Issue #805: extracted namespace stuffs

src/tmdet-extension/behavior.ts

@@ -30,7 +30,7 @@ import { PluginUIContext } from 'molstar/lib/mol-plugin-ui/context';
 
 // TMDET imports
 import { MembraneOrientationRepresentationProvider, MembraneOrientationParams, MembraneOrientationRepresentation } from './representation';
-import { MembraneOrientationProvider, MembraneOrientation, TmDetDescriptorCache, MembraneOrientationNameSpace } from './prop';
+import { MembraneOrientationProvider, TmDetDescriptorCache, isTransmembrane as tmSymbol, setMembraneOrientation } from './prop';
 import { applyTransformations, createMembraneOrientation } from './transformation';
 import { ComponentsType, PDBTMDescriptor, PMS } from './types';
 import { registerTmDetSymmetry } from './symmetry';
@@ -39,7 +39,7 @@ import { TmDetColorThemeProvider, updateSiteColors } from './tmdet-color-theme';
 //import { loadInitialSnapshot, rotateCamera, storeCameraSnapshot } from './camera';
 import { DebugUtil } from './debug-utils';
 
-const Tag = MembraneOrientationNameSpace.Tag;
+const TMDET_MEMB_ORI_REPRESENTATION_TAG = 'tmdet-membrane-orientation-3d';
 const TMDET_MEMBRANE_ORIENTATION = 'TMDET Membrane Orientation';
 export const TMDET_STRUCTURE_PRESET_ID = 'tmdet-preset-membrane-orientation';
 
@@ -65,7 +65,7 @@ export const TMDETMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
             this.ctx.representation.structure.themes.colorThemeRegistry.add(TmDetColorThemeProvider);
             this.ctx.managers.lociLabels.addProvider(TmDetLabelProvider);
 
-            this.ctx.genericRepresentationControls.set(Tag.Representation, selection => {
+            this.ctx.genericRepresentationControls.set(TMDET_MEMB_ORI_REPRESENTATION_TAG, selection => {
                 const refs: GenericRepresentationRef[] = [];
                 selection.structures.forEach(structure => {
                     const memRepr = structure.genericRepresentations?.filter(r => r.cell.transform.transformer.id === MembraneOrientation3D.id)[0];
@@ -91,7 +91,7 @@ export const TMDETMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
             this.ctx.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
             this.ctx.query.structure.registry.remove(isTransmembrane);
 
-            this.ctx.genericRepresentationControls.delete(Tag.Representation);
+            this.ctx.genericRepresentationControls.delete(TMDET_MEMB_ORI_REPRESENTATION_TAG);
             this.ctx.builders.structure.representation.unregisterPreset(MembraneOrientationPreset);
 
             this.ctx.representation.structure.themes.colorThemeRegistry.remove(TmDetColorThemeProvider);
@@ -110,7 +110,7 @@ export const isTransmembrane = StructureSelectionQuery('Residues Embedded in Mem
         MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'atom-test': MembraneOrientationNameSpace.symbols.isTransmembrane.symbol(),
+                'atom-test': tmSymbol.symbol(),
             })
         ])
     ])
@@ -132,11 +132,6 @@ export const isTransmembrane = StructureSelectionQuery('Residues Embedded in Mem
 
 
 
-export let membraneOrientation: MembraneOrientation;
-export function setMembraneOrientation(orientation: MembraneOrientation) {
-    membraneOrientation = orientation;
-}
-
 export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIContext, params: any) {
     //storeCameraSnapshot(plugin); // store if it is not stored yet
 
@@ -150,7 +145,8 @@ export async function loadWithUNITMPMembraneRepresentation(plugin: PluginUIConte
         pdbtmDescriptor.side1 = params.side1;
         TmDetDescriptorCache.add(pdbtmDescriptor);
 
-        membraneOrientation = createMembraneOrientation(pdbtmDescriptor);
+        const membraneOrientation = createMembraneOrientation(pdbtmDescriptor);
+        setMembraneOrientation(membraneOrientation);
 
         // load structure
         await loadStructure(plugin, params, pdbtmDescriptor);
@@ -275,7 +271,7 @@ async function downloadData(ctx: PluginUIContext, params: any, pdbtmDescriptor:
 
 type MembraneOrientation3DType = typeof MembraneOrientation3D
 const MembraneOrientation3D = PluginStateTransform.BuiltIn({
-    name: Tag.Representation,
+    name: TMDET_MEMB_ORI_REPRESENTATION_TAG,
     display: {
         name: TMDET_MEMBRANE_ORIENTATION,
         description: 'Membrane Orientation planes and rims. Data calculated with TMDET algorithm.'
@@ -345,6 +341,6 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
 export function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PMS>, params?: StateTransformer.Params<MembraneOrientation3DType>, initialState?: Partial<StateTransform.State>) {
     const state = plugin.state.data;
     const membraneOrientation = state.build().to(structure)
-        .applyOrUpdateTagged(Tag.Representation, MembraneOrientation3D, params, { state: initialState });
+        .applyOrUpdateTagged(TMDET_MEMB_ORI_REPRESENTATION_TAG, MembraneOrientation3D, params, { state: initialState });
     return membraneOrientation.commit({ revertOnError: true });
 }

src/tmdet-extension/prop.ts

@@ -23,9 +23,7 @@ import { Vec3 } from 'molstar/lib/mol-math/linear-algebra';
 import { QuerySymbolRuntime } from 'molstar/lib/mol-script/runtime/query/base';
 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
@@ -33,8 +31,6 @@ export const MembraneOrientationParams = {
 export type MembraneOrientationParams = typeof MembraneOrientationParams
 export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
 
-export { MembraneOrientationNameSpace };
-
 /**
  * Simple storage to made PDBTM descriptor available globally.
  *
@@ -95,32 +91,30 @@ export interface MembraneOrientation {
     readonly centroid: Vec3
 }
 
-namespace MembraneOrientationNameSpace {
-    export enum Tag {
-        Representation = 'tmdet-membrane-orientation-3d'
-    }
+const pos = Vec3();
+export const isTransmembrane = QuerySymbolRuntime.Dynamic(
+        CustomPropSymbol('computed', 'tmdet-membrane-orientation.is-transmembrane', Type.Bool),
+        ctx => {
+            const { unit, structure } = ctx.element;
+            const { x, y, z } = StructureProperties.atom;
+            if (!Unit.isAtomic(unit)) return 0;
+            const membraneOrientation = MembraneOrientationProvider.get(structure).value;
+            if (!membraneOrientation) return 0;
+            Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
+            const { normalVector, planePoint1, planePoint2 } = membraneOrientation;
+            return isInMembranePlane(pos, normalVector, planePoint1, planePoint2);
+        }
+);
 
-    const pos = Vec3();
-    export const symbols = {
-        isTransmembrane: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'tmdet-membrane-orientation.is-transmembrane', Type.Bool),
-            ctx => {
-                const { unit, structure } = ctx.element;
-                const { x, y, z } = StructureProperties.atom;
-                if (!Unit.isAtomic(unit)) return 0;
-                const membraneOrientation = MembraneOrientationProvider.get(structure).value;
-                if (!membraneOrientation) return 0;
-                Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
-                const { normalVector, planePoint1, planePoint2 } = membraneOrientation;
-                return isInMembranePlane(pos, normalVector, planePoint1, planePoint2);
-            })
-    };
+export let membraneOrientation: MembraneOrientation;
+export function setMembraneOrientation(orientation: MembraneOrientation) {
+    membraneOrientation = orientation;
 }
-
 export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
     label: 'TMDET Membrane Orientation Provider',
     descriptor: CustomPropertyDescriptor({
         name: 'tmdet_computed_membrane_orientation',
-        symbols: MembraneOrientationNameSpace.symbols,
+        symbols: { isTransmembrane: isTransmembrane },
         // TODO `cifExport`
     }),
     type: 'root',
@@ -132,7 +126,7 @@ 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/viewer/helpers/model.ts

@@ -42,6 +42,7 @@ export class ModelLoader {
     ): Promise<S | ReturnType<typeof RcsbPreset.apply> | undefined> {
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
         if (reprProvider) {
+            console.log('REPR. PROVIDER:', trajectory);
             console.log('REPR. PROVIDER:', reprProvider);
             return this.plugin.builders.structure.hierarchy.applyPreset(trajectory, reprProvider, params);
         } else {