icn3d 3.37.1 → 3.38.0

package/icn3d.js

@@ -9069,6 +9069,10 @@ class ClickMenu {
            me.htmlCls.dialogCls.openDlg('dl_cid', 'Please input PubChem Compound');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_smiles", "click", function(e) { me.icn3d; //e.preventDefault();
+         me.htmlCls.dialogCls.openDlg('dl_smiles', 'Please input a chemical SMILES');
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_pngimage", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_pngimage', 'Please append PNG images');
         });
@@ -11746,6 +11750,7 @@ class SetMenu {
         //html += this.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
 
         html += this.getLink('mn1_cid', 'PubChem CID/Name/InchI ' + me.htmlCls.wifiStr, 1, 2);
+        html += this.getLink('mn1_smiles', 'Chemical SMILES ', undefined, 2);
         
         html += "</ul>";
         html += "</li>";
@@ -14017,7 +14022,7 @@ class SetDialog {
         html += '<div style="width:550px;">You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.<br>';
         html += '<pre>refnum,11,12,,21,22,,10C,11C,20C<br>';
         html += '1TUP_A,100,101,,,132,,,,<br>';
-        html += '1TUP_B,110,111,,141,142,,,,</pre>';
+        html += '1TUP_B,110,111,,141,142,,,,<br>';
         html += '1TUP_C,,,,,,,200,201,230</pre>';
         html += 'The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.<br><br>';
         html += 'To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#selectb" target="_blank">Specification</a>. For example, "%12"  selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.<br>';
@@ -14211,6 +14216,12 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_cid'>Load</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_smiles' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_cid', 'Please input a chemical SMILES');
+        html += "Chemical SMILES: " + me.htmlCls.inputTextStr + "id='" + me.pre + "smiles' value='CC(=O)OC1=CC=CC=C1C(=O)O' size=30> ";
+        html += me.htmlCls.buttonStr + "reload_smiles'>Load</button>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_pngimage' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_pngimage', 'Please append iCn3D PNG Image files');
         html += "Multiple iCn3D PNG images: " + me.htmlCls.inputFileStr + " multiple id='" + me.pre + "pngimage' size=8><br/>";
@@ -16654,8 +16665,7 @@ class Events {
         });
 
 
-        me.myEventCls.onIds("#" + me.pre 
-        + "reload_cid", "click", function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_cid", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            thisClass.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
@@ -16663,6 +16673,18 @@ class Events {
            window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_smiles", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            // thisClass.setLogCmd("load smiles " + $("#" + me.pre + "smiles").val(), false);
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+
+            urlTarget = '_blank';
+
+            console.log("smiles: " + $("#" + me.pre + "smiles").val() + " encode: " + encodeURIComponent($("#" + me.pre + "smiles").val()));
+            window.open(hostUrl + '?smiles=' + encodeURIComponent($("#" + me.pre + "smiles").val()), urlTarget);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
@@ -49711,7 +49733,7 @@ class LineGraph {
                           }
                           else {                           
                             ++linkedNodeCnt[mappingid];   
-                            linkedNodeInterDiff[mappingid] += link.n; 
+                            linkedNodeInterDiff[mappingid] += link.n;
                             
                             linkedNodeInterDiffBool[mappingid] = (linkedNodeInterDiff[mappingid] / link.n == linkedNodeCnt[mappingid]) ? 0 : 1; 
                           }
@@ -49765,7 +49787,7 @@ class LineGraph {
                           let linkDiff = me.hashUtilsCls.cloneHash(link);
                           linkDiff.source += separatorDiff + ic.chainsMapping[chainid1][resid1];
                           linkDiff.target += separatorDiff + ic.chainsMapping[chainid2][resid2];
-                      
+                          
                           if(linkedNodeCnt[mappingid] == structureArray.length && (bIgRef || linkedNodeInterDiffBool[mappingid] == 0)) {
                               linkArraySplitCommon[index].push(linkCommon);
                           }  
@@ -50458,6 +50480,7 @@ class GetGraph {
                 nodeArray2.push(node);
             }
         }
+
         // sort array
         nodeArray1.sort(function(a,b) {
           return thisClass.compNode(a, b);
@@ -50465,6 +50488,7 @@ class GetGraph {
         nodeArray2.sort(function(a,b) {
           return thisClass.compNode(a, b, bReverseNode);
         });
+
         return {"nodeArray1": nodeArray1, "nodeArray2": nodeArray2, "name2node": name2nodeCommon};
     }
     updateGraphJson(struc, index, nodeArray1, nodeArray2, linkArray) { let ic = this.icn3d, me = ic.icn3dui;
@@ -50769,7 +50793,9 @@ class GetGraph {
         }
 
         for(let linkStr in linkstr2cnt) {
-            hbondStr += ', {' + linkStr + ', "n": ' + linkstr2cnt[linkStr] + '}';
+            // do not differentiate the number of contacts
+            let n = (value == me.htmlCls.contactInsideValue || value == me.htmlCls.contactValue) ? 1 : linkstr2cnt[linkStr];
+            hbondStr += ', {' + linkStr + ', "n": ' + n + '}';
         }
 
         return hbondStr;
@@ -57808,6 +57834,19 @@ class SdfParser {
         }
     }
 
+    async downloadSmiles(smiles) { let ic = this.icn3d, me = ic.icn3dui;
+        let urlSmiles = me.htmlCls.baseUrl + "openbabel/openbabel.cgi?smiles2pdb=" + smiles;
+        let pdbStr = await me.getAjaxPromise(urlSmiles, 'text');
+
+        ic.init();
+
+        ic.bInputfile = true;
+        ic.InputfileType = 'pdb';
+        ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + pdbStr : pdbStr;
+
+        await ic.pdbParserCls.loadPdbData(pdbStr);
+    }
+
     async loadSdfData(data) { let ic = this.icn3d, me = ic.icn3dui;
         let bResult = this.loadSdfAtomData(data);
 
@@ -69092,6 +69131,10 @@ class LoadScript {
           me.cfg.cid = id;
           await ic.sdfParserCls.downloadCid(id);
         }
+        else if(command.indexOf('load smiles') !== -1) {
+          me.cfg.smiles = id;
+          await ic.sdfParserCls.downloadSmiles(id);
+        }
         else if(command.indexOf('load alignment') !== -1) {
           me.cfg.align = id;
 
@@ -82428,7 +82471,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.37.0';
+    this.REVISION = '3.38.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -82840,6 +82883,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         await ic.sdfParserCls.downloadCid(me.cfg.cid);
     }
+    else if(me.cfg.smiles !== undefined) {
+        ic.inputid = me.cfg.smiles;
+        ic.loadCmd = 'load smiles ' + me.cfg.smiles;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        await ic.sdfParserCls.downloadSmiles(me.cfg.smiles);
+    }
     else if(me.cfg.mmcifid !== undefined) {
         ic.inputid = me.cfg.mmcifid;
         ic.loadCmd = 'load mmcif ' + me.cfg.mmcifid;