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@@ -1,5 +1,5 @@
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/**
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- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
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+ * Copyright (c) 2019-2021 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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* @author Alexander Rose <alexander.rose@weirdbyte.de>
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@@ -16,6 +16,11 @@ import { Assembly, Symmetry } from '../../mol-model/structure/model/properties/s
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import { PluginStateObject as SO } from '../objects';
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import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
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+const CommonStructureParams = {
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+ dynamicBonds: PD.Optional(PD.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules.' })),
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+};
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+type CommonStructureProps = PD.ValuesFor<typeof CommonStructureParams>
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+
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export namespace RootStructureDefinition {
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export function getParams(model?: Model, defaultValue?: 'auto' | 'model' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {
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const symmetry = model && ModelSymmetry.Provider.get(model);
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@@ -40,19 +45,22 @@ export namespace RootStructureDefinition {
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}
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const modes = {
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- auto: PD.EmptyGroup(),
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- model: PD.EmptyGroup(),
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+ auto: PD.Group(CommonStructureParams),
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+ model: PD.Group(CommonStructureParams),
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assembly: PD.Group({
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id: PD.Optional(model
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? PD.Select(assemblyIds.length ? assemblyIds[0][0] : '', assemblyIds, { label: 'Asm Id', description: 'Assembly Id' })
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- : PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' }))
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+ : PD.Text('', { label: 'Asm Id', description: 'Assembly Id (use empty for the 1st assembly)' })),
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+ ...CommonStructureParams
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}, { isFlat: true }),
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'symmetry-mates': PD.Group({
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- radius: PD.Numeric(5, { min: 0, max: 50, step: 1 })
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+ radius: PD.Numeric(5, { min: 0, max: 50, step: 1 }),
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+ ...CommonStructureParams
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}, { isFlat: true }),
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'symmetry': PD.Group({
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ijkMin: PD.Vec3(Vec3.create(-1, -1, -1), { step: 1 }, { label: 'Min IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }),
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- ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
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+ ijkMax: PD.Vec3(Vec3.create(1, 1, 1), { step: 1 }, { label: 'Max IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } }),
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+ ...CommonStructureParams
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}, { isFlat: true }),
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'symmetry-assembly': PD.Group({
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generators: PD.ObjectList({
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@@ -65,7 +73,8 @@ export namespace RootStructureDefinition {
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asymIds: PD.MultiSelect([] as string[], asymIdsOptions)
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}, e => `${e.asymIds.length} asym ids, ${e.operators.length} operators`, {
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defaultValue: [] as { operators: { index: number, shift: Vec3 }[], asymIds: string[] }[]
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- })
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+ }),
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+ ...CommonStructureParams
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}, { isFlat: true })
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};
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@@ -99,7 +108,7 @@ export namespace RootStructureDefinition {
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return true;
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}
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- async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string) {
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+ async function buildAssembly(plugin: PluginContext, ctx: RuntimeContext, model: Model, id?: string, props?: CommonStructureProps) {
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let asm: Assembly | undefined = void 0;
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const symmetry = ModelSymmetry.Provider.get(model);
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@@ -118,7 +127,7 @@ export namespace RootStructureDefinition {
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}
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}
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- const base = Structure.ofModel(model);
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+ const base = Structure.ofModel(model, props);
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if (!asm) {
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const label = { label: 'Model', description: Structure.elementDescription(base) };
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return new SO.Molecule.Structure(base, label);
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@@ -126,56 +135,57 @@ export namespace RootStructureDefinition {
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id = asm.id;
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const s = await StructureSymmetry.buildAssembly(base, id!).runInContext(ctx);
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- const props = { label: `Assembly ${id}`, description: Structure.elementDescription(s) };
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- return new SO.Molecule.Structure(s, props);
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+ const objProps = { label: `Assembly ${id}`, description: Structure.elementDescription(s) };
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+ return new SO.Molecule.Structure(s, objProps);
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}
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- async function buildSymmetry(ctx: RuntimeContext, model: Model, ijkMin: Vec3, ijkMax: Vec3) {
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- const base = Structure.ofModel(model);
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+ async function buildSymmetry(ctx: RuntimeContext, model: Model, ijkMin: Vec3, ijkMax: Vec3, props?: CommonStructureProps) {
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+ const base = Structure.ofModel(model, props);
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const s = await StructureSymmetry.buildSymmetryRange(base, ijkMin, ijkMax).runInContext(ctx);
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- const props = { label: `Symmetry [${ijkMin}] to [${ijkMax}]`, description: Structure.elementDescription(s) };
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- return new SO.Molecule.Structure(s, props);
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+ const objProps = { label: `Symmetry [${ijkMin}] to [${ijkMax}]`, description: Structure.elementDescription(s) };
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+ return new SO.Molecule.Structure(s, objProps);
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}
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- async function buildSymmetryMates(ctx: RuntimeContext, model: Model, radius: number) {
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- const base = Structure.ofModel(model);
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+ async function buildSymmetryMates(ctx: RuntimeContext, model: Model, radius: number, props?: CommonStructureProps) {
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+ const base = Structure.ofModel(model, props);
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const s = await StructureSymmetry.builderSymmetryMates(base, radius).runInContext(ctx);
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- const props = { label: `Symmetry Mates`, description: Structure.elementDescription(s) };
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- return new SO.Molecule.Structure(s, props);
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+ const objProps = { label: `Symmetry Mates`, description: Structure.elementDescription(s) };
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+ return new SO.Molecule.Structure(s, objProps);
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}
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- async function buildSymmetryAssembly(ctx: RuntimeContext, model: Model, generators: StructureSymmetry.Generators, symmetry: Symmetry) {
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- const base = Structure.ofModel(model);
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+ async function buildSymmetryAssembly(ctx: RuntimeContext, model: Model, generators: StructureSymmetry.Generators, symmetry: Symmetry, props?: CommonStructureProps) {
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+ const base = Structure.ofModel(model, props);
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const s = await StructureSymmetry.buildSymmetryAssembly(base, generators, symmetry).runInContext(ctx);
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- const props = { label: `Symmetry Assembly`, description: Structure.elementDescription(s) };
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- return new SO.Molecule.Structure(s, props);
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+ const objProps = { label: `Symmetry Assembly`, description: Structure.elementDescription(s) };
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+ return new SO.Molecule.Structure(s, objProps);
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}
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export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise<SO.Molecule.Structure> {
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+ const props = params?.params;
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const symmetry = ModelSymmetry.Provider.get(model);
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if (!symmetry || !params || params.name === 'model') {
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- const s = Structure.ofModel(model);
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+ const s = Structure.ofModel(model, props);
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return new SO.Molecule.Structure(s, { label: 'Model', description: Structure.elementDescription(s) });
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}
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if (params.name === 'auto') {
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if (symmetry.assemblies.length === 0) {
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- const s = Structure.ofModel(model);
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+ const s = Structure.ofModel(model, props);
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return new SO.Molecule.Structure(s, { label: 'Model', description: Structure.elementDescription(s) });
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} else {
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- return buildAssembly(plugin, ctx, model);
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+ return buildAssembly(plugin, ctx, model, undefined, props);
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}
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}
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if (params.name === 'assembly') {
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- return buildAssembly(plugin, ctx, model, params.params.id);
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+ return buildAssembly(plugin, ctx, model, params.params.id, props);
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}
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if (params.name === 'symmetry') {
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- return buildSymmetry(ctx, model, params.params.ijkMin, params.params.ijkMax);
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+ return buildSymmetry(ctx, model, params.params.ijkMin, params.params.ijkMax, props);
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}
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if (params.name === 'symmetry-mates') {
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- return buildSymmetryMates(ctx, model, params.params.radius);
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+ return buildSymmetryMates(ctx, model, params.params.radius, props);
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}
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if (params.name === 'symmetry-assembly') {
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- return buildSymmetryAssembly(ctx, model, params.params.generators, symmetry);
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+ return buildSymmetryAssembly(ctx, model, params.params.generators, symmetry, props);
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}
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throw new Error(`Unknown represetation type: ${(params as any).name}`);
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Alexander Rose