icn3d 3.21.0 → 3.21.2

package/icn3d.js

@@ -15321,7 +15321,7 @@ class Html {
 
     //this.baseUrl = "https://structure.ncbi.nlm.nih.gov/";
     this.baseUrl = (window && window.location && window.location.hostname == 'structure.ncbi.nlm.nih.gov') 
-        ? "https://structure.ncbi.nlm.nih.gov/Structure/" : "https://test.ncbi.nlm.nih.gov/Structure/";
+        ? "https://structure.ncbi.nlm.nih.gov/Structure/" : "https://www.ncbi.nlm.nih.gov/Structure/";
     this.divStr = "<div id='" + this.icn3dui.pre;
     this.divNowrapStr = "<div style='white-space:nowrap'>";
     this.spanNowrapStr = "<span style='white-space:nowrap'>";
@@ -34138,7 +34138,7 @@ class AnnoCddSite {
                 for(let s = 0, sl = segArray.length; s < sl; ++s) {
                     let domainFrom = Math.round(segArray[s].from);
                     let domainTo = Math.round(segArray[s].to);
-                    
+
                     // if(ic.bNCBI) {
                     //     fromArray.push(domainFrom);
                     //     toArray.push(domainTo);
@@ -34148,8 +34148,11 @@ class AnnoCddSite {
                     //     toArray.push(thisClass.getAdjustedResi(domainTo, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi) - 1);
                     // }
 
-                    fromArray.push(ic.ParserUtilsCls.getResi(chnid, domainFrom));
-                    toArray.push(ic.ParserUtilsCls.getResi(chnid, domainTo));
+                    // fromArray.push(ic.ParserUtilsCls.getResi(chnid, domainFrom));
+                    // toArray.push(ic.ParserUtilsCls.getResi(chnid, domainTo));
+
+                    fromArray.push(domainFrom);
+                    toArray.push(domainTo);
 
                     for(let i = domainFrom; i <= domainTo; ++i) {
                         resiHash[i] = 1;
@@ -38859,7 +38862,8 @@ class ShowAnno {
             if(me.cfg.blast_rep_id === undefined) {
                if(ic.bFullUi) {
                     if(me.cfg.mmtfid !== undefined) { // mmtf data do NOT have the missing residues
-                        let id = chainArray[0].substr(0, chainArray[0].indexOf('_'));
+                        //let id = chainArray[0].substr(0, chainArray[0].indexOf('_'));
+                        let id = Object.keys(ic.structures)[0];
 
                         await ic.mmcifParserCls.downloadMmcifSymmetry(id, 'mmtfid');
                     }
@@ -40408,7 +40412,7 @@ class HlSeq {
                                 to = parseInt(toArray[i]);
 
                                 for(let j = from; j <= to; ++j) {
-                                    // if(ic.bNCBI && ($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined || $(that).attr('3ddomain') !== undefined) ) {
+                                    /*
                                     if( ($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined || $(that).attr('3ddomain') !== undefined) ) {
                                         let residNCBI = chainid + '_' + (j+1).toString();
                                         // AlphaFold domains calculated on-the-fly have no conversion
@@ -40424,6 +40428,12 @@ class HlSeq {
 
                                         residueid = ic.ncbi2resid[residNCBI];
                                     }
+                                    */
+                                    
+                                    if(($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined) || $(that).attr('3ddomain') !== undefined) {
+                                        let residNCBI = chainid + '_' + (j+1).toString();
+                                        residueid = ic.ncbi2resid[residNCBI];
+                                    }
                                     else {
                                         residueid = chainid + '_' + (j+1).toString();
                                     }
@@ -40861,7 +40871,7 @@ class HlUpdate {
        // update annotation windows and alignment sequences
        let chainHash = {};
        for(let i = 0, il = residueArray.length; i < il; ++i) {
-           let pickedResidue = residueArray[i];
+           let pickedResidue = residueArray[i].trim();
            //[id$= is expensive to search id ending with
            //var resElem = $("[id$=" + ic.pre + pickedResidue + "]");
            let resElem = $("[id=giseq_" + ic.pre + pickedResidue + "]");
@@ -45814,6 +45824,16 @@ class MmdbParser {
         }
     }
 
+        //Ajax call was used to get the atom data from the NCBI "gi". This function was deferred so that
+    //it can be chained together with other deferred functions for sequential execution. Note that
+    //only one structure corresponding to the gi will be shown. If there is no structures available
+    //for the gi, a warning message will be shown.
+    async downloadGi(gi) { let ic = this.icn3d; ic.icn3dui;
+        ic.bCid = undefined;
+        let bGi = true;
+        await this.downloadMmdb(gi, bGi);
+    }
+
     //Ajax call was used to get the atom data from "sequence_id_comma_structure_id", comma-separated
     //NCBI protein accessions of a protein sequence and a chain of a 3D structure (e.g., 23491729,1TUP_A).
     //This function was deferred so that it can be chained together with other deferred functions for
@@ -46974,7 +46994,7 @@ class PdbParser {
         ic.InputfileType = type;
 
         if(type === 'pdb') {
-            await thisClass.loadPdbData(data);
+            await this.loadPdbData(data);
             await ic.loadScriptCls.loadScript(command, undefined, true);
         }
         else if(type === 'mmcif') {
@@ -52125,12 +52145,11 @@ class LoadPDB {
         //let chainMissingResidueArray = {}
 
         let id = (pdbid) ? pdbid : 'stru';
+        let structure = id;
 
         let prevMissingChain = '';
         let CSerial, prevCSerial, OSerial, prevOSerial;
-
-        let structure = "stru";
-
+        
         let bHeader = false;
 
         for (let i in lines) {
@@ -52181,7 +52200,7 @@ class LoadPDB {
 
                   if(j === startResi) helixStart.push(resid);
                   if(j === endResi) helixEnd.push(resid);
-                }               
+                }    
             } else if (record === 'SHEET ') {
                 //ic.bSecondaryStructure = true;
                 if(bOpm === undefined || !bOpm) ic.bSecondaryStructure = true;
@@ -52243,10 +52262,7 @@ class LoadPDB {
                     //let chain = line.substr(19, 1);
                     let chain = line.substr(18, 2).trim();
                     //let resi = parseInt(line.substr(21, 5));
-                    let resi = line.substr(21, 5);
-
-                    //var structure = parseInt(line.substr(13, 1));
-                    //if(line.substr(13, 1) == ' ') structure = 1;
+                    let resi = line.substr(21, 5).trim();
 
                     //var chainNum = structure + '_' + chain;
                     let chainNum = id + '_' + chain;
@@ -52718,73 +52734,81 @@ class LoadPDB {
         for(let chainNum in ic.chainsSeq) {
             if(chainMissingResidueArray[chainNum] === undefined) continue;
 
-            //let A = ic.chainsSeq[chainNum];
-            //let B = chainMissingResidueArray[chainNum];
-
-            let A = chainMissingResidueArray[chainNum];
-            let B = ic.chainsSeq[chainNum];
-
-            let m = A.length;
-            let n = B.length;
-
-            let C = new Array(m + n);
-            //var C2 = new Array(m + n);
-            //var C3 = new Array(m + n);
-
-            // http://www.algolist.net/Algorithms/Merge/Sorted_arrays
-            // m - size of A
-            // n - size of B
-            // size of C array must be equal or greater than m + n
-              let i, j, k;
-              i = 0;
-              j = 0;
-              k = 0;
-              while (i < m && j < n) {
-                    if (parseInt(A[i].resi) <= parseInt(B[j].resi)) {
-                          C[k] = A[i];
-                          //C2[k] = A2[i];
-                          //C3[k] = A3[i];
-                          i++;
-                    } else {
-                          C[k] = B[j];
-                          //if(B[j].resi % 10 === 0) {
-                          //    C2[k] = B[j].resi.toString();
-                          //}
-                          //else {
-                          //    C2[k] = '';
-                          //}
-                          //C3[k] = '-';
-                          j++;
+            ic.chainsSeq[chainNum] = this.mergeTwoSequences(chainMissingResidueArray[chainNum], ic.chainsSeq[chainNum]);     
+        }
+
+        this.setResidMapping();
+    }
+
+    mergeTwoSequences(A, B) {
+        let m = A.length; // missing residues
+        let n = B.length; // residues with coord
+
+        // inserted domain such as PRK150 in the R chain of PDB 6WW2
+        let lastResiA = parseInt(A[m - 1].resi);
+        let lastResiB = parseInt(B[n - 1].resi);
+        let lastResi = (lastResiA >= lastResiB) ? lastResiA : lastResiB;
+
+        let C = new Array(m + n);
+        // http://www.algolist.net/Algorithms/Merge/Sorted_arrays
+        // m - size of A
+        // n - size of B
+        // size of C array must be equal or greater than m + n
+          let i = 0, j = 0, k = 0;
+          let bInsertion = false;
+
+          while (i < m && j < n) {
+                let aResi = parseInt(A[i].resi), bResi = parseInt(B[j].resi);
+                if(aResi > lastResi && bResi > lastResi) bInsertion = true;
+
+                if(aResi <= lastResi &&  bResi > lastResi) {
+                    if (aResi > bResi || bInsertion) {
+                        C[k] = B[j];
+                        j++;
                     }
-                    k++;
-              }
-              if (i < m) {
-                    for (let p = i; p < m; p++) {
-                          C[k] = A[p];
-                          //C2[k] = A2[p];
-                          //C3[k] = A3[p];
-                          k++;
+                    else  {
+                        C[k] = A[i];
+                        i++;
                     }
-              } else {
-                    for (let p = j; p < n; p++) {
-                          C[k] = B[p];
-                          //if(B[p].resi % 10 === 0) {
-                          //    C2[k] = B[p].resi.toString();
-                          //}
-                          //else {
-                          //    C2[k] = '';
-                          //}
-                          //C3[k] = '-';
-                          k++;
+                }
+                else if(aResi > lastResi &&  bResi <= lastResi) {
+                    if (aResi <= bResi || bInsertion) {
+                        C[k] = A[i];
+                        i++;
                     }
-              }
+                    else  {
+                        C[k] = B[j];
+                        j++;
+                    }
+                }
+                else {
+                    if (aResi <= bResi) {
+                        C[k] = A[i];
+                        i++;
+                    }
+                    else {
+                        C[k] = B[j];
+                        j++;
+                    }
+                }
 
-            ic.chainsSeq[chainNum] = C;
-            //ic.chainsAn[chainNum][0] = C2;
-            //ic.chainsAn[chainNum][1] = C3;
-        }
+                k++;
+          }
 
-        this.setResidMapping();
+          if (i < m) {
+                for (let p = i; p < m; p++) {
+                      C[k] = A[p];
+                      k++;
+                }
+          } 
+          else {
+                for (let p = j; p < n; p++) {
+                      C[k] = B[p];
+                      k++;
+                }
+          }
+
+          return C;
     }
 
     setResidMapping() { let ic = this.icn3d; ic.icn3dui;
@@ -56582,6 +56606,10 @@ class LoadScript {
 
             await ic.chainalignParserCls.downloadMmdbAf(id);
         }
+        else if(command.indexOf('load gi') !== -1) {
+            me.cfg.gi = id;
+            await ic.mmdbParserCls.downloadGi(id);
+        }
         else if(command.indexOf('load refseq') !== -1) {
             me.cfg.refseqid = id;
             await ic.mmdbParserCls.downloadRefseq(id);
@@ -67388,7 +67416,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.21.0';
+    this.REVISION = '3.21.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -67665,6 +67693,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
        await ic.mmdbParserCls.downloadMmdb(me.cfg.mmdbid);
     }
+    else if(me.cfg.gi !== undefined) {
+        // ic.bNCBI = true;
+        ic.loadCmd = 'load gi ' + me.cfg.gi;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        await ic.mmdbParserCls.downloadGi(me.cfg.gi);
+    }
     else if(me.cfg.refseqid !== undefined) {
         ic.inputid = me.cfg.refseqid;