icn3d 3.37.2 → 3.38.1

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>";
@@ -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();
@@ -36925,6 +36947,10 @@ class Contact {
         for(let i in atomlistTarget) {
             //var oriAtom = atomlistTarget[i];
             let oriAtom = ic.atoms[i];
+
+            // skip hydrogen atoms
+            if(bInteraction && oriAtom.elem == 'H') continue;
+
             let r1 = me.parasCls.vdwRadii[oriAtom.elem.toUpperCase()];
             let chainid1 = oriAtom.structure + '_' + oriAtom.chain;
 
@@ -36951,6 +36977,10 @@ class Contact {
 
             for (let j in neighbors) {
                let atom = neighbors[j];
+
+               // skip hydrogen atoms
+               if(bInteraction && atom.elem == 'H') continue;
+
                let r2 = me.parasCls.vdwRadii[atom.elem.toUpperCase()];
                let chainid2 = atom.structure + '_' + atom.chain;
 
@@ -57812,6 +57842,19 @@ 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);
 
@@ -69096,6 +69139,10 @@ 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;
 
@@ -82389,7 +82436,7 @@ iCn3D.prototype.resetConfig = function () { let ic = this, me = ic.icn3dui;
         this.opts['nucleotides'] = 'o3 trace';
     }
 
-    if(me.cfg.cid !== undefined) {
+    if(me.cfg.cid !== undefined || me.cfg.smiles !== undefined) {
         this.opts['color'] = 'atom';
 
         this.opts['pk'] = 'atom';
@@ -82432,7 +82479,7 @@ 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;
@@ -82844,6 +82891,12 @@ 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;