/** * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose */ import { ParamDefinition as PD } from '../../../../../mol-util/param-definition' import { AssemblySymmetryProvider, AssemblySymmetry } from '../../../../../mol-model-props/rcsb/assembly-symmetry'; import { PluginBehavior } from '../../../behavior'; import { AssemblySymmetryParams, AssemblySymmetryRepresentation } from '../../../../../mol-model-props/rcsb/representations/assembly-symmetry'; import { AssemblySymmetryClusterColorThemeProvider } from '../../../../../mol-model-props/rcsb/themes/assembly-symmetry-cluster'; import { PluginStateTransform, PluginStateObject } from '../../../../../mol-plugin-state/objects'; import { Task } from '../../../../../mol-task'; import { PluginContext } from '../../../../context'; import { StateTransformer, StateAction, StateObject, StateTransform, StateObjectRef } from '../../../../../mol-state'; import { GenericRepresentationRef } from '../../../../../mol-plugin-state/manager/structure/hierarchy-state'; import { AssemblySymmetryControls } from './ui/assembly-symmetry'; import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../../../mol-plugin-state/builder/structure/representation-preset'; const Tag = AssemblySymmetry.Tag export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean }>({ name: 'rcsb-assembly-symmetry-prop', category: 'custom-props', display: { name: 'Assembly Symmetry', description: 'Assembly Symmetry data calculated with BioJava, obtained via RCSB PDB.' }, ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> { private provider = AssemblySymmetryProvider register(): void { this.ctx.state.data.actions.add(InitAssemblySymmetry3D) this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach); this.ctx.representation.structure.themes.colorThemeRegistry.add(AssemblySymmetryClusterColorThemeProvider) this.ctx.genericRepresentationControls.set(Tag.Representation, selection => { const refs: GenericRepresentationRef[] = [] selection.structures.forEach(structure => { const symmRepr = structure.genericRepresentations?.filter(r => r.cell.transform.transformer.id === AssemblySymmetry3D.id)[0] if (symmRepr) refs.push(symmRepr) }) return [refs, 'Symmetries'] }) this.ctx.customStructureControls.set(Tag.Representation, AssemblySymmetryControls as any) this.ctx.builders.structure.representation.registerPreset(AssemblySymmetryPreset) } update(p: { autoAttach: boolean }) { let updated = this.params.autoAttach !== p.autoAttach this.params.autoAttach = p.autoAttach; this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach); return updated; } unregister() { this.ctx.state.data.actions.remove(InitAssemblySymmetry3D) this.ctx.customStructureProperties.unregister(this.provider.descriptor.name); this.ctx.representation.structure.themes.colorThemeRegistry.remove(AssemblySymmetryClusterColorThemeProvider) this.ctx.genericRepresentationControls.delete(Tag.Representation) this.ctx.customStructureControls.delete(Tag.Representation) this.ctx.builders.structure.representation.unregisterPreset(AssemblySymmetryPreset) } }, params: () => ({ autoAttach: PD.Boolean(false), serverUrl: PD.Text(AssemblySymmetry.DefaultServerUrl) }) }); // export const InitAssemblySymmetry3D = StateAction.build({ display: { name: 'Assembly Symmetry', description: 'Initialize Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.' }, from: PluginStateObject.Molecule.Structure, isApplicable: (a) => AssemblySymmetry.isApplicable(a.data) })(({ a, ref, state }, plugin: PluginContext) => Task.create('Init Assembly Symmetry', async ctx => { try { await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data) } catch(e) { plugin.log.error(`Assembly Symmetry: ${e}`) return } const tree = state.build().to(ref).apply(AssemblySymmetry3D); await state.updateTree(tree).runInContext(ctx); })); export { AssemblySymmetry3D } type AssemblySymmetry3D = typeof AssemblySymmetry3D const AssemblySymmetry3D = PluginStateTransform.BuiltIn({ name: Tag.Representation, display: { name: 'Assembly Symmetry', description: 'Assembly Symmetry axes and cage. Data calculated with BioJava, obtained via RCSB PDB.' }, from: PluginStateObject.Molecule.Structure, to: PluginStateObject.Shape.Representation3D, params: (a) => { return { ...AssemblySymmetryParams, } } })({ canAutoUpdate({ oldParams, newParams }) { return true; }, apply({ a, params }, plugin: PluginContext) { return Task.create('Assembly Symmetry', async ctx => { await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data) const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') { return StateObject.Null; } const repr = AssemblySymmetryRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => AssemblySymmetryParams) await repr.createOrUpdate(params, a.data).runInContext(ctx); const { type, kind, symbol } = assemblySymmetry return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: kind, description: `${type} (${symbol})` }); }); }, update({ a, b, newParams }, plugin: PluginContext) { return Task.create('Assembly Symmetry', async ctx => { await AssemblySymmetryProvider.attach({ runtime: ctx, fetch: plugin.fetch }, a.data) const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') { return StateTransformer.UpdateResult.Recreate } const props = { ...b.data.repr.props, ...newParams } await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx); const { type, kind, symbol } = assemblySymmetry b.label = kind b.description = `${type} (${symbol})` return StateTransformer.UpdateResult.Updated; }); }, isApplicable(a) { return AssemblySymmetry.isApplicable(a.data) } }); // const AssemblySymmetryPresetParams = { ...StructureRepresentationPresetProvider.CommonParams, symmetryIndex: PD.Numeric(0) } export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({ id: 'preset-structure-representation-rcsb-assembly-symmetry', display: { name: 'Assembly Symmetry', group: 'Annotation', description: 'Shows Assembly Symmetry axes and cage; colors structure according to assembly symmetry cluster membership. Data calculated with BioJava, obtained via RCSB PDB.' }, params: () => AssemblySymmetryPresetParams, async apply(ref, params, plugin) { const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref); const structure = structureCell?.obj?.data; if (!structureCell || !structure) return {}; await plugin.runTask(Task.create('Assembly Symmetry', async runtime => { await AssemblySymmetryProvider.attach({ fetch: plugin.fetch, runtime }, structure, { symmetryIndex: params.symmetryIndex }) })) const assemblySymmetry = await tryCreateAssemblySymmetry(plugin, structureCell); const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: Tag.Cluster as any }, plugin); return { components: preset.components, representations: { ...preset.representations, assemblySymmetry } }; } }); async function tryCreateAssemblySymmetry(plugin: PluginContext, structure: StateObjectRef, params?: StateTransformer.Params, initialState?: Partial) { const state = plugin.state.data; const assemblySymmetry = state.build().to(structure) .apply(AssemblySymmetry3D, params, { state: initialState }); await plugin.updateDataState(assemblySymmetry, { revertOnError: true }); return assemblySymmetry.selector }