model.ts

/**
 * Copyright (c) 2018-2019 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>
 */

import { parsePDB } from '../../../mol-io/reader/pdb/parser';
import { Vec3, Mat4, Quat } from '../../../mol-math/linear-algebra';
import { trajectoryFromMmCIF } from '../../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../../mol-model-formats/structure/pdb';
import { Model, ModelSymmetry, Queries, QueryContext, Structure, StructureQuery, StructureSelection as Sel, StructureSymmetry, QueryFn, StructureElement } from '../../../mol-model/structure';
import { Assembly } from '../../../mol-model/structure/model/properties/symmetry';
import { PluginContext } from '../../../mol-plugin/context';
import { MolScriptBuilder } from '../../../mol-script/language/builder';
import Expression from '../../../mol-script/language/expression';
import { compile } from '../../../mol-script/runtime/query/compiler';
import { StateObject, StateTransformer } from '../../../mol-state';
import { RuntimeContext, Task } from '../../../mol-task';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { stringToWords } from '../../../mol-util/string';
import { PluginStateObject as SO, PluginStateTransform } from '../objects';
import { trajectoryFromGRO } from '../../../mol-model-formats/structure/gro';
import { parseGRO } from '../../../mol-io/reader/gro/parser';
import { shapeFromPly } from '../../../mol-model-formats/shape/ply';
import { SymmetryOperator } from '../../../mol-math/geometry';
import { ensureSecondaryStructure } from './helpers';
import { Script } from '../../../mol-script/script';
import { parse3DG } from '../../../mol-io/reader/3dg/parser';
import { trajectoryFrom3DG } from '../../../mol-model-formats/structure/3dg';

export { TrajectoryFromBlob };
export { TrajectoryFromMmCif };
export { TrajectoryFromPDB };
export { TrajectoryFromGRO };
export { TrajectoryFrom3DG };
export { ModelFromTrajectory };
export { StructureFromTrajectory };
export { StructureFromModel };
export { StructureAssemblyFromModel };
export { StructureSymmetryFromModel };
export { TransformStructureConformation };
export { TransformStructureConformationByMatrix };
export { StructureSelectionFromExpression };
export { StructureSelectionFromScript };
export { StructureSelectionFromBundle };
export { StructureComplexElement };
export { CustomModelProperties };
export { CustomStructureProperties };

type TrajectoryFromBlob = typeof TrajectoryFromBlob
const TrajectoryFromBlob = PluginStateTransform.BuiltIn({
    name: 'trajectory-from-blob',
    display: { name: 'Parse Blob', description: 'Parse format blob into a single trajectory.' },
    from: SO.Format.Blob,
    to: SO.Molecule.Trajectory
})({
    apply({ a }) {
        return Task.create('Parse Format Blob', async ctx => {
            const models: Model[] = [];
            for (const e of a.data) {
                if (e.kind !== 'cif') continue;
                const block = e.data.blocks[0];
                const xs = await trajectoryFromMmCIF(block).runInContext(ctx);
                if (xs.length === 0) throw new Error('No models found.');
                for (const x of xs) models.push(x);
            }

            const props = { label: `Trajectory`, description: `${models.length} model${models.length === 1 ? '' : 's'}` };
            return new SO.Molecule.Trajectory(models, props);