icn3d 3.29.10 → 3.29.11

package/icn3d.js

@@ -11913,12 +11913,17 @@ 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 + "'>";
@@ -11972,10 +11977,10 @@ 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;
     }
 }
@@ -36765,7 +36770,8 @@ 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;
@@ -38225,11 +38231,11 @@ 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 {
@@ -38256,6 +38262,7 @@ 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];
@@ -39657,12 +39664,16 @@ 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];
@@ -39670,15 +39681,20 @@ 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;
 			}
 		}
 
@@ -39686,7 +39702,8 @@ 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;
@@ -40355,6 +40372,8 @@ 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 ) {
@@ -40365,7 +40384,7 @@ class Domain3d {
 				sheetNeighbor[ss2][ss1] = 1;
 			}
 		}
-
+	
 		//https://www.geeksforgeeks.org/number-groups-formed-graph-friends/
 		let existing_groups = 0;
 		let sheet2sheetnum = {};
@@ -40388,12 +40407,13 @@ 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 = {};
@@ -40406,6 +40426,8 @@ class Domain3d {
 					sheetsItem.sheet_num = 0;
 					sheetsItem.adj_strand2 = 0; 
 					sheetsItem.sse = i + 1; 
+
+					invalidSheethash[sheetsItem.sse] = 1;
 				}
 
 				sheets.push(sheetsItem);
@@ -40437,7 +40459,7 @@ 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
@@ -40461,7 +40483,8 @@ 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;
 				}
 			}
 		}
@@ -40517,11 +40540,25 @@ 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;