icn3d 3.45.5 → 3.45.7

package/icn3d.js

@@ -58415,11 +58415,13 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_cameraPers", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+           ic.bChangeCamera = true;
            ic.setOptionCls.setOption('camera', 'perspective');
            thisClass.setLogCmd('set camera perspective', true);
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn6_cameraOrth", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+           ic.bChangeCamera = true;
            ic.setOptionCls.setOption('camera', 'orthographic');
            thisClass.setLogCmd('set camera orthographic', true);
         });
@@ -63779,7 +63781,7 @@ class Events {
         me.myEventCls.onIds(["#" + me.pre + "show_2ddgm", "#" + me.pre + "mn2_2ddgm"], "click", async function(e) { let ic = me.icn3d;
              me.htmlCls.dialogCls.openDlg('dl_2ddgm', '2D Diagram');
              await ic.viewInterPairsCls.retrieveInteractionData();
-             thisClass.setLogCmd("view interactions", true);
+             thisClass.setLogCmd("view 2d diagram", true);
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn2_2ddepiction", "click", async function(e) { let ic = me.icn3d;
@@ -74153,11 +74155,13 @@ class Scene {
 
         ic.fogCls.setFog();
 
-        ic.cameraCls.setCamera();
-        // set the ratio for view point, which was set in ic.transformCls.resetOrientation_base
-        if(!ic.container.whratio) {
-            ic.container.whratio = me.htmlCls.WIDTH / me.htmlCls.HEIGHT; 
-            ic.cam.aspect = ic.container.whratio;
+        if(!ic.cam || ic.bChangeCamera) {
+            ic.cameraCls.setCamera();
+            // set the ratio for view point, which was set in ic.transformCls.resetOrientation_base
+            if(!ic.container.whratio) {
+                ic.container.whratio = me.htmlCls.WIDTH / me.htmlCls.HEIGHT; 
+                ic.cam.aspect = ic.container.whratio;
+            }
         }
 
         if(ic.opts['slab'] === 'yes') ic.cameraCls.setSlab();
@@ -74341,13 +74345,17 @@ class Scene {
             }
         }
 
-        ic.perspectiveCamera = new PerspectiveCamera$1(20, ic.container.whratio, 0.1, 10000);
-        ic.perspectiveCamera.position.set(0, 0, ic.cam_z);
-        ic.perspectiveCamera.lookAt(new Vector3$1(0, 0, 0));
+        if(!ic.perspectiveCamera) {
+            ic.perspectiveCamera = new PerspectiveCamera$1(20, ic.container.whratio, 0.1, 10000);
+            ic.perspectiveCamera.position.set(0, 0, ic.cam_z);
+            ic.perspectiveCamera.lookAt(new Vector3$1(0, 0, 0));
+        }
 
-        ic.orthographicCamera = new OrthographicCamera$1();
-        ic.orthographicCamera.position.set(0, 0, ic.cam_z);
-        ic.orthographicCamera.lookAt(new Vector3$1(0, 0, 0));
+        if(!ic.orthographicCamera) {
+            ic.orthographicCamera = new OrthographicCamera$1();
+            ic.orthographicCamera.position.set(0, 0, ic.cam_z);
+            ic.orthographicCamera.lookAt(new Vector3$1(0, 0, 0));
+        }
 
         ic.cams = {
             perspective: ic.perspectiveCamera,
@@ -86361,7 +86369,7 @@ class Alternate {
             }
             
             ic.bShowHighlight = false;
-//            ic.opts['rotationcenter'] = 'highlight center';
+            ic.opts['rotationcenter'] = 'highlight center';
         }
 
         // also alternating the surfaces
@@ -104163,7 +104171,7 @@ class ChainalignParser {
                 targetOrQuery = 'query';
                 bAppend = true; 
             }
-
+console.log("### i " + i + " structArray[i] " + structArray[i]);
             //if(structArray[i].length > 4) {
             if(isNaN(structArray[i]) && structArray[i].length > 5) {  // PDB ID plus postfix could be 5 
                 //let bNoDssp = true;
@@ -104181,8 +104189,8 @@ class ChainalignParser {
             // hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
         }
 
-        let structArrayAll = Object.keys(ic.structures);
-
+        let structArrayAll = structArray; //Object.keys(ic.structures);
+console.log("### ic.chains: " + JSON.stringify(ic.chains) + " ic.structures " + JSON.stringify(ic.structures));
         ic.opts['color'] = (structArrayAll.length > 1) ? 'structure' : ((structArrayAll[0].length > 5) ? 'confidence' : 'chain');
 
         // add color for all structures
@@ -116047,7 +116055,7 @@ class ApplyCommand {
          ic.selectionCls.selectAll();
          //ic.hlObjectsCls.addHlObjects();
       }
-      else if(command == 'show all') {
+      else if(command == 'show all' || command == 'view all') {
          ic.selectionCls.showAll();
       }
       else if(command == 'select complement') {
@@ -116427,7 +116435,7 @@ class ApplyCommand {
         ic.applyCenterCls.centerSelection();
         ic.drawCls.draw();
       }
-      else if(command == 'show selection') {
+      else if(command == 'show selection' || command == 'view selection') {
         ic.selectionCls.showSelection();
       }
       else if(command == 'hide selection') {
@@ -116470,12 +116478,12 @@ class ApplyCommand {
       else if(command == 'delete selected sets') {
          ic.definedSetsCls.deleteSelectedSets();
       }
-      else if(command == 'view interactions') {
+      else if(command == 'view interactions' || command == 'view 2d diagram') {
          if(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined) {
              ic.ParserUtilsCls.set2DDiagrams(ic.inputid);
          }
       }
-      else if(command == 'show annotations all chains') {
+      else if(command == 'show annotations all chains' || command == 'view annotations all chains') {
          ic.annotationCls.showAnnoAllChains();
       }
 
@@ -116537,7 +116545,7 @@ class ApplyCommand {
       else if(command == 'clear symd symmetry') {
          ic.symdArray = [];
       }
-      else if(command == 'show axis') {
+      else if(command == 'show axis' || command == 'view axis') {
          ic.bAxisOnly = true;
       }
 
@@ -116985,7 +116993,7 @@ class ApplyCommand {
         }
       }
       else if(commandOri.indexOf('display interaction 3d') == 0
-          || commandOri.indexOf('view interaction pairs') == 0
+          || commandOri.indexOf('view interaction pairs') == 0 || commandOri.indexOf('show interaction pairs') == 0
           || commandOri.indexOf('save1 interaction pairs') == 0
           || commandOri.indexOf('save2 interaction pairs') == 0
           || commandOri.indexOf('line graph interaction pairs') == 0
@@ -117036,7 +117044,7 @@ class ApplyCommand {
                 if(commandOri.indexOf('display interaction 3d') == 0) {
                     type = '3d';
                 }
-                else if(commandOri.indexOf('view interaction pairs') == 0) {
+                else if(commandOri.indexOf('view interaction pairs') == 0 || commandOri.indexOf('show interaction pairs') == 0) {
                     type = 'view';
                 }
                 else if(commandOri.indexOf('save1 interaction pairs') == 0) {
@@ -117396,7 +117404,7 @@ class ApplyCommand {
         let dataStr = paraArray[1].replace(/\\n/g, '\n');
         await ic.refnumCls.parseCustomRefFile(dataStr);
       }
-      else if(command.indexOf('show ref number') == 0) {
+      else if(command.indexOf('show ref number') == 0 || command.indexOf('view ref number') == 0) {
         ic.bShownRefnum = true;
       }
       else if(command.indexOf('hide ref number') == 0) {
@@ -117652,7 +117660,7 @@ class ApplyCommand {
         else if(cmd.indexOf('set annotation clinvar') == 0) return seqAnnoStr + ': "ClinVar" checkbox';
         else if(cmd.indexOf('set annotation snp') == 0) return seqAnnoStr + ': "SNP" checkbox';
         else if(cmd.indexOf('set annotation 3ddomain') == 0) return seqAnnoStr + ': "3D Domains" checkbox';
-        else if(cmd.indexOf('view interactions') == 0) return 'Windows > View 2D Diagram';
+        else if(cmd.indexOf('view interactions') == 0 || cmd.indexOf('view 2d diagram') == 0) return 'Windows > View 2D Diagram';
         else if(cmd.indexOf('symmetry') == 0) return 'Analysis > Symmetry';
         else if(cmd.indexOf('realign on seq align') == 0) return 'File > Realign Selection > on Sequence Alignment';
         else if(cmd.indexOf('realign') == 0) return 'File > Realign Selection > Residue by Residue';
@@ -117744,7 +117752,7 @@ class ApplyCommand {
         else if(cmd == 'clear all') return 'Select > Clear Selection';
         else if(cmd == 'defined sets') return 'Windows > Defined Sets';
         else if(cmd == 'delete selected sets') return 'Windows > Defined Sets: "Delete Selected Sets" button';
-        else if(cmd == 'view interactions') return 'Windows > View Interactions';
+        else if(cmd == 'view interactions' || cmd == 'view 2d diagram') return 'Windows > View Interactions';
         else if(cmd == 'show annotations all chains') return seqAnnoStr + ': "Show All Chains" button';
         else if(cmd == 'save color') return 'Color > Save Color';
         else if(cmd == 'apply saved color') return 'Color > Apply Saved Color';
@@ -119015,7 +119023,7 @@ class LoadScript {
 
             await ic.annotationCls.setAnnoTabAll();
           }
-          else if(command.indexOf('view interactions') == 0 && me.cfg.align !== undefined) { // the command may have "|||{"factor"...
+          else if((command.indexOf('view interactions') == 0 || command.indexOf('view 2d diagram') == 0) && me.cfg.align !== undefined) { // the command may have "|||{"factor"...
               await thisClass.applyCommandViewinteraction(strArray[0].trim());
           }
           else if(command.indexOf('view 2d depiction') == 0) { // the command may have "|||{"factor"...
@@ -119226,7 +119234,7 @@ class LoadScript {
                         thisClass.applyCommand3ddomain(lastCommand);
                         await ic.annotationCls.setAnnoTabAll();
                     }
-                    else if(lastCommand.indexOf('view interactions') == 0 && me.cfg.align !== undefined) {
+                    else if((lastCommand.indexOf('view interactions') == 0 || lastCommand.indexOf('view 2d diagram') == 0) && me.cfg.align !== undefined) {
                         await thisClass.applyCommandViewinteraction(lastCommand);
                     }
                     else if(lastCommand.indexOf('view 2d depiction') == 0) {
@@ -119687,7 +119695,7 @@ class LoadScript {
 
         if(commandTransformation.length == 2 && commandTransformation[1].substr(0,1) == '{') ic.bTransformation = true;
 
-        ic.transformCls.resetOrientation_base(commandTransformation);
+        // ic.transformCls.resetOrientation_base(commandTransformation);
 
         ic.selectionCls.oneStructurePerWindow();
 
@@ -119753,8 +119761,12 @@ class LoadScript {
           $("#ncbi_logo").hide();
         }
 
+        ic.transformCls.resetOrientation_base(commandTransformation);
+
         // an extra render to remove artifacts in transparent surface
-        if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
+        // if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
+        ic.drawCls.applyTransformation(ic._zoomFactor, ic.mouseChange, ic.quaternion);
+        ic.drawCls.render();
 
         if(me.cfg.imageonly) ic.saveFileCls.saveFile(undefined, 'png', undefined, true);
 
@@ -132253,7 +132265,7 @@ class iCn3D {
 
     this.transparentRenderOrder = false; // false: regular transparency; true: expensive renderOrder for each face
 
-    this.AFUniprotVersion = 'v4';
+    this.AFUniprotVersion = 'v6';
     this.defaultPdbId = 'stru';
 
     if(!this.icn3dui.bNode) {
@@ -132842,7 +132854,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.45.3';
+    this.REVISION = '3.45.4';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;