icn3d 3.39.0 → 3.39.1

package/icn3d.js

@@ -52051,7 +52051,10 @@ class ViewInterPairs {
             cntHbond += result.cnt;
             svgHtmlNode += result.svgHtmlNode;
             svgHtmlLine += result.svgHtmlLine;
-            if(result.cnt > 0) residname2List += residname2 + ":hbond_" + result.cnt + " ";
+            // if(result.cnt > 0) residname2List += residname2 + ":hbond_" + result.cnt + " ";
+            // add hydrogen bond between main or side chains. result.mainside has value such as main,side,side,side  
+            // for two hydrogens between main and side, and side and side chains
+            if(result.cnt > 0) residname2List += residname2 + ":hbond_" + result.cnt + ":type_" + result.mainside + " ";
 
             labels2dist = ic.resids2inter[resids]['ionic'];
             result = this.getInteractionPairDetails(labels2dist, type, 'ionic', index2xy, xlen, ylen, xcenter, ycenter);
@@ -52059,7 +52062,7 @@ class ViewInterPairs {
             cntIonic += result.cnt;
             svgHtmlNode += result.svgHtmlNode;
             svgHtmlLine += result.svgHtmlLine;
-            if(result.cnt > 0) residname2List += residname2 + ":ionic_" + result.cnt + " ";
+            if(result.cnt > 0) residname2List += residname2 + ":ionic_" + result.cnt + ":type_" + result.mainside + " ";
 
             labels2dist = ic.resids2inter[resids]['halogen'];
             result = this.getInteractionPairDetails(labels2dist, type, 'halogen', index2xy, xlen, ylen, xcenter, ycenter);
@@ -52067,7 +52070,7 @@ class ViewInterPairs {
             cntHalegen += result.cnt;
             svgHtmlNode += result.svgHtmlNode;
             svgHtmlLine += result.svgHtmlLine;
-            if(result.cnt > 0) residname2List += residname2 + ":halogen_" + result.cnt + " ";
+            if(result.cnt > 0) residname2List += residname2 + ":halogen_" + result.cnt + ":type_" + result.mainside + " ";
 
             labels2dist = ic.resids2inter[resids]['pi-cation'];
             result = this.getInteractionPairDetails(labels2dist, type, 'pi-cation', index2xy, xlen, ylen, xcenter, ycenter);
@@ -52075,7 +52078,7 @@ class ViewInterPairs {
             cntPication += result.cnt;
             svgHtmlNode += result.svgHtmlNode;
             svgHtmlLine += result.svgHtmlLine;
-            if(result.cnt > 0) residname2List += residname2 + ":pi-cation_" + result.cnt + " ";
+            if(result.cnt > 0) residname2List += residname2 + ":pi-cation_" + result.cnt + ":type_" + result.mainside + " ";
 
             labels2dist = ic.resids2inter[resids]['pi-stacking'];
             result = this.getInteractionPairDetails(labels2dist, type, 'pi-stacking', index2xy, xlen, ylen, xcenter, ycenter);
@@ -52083,7 +52086,7 @@ class ViewInterPairs {
             cntPistacking += result.cnt;
             svgHtmlNode += result.svgHtmlNode;
             svgHtmlLine += result.svgHtmlLine;
-            if(result.cnt > 0) residname2List += residname2 + ":pi-stacking_" + result.cnt + " ";
+            if(result.cnt > 0) residname2List += residname2 + ":pi-stacking_" + result.cnt + ":type_" + result.mainside + " ";
 
             // put contact as the last one since contact will use the same node as other interactions in ligand-protein interactoin
             labels2dist = ic.resids2inter[resids]['contact'];
@@ -52137,7 +52140,7 @@ class ViewInterPairs {
         return tmpText;
     }
     getInteractionPairDetails(labels2dist, type, interactionType, index2xy, xlen, ylen, xcenter, ycenter) { let ic = this.icn3d; ic.icn3dui;
-        let svgHtmlNode = '', svgHtmlLine = '', tmpText = '', cnt = 0;
+        let svgHtmlNode = '', svgHtmlLine = '', tmpText = '', cnt = 0, mainside= '';
         let colorText1 = ' <span style="background-color:#';
         let colorText2 = '">&nbsp;&nbsp;&nbsp;</span>';
         if(labels2dist !== undefined) {
@@ -52154,6 +52157,12 @@ class ViewInterPairs {
                 let resid1 = resid1Ori.substr(0, pos1);
                 let resid2 = resid2Ori.substr(0, pos2);
 
+                let atomName1 = resid1.substr(resid1.indexOf('@') + 1);
+                resid2.substr(resid2.indexOf('@') + 1);
+                let atomType1 = (atomName1 === "N" || atomName1 === "C" || atomName1 === "O" || atomName1 === "CA") ? 'main' : 'side';
+                if(mainside) mainside += ';';
+                mainside += atomType1 + ',' + atomType1;
+
                 let resid1Real = ic.getGraphCls.convertLabel2Resid(resid1);
                 let atom1 = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid1Real]);
                 let color1 = (atom1.color) ? atom1.color.getHexString() : '';
@@ -52175,7 +52184,7 @@ class ViewInterPairs {
                 }
             }
         }
-        return {html: tmpText, cnt: cnt, svgHtmlNode: svgHtmlNode, svgHtmlLine: svgHtmlLine}
+        return {html: tmpText, cnt: cnt, svgHtmlNode: svgHtmlNode, svgHtmlLine: svgHtmlLine, mainside: mainside}
     }
 
     getContactPairDetails(labels2dist, type, interactionType, index2xy, xlen, ylen, xcenter, ycenter) { let ic = this.icn3d; ic.icn3dui;
@@ -63581,6 +63590,9 @@ class LoadPDB {
 
                 ///id = line.substr(62, 4).trim();
                 id = line.substr(62).trim();
+                // remove "_" in the id
+                id = id.replace(/_/g, '-');
+                
                 oriId = id;
 
                 if(id == '') {
@@ -64491,6 +64503,8 @@ class LoadCIF {
             
             if(block.getCategory("_entry")) {
                 id = block.getCategory("_entry").getColumn("id").getString(0);
+                // remove "_" in the id
+                id = id.replace(/_/g, '-');
 
                 if(id == '') {
                     if(bAppend) {
@@ -72213,7 +72227,6 @@ class Dssp {
             if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
               for(let chainNum in ic.chainsSeq) {
                   let pos = chainNum.indexOf('_');
-
                   // one structure at a time
                   if(chainNum.substr(0, pos) != struArray[index]) continue;
 
@@ -79425,6 +79438,11 @@ class SaveFile {
 
                 $("#" + ic.pre + "title").html("PubChem CID <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + ic.inputid.toUpperCase() + "</a>: " + title);
             }
+            else if(me.cfg.smiles !== undefined) {
+                let text = decodeURIComponent(me.cfg.smiles);
+                if(text.length > 60) text = text.substr(0, 60) + "...";
+                $("#" + ic.pre + "title").html("SMILES: " + text);
+            }
             else if(me.cfg.align !== undefined) {
                 title = 'VAST+ alignment of ' + Object.keys(ic.structures);