2.0.0-dev.9

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.0.0-dev.8",
+  "version": "2.0.0-dev.9",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/apps/viewer/index.html

@@ -49,11 +49,13 @@
             if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
                 pdbProvider: pdbProvider || 'pdbe',
                 emdbProvider: emdbProvider || 'pdbe',
             });

src/apps/viewer/index.ts

@@ -68,6 +68,7 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
+    collapseLeftPanel: false,
     disableAntialiasing: false,
     pixelScale: 1,
     enableWboit: true,
@@ -106,6 +107,12 @@ export class Viewer {
                     isExpanded: o.layoutIsExpanded,
                     showControls: o.layoutShowControls,
                     controlsDisplay: o.layoutControlsDisplay,
+                    regionState: {
+                        bottom: 'full',
+                        left: o.collapseLeftPanel ? 'collapsed' : 'full',
+                        right: 'full',
+                        top: 'full',
+                    }
                 },
             },
             components: {

src/mol-gl/compute/marching-cubes/isosurface.ts

@@ -192,6 +192,15 @@ export function createIsosurfaceBuffers(ctx: WebGLContext, activeVoxelsBase: Tex
 
 //
 
+/**
+ * GPU isosurface extraction
+ *
+ * Algorithm from "High‐speed Marching Cubes using HistoPyramids"
+ * by C Dyken, G Ziegler, C Theobalt, HP Seidel
+ * https://doi.org/10.1111/j.1467-8659.2008.01182.x
+ *
+ * Implementation based on http://www.miaumiau.cat/2016/10/stream-compaction-in-webgl/
+ */
 export function extractIsosurface(ctx: WebGLContext, volumeData: Texture, gridDim: Vec3, gridTexDim: Vec3, gridTexScale: Vec2, transform: Mat4, isoValue: number, packedGroup: boolean, vertexTexture?: Texture, groupTexture?: Texture, normalTexture?: Texture) {
     // console.time('calcActiveVoxels');
     const activeVoxelsTex = calcActiveVoxels(ctx, volumeData, gridDim, gridTexDim, isoValue, gridTexScale);

src/mol-plugin-ui/spec.ts

@@ -5,13 +5,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { StateActions } from '../mol-plugin-state/actions';
-import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
-import { StateTransforms } from '../mol-plugin-state/transforms';
+
 import { StateTransformParameters } from '../mol-plugin-ui/state/common';
 import { DefaultPluginSpec, PluginSpec } from '../mol-plugin/spec';
 import { StateAction, StateTransformer } from '../mol-state';
-import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 
 export { PluginUISpec };
 
@@ -40,50 +37,4 @@ namespace PluginUISpec {
 
 export const DefaultPluginUISpec = (): PluginUISpec => ({
     ...DefaultPluginSpec(),
-    actions: [
-        PluginSpec.Action(StateActions.Structure.DownloadStructure),
-        PluginSpec.Action(StateActions.Structure.AddTrajectory),
-        PluginSpec.Action(StateActions.Volume.DownloadDensity),
-        PluginSpec.Action(StateActions.DataFormat.DownloadFile),
-        PluginSpec.Action(StateActions.DataFormat.OpenFiles),
-        PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
-        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
-
-        // Volume streaming
-        PluginSpec.Action(InitVolumeStreaming),
-        PluginSpec.Action(BoxifyVolumeStreaming),
-        PluginSpec.Action(CreateVolumeStreamingBehavior),
-
-        PluginSpec.Action(StateTransforms.Data.Download),
-        PluginSpec.Action(StateTransforms.Data.ParseCif),
-        PluginSpec.Action(StateTransforms.Data.ParseCcp4),
-        PluginSpec.Action(StateTransforms.Data.ParseDsn6),
-
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromMmCif),
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromCifCore),
-        PluginSpec.Action(StateTransforms.Model.TrajectoryFromPDB),
-        PluginSpec.Action(StateTransforms.Model.TransformStructureConformation),
-        PluginSpec.Action(StateTransforms.Model.StructureFromModel),
-        PluginSpec.Action(StateTransforms.Model.StructureFromTrajectory),
-        PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
-        PluginSpec.Action(StateTransforms.Model.StructureSelectionFromScript),
-        PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDistance3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsAngle3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDihedral3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsLabel3D),
-        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsOrientation3D),
-        PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
-        PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
-        PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
-        PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
-
-        PluginSpec.Action(AssignColorVolume),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromDsn6),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromCube),
-        PluginSpec.Action(StateTransforms.Volume.VolumeFromDx),
-        PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
-    ]
 });

src/mol-plugin/spec.ts

@@ -17,6 +17,10 @@ import { PluginBehaviors } from './behavior';
 import { StructureFocusRepresentation } from './behavior/dynamic/selection/structure-focus-representation';
 import { PluginConfigItem } from './config';
 import { PluginLayoutStateProps } from './layout';
+import { StateActions } from '../mol-plugin-state/actions';
+import { AssignColorVolume } from '../mol-plugin-state/actions/volume';
+import { StateTransforms } from '../mol-plugin-state/transforms';
+import { BoxifyVolumeStreaming, CreateVolumeStreamingBehavior, InitVolumeStreaming } from '../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 
 export { PluginSpec };
 
@@ -55,6 +59,52 @@ namespace PluginSpec {
 }
 
 export const DefaultPluginSpec = (): PluginSpec => ({
+    actions: [
+        PluginSpec.Action(StateActions.Structure.DownloadStructure),
+        PluginSpec.Action(StateActions.Structure.AddTrajectory),
+        PluginSpec.Action(StateActions.Volume.DownloadDensity),
+        PluginSpec.Action(StateActions.DataFormat.DownloadFile),
+        PluginSpec.Action(StateActions.DataFormat.OpenFiles),
+        PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
+        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
+
+        // Volume streaming
+        PluginSpec.Action(InitVolumeStreaming),
+        PluginSpec.Action(BoxifyVolumeStreaming),
+        PluginSpec.Action(CreateVolumeStreamingBehavior),
+
+        PluginSpec.Action(StateTransforms.Data.Download),
+        PluginSpec.Action(StateTransforms.Data.ParseCif),
+        PluginSpec.Action(StateTransforms.Data.ParseCcp4),
+        PluginSpec.Action(StateTransforms.Data.ParseDsn6),
+
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromMmCif),
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromCifCore),
+        PluginSpec.Action(StateTransforms.Model.TrajectoryFromPDB),
+        PluginSpec.Action(StateTransforms.Model.TransformStructureConformation),
+        PluginSpec.Action(StateTransforms.Model.StructureFromModel),
+        PluginSpec.Action(StateTransforms.Model.StructureFromTrajectory),
+        PluginSpec.Action(StateTransforms.Model.ModelFromTrajectory),
+        PluginSpec.Action(StateTransforms.Model.StructureSelectionFromScript),
+        PluginSpec.Action(StateTransforms.Representation.StructureRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDistance3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsAngle3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsDihedral3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsLabel3D),
+        PluginSpec.Action(StateTransforms.Representation.StructureSelectionsOrientation3D),
+        PluginSpec.Action(StateTransforms.Representation.ModelUnitcell3D),
+        PluginSpec.Action(StateTransforms.Representation.ExplodeStructureRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
+        PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
+        PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
+
+        PluginSpec.Action(AssignColorVolume),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromDsn6),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromCube),
+        PluginSpec.Action(StateTransforms.Volume.VolumeFromDx),
+        PluginSpec.Action(StateTransforms.Representation.VolumeRepresentation3D),
+    ],
     behaviors: [
         PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
         PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),