icn3d 3.29.10 → 3.29.12

package/icn3d.module.js

@@ -12814,12 +12814,17 @@ class SetDialog {
 
         //html += me.htmlCls.setHtmlCls.getOptionHtml(['0', '10', '20', '30', '40', '50', '60', '70', '80', '90', '100'], 3);
         let group2tpl = {};
-        group2tpl['V'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V', 'ICOS_6x4gA_human_V', 'CD28_1yjdC_human_V', 'PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
-        group2tpl['C1'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2'];
-        group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Contactin1_3s97C_human_C2-n2'];
-        group2tpl['Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'JAM1_1nbqA_human_VorIset-n2', 'CD19_6al5A_human_C2orV-n1'];
-        group2tpl['FN3'] = ['InsulinR_8guyE_human_FN3-n1', 'IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7', 'InsulinR_8guyE_human_FN3-n2', 'Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
-        group2tpl['Other'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria', 'C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human', 'ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'LaminAC_1ifrA_human', 'IsdA_2iteA_bacteria'];  
+        group2tpl['V'] = ['CD28_1yjdC_human_V', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'ICOS_6x4gA_human_V', 'LAG3_7tzgD_human_V-n1', 'PDL1_4z18B_human_V-n1', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V'];
+        group2tpl['C1'] = ['B2Microglobulin_7phrL_human_C1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-HEAVY_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'MHCIa_7phrH_human_C1', 'TCRa_6jxrm_human_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
+        group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
+        group2tpl['I'] = ['BTLA_2aw2A_human_Iset', 'CD19_6al5A_human_C2orV-n1', 'JAM1_1nbqA_human_VorIset-n2', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152'];
+        group2tpl['E'] = ['ASF1A_2iijA_human', 'CoAtomerGamma1_1r4xA_human', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'IsdA_2iteA_bacteria', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'TEAD1_3kysC_human'];
+
+        group2tpl['FN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
+
+        group2tpl['FN3-like'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
+
+        group2tpl['Other'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];  
 
         for(let group in group2tpl) {
             html += "<optgroup label='" + group + "'>";
@@ -12874,6 +12879,7 @@ class SetDialog {
         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>";
 
@@ -37666,7 +37672,8 @@ class AnnoCddSite {
 
                 //var setname = chnid + "_" + domain + "_" + index + "_" + r; //chnid + "_" + type + "_" + index + "_" + r;
                 let setname = chnid + "_" + domain;
-                if(type != 'domain') setname += "_" + index + "_" + r; // + acc2domain[acc];
+                // if(type != 'domain') setname += "_" + index + "_" + r; 
+                if(type != 'domain') setname = chnid + "_" + index + "_" + r  + "_" + domain; 
 
                 if(type == 'domain') pssmid2fromArray[pssmid] = fromArray;
                 if(type == 'domain') pssmid2toArray[pssmid] = toArray;
@@ -37737,14 +37744,12 @@ 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);
@@ -37770,6 +37775,8 @@ 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>';
@@ -37794,6 +37801,24 @@ 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">';
@@ -38451,7 +38476,7 @@ 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';
@@ -38496,7 +38521,6 @@ 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};
 
@@ -38535,7 +38559,7 @@ 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;
 
@@ -38571,7 +38595,7 @@ 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;
                 }
 
@@ -38856,7 +38880,8 @@ 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;
@@ -38981,15 +39006,30 @@ 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) {
@@ -39023,7 +39063,6 @@ class AnnoIg {
                     }
                     else {
                         refnumStr = refnumStr_ori;
-                        refnum = parseInt(refnumStr);
                     }
 
                     let prevStrandFirstLet = (prevStrand) ? prevStrand.substr(0, 1) : '';
@@ -39126,11 +39165,11 @@ class AnnoIg {
             htmlTmp += '<span class="icn3d-residueNum"></span>';
         }
         else if(kabat_or_imgt == 1) {
-            htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="Kabat Reference Numbers ' + refStruTitle + '">Kabat Ref. No.</div>';
+            htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="Kabat Reference Numbers">Kabat Ref. No.</div>';
             htmlTmp += '<span class="icn3d-residueNum"></span>';
         }
         else if(kabat_or_imgt == 2) {
-            htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="IMGT Reference Numbers ' + refStruTitle + '">IMGT Ref. No.</div>';
+            htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="IMGT Reference Numbers">IMGT Ref. No.</div>';
             htmlTmp += '<span class="icn3d-residueNum"></span>';
         }
         else {
@@ -39157,6 +39196,7 @@ class AnnoIg {
         let igArray = ic.chain2igArray[chnid];      
         if(igArray.length == 0) return {html: '', html2: '', html3: ''};
         let rangeArray = [], titleArray = [], fullTitleArray = [], domainArray = [];
+
         for(let i = 0, il = igArray.length; i < il; ++i) {
             let domainid = igArray[i].domainid;
             let info = ic.domainid2info[domainid];
@@ -39178,9 +39218,9 @@ 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);
@@ -40558,12 +40598,16 @@ class Domain3d {
 
 		// this.elements from the this.top of the this.stack 
 		//elts = &this.elements[this.stack[this.top - 1]];
+		
 		for(i = this.stack[this.top - 1], il = this.elements.length; i < il; ++i) {
 			elts.push(this.elements[i]);
 		}
 
 		// generate the partition based on the cut //
-		for (i = ne = ne0 = ne1 = 0, prt = prt0, t = -1; i < k; i++) {
+		// for (i = ne = ne0 = ne1 = 0, prt = prt0, t = -1; i < k; i++) {
+		let bAtZero = true;
+		prt = prt0;
+		for (i = ne = ne0 = ne1 = 0, t = -1; i < k; i++) {
 			// write the this.elements into prt //
 			for (j = t + 1; j <= cut[i]; j++)
 				prt[ne++] = elts[j];
@@ -40571,15 +40615,20 @@ class Domain3d {
 			t = cut[i];
 
 			// switch the partition //
-			if (prt == prt0) {
+			// if (prt == prt0) {
+			if (bAtZero) {
 				ne0 = ne;
 				prt = prt1;
 				ne = ne1;
+
+				bAtZero = false;
 			}
 			else {
 				ne1 = ne;
 				prt = prt0;
 				ne = ne0;
+
+				bAtZero = true;
 			}
 		}
 
@@ -40587,7 +40636,8 @@ class Domain3d {
 		for (j = t + 1; j < n; j++)
 			prt[ne++] = elts[j];
 
-		if (prt == prt0)
+		// if (prt == prt0)
+		if (bAtZero)
 			ne0 = ne;
 		else
 			ne1 = ne;
@@ -41256,6 +41306,8 @@ class Domain3d {
 			let ss1 = parseInt(ssPair[0]);
 			let ss2 = parseInt(ssPair[1]);
 
+			if(ctable[pair] < this.min_contacts) ctable[pair] = 0;
+
 			// both are sheets
 			// min number of contacts: this.min_contacts
 			if(substruct[ss1 - 1].Sheet && substruct[ss2 - 1].Sheet && ctable[pair] >= this.min_contacts ) {
@@ -41266,7 +41318,7 @@ class Domain3d {
 				sheetNeighbor[ss2][ss1] = 1;
 			}
 		}
-
+	
 		//https://www.geeksforgeeks.org/number-groups-formed-graph-friends/
 		let existing_groups = 0;
 		let sheet2sheetnum = {};
@@ -41289,12 +41341,13 @@ class Domain3d {
 		// get sheet2sheetnum
 		// each neighboring sheet will be represented by the sheet with the smallest sse 
 		for(let groupnum in this.groupnum2sheet) {
-			let ssArray = this.groupnum2sheet[groupnum].sort();
+			let ssArray = this.groupnum2sheet[groupnum].sort(function(a, b){return a-b});
 			for(let i = 0, il = ssArray.length; i < il; ++i) {
 				sheet2sheetnum[ssArray[i]] = ssArray[0];
 			}
 		}
 
+		let invalidSheethash = {};	
 		for (let i = 0; i < nsse; i++) {
 			if(substruct[i].Sheet) {				
 				let sheetsItem = {};
@@ -41307,6 +41360,8 @@ class Domain3d {
 					sheetsItem.sheet_num = 0;
 					sheetsItem.adj_strand2 = 0; 
 					sheetsItem.sse = i + 1; 
+
+					invalidSheethash[sheetsItem.sse] = 1;
 				}
 
 				sheets.push(sheetsItem);
@@ -41338,7 +41393,7 @@ class Domain3d {
 			}
 		}
 
-		let minStrand = 6;
+		let minStrand = 6; // number of residues in a strand
 
 		if (hasSheets) {
 			//sheets: array of sheets, each of which has the key: sheet_num (number of strands), adj_strand1, adj_strand2
@@ -41362,7 +41417,8 @@ class Domain3d {
 			if (cnt> 0) {
 				for (let i = 0; i < sheets.length; i++) {
 					let bsrec = sheets[i];
-					this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
+					// this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
+					if(bsrec.sheet_num != 0) this.group_num[bsrec.sse - 1] = bsrec.sheet_num;
 				}
 			}
 		}
@@ -41418,11 +41474,26 @@ class Domain3d {
 				}
 			}
 		}
-		
+
 		list_parts.sort(function(v1, v2) {
 				return v1[0] - v2[0];
 			});
 
+		// remove sheets less than 3 residues
+		let list_partsTmp = [];
+		for(let i = 0, il = list_parts.length; i < il; ++i) {
+			let list_parts_item = [];
+			for(let j = 0, jl = list_parts[i].length; j < jl; ++j) {
+				let sse = list_parts[i][j];
+				if(!invalidSheethash.hasOwnProperty(sse)) {
+					list_parts_item.push(sse);
+				}
+			}
+			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++) {
 		for (let index = 0, indexl = list_parts.length; index < indexl; ++index) {
 			//vector<int> prts = *lpint;
@@ -44111,8 +44182,8 @@ 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();
@@ -67369,42 +67440,50 @@ class Dssp {
             if(!bRound1 && queryData[0].segs) {
                 let bBstrand = false, bCstrand = false, bEstrand = false, bFstrand = false;
                 let bBSheet = true, bCSheet = true, bESheet = true, bFSheet = true;
+                let BCnt = 0, CCnt = 0, ECnt = 0, FCnt = 0;
                 let chainid = domainid.split(',')[0];
 
                 for(let j = 0, jl = queryData[0].segs.length; j < jl; ++j) {
                     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;
+                        ++BCnt;
                     }
-                    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;
+                        ++CCnt;
                     }
-                    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; 
+                        ++ECnt;                    
                     }
-                    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;
+                        ++FCnt;
                     }
 
                     //if(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand) break;
                     if(bBstrand && bCstrand && bEstrand && bFstrand) break;
                 }
-
-                if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
-                //if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+   
+                if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)
+                  || BCnt < 3 || CCnt < 3 || ECnt < 3 || FCnt < 3) {
+                // 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];
@@ -67702,9 +67781,13 @@ 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()
 
@@ -68051,6 +68134,8 @@ 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;
@@ -68073,6 +68158,8 @@ class Dssp {
             dataArray3 = dataArray3.concat(currDataArray);
         }
 
+        if(!me.bNode) me.icn3d.ParserUtilsCls.hideLoading();
+
         return dataArray3;
     }
  }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "icn3d",
-  "version": "3.29.10",
+  "version": "3.29.12",
   "main": "./icn3d.js",
   "exports": {
     ".": {