icn3d 3.29.15 → 3.29.17

package/icn3d.js

@@ -36881,16 +36881,17 @@ 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) {
+                        // 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);
-                        }
-                        else {
-                            emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
-                        }
+                        // }
+                        // else {
+                        //     emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / 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 + '" ' + type + '="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + setname + '" id="' + chnid + '_domain_' + index + '_' + r + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + domain + ' </div>';
@@ -37919,19 +37920,24 @@ 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;
@@ -38331,7 +38337,9 @@ class AnnoDomain {
 
             if(me.cfg.blast_rep_id != chnid) { // regular
                 for(let i = 0, il = fromArray.length; i < il; ++i) {
-                    let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
+                    // let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
+                    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 icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
                 }
@@ -39940,7 +39948,7 @@ class Domain3d {
 		// get a list of Calpha-Calpha contacts
 		///list< pair< pair< int, let >, let > >
 		let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut, resiArray);
-		
+	
 		//
 		// Produce a "map" of the SSEs, i.e. vec_sse[i] = 0 means residue i + 1
 		// is in a loop, and vec_sse[i] = k means residue i + 1 belongs to SSE
@@ -40001,7 +40009,7 @@ class Domain3d {
 			vec_cts1.push(i + 1);
 			vec_cts2.push(i + 1);
 		}
-		
+
 		// create contact counts from the contacts/interactions
 		//map< pair< int, let >, let > ctable = this.c2b_ContactTable(vec_cts1, vec_cts2);
 		let ctable = this.c2b_ContactTable(vec_cts1, vec_cts2);
@@ -40025,7 +40033,7 @@ class Domain3d {
 				sheetNeighbor[ss2][ss1] = 1;
 			}
 		}
-	
+
 		//https://www.geeksforgeeks.org/number-groups-formed-graph-friends/
 		let existing_groups = 0;
 		let sheet2sheetnum = {};
@@ -40153,7 +40161,7 @@ class Domain3d {
 			this.parts[2*i] = this.parts[2*i + 1] = 0;
 			ratios[i] = 0.0;
 		}
-		
+
 		n_saved = this.new_split_chain(nsse, sratio, minSize, minSSE, maxCsz, avgCts, cDelta, ncFact, this.parts, n_saved, ratios);
 
 		// save domain data
@@ -40201,6 +40209,36 @@ class Domain3d {
 		
 		list_parts = list_partsTmp;
 
+		// if there is only one domain, add all
+		if(list_parts.length == 0) {
+			let groupnum2cnt = {}, groupnum2sseList = {}, chosenGroupnum = 0;
+			for(let i = 0, il = this.group_num.length; i < il; ++i) {
+				let groupnum = this.group_num[i];
+				let sse = i + 1;
+				if(groupnum && groupnum != i + 1) {
+					if(!groupnum2sseList[groupnum]) groupnum2sseList[groupnum] = [];
+					// collect all sse for this groupnum
+					groupnum2sseList[groupnum].push(sse);
+
+					if(!groupnum2cnt[groupnum]) {
+						groupnum2cnt[groupnum] = 1;
+					}
+					else {
+						++groupnum2cnt[groupnum];
+						if(groupnum2cnt[groupnum] >= 3) { // minimum 3 sse
+							chosenGroupnum = groupnum;
+						}
+					}
+				}
+			}
+
+			if(chosenGroupnum != 0) { // found a domain
+				let sseArray = [chosenGroupnum].concat(groupnum2sseList[chosenGroupnum]);
+
+				list_parts.push(sseArray);
+			}
+		}
+
 		//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;
@@ -40338,7 +40376,7 @@ class Domain3d {
 					ic.tddomains[domainName][resid] = 1;
 				}
 			}
-		}			
+		}
 
 		return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
 	} // end c2b_NewSplitChain
@@ -65992,9 +66030,9 @@ 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);
@@ -66015,7 +66053,7 @@ class Dssp {
         let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms, undefined);
         let subdomains = result.subdomains;
         let pos2resi = result.pos2resi;
-
+/*
         if(subdomains.length <= 1) {
             let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
             if(residueArray.length < minResidues) return domainAtomsArray;
@@ -66032,25 +66070,27 @@ class Dssp {
 
             domainAtomsArray.push(currAtoms);
         }
-        else {
+        else 
+*/
+
+        if(subdomains.length >= 1) {
             for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                 let domainAtoms = {};
                 let segArray = subdomains[k];
 
                 let resCnt = 0;
                 for(let m = 0, ml = segArray.length; m < ml; m += 2) {
-                    let startResi = segArray[m];
-                    let endResi = segArray[m+1];
-                    for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
+                    let startResi = parseInt(segArray[m]);
+                    let endResi = parseInt(segArray[m+1]);
+
+                    for(let n = startResi; n <= endResi; ++n) {
                         let resid = chainid + '_' + pos2resi[n];
                         ++resCnt;
                         domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
 
                         // clear previous refnum assignment if any
-                        // if(bRerunDomain) {
-                            delete ic.resid2refnum[resid];
-                            delete ic.residIgLoop[resid];
-                        // }
+                        delete ic.resid2refnum[resid];
+                        delete ic.residIgLoop[resid];
                     }
                 }
 
@@ -66247,11 +66287,12 @@ class Dssp {
                 domainid2refpdbnamelist[domainid][refpdbname] = score;
             }
         }
-/* !!!
-        // 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) {
-                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);
@@ -66259,12 +66300,11 @@ class Dssp {
                         return refpdbname2score[b] - refpdbname2score[a]
                     });
                     // top 3 templates
-                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,3);
+                    ic.domainid2refpdbname[domainid] = refpdbnameList.slice(0,4);
                 }
-                console.log("###bb ic.domainid2refpdbname[domainid] " + ic.domainid2refpdbname[domainid])
             }
         }
-*/
+
         return domainid2segs; // only used in round 2
     }
 
@@ -67131,6 +67171,7 @@ 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;
@@ -67164,6 +67205,7 @@ 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;
@@ -67171,15 +67213,13 @@ class Dssp {
                 }
             }
         }
-/*
+
         // 2b. remove strands with less than 3 residues except G strand
         for(let il = strandArray.length, i = il - 1; i >= 0; --i) {
             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 removed since they are too short...");
-
-                    console.log("### strandTmp " + strandTmp + " strandArray[i].endRefnum - strandArray[i].startRefnum + 1 " + (strandArray[i].endRefnum - strandArray[i].startRefnum + 1))
                     return false;
                 }
 
@@ -67190,7 +67230,7 @@ class Dssp {
                 strandArray.splice(i, 1);
             }
         }
-*/
+
         // 3. assign refnumLabel for each resid
         strandCnt = 0;
         let loopCnt = 0;