Select Git revision
root-structure.ts 8.50 KiB
/**
* Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Model, Structure, StructureSymmetry } from '../../mol-model/structure';
import { stringToWords } from '../../mol-util/string';
import { SpacegroupCell, Spacegroup } from '../../mol-math/geometry';
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Vec3 } from '../../mol-math/linear-algebra';
import { RuntimeContext } from '../../mol-task';
import { PluginContext } from '../../mol-plugin/context';
import { Assembly, Symmetry } from '../../mol-model/structure/model/properties/symmetry';
import { PluginStateObject as SO } from '../objects';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
export namespace RootStructureDefinition {
export function getParams(model?: Model, defaultValue?: 'auto' | 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {
const symmetry = model && ModelSymmetry.Provider.get(model)
const assemblyIds = symmetry ? symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : [];
const showSymm = !symmetry ? true : !SpacegroupCell.isZero(symmetry.spacegroup.cell);
const operatorOptions: [number, string][] = []
if (symmetry) {
const { operators } = symmetry.spacegroup
for (let i = 0, il = operators.length; i < il; i++) {
operatorOptions.push([i, `${i + 1}: ${Spacegroup.getOperatorXyz(operators[i])}`])
}
}
const asymIdsOptions: [string, string][] = []
if (model) {
model.properties.structAsymMap.forEach(v => {
const label = v.id === v.auth_id ? v.id : `${v.id} [auth ${v.auth_id}]`
asymIdsOptions.push([v.id, label])
})
}
const modes = {
auto: PD.EmptyGroup(),
deposited: PD.EmptyGroup(),
assembly: PD.Group({
id: PD.Optional(model
? PD.Select(assemblyIds.length ? assemblyIds[0][0] : '', assemblyIds, { label: 'Asm Id', description: 'Assembly Id' })
: PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' }))
}, { isFlat: true }),
'symmetry-mates': PD.Group({
radius: PD.Numeric(5, { min: 0, max: 50, step: 1 })
}, { isFlat: true }),
'symmetry': PD.Group({
ijkMin: PD.Vec3(Vec3.create(-1, -1, -1), { step: 1 }, { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }),
ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
}, { isFlat: true }),
'symmetry-assembly': PD.Group({
generators: PD.ObjectList({
operators: PD.ObjectList({
index: PD.Select(0, operatorOptions),
shift: PD.Vec3(Vec3(), { step: 1 }, { label: 'IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
}, e => `${e.index + 1}_${e.shift.map(a => a + 5).join('')}`, {
defaultValue: [] as { index: number, shift: Vec3 }[]
}),
asymIds: PD.MultiSelect([] as string[], asymIdsOptions)
}, e => `${e.asymIds.length} asym ids, ${e.operators.length} operators`, {
defaultValue: [] as { operators: { index: number, shift: Vec3 }[], asymIds: string[] }[]
})
}, { isFlat: true })
};
const options: [keyof typeof modes, string][] = [];
if (defaultValue === 'auto') {
options.push(['auto', 'Auto']);
}
options.push(['deposited', 'Deposited']);
if (assemblyIds.length > 0) {
options.push(['assembly', 'Assembly']);
}
if (showSymm) {
options.push(['symmetry-mates', 'Symmetry Mates']);
options.push(['symmetry', 'Symmetry (indices)']);
options.push(['symmetry-assembly', 'Symmetry (assembly)']);
}
return {
type: PD.MappedStatic(defaultValue || 'deposited', modes, { options })
};
}
export type Params = PD.Values<ReturnType<typeof getParams>>['type']
export function isSymmetryType(params: Params) {
return params.name.indexOf('symmetry') >= 0;
}
async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string) {
let asm: Assembly | undefined = void 0;
const symmetry = ModelSymmetry.Provider.get(model)
// if no id is specified, use the 1st assembly.
if (!id && symmetry && symmetry.assemblies.length !== 0) {
id = symmetry.assemblies[0].id;
}
if (!symmetry || symmetry.assemblies.length === 0) {
if (id !== 'deposited') {
plugin.log.warn(`Model '${model.entryId}' has no assembly, returning deposited structure.`);
}
} else {
asm = Symmetry.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) {
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);
const props = { label: `Assembly ${id}`, description: Structure.elementDescription(s) };
return new SO.Molecule.Structure(s, props);
}
async function buildSymmetry(ctx: RuntimeContext, model: Model, ijkMin: Vec3, ijkMax: Vec3) {
const base = Structure.ofModel(model);
const s = await StructureSymmetry.buildSymmetryRange(base, ijkMin, ijkMax).runInContext(ctx);
const props = { label: `Symmetry [${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);
const props = { label: `Symmetry Mates`, description: Structure.elementDescription(s) };
return new SO.Molecule.Structure(s, props);
}
async function buildSymmetryAssembly(ctx: RuntimeContext, model: Model, generators: StructureSymmetry.Generators, symmetry: Symmetry) {
const base = Structure.ofModel(model);
const s = await StructureSymmetry.buildSymmetryAssembly(base, generators, symmetry).runInContext(ctx);
const props = { label: `Symmetry Assembly`, description: Structure.elementDescription(s) };
return new SO.Molecule.Structure(s, props);
}
export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise<SO.Molecule.Structure> {
const symmetry = ModelSymmetry.Provider.get(model)
if (!symmetry || !params || params.name === 'deposited') {
const s = Structure.ofModel(model);
return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
}
if (params.name === 'auto') {
if (symmetry.assemblies.length === 0) {
const s = Structure.ofModel(model);
return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
} else {
return buildAssembly(plugin, ctx, model);
}
}
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)
}
if (params.name === 'symmetry-assembly') {
return buildSymmetryAssembly(ctx, model, params.params.generators, symmetry)
}
throw new Error(`Unknown represetation type: ${(params as any).name}`);
}
}