icn3d 3.44.0 → 3.44.1

package/README.md

@@ -102,11 +102,11 @@ Usage
     If your typescript compiler complains about missing type definition files, create a file named icn3d.d.ts in your project's root directory and fill it with the following:
 
 		declare module 'icn3d/module' {
-			export class iCn3DUI {
-				constructor(cfg: object);
+		export class iCn3DUI {
+			constructor(cfg: object);
 
-				show3DStructure(): Promise<void>;
-			}
+			show3DStructure(): Promise<void>;
+		}
 		}
 
 		declare module 'icn3d/three' {}

package/icn3d.js

@@ -56237,6 +56237,13 @@ class ClickMenu {
          }
       }
     }
+
+    //https://stackoverflow.com/questions/105034/how-do-i-create-a-guid-uuid
+    uuidv4() {
+      return "10000000-1000-4000-8000-100000000000".replace(/[018]/g, c =>
+         (+c ^ crypto.getRandomValues(new Uint8Array(1))[0] & 15 >> +c / 4).toString(16)
+      );
+    }
     
     displayShownMenus() { let me = this.icn3dui; me.icn3d;
         let html = "<form name='" + me.pre + "selmenu'>";
@@ -56525,6 +56532,132 @@ class ClickMenu {
            ic.saveFileCls.saveFile(file_pref + '_statefile.txt', 'command');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_exportCamera", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+            thisClass.setLogCmd("export bcf viewpoint", false);
+            let file_pref = Object.keys(ic.structures).join(',');
+            //ic.saveFileCls.saveFile(file_pref + '_camera.bcf', 'bcf');
+
+            let url = './script/jszip.min.js';
+            await me.getAjaxPromise(url, 'script');
+
+            let data, jszip = new JSZip();
+
+            let uuid1 = thisClass.uuidv4();
+            let uuid2 = thisClass.uuidv4();
+
+            data = '';
+            data += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n';
+            data += '    <Version VersionId="3.0"/>\n';
+
+            jszip.file("bcf.version", data);
+
+            data = '';
+            data += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n';
+            data += '    <Extensions>\n';
+            data += '        <TopicTypes>\n';
+            data += '          <TopicType>ERROR</TopicType>\n';
+            data += '          <TopicType>WARNING</TopicType>\n';
+            data += '          <TopicType>INFORMATION</TopicType>\n';
+            data += '          <TopicType>CLASH</TopicType>\n';
+            data += '          <TopicType>OTHER</TopicType>\n';
+            data += '        </TopicTypes>\n';
+            data += '          <TopicStatuses>\n';
+            data += '          <TopicStatus>OPEN</TopicStatus>\n';
+            data += '          <TopicStatus>IN_PROGRESS</TopicStatus>\n';
+            data += '          <TopicStatus>SOLVED</TopicStatus>\n';
+            data += '          <TopicStatus>CLOSED</TopicStatus>\n';
+            data += '        </TopicStatuses>\n';
+            data += '        <Priorities>\n';
+            data += '          <Priority>LOW</Priority>\n';
+            data += '          <Priority>MEDIUM</Priority>\n';
+            data += '          <Priority>HIGH</Priority>\n';
+            data += '          <Priority>CRITICAL</Priority>\n';
+            data += '        </Priorities>\n';
+            data += '        <TopicLabels/>\n';
+            data += '        <Users/>\n';
+            data += '        <SnippetTypes/>\n';
+            data += '        <Stages/>\n';
+            data += '    </Extensions>\n';
+
+            jszip.file("extensions.xml", data);
+
+            let folder = jszip.folder(uuid1);
+
+            data = '';
+            data += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n';
+            data += '    <Markup>\n';
+            data += '        <Header>\n';
+            data += '          <Files/>\n';
+            data += '        </Header>		\n';
+            data += '        <Topic Guid="' + uuid1 + '">\n';
+            data += '        <Title>Perspective camera</Title>\n';
+
+            let now = new Date();
+            const isoString = now.toISOString();
+
+            data += '        <CreationDate>' + isoString + '</CreationDate>\n';
+            data += '        <CreationAuthor>https://www.ncbi.nlm.nih.gov/Structure/icn3d</CreationAuthor>\n';
+            data += '        <DocumentReferences/>\n';
+            data += '        <RelatedTopics/>\n';
+            data += '        <Comments/>\n';
+            data += '        <Viewpoints>\n';
+            data += '          <ViewPoint Guid="' + uuid2 + '">\n';
+            data += '            <Viewpoint>viewpoint-' + uuid2 + '.bcfv</Viewpoint>\n';
+            data += '            <Snapshot>snapshot-' + uuid2 + '.png</Snapshot>\n';
+            data += '          </ViewPoint>\n';
+            data += '        </Viewpoints>\n';
+            data += '      </Topic>\n';
+            data += '    </Markup>\n';
+
+            folder.file("markup.bcf", data);
+            let blob = await ic.saveFileCls.saveFile('any', 'png', undefined, undefined, true);
+
+            folder.file("snapshot-" + uuid2 + ".png", blob);
+
+            data = '';
+            
+            data += '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n';
+            data += '    <VisualizationInfo Guid="' + uuid2 + '">\n';
+            data += '      <Components>\n';
+            data += '        <Selection/>\n';
+            data += '        <Visibility DefaultVisibility="true" />\n';
+            data += '        <Coloring/>\n';
+            data += '      </Components>\n';
+            data += '      <PerspectiveCamera>\n';
+            data += '        <CameraViewPoint>\n';
+            data += '          <X>' + ic.cam.position.x + '</X>\n';
+            data += '          <Y>' + ic.cam.position.y + '</Y>\n';
+            data += '          <Z>' + ic.cam.position.z + '</Z>\n';
+            data += '        </CameraViewPoint>\n';
+
+            let direction = (new Vector3$1(0, 0, -1)).applyQuaternion(ic.cam.quaternion);
+
+            data += '        <CameraDirection>\n';
+            data += '          <X>' + direction.x + '</X>\n';
+            data += '          <Y>' + direction.y + '</Y>\n';
+            data += '          <Z>' + direction.z + '</Z>\n';
+            data += '        </CameraDirection>\n';
+            data += '        <CameraUpVector>\n';
+            data += '          <X>' + ic.cam.up.x + '</X>\n';
+            data += '          <Y>' + ic.cam.up.y + '</Y>\n';
+            data += '          <Z>' + ic.cam.up.z + '</Z>\n';
+            data += '        </CameraUpVector>\n';
+            data += '        <FieldOfView>' + ic.cam.fov + '</FieldOfView>\n'; // 20
+            data += '        <AspectRatio>' + ic.container.whratio + '</AspectRatio>\n';
+            data += '      </PerspectiveCamera>\n';
+            data += '      <Lines/>\n';
+            data += '      <ClippingPlanes/>\n';
+            data += '      <Bitmaps/>  \n';
+            data += '    </VisualizationInfo>\n';
+
+            folder.file("viewpoint-" + uuid2 + ".bcfv", data);
+
+            jszip.generateAsync({type:"blob"})
+               .then(function(content) {
+                  saveAs(content, file_pref + "_viewpoint.bcf");
+               });
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_exportVideo", "click", function(e) { me.icn3d; //e.preventDefault();
          thisClass.setLogCmd("export video", false);
          me.htmlCls.dialogCls.openDlg('dl_video', 'Save canvas changes in a video');
@@ -58265,13 +58398,13 @@ class ClickMenu {
           thisClass.setLogCmd(value, true);
           let axis;
           if(direction == 'x') {
-              axis = new THREE.Vector3(1,0,0);
+              axis = new Vector3$1(1,0,0);
           }
           else if(direction == 'y') {
-              axis = new THREE.Vector3(0,1,0);
+              axis = new Vector3$1(0,1,0);
           }
           else if(direction == 'z') {
-              axis = new THREE.Vector3(0,0,1);
+              axis = new Vector3$1(0,0,1);
           }
           let angle = 0.5 * Math.PI;
           ic.transformCls.setRotation(axis, angle);
@@ -58582,8 +58715,8 @@ class ClickMenu {
       if(!ic.quaternion) {
          // reset parameters
          ic._zoomFactor = 1.0;
-         ic.mouseChange = new THREE.Vector2(0,0);
-         ic.quaternion = new THREE.Quaternion(0,0,0,1);
+         ic.mouseChange = new Vector2$1(0,0);
+         ic.quaternion = new Quaternion(0,0,0,1);
       }
 
       transformation.factor = ic._zoomFactor;
@@ -59388,6 +59521,7 @@ class SetMenu {
         html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
         html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
         html += "</ul>";
+        html += this.getLink('mn1_exportCamera', 'BCF Viewpoint', undefined, 2);
 
         html += "<li><br/></li>";
 
@@ -60602,6 +60736,7 @@ class SetMenu {
 
         html += this.getMenuText('mn6_develop', 'Develop', undefined, undefined, 1);
         html += "<ul>";
+        html += this.getMenuUrl('dev_contribute', me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToContribute", "Become a Contributor", undefined, 2);
         html += this.getMenuUrl('dev_embedicn3d2', me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse", "Embed iCn3D", undefined, 2);
         html += this.getMenuUrl('dev_urlpara', me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters", "URL Parameters", undefined, 2);
         html += this.getMenuUrl('dev_command', me.htmlCls.baseUrl + "icn3d/icn3d.html#commands", "Commands", undefined, 2);
@@ -62831,9 +62966,9 @@ class SetDialog {
 
         group2tpl['IgFN3'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'Sidekick2_1wf5A_human_FN3-n7'];
 
-        group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TEAD1_3kysC_human'];
+        group2tpl['IgFN3-like'] = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'RBPJ_6py8C_human_Unk-n1', 'TEAD1_3kysC_human'];
 
-        group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus'];  
+        group2tpl['Other Ig'] = ['CD19_6al5A_human-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'LaminAC_1ifrA_human', 'ORF7a_1xakA_virus', 'RBPJ_6py8C_human_Unk-n2'];  
 
         let tpl2strandsig = {};
         tpl2strandsig['ASF1A_2iijA_human']                          = "A A' B C C' E F G G+";
@@ -94044,9 +94179,12 @@ class Domain3d {
 
 		// let subdomains = result.subdomains;
 		// let substruct = result.substruct;
+		let jsonStr = '{"data": [';
 
 		let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
 		let residueArray = Object.keys(residueHash);
+		if(residueArray.length == 0) return jsonStr + ']}';
+
 		let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
 		// let resid1 = residueArray[0];
@@ -94097,7 +94235,7 @@ class Domain3d {
 		substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
 
 		// m_domains1: {"data": [ {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]], "domain": [[1,43,x,y,z],[2,58,x,y,z], ...]}, {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]],"domain": [[1,43,x,y,z],[2,58,x,y,z], ...]} ] }
-		let jsonStr = '{"data": [';
+
 		//merge all subdomains into one domain
 		jsonStr += '{"ss": ['; //secondary structure
 
@@ -117489,12 +117627,12 @@ class DefinedSets {
     }
 
     setPredefinedInMenu() { let ic = this.icn3d, me = ic.icn3dui;
-          // predefined sets: all chains
-          this.setChainsInMenu();
-
           // predefined sets: proteins,nucleotides, chemicals
           this.setProtNuclLigInMenu();
 
+          // predefined sets: all chains
+          this.setChainsInMenu();
+
           // show 3d domains for mmdbid
           if(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined  || me.cfg.chainalign !== undefined || me.cfg.mmdbafid !== undefined) {
               for(let tddomainName in ic.tddomains) {
@@ -117592,10 +117730,15 @@ class DefinedSets {
       return html;
     }
 
-    setChainsInMenu() { let ic = this.icn3d; ic.icn3dui;
+    setChainsInMenu() { let ic = this.icn3d, me = ic.icn3dui;
+        let nonProtNuclResHash = {};
+
         for(let chainid in ic.chains) {
-            // skip chains with one residue/chemical
-            if(ic.chainsSeq[chainid] && ic.chainsSeq[chainid].length > 1) {
+            let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
+
+            // protein or nucleotide
+            // if(ic.chainsSeq[chainid] && ic.chainsSeq[chainid].length > 1) {
+            if(ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial)) {
               //ic.defNames2Atoms[chainid] = Object.keys(ic.chains[chainid]);
               ic.defNames2Residues[chainid] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(ic.chains[chainid]));
               ic.defNames2Descr[chainid] = chainid;
@@ -117606,6 +117749,25 @@ class DefinedSets {
 
               ic.defNames2Command[chainid] = 'select $' + structure + '.' + chain;
             }
+            else { // chemicals, etc
+              let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
+              let resn = atom.resn.substr(0, 3);
+
+              if(!nonProtNuclResHash[resn]) {
+                nonProtNuclResHash[resn] = ic.residues[resid];
+              }
+              else {
+                nonProtNuclResHash[resn] = me.hashUtilsCls.unionHash(nonProtNuclResHash[atom.resn], ic.residues[resid]);
+              }
+            }
+        }
+
+        // chemicals etc
+        for(let resn in nonProtNuclResHash) {
+            ic.defNames2Residues[resn] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(nonProtNuclResHash[resn]));
+            ic.defNames2Descr[resn] = resn;
+
+            ic.defNames2Command[resn] = 'select :3' + resn;
         }
 
         // select whole structure
@@ -121884,7 +122046,7 @@ class Dssp {
         ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
         ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
         ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
-        ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
+        //ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
         ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
         ic.ref2igtype['Siglec3_5j0bB_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
@@ -127978,7 +128140,7 @@ class SaveFile {
     //The type "png" is used to save the current canvas image. The type "html" is used to save html file with the
     //"data". This can be used to save any text. The type "text" is used to save an array of text, where "data" is
     //actually an array. The type "binary" is used to save an array of binary, where "data" is actually an array.
-    saveFile(filename, type, text, bBlob) { let ic = this.icn3d, me = ic.icn3dui;
+    async saveFile(filename, type, text, bBlob, bReturnBlobOnly) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         //Save file
@@ -128020,7 +128182,12 @@ class SaveFile {
 
             if(me.utilsCls.isIE()) {
                 blob = ic.renderer.domElement.msToBlob();
+            }
+            else {
+                blob = await this.getBlobFromNonIE();
+            }
 
+            if(!bReturnBlobOnly) {
                 if(bAddURL) {
                     let reader = new FileReader();
                     reader.onload = function(e) {
@@ -128046,33 +128213,7 @@ class SaveFile {
                 }
             }
             else {
-                ic.renderer.domElement.toBlob(function(data) {
-                    if(bAddURL) {
-                        let reader = new FileReader();
-                        reader.onload = function(e) {
-                            let arrayBuffer = e.target.result; // or = reader.result;
-
-                            let text = ic.shareLinkCls.getPngText();
-
-                            blob = me.convertTypeCls.getBlobFromBufferAndText(arrayBuffer, text);
-
-                            //ic.createLinkForBlob(blob, filename);
-                            thisClass.saveBlob(blob, filename, bBlob, width, height);
-
-                            return blob;
-                        };
-
-                        reader.readAsArrayBuffer(data);
-                    }
-                    else {
-                        blob = data;
-
-                        //ic.createLinkForBlob(blob, filename);
-                        thisClass.saveBlob(blob, filename, bBlob, width, height);
-
-                        return blob;
-                    }
-                });
+                return blob;
             }
 
             // reset the image size
@@ -128106,12 +128247,20 @@ class SaveFile {
 
         if(type !== 'png') {
             //https://github.com/eligrey/FileSaver.js/
-            saveAs(blob, filename);
+            if(!bReturnBlobOnly) saveAs(blob, filename);
         }
 
         return blob;
     }
 
+    getBlobFromNonIE() { let ic = this.icn3d; ic.icn3dui;
+        return new Promise(function(resolve, reject) {
+            ic.renderer.domElement.toBlob(function(data) {
+                resolve(data);
+            });
+        })
+    }
+
     saveBlob(blob, filename, bBlob, width, height) { let ic = this.icn3d; ic.icn3dui;
         if(bBlob) {
             let urlCreator = window.URL || window.webkitURL;
@@ -132411,7 +132560,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.44.0';
+    this.REVISION = '3.44.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;