icn3d 3.29.11 → 3.29.13

package/icn3d.js

@@ -11977,10 +11977,11 @@ class SetDialog {
         html += "<td></td>";
         html += "</tr><tr>";
         html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ig'>Ig Domains" + me.htmlCls.space2 + "</span></td>";
+*/
 
         html += "<td></td>";
         html += "</tr></table></div></div>";
-*/
+
         return html;
     }
 }
@@ -36842,14 +36843,12 @@ class AnnoCddSite {
 
                 if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
 
-                let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
-                let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
-                let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
-
                 if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
 
                 if(me.cfg.blast_rep_id != chnid) { // regular
                     for(let i = 0, il = fromArray.length; i < il; ++i) {
+                        let color = this.getColorFromPos(chnid, i, titleArray);
+        
                         let emptyWidth;
                         if(titleArray) {
                             emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
@@ -36875,6 +36874,8 @@ class AnnoCddSite {
                         toArray2.push(toArray[i]);
                     }
                     for(let i = 0, il = fromArray2.length; i < il; ++i) {
+                        let color = this.getColorFromPos(chnid, i, titleArray);
+        
                         html2 += ic.showSeqCls.insertGapOverview(chnid, fromArray2[i]);
                         let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray2[i] - ic.baseResi[chnid] - 1) /(ic.maxAnnoLength + ic.nTotalGap)) : Math.round(ic.seqAnnWidth *(fromArray2[i] - toArray2[i-1] - 1) /(ic.maxAnnoLength + ic.nTotalGap));
                         html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
@@ -36899,6 +36900,24 @@ class AnnoCddSite {
     // getAdjustedResi(resi, chnid, matchedPos, chainsSeq, baseResi) { let ic = this.icn3d, me = ic.icn3dui;
     //     return (resi >= matchedPos[chnid] && resi - matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][resi - matchedPos[chnid]].resi : baseResi[chnid] + 1 + resi;
     // }
+    getColorFromPos(chainid, pos, bIg) { let ic = this.icn3d; ic.icn3dui;
+        let color;
+
+        let resid =  chainid + '_' + ic.ParserUtilsCls.getResi(chainid, pos);
+        // if(!bIg) {
+            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";
+        // }
+        // else {
+            // let refnumLabel = ic.resid2refnum[resid];
+            // let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+            // let currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
+            // color = ic.annoIgCls.getRefnumColor(currStrand, true).substr(1);
+        // }
+
+        return color;
+    }
 
     showAnnoType(chnid, chnidBase, type, title, residueArray, resid2resids) { let ic = this.icn3d, me = ic.icn3dui;
         let html = '<div id="' + ic.pre + chnid + '_' + type + 'seq_sequence" class="icn3d-dl_sequence">';
@@ -37556,7 +37575,7 @@ class AnnoIg {
     async showIg(chnid, template) { let ic = this.icn3d; ic.icn3dui;
         if(!ic.bRunRefnum || Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
             await ic.refnumCls.showIgRefNum(template);
-            ic.bRunRefnum = true;
+            ic.bRunRefnum = true;    
         }
 
         let type = 'ig';
@@ -37601,7 +37620,6 @@ class AnnoIg {
 
     showRefNum(giSeq, chnid, kabat_or_imgt, bCustom) {  let ic = this.icn3d, me = ic.icn3dui;
         let html = '', html2 = '', html3 = '';
-        let type = 'ig';
 
         if(!ic.chainid2refpdbname[chnid]) return {html: html, html2: html2, html3: html3};
 
@@ -37640,7 +37658,7 @@ class AnnoIg {
         }
 
         // auto-generate ref numbers for loops 
-        let bLoop = false, currStrand = '', prevStrand = '';
+        let currStrand = '', prevStrand = '';
         let refnumLabel, refnumStr_ori, refnumStr, postfix, strandPostfix, refnum, refnum3c, refnum2c;
         let bExtendedStrand = false, bSecThird9 = false;
 
@@ -37676,7 +37694,7 @@ class AnnoIg {
                     bFoundAnchor = false;
                 }
 
-                if(prevStrand.substr(0,1) == 'G' && !refnumLabel) { // indicate the end of an IG domain
+                if((prevStrand.substr(0,1) == 'F' || prevStrand.substr(0,1) == 'G') && !refnumLabel) { // indicate the end of an IG domain
                     bStart = false;
                 }
 
@@ -37810,7 +37828,13 @@ class AnnoIg {
 
             // 2. remove strands with less than 3 residues except G strand
             for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
-                if(strandArray[i].strand.substr(0, 1) != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
+                let strandTmp = strandArray[i].strand.substr(0, 1);
+                if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
+                    if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
+                        if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing...");
+                        return {html: '', html2: '', html3: ''};
+                    }
+
                     if(i != il - 1) { // modify 
                         strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                     }
@@ -37961,7 +37985,8 @@ class AnnoIg {
                                 }                        
                             }
                             else {
-                                if(prevStrandCnt >= 0 && strandArray[prevStrandCnt].strand.substr(0, 1) == 'G') {
+                                if(prevStrandCnt >= 0 
+                                  && (strandArray[prevStrandCnt].strand.substr(0, 1) == 'F' || strandArray[prevStrandCnt].strand.substr(0, 1) == 'G')) {
                                     if(!bAfterGstrand) {
                                         //loopCnt = 0;
                                         refnumLabelNoPostfix = undefined;
@@ -38086,15 +38111,30 @@ class AnnoIg {
             }
         }
 
+        // add color to atoms
+        if(ic.bShowRefnum) {
+            ic.opts.color = 'ig strand';
+            ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
+        }
+
+        return this.getIgAnnoHtml(chnid, giSeq, bCustom, kabat_or_imgt);
+    }
+
+    getIgAnnoHtml(chnid, giSeq, bCustom, kabat_or_imgt) { let ic = this.icn3d, me = ic.icn3dui;
+        let html = '', html2 = '', html3 = '';
+        let type = 'ig';
+
         if(!ic.chain2igArray) ic.chain2igArray = {};
         ic.chain2igArray[chnid] = [];
 
         let igElem = {};
-        bStart = false;
         let currStrand_ori;
-        prevStrand = undefined;
+        let prevStrand = undefined;
         let prevPos;
 
+        let bLoop = false, currStrand = '';
+        let refnumLabel, refnumStr_ori, refnumStr;
+
         // show tracks
         let htmlIg = '';
         for(let i = 0, il = giSeq.length; i < il; ++i) {
@@ -38128,7 +38168,6 @@ class AnnoIg {
                     }
                     else {
                         refnumStr = refnumStr_ori;
-                        refnum = parseInt(refnumStr);
                     }
 
                     let prevStrandFirstLet = (prevStrand) ? prevStrand.substr(0, 1) : '';
@@ -38284,9 +38323,9 @@ class AnnoIg {
         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.getFirstCalphaAtomObj(ic.residues[resid]);
-            let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
-            let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
+            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 emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : 
                 Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
@@ -40557,6 +40596,7 @@ class Domain3d {
 			}
 			if(list_parts_item.length >= this.min_sse) list_partsTmp.push(list_parts[i]);
 		}
+		
 		list_parts = list_partsTmp;
 
 		//for (lplet = list_parts.begin(); lplet != list_parts.end(); lpint++) {
@@ -43247,8 +43287,8 @@ class Annotation {
         // ic.bIgShown = true;
 
         if(ic.bShowRefnum) {
-            ic.opts.color = 'ig strand';
-            ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
+            // ic.opts.color = 'ig strand';
+            // ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
 
             ic.hlUpdateCls.updateHlAll();
             ic.drawCls.draw();
@@ -66511,26 +66551,27 @@ class Dssp {
                     let seg = queryData[0].segs[j];
                     let resi = seg.t_start;
                     let resid = chainid + '_' + resi;
+                    let q_start = parseInt(seg.q_start);
 
-                    if(seg.q_start.indexOf('2550') != -1) {
+                    if(q_start > 2540 && q_start < 2560) {
                         bBstrand = true;
                         let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        bBSheet = (atom.ss == 'sheet');
+                        if(atom.ss == 'helix') bBSheet = false;
                     }
-                    else if(seg.q_start.indexOf('3550') != -1) {
+                    else if(q_start > 3540 && q_start < 3560) {
                         bCstrand = true;
                         let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        bBSheet = (atom.ss == 'sheet');
+                        if(atom.ss == 'helix') bCSheet = false;
                     }
-                    else if(seg.q_start.indexOf('7550') != -1) {
+                    else if(q_start > 7540 && q_start < 7560) {
                         bEstrand = true;
                         let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        bBSheet = (atom.ss == 'sheet');
+                        if(atom.ss == 'helix') bESheet = false; 
                     }
-                    else if(seg.q_start.indexOf('8550') != -1) {
+                    else if(q_start > 8540 && q_start < 8560) {
                         bFstrand = true;
                         let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
-                        bBSheet = (atom.ss == 'sheet');
+                        if(atom.ss == 'helix') bFSheet = false;
                     }
 
                     //if(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand) break;
@@ -66538,9 +66579,10 @@ class Dssp {
                 }
 
                 if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
-                //if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+                // if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
                     if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
                     if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
+                    // if(!me.bNode && (BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
                     if(ic.domainid2refpdbname[domainid] == refpdbname) {
                         delete ic.domainid2refpdbname[domainid];
                         delete ic.domainid2score[domainid];
@@ -66838,9 +66880,13 @@ class Dssp {
                         refnumLabel = this.getLabelFromRefnum(refnum, currStrandFinal);
                     }
 
-                    ic.resid2refnum[resid] = refnumLabel;
-                    ic.resid2refnum_ori[resid] = refnumLabel;
-                    ic.resid2domainid[resid] = domainid;
+                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    // only sheet or loop will be aligned
+                    if(atom.ss != 'helix') {
+                        ic.resid2refnum[resid] = refnumLabel;
+                        ic.resid2refnum_ori[resid] = refnumLabel;
+                        ic.resid2domainid[resid] = domainid;
+                    }
 
                     // final reference numbers will be assign in ic.annoIgCls.showRefNum()
 
@@ -67187,6 +67233,8 @@ class Dssp {
     }
 
     async promiseWithFixedJobs(ajaxArray) { let ic = this.icn3d, me = ic.icn3dui;
+        if(!me.bNode) me.icn3d.ParserUtilsCls.showLoading();
+
         let dataArray3 = [];
         //let allPromise = Promise.allSettled(ajaxArray);
         //dataArray3 = await allPromise;
@@ -67209,6 +67257,8 @@ class Dssp {
             dataArray3 = dataArray3.concat(currDataArray);
         }
 
+        if(!me.bNode) me.icn3d.ParserUtilsCls.hideLoading();
+
         return dataArray3;
     }
  }