icn3d 3.31.7 → 3.31.9

package/icn3d.js

@@ -40933,6 +40933,7 @@ class AnnoIg {
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
 
+
         // remove Igs without BCEF strands one more time
         let igArray = ic.chain2igArray[chnid];    
 
@@ -41005,6 +41006,7 @@ class AnnoIg {
             }
         }
 
+
         // reset ic.chain2igArray
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
@@ -44422,7 +44424,8 @@ 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 + ', Exon ' + (exonIndex + 1) + '" title="Exon ' + (exonIndex + 1) + ': ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+        // 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 + ', Exon ' + (exonIndex + 1) + '" title="Exon ' + (exonIndex + 1) + ': ' + genomeRange + ' genomic interval" anno="sequence" chain="' + chainid + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+        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>';
     }
 
     getExonColor(start, end, pos) { let ic = this.icn3d; ic.icn3dui;
@@ -51629,7 +51632,7 @@ class ContactMap {
                 let color2 = rHex + gHex + bHex;
 
                 if(bLink) linkStr += ', ';
-                linkStr += '{"source": "' + idStr + postA + '", "target": "' + idStr2 + postB + '", "v": 11, "c": "' + color2 + '"}\n';
+                linkStr += '{"source": "' + idStr + postA + '", "target": "' + idStr2 + postB + '", "v": 11, "c": "' + color2 + '", "pae": ' + parseInt(distMatrix[i][j]) + '}\n';
                 bLink = true;
             }
         }
@@ -55248,10 +55251,12 @@ class BcifParser {
             let conf_type_idArray = struct_conf.getColumn("conf_type_id");
 
             let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
 
             let chain2Array = struct_conf.getColumn("end_auth_asym_id");
-            let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            // let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            let resi2Array = struct_conf.getColumn("end_auth_seq_id");
 
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
@@ -55296,10 +55301,12 @@ class BcifParser {
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
 
             let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
 
             let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id");
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
 
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
@@ -58804,9 +58811,13 @@ class ParserUtils {
 
         for(let i = 0, il = ic.realignResid[chainid_t].length; i < il && i < ic.realignResid[chainid_q].length; ++i) {
             let resid_t = ic.realignResid[chainid_t][i].resid;
+            if(!resid_t) continue;
+
             let pos_t = resid_t.lastIndexOf('_');
             let resi_t = parseInt(resid_t.substr(pos_t + 1));
             let resid_q = ic.realignResid[chainid_q][i].resid;
+            if(!resid_q) continue;
+
             let pos_q = resid_q.lastIndexOf('_');
             let resi_q = parseInt(resid_q.substr(pos_q + 1));
 
@@ -62819,10 +62830,12 @@ class LoadCIF {
             let conf_type_idArray = struct_conf.getColumn("conf_type_id");
         
             let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+            let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
         
             struct_conf.getColumn("end_auth_asym_id");
-            let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            // let resi2Array = struct_conf.getColumn("end_label_seq_id");
+            let resi2Array = struct_conf.getColumn("end_auth_seq_id");
         
             // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
             let confSize = struct_conf.rowCount;
@@ -62861,10 +62874,12 @@ class LoadCIF {
             let struct_sheet_range = block.getCategory("_struct_sheet_range");
         
             let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
         
             struct_sheet_range.getColumn("end_auth_asym_id");
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+            let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
         
             // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
             let sheetSize = struct_sheet_range.rowCount;
@@ -62872,7 +62887,7 @@ class LoadCIF {
                 let startChain = chain1Array.getString(i);
                 let startResi = parseInt(resi1Array.getString(i));
                 let endResi = parseInt(resi2Array.getString(i));
-            
+
                 for(let j = startResi; j <= endResi; ++j) {
                     let resid = structure + "_" + startChain + "_" + j;
                     sheetArray.push(resid);
@@ -70476,7 +70491,7 @@ class Dssp {
         ic.ref2igtype['LaminAC_1ifrA_human'] = 'Lamin';
         ic.ref2igtype['MHCIa_7phrH_human_C1'] = 'IgC1';
         ic.ref2igtype['MPT63_1lmiA_bacteria'] = 'IgE';
-        ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgE';
+        ic.ref2igtype['NaCaExchanger_2fwuA_dog_n2'] = 'IgFN3-like';
         ic.ref2igtype['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = 'IgE';
         ic.ref2igtype['ORF7a_1xakA_virus'] = 'ORF';
         ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
@@ -70903,12 +70918,13 @@ class Dssp {
                     // 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][0] == refpdbname) {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        continue;                     }
+                        continue;  
+                  }
                 // }
 
             }
@@ -71202,14 +71218,16 @@ class Dssp {
                         let resiDistToC = (bCpstrand) ? parseInt(CpAtom.resi) - parseInt(CAtom.resi) : parseInt(DAtom.resi) - parseInt(CAtom.resi);
                         let resiDistToE = (bCpstrand) ? parseInt(EAtom.resi) - parseInt(CpAtom.resi) : parseInt(EAtom.resi) - parseInt(DAtom.resi);
 
+                        let adjust = 1;
+
                         if(bCpstrand) {
-                            if(distToC > distToE || (distToC == distToE && resiDistToC > resiDistToE)) { // rename C' to D
+                            if(distToC > distToE + adjust || (distToC == distToE + adjust && resiDistToC > resiDistToE + adjust)) { // rename C' to D
                                 CpToDResi.push(CpAtom.resi);
                                 if(!me.bNode) console.log("Rename strand C' to D: distToC " + distToC + " distToE " + distToE + " resiDistToC " + resiDistToC + " resiDistToE " + resiDistToE);
                             }
                         }
                         else if(bDstrand) {
-                            if(distToC < distToE || (distToC == distToE && resiDistToC < resiDistToE)) { // rename D to C'
+                            if(distToC + adjust < distToE || (distToC + adjust == distToE && resiDistToC + adjust < resiDistToE)) { // rename D to C'
                                 DToCpResi.push(DAtom.resi);
                                 if(!me.bNode) console.log("Rename strand D to C': distToC " + distToC + " distToE " + distToE + " resiDistToC " + resiDistToC + " resiDistToE " + resiDistToE);
                             }
@@ -71229,7 +71247,8 @@ class Dssp {
 
                 seg.q_start;
                 let qStartInt = parseInt(seg.q_start);
-                if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
+                let postfix = '';
+                if(isNaN(seg.q_start)) postfix = seg.q_start.substr(seg.q_start.length - 1, 1);
 
                 // one item in "seq"
                 // q_start and q_end are numbers, but saved in string
@@ -71244,7 +71263,7 @@ class Dssp {
                     //let refnum = qStart;
                     let refnum = qStartInt;
 
-                    let refnumLabel = this.getLabelFromRefnum(refnum);
+                    let refnumLabel = this.getLabelFromRefnum(refnum, postfix);
                     currStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
 
                     let currStrandFinal = currStrand;
@@ -71266,7 +71285,7 @@ class Dssp {
                     }
 
                     if(currStrand != currStrandFinal) {
-                        refnumLabel = this.getLabelFromRefnum(refnum, currStrandFinal);
+                        refnumLabel = this.getLabelFromRefnum(refnum, postfix, currStrandFinal);
                     }
 
                     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
@@ -71302,7 +71321,7 @@ class Dssp {
         }
     }
 
-    getStrandFromRefnum(oriRefnum, prevStrand) { let ic = this.icn3d; ic.icn3dui;
+    getStrandFromRefnum(oriRefnum, finalStrand) { let ic = this.icn3d; ic.icn3dui;
         let refnum = parseInt(oriRefnum);
 
         //N-terminus = 0999-0001
@@ -71381,16 +71400,25 @@ class Dssp {
         else if(refnum > 9900) strand = undefined;
         else strand = " ";
 
-        if(prevStrand) strand = prevStrand;
+        if(finalStrand) strand = finalStrand;
 
         return strand
     }
 
-    getLabelFromRefnum(oriRefnum, prevStrand) { let ic = this.icn3d; ic.icn3dui;
-        let strand = this.getStrandFromRefnum(oriRefnum, prevStrand);
+    getLabelFromRefnum(oriRefnum, postfix, finalStrand) { let ic = this.icn3d; ic.icn3dui;
+        let strand = this.getStrandFromRefnum(oriRefnum, finalStrand);
+
+        // rename C' to D or D to C'
+        let refnum = oriRefnum.toString();
+        if(finalStrand == "C'" && refnum.substr(0, 1) == '6') { // previous D
+            refnum = '4' + refnum.substr(1);
+        }
+        else if(finalStrand == "D" && refnum.substr(0, 1) == '4') { // previous C'
+            refnum = '6' + refnum.substr(1);
+        }
 
         if(strand) {
-            return strand + oriRefnum;
+            return strand + refnum + postfix;
         }
         else {
             return undefined;
@@ -80309,7 +80337,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.1';
+    this.REVISION = '3.31.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;