icn3d 3.29.16 → 3.30.0

package/icn3d.js

@@ -5810,6 +5810,26 @@ class ClickMenu {
         $("#" + me.pre + "menulist").html(html);
     }
 
+    async setIgTemplate(template) { let me = this.icn3dui, ic = me.icn3d;
+      ic.bRunRefnumAgain = true;
+
+      // reset for the selection
+      let residueArray = ic.resid2specCls.atoms2residues(Object.keys(ic.hAtoms));
+      for(let i = 0, il = residueArray.length; i < il; ++i) {
+         let resid = residueArray[i];
+
+         if(ic.resid2refnum) delete ic.resid2refnum[resid];
+         if(ic.resid2refnum_ori) delete ic.resid2refnum_ori[resid];
+         if(ic.resid2domainid) delete ic.resid2domainid[resid];
+      }
+
+      let bSelection = true;
+      // await ic.refnumCls.showIgRefNum(template);
+      if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
+      await ic.annotationCls.setAnnoTabIg(bSelection, template);
+
+      // ic.bRunRefnumAgain = false;
+    }
 
     clickMenu1() { let me = this.icn3dui; me.icn3d;
         if(me.bNode) return;
@@ -7375,6 +7395,8 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_igrefYes", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+            ic.bRunRefnumAgain = true;
+
             thisClass.setLogCmd('ig refnum on', true);
             // await ic.refnumCls.showIgRefNum();
             // thisClass.setLogCmd('set annotation ig', true);
@@ -7391,21 +7413,22 @@ class ClickMenu {
             //    ic.hlUpdateCls.updateHlAll();
             //    ic.drawCls.draw();
             // }
+
+            // ic.bRunRefnumAgain = false;
          });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
             me.htmlCls.dialogCls.openDlg('dl_igrefTpl', 'Choose an Ig template');
          });
 
-        me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+        me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { me.icn3d; //e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-                  
+
             let template = $("#" + me.pre + "refTpl").val();
+
+            await thisClass.setIgTemplate(template);
+
             thisClass.setLogCmd('ig template ' + template, true);
-            let bSelection = true;
-            // await ic.refnumCls.showIgRefNum(template);
-            if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
-            await ic.annotationCls.setAnnoTabIg(bSelection, template);
          });
 
          me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
@@ -7414,18 +7437,26 @@ class ClickMenu {
 
          me.myEventCls.onIds("#" + me.pre + "mn6_alignrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-                  
+   
             let template = $("#" + me.pre + "refTpl2").val();
 
+            let selAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+
             // load the template
             let url = me.htmlCls.baseUrl + "icn3d/refpdb/" + template + ".pdb";
             await ic.pdbParserCls.downloadUrl(url, 'pdb', undefined, template);
             thisClass.setLogCmd('load url ' + url + ' | type pdb', true);
+   
+            let structure = template.replace(/_/g, '').substr(0,4);
+
+            let chainid = ic.structures[structure][0];
+
+            ic.hAtoms = me.hashUtilsCls.unionHash(selAtoms, ic.chains[chainid]);
 
             // align the template with the selection
             me.cfg.aligntool = 'tmalign';
             await ic.realignParserCls.realignOnStructAlign();
-            thisClass.setLogCmd('realign on tmalign', true);
+            thisClass.setLogCmd('realign on tmalign', true);   
          });
 
          me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
@@ -36881,8 +36912,9 @@ class AnnoCddSite {
                 if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
 
                 if(me.cfg.blast_rep_id != chnid) { // regular
+                    let color;
                     for(let i = 0, il = fromArray.length; i < il; ++i) {
-                        let color = this.getColorFromPos(chnid, fromArray[i], titleArray);
+                        if(i == 0) color = this.getColorFromPos(chnid, fromArray[i], titleArray);
         
                         let emptyWidth;
                         // if(titleArray) {
@@ -37608,9 +37640,10 @@ class AnnoIg {
 
     //Show the annotations of CDD domains and binding sites.
     async showIg(chnid, template) { let ic = this.icn3d; ic.icn3dui;
-        if(!ic.bRunRefnum || Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
+        // if(!ic.bRunRefnum || Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
+        if(ic.bRunRefnumAgain) {
             await ic.refnumCls.showIgRefNum(template);
-            ic.bRunRefnum = true;    
+            // ic.bRunRefnum = true;    
         }
 
         let type = 'ig';
@@ -37628,6 +37661,8 @@ class AnnoIg {
         $("#" + ic.pre + "dt_" + type + "_" + chnid).html(html);
         $("#" + ic.pre + "ov_" + type + "_" + chnid).html(html2);
         $("#" + ic.pre + "tt_" + type + "_" + chnid).html(html3);
+
+        ic.bRunRefnumAgain = false;
     }
 
     showAllRefNum(giSeq, chnid) {  let ic = this.icn3d; ic.icn3dui;
@@ -37919,19 +37954,24 @@ class AnnoIg {
             html2 += htmlTitle; 
             html2 += htmlCnt + '<span class="icn3d-seqLine">';
 
+            let prevDomainindex, color;
             for(let i = 0, il = fromArray.length; i < il; ++i) {
                 let resi = ic.ParserUtilsCls.getResi(chnid, fromArray[i]);
                 let resid = chnid + "_" + resi;
-                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                let colorStr =(!atom || atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
-                let color =(atom && atom.color !== undefined) ? colorStr : "CCCCCC";
 
                 let domainindex = posindex2domainindex[fromArray[i]];
+                if(domainindex != prevDomainindex) {
+                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    let colorStr =(!atom || atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
+                    color =(atom && atom.color !== undefined) ? colorStr : "CCCCCC";
+                }
 
                 let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : 
                     Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
                 html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
                 html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[domainindex] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[domainindex] + '">' +  domainArray[domainindex] + ' </div>';
+
+                prevDomainindex = domainindex;
             }
 
             html2 += htmlCnt;
@@ -38125,6 +38165,7 @@ class AnnoDomain {
         let pdbid = pdbArray[index];
         //let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&domain&molinfor&uid=" + pdbid;
 
+/*
         if(!ic.bResetAnno && index == 0 && ic.mmdb_data !== undefined) {      
             for(let chnid in ic.protein_chainid) {
                 if(chnid.indexOf(pdbid) !== -1) {
@@ -38140,6 +38181,7 @@ class AnnoDomain {
             }
         }
         else {
+*/
             // calculate 3D domains on-the-fly
             //ic.protein_chainid[chainArray[i]] 
             let data = {};
@@ -38181,7 +38223,7 @@ class AnnoDomain {
 
             ic.bAjax3ddomain = true;
             ic.bAjaxDoneArray[index] = true;          
-        }
+        // }
     }
 
     //Show the annotations of 3D domains.
@@ -39216,6 +39258,10 @@ class Domain3d {
     constructor(icn3d) {
 		this.icn3d = icn3d;
 
+		this.init3ddomain();
+	}
+
+	init3ddomain() { let ic = this.icn3d; ic.icn3dui;
         //this.dcut = 8; // threshold for C-alpha interactions
 
 		// It seemed the threshold 7 angstrom works better
@@ -39223,7 +39269,8 @@ class Domain3d {
 		this.dcut = 8; // threshold for C-alpha interactions
 
 		// added by Jiyao
-		this.min_contacts = 5; //3;			// minimum number of contacts to be considered as neighbors
+		// pdbid 1CD8 requires a min contact 4, not 5
+		this.min_contacts = 4; //5; //3;			// minimum number of contacts to be considered as neighbors
 
 		this.MAX_SSE = 512;
 
@@ -39235,6 +39282,7 @@ class Domain3d {
 
         //let this.elt_size[this.MAX_SSE];			// element sizes in residues
         this.elt_size = [];
+
         this.elt_size.length = this.MAX_SSE;
 
         //let this.group_num[this.MAX_SSE];			// indicates required element groupings
@@ -39844,6 +39892,8 @@ class Domain3d {
 	// x0, y0, z0: array of x,y,z coordinates of C-alpha atoms
 	//c2b_NewSplitChain(chnid, dcut) { let ic = this.icn3d, me = ic.icn3dui;
 	c2b_NewSplitChain(atoms, dcut) { let ic = this.icn3d; ic.icn3dui;
+		this.init3ddomain();
+
 		let x0 = [], y0 = [], z0 = [], resiArray = [];
 
 		//substruct: array of secondary structures, each of which has the keys: From (1-based), To (1-based), Sheet (0 or 1), also add these paras: x1, y1, z1, x2, y2, z2
@@ -42377,7 +42427,11 @@ class Annotation {
         this.updateSsbond();
         this.updateCrosslink();
         await this.updateTransmem();
+
+        ic.bRunRefnumAgain = true;
         await this.updateIg();
+        // ic.bRunRefnumAgain = false;
+
         this.updateInteraction();
     }
     hideAnnoTabAll() {  let ic = this.icn3d; ic.icn3dui;
@@ -42459,10 +42513,13 @@ class Annotation {
             $("[id^=" + ic.pre + "transmem]").show();
         }
         if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked) {
-            ic.bRunRefnum = false;
+            // ic.bRunRefnumAgain = true;
+
             await this.updateIg();
 
             $("[id^=" + ic.pre + "ig]").show();
+
+            // ic.bRunRefnumAgain = false;
         }
     }
     setAnnoTabCustom() {  let ic = this.icn3d; ic.icn3dui;
@@ -42723,12 +42780,15 @@ class Annotation {
 
         me.myEventCls.onIds("#" + ic.pre + "anno_ig", "click", async function(e) {
             if($("#" + ic.pre + "anno_ig").length && $("#" + ic.pre + "anno_ig")[0].checked) {
-                if(Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
-                    ic.bRunRefnum = false;
-                }
+                // if(Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
+                //     ic.bRunRefnum = false;
+                // }
 
+                ic.bRunRefnumAgain = true;
                 await thisClass.setAnnoTabIg();
                 me.htmlCls.clickMenuCls.setLogCmd("set annotation ig", true);
+
+                // ic.bRunRefnumAgain = false;
             }
             else {
                 thisClass.hideAnnoTabIg();
@@ -59953,11 +60013,17 @@ class ApplyCommand {
           await ic.annotationCls.setAnnoTabTransmem();
       }
       else if(command == 'set annotation ig') {
+          ic.bRunRefnumAgain = true;
           await ic.annotationCls.setAnnoTabIg();
+          // ic.bRunRefnumAgain = false;
       }
       else if(command == 'ig refnum on') {
+        ic.bRunRefnumAgain = true;
+
         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
         await ic.annotationCls.setAnnoTabIg(true);
+
+        // ic.bRunRefnumAgain = false;
     }
       else if(command == 'highlight level up') {
           ic.resid2specCls.switchHighlightLevelUp();
@@ -62445,9 +62511,7 @@ class LoadScript {
           // }
           else if(command.indexOf('ig template') == 0 ) { 
             let template = command.substr(command.lastIndexOf(' ') + 1);
-            // await ic.refnumCls.showIgRefNum(template);
-            if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
-            await ic.annotationCls.setAnnoTabIg(true, template);
+            await me.htmlCls.clickMenuCls.setIgTemplate(template);
           }
           else if(command.indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
               if(Object.keys(ic.proteins).length > 0) {
@@ -62650,8 +62714,12 @@ class LoadScript {
                     }
                     else if(lastCommand.indexOf('ig refnum on') == 0) {
                         // await ic.refnumCls.showIgRefNum();
+                        ic.bRunRefnumAgain = true;
+
                         if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
                         await ic.annotationCls.setAnnoTabIg(true);
+
+                        // ic.bRunRefnumAgain = false;
                     }
                     else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
                         thisClass.applyCommand3ddomain(lastCommand);
@@ -65648,7 +65716,7 @@ class Dssp {
 
     async hideIgRefNum() { let ic = this.icn3d; ic.icn3dui;
         ic.bShowRefnum = false;
-        ic.bRunRefnum = false;
+        // ic.bRunRefnum = false;
 
         // redo all ref numbers
         ic.resid2refnum = {};
@@ -66024,9 +66092,9 @@ class Dssp {
 
         if(bRerunDomain) {
             let atomsAssigned = {};
-            //ic.resid2refnum_ori should be used
-            for(let resid in ic.resid2refnum_ori) {
-                atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            // for(let resid in ic.resid2refnum_ori) {
+            for(let resid in ic.resid2domainid) {
+                if(ic.resid2domainid[resid]) atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
             }
 
             currAtoms = me.hashUtilsCls.exclHash(currAtoms, atomsAssigned);
@@ -66251,7 +66319,7 @@ class Dssp {
                 strandHash[strand] = 1;
             }
             let score = parseFloat(queryData[0].score);
-            //!!!
+
             // if the TM score difference is within 0.1 and more strands are found, use the template with more strands
             // if(!domainid2segs.hasOwnProperty(domainid) || 
             //     (score >= parseFloat(ic.domainid2score[domainid].split('_')[0]) + tmAdjust)
@@ -66283,24 +66351,22 @@ class Dssp {
         }
 
         //!!!
-/*
-        // combine the top three clusters for the 2nd round alignment
+
+        // combine the top four clusters for the 2nd round alignment
         if(bRound1) {
             for(let domainid in domainid2refpdbnamelist) {
-                if(!me.bNode) console.log("###score " + ic.domainid2score[domainid].split('_')[0] + " ic.domainid2refpdbname[domainid][0] " + ic.domainid2refpdbname[domainid][0])
                 if(!me.bNode && ic.domainid2refpdbname[domainid][0] == 'all_templates') {
                     let refpdbname2score = domainid2refpdbnamelist[domainid];
                     let refpdbnameList = Object.keys(refpdbname2score);
                     refpdbnameList.sort(function(a, b) {
                         return refpdbname2score[b] - refpdbname2score[a]
                     });
-                    // top 3 templates
-                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,3);
+                    // top 4 templates
+                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,4);
                 }
-                if(!me.bNode) console.log("###bb ic.domainid2refpdbname[domainid] " + ic.domainid2refpdbname[domainid])
             }
         }
-*/
+
         return domainid2segs; // only used in round 2
     }
 
@@ -66309,7 +66375,7 @@ class Dssp {
 
         let domainid2segs = this.parseAlignData_part1(dataArray, domainidpairArray, bRound1);
 
-        // !!!no more Igs to detect
+        // no more Igs to detect
         if(Object.keys(domainid2segs).length == 0) {
             bNoMoreIg = true;
             return bNoMoreIg;
@@ -67058,7 +67124,7 @@ class Dssp {
                             }
                             
                             // in case A1550 is not found, but A1551 is found
-                            if(!bFoundAnchor && (lastTwo == 51 || lastTwo == 52 || lastTwo == 53 || lastTwo == 54) ) {
+                            if(!bFoundAnchor && (lastTwo >= 46 && lastTwo <= 54) ) {
                                 let offset = lastTwo - 50;
                                 strandArray[strandCnt].anchorRefnum = refnum - offset;
                                 strandArray[strandCnt].resCntBfAnchor = resCntBfAnchor - offset;
@@ -67167,6 +67233,7 @@ class Dssp {
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
                             ic.resid2domainid[currResid] = domainid;
+                            ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;
@@ -67200,6 +67267,7 @@ class Dssp {
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
                             ic.resid2domainid[currResid] = domainid;
+                            ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
 
                         break;
@@ -75587,7 +75655,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.29.5';
+    this.REVISION = '3.30.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;