TmMolStar/src/apps/viewer/extensions/jolecule.ts

/**
 * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 */

import { StateTree, StateBuilder, StateAction, State } from '../../../mol-state';
import { StateTransforms } from '../../../mol-plugin/state/transforms';
import { createModelTree, complexRepresentation } from '../../../mol-plugin/state/actions/structure';
import { PluginContext } from '../../../mol-plugin/context';
import { PluginStateObject } from '../../../mol-plugin/state/objects';
import { ParamDefinition } from '../../../mol-util/param-definition';
import { PluginCommands } from '../../../mol-plugin/command';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { PluginStateSnapshotManager } from '../../../mol-plugin/state/snapshots';
import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
import { Text } from '../../../mol-geo/geometry/text/text';
import { UUID } from '../../../mol-util';
import { ColorNames } from '../../../mol-util/color/tables';
import { Camera } from '../../../mol-canvas3d/camera';
import { StructureRepresentation3DHelpers } from '../../../mol-plugin/state/transforms/representation';

export const CreateJoleculeState = StateAction.build({
    display: { name: 'Jolecule State Import' },
    params: { id: ParamDefinition.Text('1mbo') },
    from: PluginStateObject.Root
})(async ({ ref, state, params }, plugin: PluginContext) => {
    try {
        const id = params.id.trim().toLowerCase();
        const data = await plugin.runTask(plugin.fetch({ url: `https://jolecule.appspot.com/pdb/${id}.views.json`, type: 'json' })) as JoleculeSnapshot[];

        data.sort((a, b) => a.order - b.order);

        await PluginCommands.State.RemoveObject.dispatch(plugin, { state, ref });
        plugin.state.snapshots.clear();

        const template = createTemplate(plugin, state, id);
        const snapshots = data.map((e, idx) => buildSnapshot(plugin, template, { e, idx, len: data.length }));
        for (const s of snapshots) {
            plugin.state.snapshots.add(s);
        }

        PluginCommands.State.Snapshots.Apply.dispatch(plugin, { id: snapshots[0].snapshot.id });
    } catch (e) {
        plugin.log.error(`Jolecule Failed: ${e}`);
    }
});

interface JoleculeSnapshot {
    order: number,
    distances: { i_atom1: number, i_atom2: number }[],
    labels: { i_atom: number, text: string }[],
    camera: { up: Vec3, pos: Vec3, in: Vec3, slab: { z_front: number, z_back: number, zoom: number } },
    selected: number[],
    text: string
}

function createTemplate(plugin: PluginContext, state: State, id: string) {
    const b = new StateBuilder.Root(state.tree);
    const data = b.toRoot().apply(StateTransforms.Data.Download, { url: `https://www.ebi.ac.uk/pdbe/static/entry/${id}_updated.cif` }, { state: { isGhost: true }});
    const model = createModelTree(data, 'cif');
    const structure = model.apply(StateTransforms.Model.StructureFromModel, {});
    complexRepresentation(plugin, structure, { hideWater: true });
    return { tree: b.getTree(), structure: structure.ref };
}

const labelOptions: ParamDefinition.Values<Text.Params> = {
    ...ParamDefinition.getDefaultValues(Text.Params),
    tether: true,
    sizeFactor: 1.3,
    attachment: 'bottom-right',
    offsetZ: 10,
    background: true,
    backgroundMargin: 0.2,
    backgroundColor: ColorNames.skyblue,
    backgroundOpacity: 0.9
}

// const distanceLabelOptions = {
//     ...ParamDefinition.getDefaultValues(Text.Params),
//     sizeFactor: 1,
//     offsetX: 0,
//     offsetY: 0,
//     offsetZ: 10,
//     background: true,
//     backgroundMargin: 0.2,
//     backgroundColor: ColorNames.snow,
//     backgroundOpacity: 0.9
// }

function buildSnapshot(plugin: PluginContext, template: { tree: StateTree, structure: string }, params: { e: JoleculeSnapshot, idx: number, len: number }): PluginStateSnapshotManager.Entry {
    const b = new StateBuilder.Root(template.tree);

    let i = 0;
    for (const l of params.e.labels) {
        const query = createQuery([l.i_atom]);
        const group = b.to(template.structure)
            .group(StateTransforms.Misc.CreateGroup, { label: `Label ${++i}` });

        group
            .apply(StateTransforms.Model.StructureSelection, { query, label: 'Atom' })
            .apply(StateTransforms.Representation.StructureLabels3D, {
                target: { name: 'static-text', params: { value: l.text || '' } },
                options: labelOptions
            });

        group
            .apply(StateTransforms.Model.StructureSelection, { query: MS.struct.modifier.wholeResidues([query]), label: 'Residue' })
            .apply(StateTransforms.Representation.StructureRepresentation3D,
                StructureRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'ball-and-stick', {  }));
    }
    if (params.e.selected && params.e.selected.length > 0) {
        b.to(template.structure)
            .apply(StateTransforms.Model.StructureSelection, { query: createQuery(params.e.selected), label: `Selected` })
            .apply(StateTransforms.Representation.StructureRepresentation3D,
                StructureRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'ball-and-stick'));
    }
    // TODO
    // for (const l of params.e.distances) {
    //     b.to('structure')
    //         .apply(StateTransforms.Model.StructureSelection, { query: createQuery([l.i_atom1, l.i_atom2]), label: `Distance ${++i}` })
    //         .apply(StateTransforms.Representation.StructureLabels3D, {
    //             target: { name: 'static-text', params: { value: l. || '' } },
    //             options: labelOptions
    //         });
    // }
    return PluginStateSnapshotManager.Entry({
        id: UUID.create22(),
        data: { tree: StateTree.toJSON(b.getTree()) },
        camera: {
            current: getCameraSnapshot(params.e.camera),
            transitionStyle: 'animate',
            transitionDurationInMs: 350
        }
    }, {
        name:  params.e.text
    });
}

function getCameraSnapshot(e: JoleculeSnapshot['camera']): Camera.Snapshot {
    const direction = Vec3.sub(Vec3.zero(), e.pos, e.in);
    Vec3.normalize(direction, direction);
    const up = Vec3.sub(Vec3.zero(), e.pos, e.up);
    Vec3.normalize(up, up);

    const s: Camera.Snapshot = {
        mode: 'perspective',
        position: Vec3.scaleAndAdd(Vec3.zero(), e.pos, direction, e.slab.zoom),
        target: e.pos,
        direction,
        up,
        near: e.slab.zoom + e.slab.z_front,
        far: e.slab.zoom + e.slab.z_back,
        fogNear: e.slab.zoom + e.slab.z_front,
        fogFar: e.slab.zoom + e.slab.z_back,
        fov: Math.PI / 4,
        zoom: 1
    };
    return s;
}

function createQuery(atomIndices: number[]) {
    if (atomIndices.length === 0) return MS.struct.generator.empty();

    return MS.struct.generator.atomGroups({
        'atom-test': atomIndices.length === 1
            ? MS.core.rel.eq([MS.struct.atomProperty.core.sourceIndex(), atomIndices[0]])
            : MS.core.set.has([MS.set.apply(null, atomIndices), MS.struct.atomProperty.core.sourceIndex()]),
        'group-by': 0
    });
}