icn3d 3.19.2 → 3.19.4

package/icn3d.js

@@ -19929,7 +19929,7 @@ class Symd {
           url: url,
           type: 'POST',
           data : dataObj,
-          dataType: "jsonp",
+          dataType: "json",
           cache: true,
           tryCount : 0,
           retryLimit : 0, //1
@@ -22783,7 +22783,6 @@ class Dssp {
 
       let url = (window && window.location && window.location.hostname.indexOf('ncbi.nlm.nih.gov') != -1) ? "/Structure/mmcifparser/mmcifparser.cgi" :
         me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-      //let url = "https://www.ncbi.nlm.nih.gov/Structure/mmcifparser/mmcifparser.cgi";
         
       for(let i = 0, il = struArray.length; i < il; ++i) {
            let pdbStr = '';
@@ -22802,7 +22801,8 @@ class Dssp {
               url: url,
               type: 'POST',
               data: {'dssp':'t', 'calphaonly': calphaonly, 'pdbfile': pdbStr},
-              dataType: 'jsonp',
+              //dataType: 'jsonp',
+              dataType: 'json',
               cache: true
            });
 
@@ -25061,7 +25061,7 @@ class RealignParser {
                                 url: urlalign,
                                 type: 'POST',
                                 data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
-                                dataType: 'jsonp',
+                                dataType: 'json',
                                 cache: true
                             });
                         }
@@ -25076,7 +25076,7 @@ class RealignParser {
                                 url: urltmalign,
                                 type: 'POST',
                                 data: {'pdb_query': pdb_query, 'pdb_target': pdb_target},
-                                dataType: 'jsonp',
+                                dataType: 'json',
                                 cache: true
                             });                            
                         }
@@ -25285,7 +25285,7 @@ class RealignParser {
                         url: url,
                         type: 'POST',
                         data : {'targets': seq1, 'queries': seq2},
-                        dataType: 'jsonp',
+                        dataType: 'json',
                         cache: true
                     });
 
@@ -25357,7 +25357,7 @@ class RealignParser {
                         url: url,
                         type: 'POST',
                         data : {'targets': seq1, 'queries': seq2},
-                        dataType: 'jsonp',
+                        dataType: 'json',
                         cache: true
                     });
 
@@ -25562,7 +25562,7 @@ class ChainalignParser {
                             url: urlalign,
                             type: 'POST',
                             data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
-                            dataType: 'jsonp',
+                            dataType: 'json',
                             cache: true
                         });
                     }
@@ -25574,7 +25574,7 @@ class ChainalignParser {
                             url: urltmalign,
                             type: 'POST',
                             data: {'pdb_query': pdb_query, 'pdb_target': pdb_target},
-                            dataType: 'jsonp',
+                            dataType: 'json',
                             cache: true
                         });                        
                     }
@@ -29029,6 +29029,7 @@ class LoadScript {
         if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
 
         if(me.deferred !== undefined) me.deferred.resolve(); if(ic.deferred2 !== undefined) ic.deferred2.resolve();
+        if(me.deferredMmdbaf !== undefined) me.deferredMmdbaf.resolve();
     }
 
     replayFirstStep(currentNumber) { let  ic = this.icn3d, me = ic.icn3dui;
@@ -29738,7 +29739,7 @@ class Domain3d {
 	//list< pair< pair< int, let >, let > >
 	//c2b_AlphaContacts(let n0, let* x0, let* y0, let* z0,
 	//	const let incr = 4, const let dcut = 8.0) { let ic = this.icn3d, me = ic.icn3dui;
-	c2b_AlphaContacts(n0, x0, y0, z0, dcut) { let ic = this.icn3d; ic.icn3dui;
+	c2b_AlphaContacts(n0, x0, y0, z0, dcut, resiArray) { let ic = this.icn3d; ic.icn3dui;
 		//if(!incr) incr = 4;
 		if(!dcut) dcut = this.dcut;
 
@@ -29752,7 +29753,8 @@ class Domain3d {
 
 			//ResRec rr0;
 			let rr0 = {};
-			rr0.rnum = i + 1;
+			//rr0.rnum = i + 1;
+			rr0.rnum = resiArray[i];
 			rr0.x = x0[i];
 			rr0.y = y0[i];
 			rr0.z = z0[i];
@@ -29780,7 +29782,7 @@ class Domain3d {
 			for (j = i + 1; j < len; ++j) {	
 				//ResRec rr2 = *rrit2;
 				let rr2 = list_rr[j];
-				if ((rr1.rnum - rr2.rnum <= 3) && (rr2.rnum - rr1.rnum <= 3)) continue;
+				if ((parseInt(rr1.rnum) - parseInt(rr2.rnum) <= 3) && (parseInt(rr2.rnum) - parseInt(rr1.rnum) <= 3)) continue;
 				let x2 = rr2.x;
 				let y2 = rr2.y;
 				let z2 = rr2.z;
@@ -29798,7 +29800,7 @@ class Domain3d {
 				//pair< int, let > rpair;
 				let lpair = {}, rpair = {};
 
-				if (rr1.rnum < rr2.rnum) {
+				if (parseInt(rr1.rnum) < parseInt(rr2.rnum)) {
 					rpair.first = rr1.rnum;
 					rpair.second = rr2.rnum;
 				}
@@ -29888,7 +29890,7 @@ class Domain3d {
 	// x0, y0, z0: array of x,y,z coordinates of C-alpha atoms
 	//c2b_NewSplitChain(chnid, dcut) { let ic = this.icn3d, me = ic.icn3dui;
 	c2b_NewSplitChain(atoms, dcut) { let ic = this.icn3d; ic.icn3dui;
-		let x0 = [], y0 = [], z0 = [];
+		let x0 = [], y0 = [], z0 = [], resiArray = [];
 
 		//substruct: array of secondary structures, each of which has the keys: From (1-based), To (1-based), Sheet (0 or 1), also add these paras: x1, y1, z1, x2, y2, z2
 		let substruct = [];
@@ -29903,11 +29905,11 @@ class Domain3d {
 		residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
 		let substructItem = {};
-		let resiOffset = 0;
 		for(let i = 0; i < residueArray.length; ++i) {
 			let resid = residueArray[i];
 
             let resi = resid.substr(resid.lastIndexOf('_') + 1);
+/*			
 			if(i == 0) {
 				resiOffset = resi - 1;
 
@@ -29917,10 +29919,13 @@ class Domain3d {
 					z0.push(undefined);					
 				}
 			}
+*/
 
 			//let resid = chnid + "_" + resi;
 			let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
 
+			if(!atom) continue;    
+/*
 			if(atom) {
 				x0.push(atom.coord.x);
 				y0.push(atom.coord.y);
@@ -29931,8 +29936,13 @@ class Domain3d {
 				y0.push(undefined);
 				z0.push(undefined);
 			}
-
-			if(!atom) continue;           
+*/
+			//if(!atom) continue;   
+			
+			x0.push(atom.coord.x);
+			y0.push(atom.coord.y);
+			z0.push(atom.coord.z);
+			resiArray.push(resi);
 
 			if(atom.ssend) {
 				substructItem.To = parseInt(resi);
@@ -29966,12 +29976,13 @@ class Domain3d {
 			return {subdomains: subdomains, substruct: substruct};
 		}
 
-		let seqLen = residueArray.length + resiOffset;
+		let seqLen = residueArray.length; // + resiOffset;
+		let lastResi = resiArray[seqLen - 1];
 
 		// get a list of Calpha-Calpha contacts
 		///list< pair< pair< int, let >, let > >
-		let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut);
-
+		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
@@ -30216,13 +30227,17 @@ class Domain3d {
 			let prts = list_parts[index];
 			//vector<int> resflags;
 			//resflags.clear();
-			let resflags = [];
+
+			//let resflags = [];
+			let resflags = {};
 
 			// a domain must have at least 3 SSEs...
 			if (prts.length <= 2) continue;
 
-			for (let i = 0; i < seqLen; i++)
-				resflags.push(0);
+			for (let i = 0; i < seqLen; i++) {
+				//resflags.push(0);
+				resflags[resiArray[i]] = 0;
+			}
 
 			for (let i = 0; i < prts.length; i++) {
 				let k = prts[i] - 1;
@@ -30236,8 +30251,10 @@ class Domain3d {
 				let From = sserec.From;
 				let To = sserec.To;
 
-				for (let j = From; j <= To; j++)
-					resflags[j - 1] = 1;
+				for (let j = From; j <= To; j++) {
+					//resflags[j - 1] = 1;
+					resflags[j] = 1;
+				}
 
 				if ((k == 0) && (From > 1)) {
 					// residues with negative residue numbers will not be included
@@ -30245,17 +30262,21 @@ class Domain3d {
 						//resflags[j - 1] = 1;
 						// include at most 10 residues
 						if(From - j <= 10) {
-							resflags[j - 1] = 1;
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
 						}
 					}
 				}
 
-				if ((k == substruct.length - 1) && (To < seqLen)) {
-					for (let j = To + 1; j <= seqLen; j++) {
+				//if ((k == substruct.length - 1) && (To < seqLen)) {
+				if ((k == substruct.length - 1) && (To < parseInt(lastResi))) {
+					//for (let j = To + 1; j <= seqLen; j++) {
+					for (let j = To + 1; j <= parseInt(lastResi); j++) {
 						//resflags[j - 1] = 1;
 						// include at most 10 residues
 						if(j - To <= 10) {
-							resflags[j - 1] = 1;
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
 						}
 					}
 				}
@@ -30269,8 +30290,10 @@ class Domain3d {
 					let ll = parseInt(0.5 * (From - To1 - 1));
 
 					if (ll > 0) {
-						for (let j = From - ll; j <= From - 1; j++)
-							resflags[j - 1] = 1;
+						for (let j = From - ll; j <= From - 1; j++) {
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
+						}
 					}
 				}
 
@@ -30286,8 +30309,10 @@ class Domain3d {
 					let ll = parseInt(0.5 * (From1 - To - 1) + 0.5);
 
 					if (ll > 0) {
-						for (let j = To + 1; j <= To + ll; j++)
-							resflags[j - 1] = 1;
+						for (let j = To + 1; j <= To + ll; j++) {
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
+						}
 					}
 				}
 			}
@@ -30300,11 +30325,13 @@ class Domain3d {
 			let segments = [];
 
 			for (let i = 0; i < seqLen; i++) {
-				let rf = resflags[i];
+				//let rf = resflags[i];
+				let rf = resflags[resiArray[i]];
 
 				if (!inseg && (rf == 1)) {
 					// new segment starts here
-					startseg = i + 1;
+					//startseg = i + 1;
+					startseg = resiArray[i];
 					inseg = true;
 					continue;
 				}
@@ -30312,7 +30339,8 @@ class Domain3d {
 				if (inseg && (rf == 0)) {
 					// segment ends
 					segments.push(startseg);
-					segments.push(i);
+					//segments.push(i);
+					segments.push(resiArray[i]);
 					inseg = false;
 				}
 			}
@@ -30320,7 +30348,8 @@ class Domain3d {
 			// check for the last segment
 			if (inseg) {
 				segments.push(startseg);
-				segments.push(seqLen);
+				//segments.push(seqLen);
+				segments.push(lastResi);
 			}
 
 			subdomains.push(segments);
@@ -31127,7 +31156,7 @@ class AddTrack {
               url: url,
               type: 'POST',
               data : {'targets': chainid, 'queries': gi},
-              dataType: 'jsonp',
+              dataType: 'json',
               //dataType: 'json',
               tryCount : 0,
               retryLimit : 0, //1
@@ -31176,7 +31205,7 @@ class AddTrack {
               url: url,
               type: 'POST',
               data : {'targets': targets, 'queries': fasta},
-              dataType: 'jsonp',
+              dataType: 'json',
               //dataType: 'json',
               tryCount : 0,
               retryLimit : 0, //1
@@ -37710,7 +37739,7 @@ class ParserUtils {
           ic.selectionCls.saveSelectionIfSelected();
           ic.drawCls.draw();
       }
-
+      
 //      if(ic.bInitial && me.cfg.command !== undefined && me.cfg.command !== '') {
       if(!ic.bCommandLoad && ic.bInitial && me.cfg.command !== undefined && me.cfg.command !== '') {
           if(Object.keys(ic.structures).length == 1) {
@@ -37718,11 +37747,13 @@ class ParserUtils {
               me.cfg.command = me.cfg.command.replace(new RegExp('!','g'), id + '_');
           }
           // final step resolved ic.deferred
-          if(me.cfg.mmdbafid === undefined && me.cfg.afid === undefined) ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
+          //if(me.cfg.mmdbafid === undefined && me.cfg.afid === undefined) ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
+          ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
           //ic.loadScriptCls.loadScript(me.cfg.command);
       }
       else {
           if(me.deferred !== undefined) me.deferred.resolve(); if(ic.deferred2 !== undefined) ic.deferred2.resolve();
+          if(me.deferredMmdbaf !== undefined) me.deferredMmdbaf.resolve();
       }
       //if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined || ic.bRealign ||( ic.bInputfile && ic.InputfileType == 'pdb' && Object.keys(ic.structures).length >= 2) ) {
       if(Object.keys(ic.structures).length >= 2) {
@@ -37961,7 +37992,7 @@ class MmcifParser {
            url: url,
            type: 'POST',
            data : {'mmciffile': data},
-           dataType: 'jsonp',
+           dataType: 'json',
            cache: true,
            tryCount : 0,
            retryLimit : 0, //1
@@ -38175,7 +38206,7 @@ class MmcifParser {
                   url: url,
                   type: 'POST',
                   data : {'mmcifheader': data},
-                  dataType: 'jsonp',
+                  dataType: 'json',
                   cache: true,
                   tryCount : 0,
                   retryLimit : 0, //1
@@ -39001,7 +39032,7 @@ class ShowAnno {
                   url: url,
                   type: 'POST',
                   data : dataObj,
-                  dataType: 'jsonp',
+                  dataType: 'json',
                   //dataType: 'json',
                   tryCount : 0,
                   retryLimit : 0, //1
@@ -62429,7 +62460,7 @@ class Events {
                   url: url,
                   type: 'POST',
                   data : {'mmciffile': dataStr},
-                  dataType: 'jsonp',
+                  dataType: 'json',
                   cache: true,
                   tryCount : 0,
                   retryLimit : 0, //1
@@ -67146,7 +67177,7 @@ class Vastplus {
             url: urltmalign,
             type: 'POST',
             data: {'pdb_query': pdb_query, 'pdb_target': pdb_target},
-            dataType: 'jsonp',
+            dataType: 'json',
             cache: true
         });
 
@@ -67857,7 +67888,8 @@ class Vastplus {
 
                 let pdbAjaxArray = [];
                 for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
-                    let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
+                    //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
+                    let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
 
                     let pdbAjax = $.ajax({
                         url: urlpdb,
@@ -67906,7 +67938,7 @@ class Vastplus {
                 // align each 3D domain with reference structure
                 let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
                 let subdomains = result.subdomains;
-
+                
                 let domainAtomsArray = [];
                 if(subdomains.length <= 1) {
                     domainAtomsArray.push(ic.chains[chainid]);
@@ -67920,6 +67952,7 @@ class Vastplus {
                     for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                         let domainAtoms = {};
                         let segArray = subdomains[k];
+
                         for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                             let startResi = segArray[m];
                             let endResi = segArray[m+1];
@@ -67933,10 +67966,9 @@ class Vastplus {
                         domainAtomsArray.push(domainAtoms);
                     }
                 }
-
+                
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
-
                     let domainid = chainid + '-' + k;
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
                         let struct2 = "stru" + index;
@@ -67949,7 +67981,7 @@ class Vastplus {
                             url: urltmalign,
                             type: 'POST',
                             data: {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]},
-                            dataType: 'jsonp',
+                            dataType: 'json',
                             cache: true
                         });
 
@@ -68028,14 +68060,14 @@ console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' +
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
             }
         }
-
+        
         // combine domainid into chainid
         for(let domainid in domainid2segs) {
             let chainid = domainid.split('-')[0];
             if(!chainid2segs[chainid]) chainid2segs[chainid] = [];
             chainid2segs[chainid] = chainid2segs[chainid].concat(domainid2segs[domainid]);
         }
-
+        
         // assign ic.resid2refnum, ic.refnum2residArray, ic.chainsMapping
         if(!ic.resid2refnum) ic.resid2refnum = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};