molstar
Version:
A comprehensive macromolecular library.
205 lines • 10.9 kB
JavaScript
/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { __awaiter, __generator, __spreadArray } from "tslib";
import { StateObjectRef } from '../../mol-state';
import { PluginStateObject as SO } from '../objects';
import { StateTransforms } from '../transforms';
import { StructureRepresentationBuilder } from './structure/representation';
import { Task } from '../../mol-task';
import { StructureElement } from '../../mol-model/structure';
import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
import { SpacegroupCell } from '../../mol-math/geometry';
import { TrajectoryHierarchyBuilder } from './structure/hierarchy';
var StructureBuilder = /** @class */ (function () {
function StructureBuilder(plugin) {
this.plugin = plugin;
this.hierarchy = new TrajectoryHierarchyBuilder(this.plugin);
this.representation = new StructureRepresentationBuilder(this.plugin);
}
Object.defineProperty(StructureBuilder.prototype, "dataState", {
get: function () {
return this.plugin.state.data;
},
enumerable: false,
configurable: true
});
StructureBuilder.prototype.parseTrajectoryData = function (data, format) {
return __awaiter(this, void 0, void 0, function () {
var provider, trajectory;
return __generator(this, function (_a) {
switch (_a.label) {
case 0:
provider = typeof format === 'string' ? this.plugin.dataFormats.get(format) : format;
if (!provider)
throw new Error("'" + format + "' is not a supported data format.");
return [4 /*yield*/, provider.parse(this.plugin, data)];
case 1:
trajectory = (_a.sent()).trajectory;
return [2 /*return*/, trajectory];
}
});
});
};
StructureBuilder.prototype.parseTrajectoryBlob = function (data, params) {
var state = this.dataState;
var trajectory = state.build().to(data)
.apply(StateTransforms.Data.ParseBlob, params, { state: { isGhost: true } })
.apply(StateTransforms.Model.TrajectoryFromBlob, void 0);
return trajectory.commit({ revertOnError: true });
};
StructureBuilder.prototype.parseTrajectory = function (data, params) {
var cell = StateObjectRef.resolveAndCheck(this.dataState, data);
if (!cell)
throw new Error('Invalid data cell.');
if (SO.Data.Blob.is(cell.obj)) {
return this.parseTrajectoryBlob(data, params);
}
else {
return this.parseTrajectoryData(data, params);
}
};
StructureBuilder.prototype.createModel = function (trajectory, params, initialState) {
var state = this.dataState;
var model = state.build().to(trajectory)
.apply(StateTransforms.Model.ModelFromTrajectory, params || { modelIndex: 0 }, { state: initialState });
return model.commit({ revertOnError: true });
};
StructureBuilder.prototype.insertModelProperties = function (model, params, initialState) {
var state = this.dataState;
var props = state.build().to(model)
.apply(StateTransforms.Model.CustomModelProperties, params, { state: initialState });
return props.commit({ revertOnError: true });
};
StructureBuilder.prototype.tryCreateUnitcell = function (model, params, initialState) {
var _a, _b, _c;
var state = this.dataState;
var m = (_b = (_a = StateObjectRef.resolveAndCheck(state, model)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
if (!m)
return;
var cell = (_c = ModelSymmetry.Provider.get(m)) === null || _c === void 0 ? void 0 : _c.spacegroup.cell;
if (SpacegroupCell.isZero(cell))
return;
var unitcell = state.build().to(model)
.apply(StateTransforms.Representation.ModelUnitcell3D, params, { state: initialState });
return unitcell.commit({ revertOnError: true });
};
StructureBuilder.prototype.createStructure = function (modelRef, params, initialState) {
var _a;
var state = this.dataState;
if (!params) {
var model = StateObjectRef.resolveAndCheck(state, modelRef);
if (model) {
var symm = 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: {} };
}
}
var structure = state.build().to(modelRef)
.apply(StateTransforms.Model.StructureFromModel, { type: params || { name: 'assembly', params: {} } }, { state: initialState });
return structure.commit({ revertOnError: true });
};
StructureBuilder.prototype.insertStructureProperties = function (structure, params) {
var state = this.dataState;
var props = state.build().to(structure)
.apply(StateTransforms.Model.CustomStructureProperties, params);
return props.commit({ revertOnError: true });
};
StructureBuilder.prototype.isComponentTransform = function (cell) {
return cell.transform.transformer === StateTransforms.Model.StructureComponent;
};
/** returns undefined if the component is empty/null */
StructureBuilder.prototype.tryCreateComponent = function (structure, params, key, tags) {
var _a, _b;
return __awaiter(this, void 0, void 0, function () {
var state, root, keyTag, component, selector;
return __generator(this, function (_c) {
switch (_c.label) {
case 0:
state = this.dataState;
root = state.build().to(structure);
keyTag = "structure-component-" + key;
component = root.applyOrUpdateTagged(keyTag, StateTransforms.Model.StructureComponent, params, {
tags: tags ? __spreadArray(__spreadArray([], tags, true), [keyTag], false) : [keyTag]
});
return [4 /*yield*/, component.commit()];
case 1:
_c.sent();
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)) return [3 /*break*/, 3];
return [4 /*yield*/, state.build().delete(selector.ref).commit()];
case 2:
_c.sent();
return [2 /*return*/];
case 3: return [2 /*return*/, selector];
}
});
});
};
StructureBuilder.prototype.tryCreateComponentFromExpression = function (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);
};
StructureBuilder.prototype.tryCreateComponentStatic = function (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);
};
StructureBuilder.prototype.tryCreateComponentFromSelection = function (structure, selection, key, params) {
var _this = this;
return this.plugin.runTask(Task.create('Query Component', function (taskCtx) { return __awaiter(_this, void 0, void 0, function () {
var _a, label, tags, structureData, transformParams, _b, _c, _d;
var _e, _f;
var _g, _h;
return __generator(this, function (_j) {
switch (_j.label) {
case 0:
_a = params || {}, label = _a.label, tags = _a.tags;
label = (label || '').trim();
structureData = (_h = (_g = StateObjectRef.resolveAndCheck(this.dataState, structure)) === null || _g === void 0 ? void 0 : _g.obj) === null || _h === void 0 ? void 0 : _h.data;
if (!structureData)
return [2 /*return*/];
if (!selection.referencesCurrent) return [3 /*break*/, 2];
_e = {};
_f = {
name: 'bundle'
};
_d = (_c = StructureElement.Bundle).fromSelection;
return [4 /*yield*/, selection.getSelection(this.plugin, taskCtx, structureData)];
case 1:
_b = (_e.type = (_f.params = _d.apply(_c, [_j.sent()]),
_f),
_e.nullIfEmpty = true,
_e.label = label || selection.label,
_e);
return [3 /*break*/, 3];
case 2:
_b = {
type: { name: 'expression', params: selection.expression },
nullIfEmpty: true,
label: label || selection.label
};
_j.label = 3;
case 3:
transformParams = _b;
if (!selection.ensureCustomProperties) return [3 /*break*/, 5];
return [4 /*yield*/, selection.ensureCustomProperties({ runtime: taskCtx, assetManager: this.plugin.managers.asset }, structureData)];
case 4:
_j.sent();
_j.label = 5;
case 5: return [2 /*return*/, this.tryCreateComponent(structure, transformParams, key, tags)];
}
});
}); }));
};
return StructureBuilder;
}());
export { StructureBuilder };
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