/** * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author David Sehnal */ import { Model, Structure, StructureSymmetry } from '../../../mol-model/structure'; import { stringToWords } from '../../../mol-util/string'; import { SpacegroupCell } from '../../../mol-math/geometry'; import { ParamDefinition as PD } from '../../../mol-util/param-definition'; import { Vec3 } from '../../../mol-math/linear-algebra'; import { ensureSecondaryStructure } from '../transforms/helpers'; import { RuntimeContext } from '../../../mol-task'; import { PluginContext } from '../../context'; import { Assembly, ModelSymmetry } from '../../../mol-model/structure/model/properties/symmetry'; import { PluginStateObject as SO } from '../objects'; export namespace ModelStructureRepresentation { export function getParams(model?: Model, defaultValue?: 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates') { const assemblyIds = model ? model.symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : []; const showSymm = !model ? true : !SpacegroupCell.isZero(model.symmetry.spacegroup.cell); const modes = { deposited: PD.EmptyGroup(), assembly: PD.Group({ id: PD.Optional(model ? PD.Select(assemblyIds.length ? assemblyIds[0][0] : '', assemblyIds, { label: 'Asm Id', description: 'Assembly Id' }) : PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' })) }, { isFlat: true }), 'symmetry-mates': PD.Group({ radius: PD.Numeric(5) }, { isFlat: true }), 'symmetry': PD.Group({ ijkMin: PD.Vec3(Vec3.create(-1, -1, -1), { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }), ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }) }, { isFlat: true }) }; const options: [keyof typeof modes, string][] = [ ['deposited', 'Deposited'] ]; if (assemblyIds) { options.push(['assembly', 'Assembly']); } if (showSymm) { options.push(['symmetry-mates', 'Symmetry Mates']); options.push(['symmetry', 'Symmetry (indices)']); } return { type: PD.MappedStatic(defaultValue || 'deposited', modes, { options }) }; } export type Params = PD.Values>['type'] async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string) { let asm: Assembly | undefined = void 0; // if no id is specified, use the 1st assembly. if (!id && model.symmetry.assemblies.length !== 0) { id = model.symmetry.assemblies[0].id; } if (model.symmetry.assemblies.length === 0) { if (id !== 'deposited') { plugin.log.warn(`Model '${model.entryId}' has no assembly, returning deposited structure.`); } } else { asm = ModelSymmetry.findAssembly(model, id || ''); if (!asm) { plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning deposited structure.`); } } const base = Structure.ofModel(model); if (!asm) { await ensureSecondaryStructure(base) const label = { label: 'Deposited', description: Structure.elementDescription(base) }; return new SO.Molecule.Structure(base, label); } id = asm.id; const s = await StructureSymmetry.buildAssembly(base, id!).runInContext(ctx); await ensureSecondaryStructure(s) const props = { label: `Assembly ${id}`, description: Structure.elementDescription(s) }; return new SO.Molecule.Structure(s, props); } async function buildSymmetry(ctx: RuntimeContext, model: Model, ijkMin: Vec3, ijkMax: Vec3) { const base = Structure.ofModel(model); const s = await StructureSymmetry.buildSymmetryRange(base, ijkMin, ijkMax).runInContext(ctx); await ensureSecondaryStructure(s) const props = { label: `Symmetry [${ijkMin}] to [${ijkMax}]`, description: Structure.elementDescription(s) }; return new SO.Molecule.Structure(s, props); } async function buildSymmetryMates(ctx: RuntimeContext, model: Model, radius: number) { const base = Structure.ofModel(model); const s = await StructureSymmetry.builderSymmetryMates(base, radius).runInContext(ctx); await ensureSecondaryStructure(s) const props = { label: `Symmetry Mates`, description: Structure.elementDescription(s) }; return new SO.Molecule.Structure(s, props); } export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise { if (!params || params.name === 'deposited') { const s = Structure.ofModel(model); await ensureSecondaryStructure(s); return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) }); } if (params.name === 'assembly') { return buildAssembly(plugin, ctx, model, params.params.id) } if (params.name === 'symmetry') { return buildSymmetry(ctx, model, params.params.ijkMin, params.params.ijkMax) } if (params.name === 'symmetry-mates') { return buildSymmetryMates(ctx, model, params.params.radius) } throw new Error(`Unknown represetation type: ${(params as any).name}`); } }