molstar
Version:
A comprehensive macromolecular library.
161 lines (160 loc) • 8.09 kB
JavaScript
"use strict";
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.StructureBuilder = void 0;
const mol_state_1 = require("../../mol-state");
const objects_1 = require("../objects");
const transforms_1 = require("../transforms");
const representation_1 = require("./structure/representation");
const mol_task_1 = require("../../mol-task");
const structure_1 = require("../../mol-model/structure");
const symmetry_1 = require("../../mol-model-formats/structure/property/symmetry");
const geometry_1 = require("../../mol-math/geometry");
const hierarchy_1 = require("./structure/hierarchy");
class StructureBuilder {
get dataState() {
return this.plugin.state.data;
}
async parseTrajectoryData(data, format) {
const provider = typeof format === 'string' ? this.plugin.dataFormats.get(format) : format;
if (!provider)
throw new Error(`'${format}' is not a supported data format.`);
const { trajectory } = await provider.parse(this.plugin, data);
return trajectory;
}
parseTrajectoryBlob(data, params) {
const state = this.dataState;
const trajectory = state.build().to(data)
.apply(transforms_1.StateTransforms.Data.ParseBlob, params, { state: { isGhost: true } })
.apply(transforms_1.StateTransforms.Model.TrajectoryFromBlob, void 0);
return trajectory.commit({ revertOnError: true });
}
parseTrajectory(data, params) {
const cell = mol_state_1.StateObjectRef.resolveAndCheck(this.dataState, data);
if (!cell)
throw new Error('Invalid data cell.');
if (objects_1.PluginStateObject.Data.Blob.is(cell.obj)) {
return this.parseTrajectoryBlob(data, params);
}
else {
return this.parseTrajectoryData(data, params);
}
}
createModel(trajectory, params, initialState) {
const state = this.dataState;
const model = state.build().to(trajectory)
.apply(transforms_1.StateTransforms.Model.ModelFromTrajectory, params || { modelIndex: 0 }, { state: initialState });
return model.commit({ revertOnError: true });
}
insertModelProperties(model, params, initialState) {
const state = this.dataState;
const props = state.build().to(model)
.apply(transforms_1.StateTransforms.Model.CustomModelProperties, params, { state: initialState });
return props.commit({ revertOnError: true });
}
tryCreateUnitcell(model, params, initialState) {
var _a, _b, _c;
const state = this.dataState;
const m = (_b = (_a = mol_state_1.StateObjectRef.resolveAndCheck(state, model)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
if (!m)
return;
const cell = (_c = symmetry_1.ModelSymmetry.Provider.get(m)) === null || _c === void 0 ? void 0 : _c.spacegroup.cell;
if (geometry_1.SpacegroupCell.isZero(cell))
return;
const unitcell = state.build().to(model)
.apply(transforms_1.StateTransforms.Representation.ModelUnitcell3D, params, { state: initialState });
return unitcell.commit({ revertOnError: true });
}
createStructure(modelRef, params, initialState, tags) {
var _a;
const state = this.dataState;
if (!params) {
const model = mol_state_1.StateObjectRef.resolveAndCheck(state, modelRef);
if (model) {
const symm = symmetry_1.ModelSymmetry.Provider.get((_a = model.obj) === null || _a === void 0 ? void 0 : _a.data);
if (!symm || (symm === null || symm === void 0 ? void 0 : symm.assemblies.length) === 0)
params = { name: 'model', params: {} };
}
}
const structure = state.build().to(modelRef)
.apply(transforms_1.StateTransforms.Model.StructureFromModel, { type: params || { name: 'assembly', params: {} } }, { state: initialState, tags });
return structure.commit({ revertOnError: true });
}
insertStructureProperties(structure, params) {
const state = this.dataState;
const props = state.build().to(structure)
.apply(transforms_1.StateTransforms.Model.CustomStructureProperties, params);
return props.commit({ revertOnError: true });
}
isComponentTransform(cell) {
return cell.transform.transformer === transforms_1.StateTransforms.Model.StructureComponent;
}
/** returns undefined if the component is empty/null */
async tryCreateComponent(structure, params, key, tags) {
var _a, _b;
const state = this.dataState;
const root = state.build().to(structure);
const keyTag = `structure-component-${key}`;
const component = root.applyOrUpdateTagged(keyTag, transforms_1.StateTransforms.Model.StructureComponent, params, {
tags: tags ? [...tags, keyTag] : [keyTag]
});
await component.commit();
const selector = component.selector;
if (!selector.isOk || ((_b = (_a = selector.cell) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data.elementCount) === 0) {
await state.build().delete(selector.ref).commit();
return;
}
return selector;
}
tryCreateComponentFromExpression(structure, expression, key, params) {
return this.tryCreateComponent(structure, {
type: { name: 'expression', params: expression },
nullIfEmpty: true,
label: ((params === null || params === void 0 ? void 0 : params.label) || '').trim()
}, key, params === null || params === void 0 ? void 0 : params.tags);
}
tryCreateComponentStatic(structure, type, params) {
return this.tryCreateComponent(structure, {
type: { name: 'static', params: type },
nullIfEmpty: true,
label: ((params === null || params === void 0 ? void 0 : params.label) || '').trim()
}, `static-${type}`, params === null || params === void 0 ? void 0 : params.tags);
}
tryCreateComponentFromSelection(structure, selection, key, params) {
return this.plugin.runTask(mol_task_1.Task.create('Query Component', async (taskCtx) => {
var _a, _b;
let { label, tags } = params || {};
label = (label || '').trim();
const structureData = (_b = (_a = mol_state_1.StateObjectRef.resolveAndCheck(this.dataState, structure)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
if (!structureData)
return;
const transformParams = selection.referencesCurrent
? {
type: {
name: 'bundle',
params: structure_1.StructureElement.Bundle.fromSelection(await selection.getSelection(this.plugin, taskCtx, structureData))
},
nullIfEmpty: true,
label: label || selection.label
} : {
type: { name: 'expression', params: selection.expression },
nullIfEmpty: true,
label: label || selection.label
};
if (selection.ensureCustomProperties) {
await selection.ensureCustomProperties({ runtime: taskCtx, assetManager: this.plugin.managers.asset, errorContext: this.plugin.errorContext }, structureData);
}
return this.tryCreateComponent(structure, transformParams, key, tags);
}));
}
constructor(plugin) {
this.plugin = plugin;
this.hierarchy = new hierarchy_1.TrajectoryHierarchyBuilder(this.plugin);
this.representation = new representation_1.StructureRepresentationBuilder(this.plugin);
}
}
exports.StructureBuilder = StructureBuilder;