molstar
Version:
A comprehensive macromolecular library.
154 lines (153 loc) • 7.06 kB
JavaScript
;
/**
* Copyright (c) 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>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.G3DFormat = exports.LoadG3D = exports.G3DTrajectory = exports.G3DHeaderFromUrl = exports.G3DHeaderFromFile = exports.G3dHeaderObject = exports.G3dProvider = void 0;
const trajectory_1 = require("../../mol-plugin-state/formats/trajectory");
const objects_1 = require("../../mol-plugin-state/objects");
const behavior_1 = require("../../mol-plugin/behavior");
const base_1 = require("../../mol-script/runtime/query/base");
const mol_state_1 = require("../../mol-state");
const mol_task_1 = require("../../mol-task");
const param_definition_1 = require("../../mol-util/param-definition");
const data_1 = require("./data");
const model_1 = require("./model");
const transforms_1 = require("../../mol-plugin-state/transforms");
const structure_representation_params_1 = require("../../mol-plugin-state/helpers/structure-representation-params");
const string_1 = require("../../mol-util/string");
const object_1 = require("../../mol-util/object");
exports.G3dProvider = {
label: 'G3D',
description: 'G3D',
category: trajectory_1.TrajectoryFormatCategory,
binaryExtensions: ['g3d'],
parse: async (plugin, data) => {
const trajectory = await plugin.state.data.build()
.to(data)
.apply(exports.G3DHeaderFromFile, {}, { state: { isGhost: true } })
.apply(exports.G3DTrajectory)
.commit();
return { trajectory };
},
visuals: defaultStructure
};
async function defaultStructure(plugin, data) {
const builder = plugin.builders.structure;
const model = await builder.createModel(data.trajectory);
if (!model)
return;
const structure = await builder.createStructure(model);
const info = model_1.G3dInfoDataProperty.get(model.data);
if (!info)
return;
const components = plugin.build().to(structure);
const repr = (0, structure_representation_params_1.createStructureRepresentationParams)(plugin, void 0, {
type: 'cartoon',
color: 'polymer-index',
size: 'uniform',
sizeParams: { value: 0.25 }
});
for (const h of info.haplotypes) {
components
.apply(transforms_1.StateTransforms.Model.StructureSelectionFromExpression, { expression: (0, model_1.g3dHaplotypeQuery)(h), label: (0, string_1.stringToWords)(h) })
.apply(transforms_1.StateTransforms.Representation.StructureRepresentation3D, repr);
}
await components.commit();
}
class G3dHeaderObject extends objects_1.PluginStateObject.Create({ name: 'G3D Header', typeClass: 'Data' }) {
}
exports.G3dHeaderObject = G3dHeaderObject;
exports.G3DHeaderFromFile = objects_1.PluginStateTransform.BuiltIn({
name: 'g3d-header-from-file',
display: { name: 'G3D Header', description: 'Parse G3D Header' },
from: objects_1.PluginStateObject.Data.Binary,
to: G3dHeaderObject
})({
apply({ a }, plugin) {
return mol_task_1.Task.create('Parse G3D', async () => {
const header = await (0, data_1.getG3dHeader)(plugin, a.data);
return new G3dHeaderObject({ header, urlOrData: a.data, cache: {} }, { label: header.name, description: header.genome });
});
}
});
exports.G3DHeaderFromUrl = objects_1.PluginStateTransform.BuiltIn({
name: 'g3d-header-from-url',
display: { name: 'G3D Header', description: 'Parse G3D Header' },
params: { url: param_definition_1.ParamDefinition.Text('') },
from: objects_1.PluginStateObject.Root,
to: G3dHeaderObject
})({
apply({ params }, plugin) {
return mol_task_1.Task.create('Parse G3D', async () => {
const header = await (0, data_1.getG3dHeader)(plugin, params.url);
return new G3dHeaderObject({ header, urlOrData: params.url, cache: {} }, { label: header.name, description: header.genome });
});
}
});
exports.G3DTrajectory = objects_1.PluginStateTransform.BuiltIn({
name: 'g3d-trajecotry',
display: { name: 'G3D Trajectory', description: 'Create G3D Trajectory' },
params: a => {
if (!a)
return { resolution: param_definition_1.ParamDefinition.Numeric(200000) };
const rs = a.data.header.resolutions;
return {
resolution: param_definition_1.ParamDefinition.Select(rs[rs.length - 1], rs.map(r => [r, '' + r]))
};
},
from: G3dHeaderObject,
to: objects_1.PluginStateObject.Molecule.Trajectory
})({
apply({ a, params }, plugin) {
return mol_task_1.Task.create('G3D Trajectory', async (ctx) => {
if (a.data.cache[params.resolution]) {
return new objects_1.PluginStateObject.Molecule.Trajectory(a.data.cache[params.resolution], { label: a.label, description: a.description });
}
const data = await (0, data_1.getG3dDataBlock)(plugin, a.data.header, a.data.urlOrData, params.resolution);
const traj = await (0, model_1.trajectoryFromG3D)(data).runInContext(ctx);
a.data.cache[params.resolution] = traj;
return new objects_1.PluginStateObject.Molecule.Trajectory(traj, { label: a.label, description: a.description });
});
}
});
exports.LoadG3D = mol_state_1.StateAction.build({
display: { name: 'Load Genome 3D (G3D)', description: 'Load G3D file from the specified URL.' },
from: objects_1.PluginStateObject.Root,
params: { url: param_definition_1.ParamDefinition.Text('') }
})(({ params, state }, ctx) => mol_task_1.Task.create('Genome3D', taskCtx => {
return state.transaction(async () => {
if (params.url.trim().length === 0) {
throw new Error('Specify URL');
}
ctx.behaviors.layout.leftPanelTabName.next('data');
const trajectory = await state.build().toRoot()
.apply(exports.G3DHeaderFromUrl, { url: params.url })
.apply(exports.G3DTrajectory)
.commit();
await defaultStructure(ctx, { trajectory });
}).runInContext(taskCtx);
}));
exports.G3DFormat = behavior_1.PluginBehavior.create({
name: 'g3d',
category: 'misc',
display: {
name: 'G3D',
description: 'G3D Format Support'
},
ctor: class extends behavior_1.PluginBehavior.Handler {
register() {
this.ctx.state.data.actions.add(exports.LoadG3D);
(0, object_1.objectForEach)(model_1.G3dSymbols, s => base_1.DefaultQueryRuntimeTable.addSymbol(s));
this.ctx.managers.lociLabels.addProvider(model_1.G3dLabelProvider);
}
unregister() {
this.ctx.state.data.actions.remove(exports.LoadG3D);
(0, object_1.objectForEach)(model_1.G3dSymbols, s => base_1.DefaultQueryRuntimeTable.removeSymbol(s));
this.ctx.managers.lociLabels.removeProvider(model_1.G3dLabelProvider);
}
}
});