Issue #805: preset2 for PRACTICE - TODO: memb.ori. is not set

src/examples/assembly-tm/preset2.ts

@@ -0,0 +1,159 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
+import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
+import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
+import { RootStructureDefinition } from 'molstar/lib/mol-plugin-state/helpers/root-structure';
+import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';
+import {
+    StateObjectSelector,
+    StateObject,
+    StateTransformer,
+    StateObjectRef,
+    StateTransform
+} from 'molstar/lib/mol-state';
+import { Mat4, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+import { MembraneOrientationPreset } from 'molstar/lib/extensions/anvil/behavior';
+import { Target } from '@rcsb/rcsb-molstar/build/src/viewer/helpers/selection';
+import { TMDET_STRUCTURE_PRESET_ID } from './tmdet-extension/behavior';
+import { TmDetDescriptorCache } from './tmdet-extension/prop';
+import { DebugUtil } from './tmdet-extension/debug-utils';
+import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
+import { applyTransformations } from './tmdet-extension/transformation';
+
+type BaseProps = {
+    assemblyId?: string
+    modelIndex?: number
+    plddt?: 'off' | 'single-chain' | 'on'
+}
+
+export { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
+
+export type AlignmentProps = {
+    kind: 'alignment',
+    targets?: (Target & {
+        matrix?: Mat4
+    })[],
+    colors: {
+        value: number,
+        targets: Target[]
+    }[]
+} & BaseProps
+
+export type EmptyProps = {
+    kind: 'empty'
+} & BaseProps
+
+type ValidationProps = {
+    kind: 'validation'
+    colorTheme?: string
+    showClashes?: boolean
+} & BaseProps
+
+type StandardProps = {
+    kind: 'standard'
+} & BaseProps
+
+type SymmetryProps = {
+    kind: 'symmetry'
+    symmetryIndex?: number
+} & BaseProps
+
+type FeatureProps = {
+    kind: 'feature'
+    target: Target
+} & BaseProps
+
+type DensityProps = {
+    kind: 'density'
+} & BaseProps
+
+type MembraneProps = {
+    kind: 'membrane',
+} & BaseProps
+
+type FeatureDensityProps = {
+    kind: 'feature-density',
+    target: Target,
+    radius?: number,
+    hiddenChannels?: string[]
+} & BaseProps
+
+export type MotifProps = {
+    kind: 'motif',
+    label?: string,
+    targets: Target[],
+    color?: number
+} & BaseProps
+
+export type NakbProps = {
+    kind: 'nakb'
+} & BaseProps
+
+export type PresetProps = ValidationProps | StandardProps | SymmetryProps | FeatureProps | DensityProps | AlignmentProps |
+MembraneProps | FeatureDensityProps | MotifProps | NakbProps | EmptyProps;
+
+const RcsbParams = () => ({
+    preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
+});
+
+type StructureObject = StateObjectSelector<PluginStateObject.Molecule.Structure, StateTransformer<StateObject<any, StateObject.Type<any>>, StateObject<any, StateObject.Type<any>>, any>>
+
+export const TmDetRcsbPreset = TrajectoryHierarchyPresetProvider({
+    id: 'tmdet-preset-trajectory-rcsb',
+    display: { name: 'TMDET RCSB Preset' },
+    isApplicable: () => true,
+    params: RcsbParams,
+    async apply(trajectory: StateObjectRef<PluginStateObject.Molecule.Trajectory>, params, plugin) {
+        console.log('TMDET RCSB PRESET: apply start', params);
+
+        const modelParams = { modelIndex: 0 };
+
+        const props = {
+            type: {
+                name: 'assembly' as const,
+                params: { id: '1' }
+            }
+        };
+
+        await plugin.state.data.build().to(trajectory)
+            .apply(StateTransforms.Model.ModelFromTrajectory, modelParams, { ref: 'model' })
+            .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'assembly' })
+            .apply(StateTransforms.Model.TransformStructureConformation, {
+                    transform: {
+                        name: 'components',
+                        params: { axis: Vec3.unitY, angle: 90, translation: Vec3.zero() }
+                    }
+                })
+            .commit();
+
+        const builder = plugin.builders.structure;
+        const model = new StateObjectSelector(plugin.state.data.build().to('model').ref, plugin.state.data);
+        const modelProperties = await builder.insertModelProperties(model.ref);
+        const structure = new StateObjectSelector(plugin.state.data.build().to('assembly').ref, plugin.state.data);
+        const structureProperties = await builder.insertStructureProperties(structure);
+        const representation = await plugin.builders.structure.representation.applyPreset(
+            structureProperties, 'auto', { theme: { globalName: 'tmdet-custom-color-theme' } });
+
+        // await plugin.builders.structure.hierarchy.applyPreset(
+        //     trajectory, 'default', { representationPreset: TMDET_STRUCTURE_PRESET_ID as any });
+
+        (window as any).plugin = plugin;
+
+        const result = {
+            model,
+            modelProperties,
+            unitcell: undefined,
+            structure,
+            structureProperties,
+            representation
+        };
+        console.log(result);
+
+        return result;
+    }
+});