Issue #805: applying color theme from trajectory hierarchy preset

src/tmdet-extension/behavior.ts

@@ -161,6 +161,13 @@ export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIConte
     })(); }, 500);
 }
 
+export async function registerRegionDescriptor(plugin: PluginUIContext, url: string, side1: "Inside"|"Outside"|null) {
+    const params = { regionDescriptorUrl: url };
+    const pdbtmDescriptor: PDBTMDescriptor = await downloadRegionDescriptor(plugin, params);
+    pdbtmDescriptor.side1 = side1;
+    TmDetDescriptorCache.add(pdbtmDescriptor);
+}
+
 async function downloadRegionDescriptor(plugin: PluginUIContext, params: any): Promise<any> {
     // run a fetch task
     const downloadResult: string = await plugin.runTask(plugin.fetch({ url: params.regionDescriptorUrl })) as string;
@@ -173,7 +180,7 @@ async function createStructureRepresentation(plugin: PluginUIContext, pdbtmDescr
     const structure: StateObjectRef<PMS> = plugin.managers.structure.hierarchy.current.models[0].structures[0].cell;
     const components = await createStructureComponents(plugin, structure);
 
-    await applyTransformations(plugin, pdbtmDescriptor);
+    applyTransformations(plugin, pdbtmDescriptor);
 
     await buildStructureRepresentation(plugin, pdbtmDescriptor, components);
 }

src/tmdet-extension/camera.ts

@@ -13,7 +13,6 @@ import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { Camera } from 'molstar/lib/mol-canvas3d/camera';
 import { DebugUtil } from './debug-utils';
 
-
 let initialSnapshot: Camera.Snapshot;
 
 export function storeCameraSnapshot(plugin: PluginUIContext): void {

src/tmdet-extension/prop.ts

@@ -25,6 +25,7 @@ import { CustomPropSymbol } from 'molstar/lib/mol-script/language/symbol';
 import { Type } from 'molstar/lib/mol-script/language/type';
 import { membraneOrientation } from './behavior';
 import { ChainList, PDBTMDescriptor } from './types';
+import { DebugUtil } from './debug-utils';
 
 export const MembraneOrientationParams = {
     ...TMDETParams
@@ -131,7 +132,7 @@ export const MembraneOrientationProvider: CustomStructureProperty.Provider<Membr
     },
     isApplicable: (data: Structure) => true,
     obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneOrientationProps>) => {
-        //DebugUtil.log('obtain:: DEBUG', data.customPropertyDescriptors);
+        DebugUtil.log('obtain:: DEBUG', data.customPropertyDescriptors);
         let result = membraneOrientation;
         //DebugUtil.log("RESULT of 'obtain:'", result);
         return { value: result };

src/tmdet-extension/representation.ts

@@ -10,7 +10,7 @@ import { Vec3, Mat4 } from 'molstar/lib/mol-math/linear-algebra';
 import { Representation, RepresentationContext, RepresentationParamsGetter } from 'molstar/lib/mol-repr/representation';
 import { Structure } from 'molstar/lib/mol-model/structure';
 import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from 'molstar/lib/mol-repr/structure/representation';
-import { MembraneOrientation } from './prop';
+import { MembraneOrientation, MembraneOrientationProvider } from './prop';
 import { ThemeRegistryContext } from 'molstar/lib/mol-theme/theme';
 import { ShapeRepresentation } from 'molstar/lib/mol-repr/shape/representation';
 import { Shape } from 'molstar/lib/mol-model/shape';
@@ -21,7 +21,6 @@ import { LinesBuilder } from 'molstar/lib/mol-geo/geometry/lines/lines-builder';
 import { Circle } from 'molstar/lib/mol-geo/primitive/circle';
 import { transformPrimitive } from 'molstar/lib/mol-geo/primitive/primitive';
 import { MeshBuilder } from 'molstar/lib/mol-geo/geometry/mesh/mesh-builder';
-import { MembraneOrientationProvider } from './prop';
 import { MarkerActions } from 'molstar/lib/mol-util/marker-action';
 import { lociLabel } from 'molstar/lib/mol-theme/label';
 import { ColorNames } from 'molstar/lib/mol-util/color/names';

src/tmdet-extension/transformation.ts

@@ -19,7 +19,6 @@ import { MembraneOrientation } from './prop';
 import { TmDetColorThemeProvider } from './tmdet-color-theme';
 import { DebugUtil } from './debug-utils';
 
-
 export function applyTransformations(plugin: PluginUIContext, pdbtmDescriptor: PDBTMDescriptor) {
     const annotations = pdbtmDescriptor.additional_entry_annotations;
 

src/viewer/helpers/preset.ts

@@ -279,7 +279,9 @@ export const RcsbPreset = TrajectoryHierarchyPresetProvider({
             representation = await plugin.builders.structure.representation.applyPreset<any>(structureProperties!, 'auto', { ...presetParams, theme: { globalName: 'nakb', focus: { name: 'nakb' } } });
         } else {
             console.log('HERE WE GO:', { structure: structure, structureProps: structureProperties, presetParams: presetParams });
-            representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', presetParams);
+            //representation = await plugin.builders.structure.representation.applyPreset(structureProperties!, 'auto', presetParams);
+            representation = await plugin.builders.structure.representation.applyPreset(
+                structureProperties!, 'auto', { theme: { globalName: 'tmdet-custom-color-theme' } });
         }
 
         console.log('STRUCTURE REPRESENTATION:', representation);

src/viewer/index.ts

@@ -53,7 +53,7 @@ import { AssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/
 import { wwPDBChemicalComponentDictionary } from 'molstar/lib/extensions/wwpdb/ccd/behavior';
 import { ChemicalCompontentTrajectoryHierarchyPreset } from 'molstar/lib/extensions/wwpdb/ccd/representation';
 import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
-import { TMDETMembraneOrientation, loadWithUNITMPMembraneRepresentation } from '../tmdet-extension/behavior';
+import { TMDETMembraneOrientation, registerRegionDescriptor } from '../tmdet-extension/behavior';
 
 /** package version, filled in at bundle build time */
 declare const __RCSB_MOLSTAR_VERSION__: string;
@@ -345,12 +345,10 @@ export class Viewer {
     loadStructureFromUrl<P, S>(url: string, format: BuiltInTrajectoryFormat, isBinary: boolean, config?: {props?: PresetProps & { dataLabel?: string }; matrix?: Mat4; reprProvider?: TrajectoryHierarchyPresetProvider<P, S>, params?: P}) {
         console.log('RCSB loadStructureFromUrl II', this.customState);
         const pdbId = '1afo';
-        //return this.customState.modelLoader.load({ fileOrUrl: url, format, isBinary }, config?.props, config?.matrix, config?.reprProvider, config?.params);
-        return loadWithUNITMPMembraneRepresentation(this._plugin, {
-            structureUrl: `https://www.ebi.ac.uk/pdbe/entry-files/download/${pdbId}_updated.cif`,
-            regionDescriptorUrl: `/${pdbId}.json`,
-            side1: "Periplasm"
-        });
+        const descriptorUrl = `/${pdbId}.json`;
+        registerRegionDescriptor(this._plugin, descriptorUrl, "Inside");
+
+        return this.customState.modelLoader.load({ fileOrUrl: url, format, isBinary }, config?.props, config?.matrix, config?.reprProvider, config?.params);
     }
 
     loadSnapshotFromUrl(url: string, type: PluginState.SnapshotType) {