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+/**
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+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ *
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+ * @author David Sehnal <david.sehnal@gmail.com>
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+ */
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+
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+import { StateTree, StateBuilder, StateAction } from 'mol-state';
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+import { StateTransforms } from 'mol-plugin/state/transforms';
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+import { createModelTree, complexRepresentation } from 'mol-plugin/state/actions/structure';
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+import { PluginContext } from 'mol-plugin/context';
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+import { PluginStateObject } from 'mol-plugin/state/objects';
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+import { ParamDefinition } from 'mol-util/param-definition';
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+import { PluginCommands } from 'mol-plugin/command';
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+import { Vec3 } from 'mol-math/linear-algebra';
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+import { PluginStateSnapshotManager } from 'mol-plugin/state/snapshots';
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+import { MolScriptBuilder as MS } from 'mol-script/language/builder';
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+import { Text } from 'mol-geo/geometry/text/text';
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+import { UUID } from 'mol-util';
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+import { ColorNames } from 'mol-util/color/tables';
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+import { Camera } from 'mol-canvas3d/camera';
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+import { StructureRepresentation3DHelpers } from 'mol-plugin/state/transforms/representation';
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+
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+export const CreateJoleculeState = StateAction.build({
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+ display: { name: 'Jolecule State' },
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+ params: { id: ParamDefinition.Text('1mbo') },
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+ from: PluginStateObject.Root
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+})(async ({ ref, state, params }, plugin: PluginContext) => {
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+ try {
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+ const id = params.id.trim().toLowerCase();
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+ const data = await plugin.runTask(plugin.fetch({ url: `https://jolecule.appspot.com/pdb/${id}.views.json`, type: 'json' })) as JoleculeSnapshot[];
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+
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+ data.sort((a, b) => a.order - b.order);
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+
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+ await PluginCommands.State.RemoveObject.dispatch(plugin, { state, ref }, true);
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+ plugin.state.snapshots.clear();
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+
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+ const template = createTemplate(plugin, state.tree, id);
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+ const snapshots = data.map((e, idx) => buildSnapshot(plugin, template, { e, idx, len: data.length }));
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+ for (const s of snapshots) {
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+ plugin.state.snapshots.add(s);
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+ }
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+
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+ PluginCommands.State.Snapshots.Apply.dispatch(plugin, { id: snapshots[0].snapshot.id }, true);
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+ } catch (e) {
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+ plugin.log.error(`Jolecule Failed: ${e}`);
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+ }
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+});
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+
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+interface JoleculeSnapshot {
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+ order: number,
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+ distances: { i_atom1: number, i_atom2: number }[],
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+ labels: { i_atom: number, text: string }[],
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+ camera: { up: Vec3, pos: Vec3, in: Vec3, slab: { z_front: number, z_back: number, zoom: number } },
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+ selected: number[],
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+ text: string
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+}
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+
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+function createTemplate(plugin: PluginContext, tree: StateTree, id: string) {
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+ const b = new StateBuilder.Root(tree);
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+ const data = b.toRoot().apply(StateTransforms.Data.Download, { url: `https://www.ebi.ac.uk/pdbe/static/entry/${id}_updated.cif` }, { props: { isGhost: true }});
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+ const model = createModelTree(data, 'cif');
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+ const structure = model.apply(StateTransforms.Model.StructureFromModel, {}, { ref: 'structure' });
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+ complexRepresentation(plugin, structure, { hideWater: true });
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+ return b.getTree();
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+}
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+
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+const labelOptions = {
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+ ...ParamDefinition.getDefaultValues(Text.Params),
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+ sizeFactor: 1.5,
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+ offsetX: 1,
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+ offsetY: 1,
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+ offsetZ: 10,
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+ background: true,
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+ backgroundMargin: 0.2,
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+ backgroundColor: ColorNames.snow,
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+ backgroundOpacity: 0.9
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+}
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+
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+// const distanceLabelOptions = {
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+// ...ParamDefinition.getDefaultValues(Text.Params),
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+// sizeFactor: 1,
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+// offsetX: 0,
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+// offsetY: 0,
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+// offsetZ: 10,
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+// background: true,
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+// backgroundMargin: 0.2,
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+// backgroundColor: ColorNames.snow,
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+// backgroundOpacity: 0.9
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+// }
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+
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+function buildSnapshot(plugin: PluginContext, template: StateTree, params: { e: JoleculeSnapshot, idx: number, len: number }): PluginStateSnapshotManager.Entry {
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+ const b = new StateBuilder.Root(template);
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+
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+ let i = 0;
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+ for (const l of params.e.labels) {
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+ b.to('structure')
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+ .apply(StateTransforms.Model.StructureSelection, { query: createQuery([l.i_atom]), label: `Label ${++i}` })
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+ .apply(StateTransforms.Representation.StructureLabels3D, {
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+ target: { name: 'static-text', params: { value: l.text || '' } },
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+ options: labelOptions
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+ });
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+ }
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+ if (params.e.selected && params.e.selected.length > 0) {
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+ b.to('structure')
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+ .apply(StateTransforms.Model.StructureSelection, { query: createQuery(params.e.selected), label: `Selected` })
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+ .apply(StateTransforms.Representation.StructureRepresentation3D,
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+ StructureRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'ball-and-stick'));
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+ }
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+ // TODO
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+ // for (const l of params.e.distances) {
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+ // b.to('structure')
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+ // .apply(StateTransforms.Model.StructureSelection, { query: createQuery([l.i_atom1, l.i_atom2]), label: `Distance ${++i}` })
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+ // .apply(StateTransforms.Representation.StructureLabels3D, {
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+ // target: { name: 'static-text', params: { value: l. || '' } },
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+ // options: labelOptions
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+ // });
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+ // }
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+ return PluginStateSnapshotManager.Entry({
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+ id: UUID.create22(),
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+ data: { tree: StateTree.toJSON(b.getTree()) },
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+ camera: {
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+ current: getCameraSnapshot(params.e.camera),
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+ transitionStyle: 'animate',
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+ transitionDurationInMs: 350
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+ }
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+ }, {
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+ name: params.e.text
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+ });
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+}
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+
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+function getCameraSnapshot(e: JoleculeSnapshot['camera']): Camera.Snapshot {
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+ const direction = Vec3.sub(Vec3.zero(), e.pos, e.in);
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+ Vec3.normalize(direction, direction);
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+ const up = Vec3.sub(Vec3.zero(), e.pos, e.up);
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+ Vec3.normalize(up, up);
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+
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+ const s: Camera.Snapshot = {
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+ mode: 'perspective',
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+ position: Vec3.scaleAndAdd(Vec3.zero(), e.pos, direction, e.slab.zoom),
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+ target: e.pos,
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+ direction,
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+ up,
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+ near: e.slab.zoom + e.slab.z_front,
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+ far: e.slab.zoom + e.slab.z_back,
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+ fogNear: e.slab.zoom + e.slab.z_front,
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+ fogFar: e.slab.zoom + e.slab.z_back,
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+ fov: Math.PI / 4,
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+ zoom: 1
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+ };
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+ return s;
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+}
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+
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+function createQuery(atomIndices: number[]) {
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+ if (atomIndices.length === 0) return MS.struct.generator.empty();
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+
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+ return MS.struct.generator.atomGroups({
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+ 'atom-test': atomIndices.length === 1
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+ ? MS.core.rel.eq([MS.struct.atomProperty.core.sourceIndex(), atomIndices[0]])
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+ : MS.core.set.has([MS.set.apply(null, atomIndices), MS.struct.atomProperty.core.sourceIndex()]),
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+ 'group-by': 0
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+ });
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+}
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David Sehnal