TmMolStar/src/TmFv3DApp/TmTrajectoryHierarchyPreset.ts

/**
 * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
/**
 * Copyright (C) 2023, Protein Bioinformatics Research Group, RCNS
 *
 * Licensed under CC BY-NC 4.0, see LICENSE file for more info.
 *
 * @author Gabor Tusnady <tusnady.gabor@ttk.hu>
 * @author Csongor Gerdan <gerdan.csongor@ttk.hu>
 */

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 {
    StateObjectSelector,
    StateObjectRef,
} from 'molstar/lib/mol-state';
import { MembraneOrientationPreset } from './tmdet-extension/behavior';
import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
import { applyTransformations } from './tmdet-extension/transformation';
import { TmDetDescriptorCache } from './tmdet-extension/prop';
import { registerTmDetSymmetry } from './tmdet-extension/symmetry';
import { PresetProps } from '@rcsb/rcsb-molstar/build/src/viewer/helpers/preset';

const RcsbParams = () => ({
    preset: PD.Value<PresetProps>({ kind: 'standard', assemblyId: '' }, { isHidden: true })
});

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 entryId = (trajectory as any).obj?.data.representative.entryId;
        console.log('TRAJECTORY entry ID:', entryId);
        const descriptor = TmDetDescriptorCache.get(entryId);
        registerTmDetSymmetry(descriptor!);

        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' })
            .commit();

        //applyTransformations(plugin, descriptor!);

        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<any>(structureProperties, MembraneOrientationPreset, {});


        (window as any).plugin = plugin;

        const result = {
            model,
            modelProperties,
            unitcell: undefined,
            structure,
            structureProperties,
            representation
        };
        console.log('TmDetRcsbPreset apply result', result);

        return result;
    }
});