molstar
Version:
A comprehensive macromolecular library.
210 lines (209 loc) • 11.9 kB
JavaScript
/**
* Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { AssemblySymmetryProvider, AssemblySymmetryData, AssemblySymmetryDataProvider, AssemblySymmetryDataParams } from './prop';
import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
import { AssemblySymmetryParams, AssemblySymmetryRepresentation } from './representation';
import { AssemblySymmetryClusterColorThemeProvider } from './color';
import { PluginStateTransform, PluginStateObject } from '../../mol-plugin-state/objects';
import { Task } from '../../mol-task';
import { PluginConfigItem } from '../../mol-plugin/config';
import { StateTransformer, StateAction, StateObject, StateObjectRef } from '../../mol-state';
import { AssemblySymmetryControls } from './ui';
import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
const Tag = AssemblySymmetryData.Tag;
export const AssemblySymmetry = PluginBehavior.create({
name: 'assembly-symmetry-prop',
category: 'custom-props',
display: {
name: 'Assembly Symmetry',
description: 'Assembly Symmetry data provided by RCSB PDB (calculated with BioJava) or by PDBe.'
},
ctor: class extends PluginBehavior.Handler {
constructor() {
super(...arguments);
this.provider = AssemblySymmetryProvider;
}
register() {
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 = [];
selection.structures.forEach(structure => {
var _a;
const symmRepr = (_a = structure.genericRepresentations) === null || _a === void 0 ? void 0 : _a.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);
this.ctx.builders.structure.representation.registerPreset(AssemblySymmetryPreset);
}
update(p) {
const 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(AssemblySymmetryData.DefaultServerUrl)
})
});
//
export const InitAssemblySymmetry3D = StateAction.build({
display: {
name: 'Assembly Symmetry',
description: 'Initialize Assembly Symmetry axes and cage. Data provided by RCSB PDB (calculated with BioJava) or by PDBe.'
},
from: PluginStateObject.Molecule.Structure,
isApplicable: (a) => AssemblySymmetryData.isApplicable(a.data),
params: (a, plugin) => getConfiguredDefaultParams(plugin)
})(({ a, ref, state, params }, plugin) => Task.create('Init Assembly Symmetry', async (ctx) => {
try {
const propCtx = { runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext };
await AssemblySymmetryDataProvider.attach(propCtx, a.data, params);
const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
const symmetryIndex = assemblySymmetryData ? AssemblySymmetryData.firstNonC1(assemblySymmetryData) : -1;
await AssemblySymmetryProvider.attach(propCtx, a.data, { ...params, symmetryIndex });
}
catch (e) {
plugin.log.error(`Assembly Symmetry: ${e}`);
return;
}
const tree = state.build().to(ref)
.applyOrUpdateTagged(AssemblySymmetryData.Tag.Representation, AssemblySymmetry3D);
await state.updateTree(tree).runInContext(ctx);
}));
export { AssemblySymmetry3D };
const AssemblySymmetry3D = PluginStateTransform.BuiltIn({
name: Tag.Representation,
display: {
name: 'Assembly Symmetry',
description: 'Assembly Symmetry axes and cage. Data provided by RCSB PDB (calculated with BioJava) or by PDBe.'
},
from: PluginStateObject.Molecule.Structure,
to: PluginStateObject.Shape.Representation3D,
params: (a) => {
return {
...AssemblySymmetryParams,
};
}
})({
canAutoUpdate({ oldParams, newParams }) {
return true;
},
apply({ a, params }, plugin) {
return Task.create('Assembly Symmetry', async (ctx) => {
var _a;
await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
return StateObject.Null;
}
const repr = AssemblySymmetryRepresentation({ webgl: (_a = plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl, ...plugin.representation.structure.themes }, () => AssemblySymmetryParams);
await repr.createOrUpdate(params, a.data).runInContext(ctx);
const { type, kind, symbol } = assemblySymmetry;
return new PluginStateObject.Shape.Representation3D({ repr, sourceData: a.data }, { label: kind, description: `${type} (${symbol})` });
});
},
update({ a, b, newParams }, plugin) {
return Task.create('Assembly Symmetry', async (ctx) => {
await AssemblySymmetryProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset, errorContext: plugin.errorContext }, a.data);
const assemblySymmetry = AssemblySymmetryProvider.get(a.data).value;
if (!assemblySymmetry || assemblySymmetry.symbol === 'C1') {
// this should NOT be StateTransformer.UpdateResult.Null
// because that keeps the old object
return StateTransformer.UpdateResult.Recreate;
}
const props = { ...b.data.repr.props, ...newParams };
await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
b.data.sourceData = a.data;
const { type, kind, symbol } = assemblySymmetry;
b.label = kind;
b.description = `${type} (${symbol})`;
return StateTransformer.UpdateResult.Updated;
});
},
isApplicable(a) {
return AssemblySymmetryData.isApplicable(a.data);
}
});
//
export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
id: 'preset-structure-representation-assembly-symmetry',
display: {
name: 'Assembly Symmetry', group: 'Annotation',
description: 'Shows Assembly Symmetry axes and cage; colors structure according to assembly symmetry cluster membership. Data provided by RCSB PDB (calculated with BioJava) or by PDBe.'
},
isApplicable(a) {
return AssemblySymmetryData.isApplicable(a.data);
},
params: (a, plugin) => {
return {
...StructureRepresentationPresetProvider.CommonParams,
...getConfiguredDefaultParams(plugin)
};
},
async apply(ref, params, plugin) {
var _a;
const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
const structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!structureCell || !structure)
return {};
if (!AssemblySymmetryDataProvider.get(structure).value) {
await plugin.runTask(Task.create('Assembly Symmetry', async (runtime) => {
const propCtx = { runtime, assetManager: plugin.managers.asset, errorContext: plugin.errorContext };
const propProps = { serverType: params.serverType, serverUrl: params.serverUrl };
await AssemblySymmetryDataProvider.attach(propCtx, structure, propProps);
const assemblySymmetryData = AssemblySymmetryDataProvider.get(structure).value;
const symmetryIndex = assemblySymmetryData ? AssemblySymmetryData.firstNonC1(assemblySymmetryData) : -1;
await AssemblySymmetryProvider.attach(propCtx, structure, { ...propProps, symmetryIndex });
}));
}
const assemblySymmetry = await tryCreateAssemblySymmetry(plugin, structureCell);
const colorTheme = getAssemblySymmetryConfig(plugin).ApplyColors && assemblySymmetry.isOk ? Tag.Cluster : undefined;
const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
return { components: preset.components, representations: { ...preset.representations, assemblySymmetry } };
}
});
export function tryCreateAssemblySymmetry(plugin, structure, params, initialState) {
const state = plugin.state.data;
const assemblySymmetry = state.build().to(structure)
.applyOrUpdateTagged(AssemblySymmetryData.Tag.Representation, AssemblySymmetry3D, params, { state: initialState });
return assemblySymmetry.commit({ revertOnError: true });
}
//
export const AssemblySymmetryConfig = {
DefaultServerType: new PluginConfigItem('assembly-symmetry.server-type', AssemblySymmetryDataParams.serverType.defaultValue),
DefaultServerUrl: new PluginConfigItem('assembly-symmetry.server-url', AssemblySymmetryDataParams.serverUrl.defaultValue),
ApplyColors: new PluginConfigItem('assembly-symmetry.apply-colors', true),
};
export function getAssemblySymmetryConfig(plugin) {
var _a, _b, _c, _d, _e, _f;
return {
ApplyColors: (_b = (_a = plugin.config.get(AssemblySymmetryConfig.ApplyColors)) !== null && _a !== void 0 ? _a : AssemblySymmetryConfig.ApplyColors.defaultValue) !== null && _b !== void 0 ? _b : true,
DefaultServerType: (_d = (_c = plugin.config.get(AssemblySymmetryConfig.DefaultServerType)) !== null && _c !== void 0 ? _c : AssemblySymmetryConfig.DefaultServerType.defaultValue) !== null && _d !== void 0 ? _d : AssemblySymmetryDataParams.serverType.defaultValue,
DefaultServerUrl: (_f = (_e = plugin.config.get(AssemblySymmetryConfig.DefaultServerUrl)) !== null && _e !== void 0 ? _e : AssemblySymmetryConfig.DefaultServerUrl.defaultValue) !== null && _f !== void 0 ? _f : AssemblySymmetryDataParams.serverUrl.defaultValue,
};
}
function getConfiguredDefaultParams(plugin) {
const config = getAssemblySymmetryConfig(plugin);
const params = PD.clone(AssemblySymmetryDataParams);
PD.setDefaultValues(params, { serverType: config.DefaultServerType, serverUrl: config.DefaultServerUrl });
return params;
}