exports": {
     ".": {