icn3d 3.24.1 → 3.24.2

package/icn3d.js

@@ -7361,6 +7361,13 @@ class ClickMenu {
            ic.drawCls.draw();
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn6_addlabelRefnum", "click", function(e) { let ic = me.icn3d; e.preventDefault();
+         ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
+         ic.selectionCls.saveSelectionIfSelected();
+         thisClass.setLogCmd('add reference number labels', true);
+         ic.drawCls.draw();
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mn6_addlabelChains", "click", function(e) { let ic = me.icn3d; e.preventDefault();
            ic.analysisCls.addChainLabels(ic.hAtoms);
            ic.selectionCls.saveSelectionIfSelected();
@@ -9389,8 +9396,8 @@ class SetMenu {
             //}
 
             //!!!
-            //!!!html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            //!!!html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9520,6 +9527,8 @@ class SetMenu {
         if(me.cfg.cid === undefined) {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
+            //!!!
+            html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9611,12 +9620,11 @@ class SetMenu {
 
             html += "<ul>";
 //!!!
-/*
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
 
             html += this.getMenuSep();
-*/
+
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -11534,7 +11542,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_copyurl' style='width:520px;' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_copyurl', 'Share Link');
-
+        html += "<br>";
         html += "1. <b>URLs Used in Browsers</b><br><br>";
 
         html += "Please copy one of the URLs below. They show the same result.<br>(To add a title to share link, click \"Windows > Your Note\" and click \"File > Share Link\" again.)<br><br>";
@@ -11543,7 +11551,6 @@ class SetDialog {
             html += "Lifelong Short URL:(To replace this URL, send a pull request to update share.html at <a href='https://github.com/ncbi/icn3d' target='_blank'>iCn3D GitHub</a>)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url' value='' style='width:100%'><br><br>";
             html += "Lifelong Short URL + Window Title:(To update the window title, click \"Analysis > Your Note/Window Title\".)<br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "short_url_title' value='' style='width:100%'><br><br>";
         }
-        html += "<br>";
 
         html += "2. <b>Commands Used in Jupyter Noteboook</b><br><br>";
         html += "Please copy the following commands into a cell in Jupyter Notebook to show the same result.<br><br>";
@@ -30739,7 +30746,7 @@ class ResidueLabels {
 
     //Add labels for all residues containing the input "atoms". The labels are one-letter residue abbreviations.
     //If "bSchematic" is true, the labels are in circles. Otherwise, they are in round-corner rectangles.
-    addResidueLabels(atoms, bSchematic, alpha, bNumber) { let ic = this.icn3d, me = ic.icn3dui;
+    addResidueLabels(atoms, bSchematic, alpha, bNumber, bRefnum) { let ic = this.icn3d, me = ic.icn3dui;
         if(me.bNode) return;
 
         let size = 18;
@@ -30779,6 +30786,15 @@ class ResidueLabels {
                     label.text += atom.resi;
                     //label.factor = 0.3;
                 }
+                else if(bRefnum) {
+                    let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
+                    let refnum = '';
+                    if(ic.resid2refnum[resid]) {
+                        refnum = (ic.resid2refnum[resid].substr(0, 1) == ' ') ? '' : ic.resid2refnum[resid];
+                    }
+
+                    label.text = refnum;
+                }
                 label.size = size;
                 label.factor = 0.3;
 
@@ -30789,6 +30805,9 @@ class ResidueLabels {
                 if(bNumber) {
                     label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd;
                 }
+                else if(bRefnum) {
+                    label.color = '#00FFFF';
+                }
                 else {
                     label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
                 }
@@ -30994,7 +31013,7 @@ class Impostor {
 
     setParametersForShader (opacity) { let ic = this.icn3d, me = ic.icn3dui;
         let background = me.parasCls.backgroundColors[ic.opts.background.toLowerCase()];
-        if(!background) background = me.parasCls.thr(0x000000);      
+        //if(!background) background = me.parasCls.thr(0x000000);      
 
         let near = 2.5*ic.maxD;
         let far = 4*ic.maxD;
@@ -31999,6 +32018,8 @@ class Alternate {
     // change the display atom when alternating
     //Show structures one by one.
     alternateStructures() { let ic = this.icn3d, me = ic.icn3dui;
+        //ic.transformCls.zoominSelection();
+        
         // default ic.ALTERNATE_STRUCTURE = -1
         if(ic.ALTERNATE_STRUCTURE == -1) {
             ic.viewSelectionAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
@@ -35592,23 +35613,27 @@ class SetOption {
         let html = '';
 
         const name2color = {
+            "<b>Protodomain 1</b>": "",
             "A Strand": "0000FF",
             "B Strand": "006400",
             "C Strand": "FFFF00", //"F0E68C",
             "C' Strand": "FFA500",
+            "<br><b>Linker</b>": "",
             "C'' Strand": "FF0000",
+            "<br><b>Protodomain 2</b>": "",
             "D Strand": "0000FF",
             "E Strand": "006400",
             "F Strand": "FFFF00", //"F0E68C",
             "G Strand": "FFA500",
+            "": "",
             "Loop": "CCCCCC"
         };
 
-        html += "<div>";
+        html += "<div>A protodomain is a supersecondary structure <br>that by its duplication, symmetry operations <br>can generate a structural domain.<br><br>";
         for (let name in name2color) {
             let color = name2color[name];
             html += "<span>";
-            html += "<div style='width: 10px; height: 10px; background-color:#" + color + "; border: 0px;display:inline-block;' ></div> ";
+            if(color) html += "<div style='width: 10px; height: 10px; background-color:#" + color + "; border: 0px;display:inline-block;' ></div> ";
             html += name;
             html +=  "</span><br>";
         }
@@ -37856,7 +37881,7 @@ class Domain3d {
         this.nc_fact = 0.0;				// size factor for internal contacts
 
 		// added by Jiyao
-		this.min_contacts = 10;			// minimum number of contacts to be considered as neighbors
+		this.min_contacts = 3;			// minimum number of contacts to be considered as neighbors
 
         //let this.elements[2*this.MAX_SSE];			// sets of this.elements to be split
         this.elements = [];
@@ -38911,7 +38936,7 @@ class Domain3d {
 				}
 			}
 		}
-		
+				
 		return {subdomains: subdomains, substruct: substruct, pos2resi:pos2resi };
 	} // end c2b_NewSplitChain
 
@@ -56539,6 +56564,11 @@ class ApplyCommand {
 
         ic.drawCls.draw();
       }
+      else if(command == 'add reference number labels') {
+        ic.residueLabelsCls.addResidueLabels(ic.hAtoms, undefined, undefined, undefined, true);
+
+        ic.drawCls.draw();
+      }
       else if(command == 'add atom labels') {
         ic.residueLabelsCls.addAtomLabels(ic.hAtoms);
 
@@ -64490,14 +64520,17 @@ class Diagram2d {
 
             ic.hlUpdateCls.updateHlAll();
 
+            ic.transformCls.zoominSelection();
+
             me.htmlCls.clickMenuCls.setLogCmd(select, true);
         });
 
         //$("#" + ic.pre + "dl_scatterplot .icn3d-interaction", "click", function(e) { let ic = this.icn3d, me = ic.icn3dui;
-        $(document).on("click", "#" + ic.pre + "dl_scatterplot .icn3d-interaction", function(e) { thisClass.icn3d;
+        $(document).on("click", "#" + ic.pre + "dl_scatterplot .icn3d-interaction", function(e) { let ic = thisClass.icn3d;
             e.stopImmediatePropagation();
 
             thisClass.clickInteraction(this);
+            ic.transformCls.zoominSelection();
         });
 
         $(document).on("click", "#" + ic.pre + "dl_contactmap .icn3d-interaction", function(e) { thisClass.icn3d;
@@ -66536,7 +66569,6 @@ class SaveFile {
         let bMulStruc =(struArray.length > 1) ? true : false;
 
         let molNum = 1, prevStru = '', prevChain = '';
-        //pdbStr += '\n';
 
         let addedChainResiHash = {};
         for(let i in atomHash) {
@@ -66556,20 +66588,24 @@ class SaveFile {
 
                 // add header            
                 let mutantInfo = (chainResi2pdb) ? "Mutated chain_residue " + Object.keys(chainResi2pdb) + '; ' : '';
-                if(!bNoHeader) pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, pdbid);
+                if(!bNoHeader) {
+                    pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, pdbid);
+                    //pdbStr += '\n'; // separate from incomplete secondary structures 
+                }
 
-                prevStru = atom.structure;
+                //prevStru = atom.structure;
                 ++molNum;
             }
-            else {
-                if(atom.chain != prevChain) {
+            //else {
+                //if(atom.chain != prevChain) {
+                if(atom.chain != prevChain && atom.structure == prevStru) {
                     // add a line "TER" to work with scap/profix to add missing atoms
                     if(prevChain) {
                         pdbStr += 'TER\n';
                     }
-                    prevChain = atom.chain;
+                    //prevChain = atom.chain;
                 }
-            }
+            //}
 
             let chainResi = atom.chain + '_' + atom.resi;
             if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {    
@@ -66734,6 +66770,9 @@ class SaveFile {
             }
 
             pdbStr += line + '\n';
+
+            prevStru = atom.structure;
+            prevChain = atom.chain;
         }
 
         pdbStr += connStr;