molstar
Version:
A comprehensive macromolecular library.
166 lines (165 loc) • 6.86 kB
JavaScript
;
/**
* Copyright (c) 2018-2024 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>
* @author Ludovic Autin <ludovic.autin@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.BuiltInTrajectoryFormats = exports.Mol2Provider = exports.SdfProvider = exports.MolProvider = exports.GroProvider = exports.LammpsTrajectoryDataProvider = exports.LammpsDataProvider = exports.XyzProvider = exports.PdbqtProvider = exports.PdbProvider = exports.CifCoreProvider = exports.MmcifProvider = exports.TrajectoryFormatCategory = void 0;
const transforms_1 = require("../transforms");
const provider_1 = require("./provider");
exports.TrajectoryFormatCategory = 'Trajectory';
function defaultVisuals(plugin, data) {
return plugin.builders.structure.hierarchy.applyPreset(data.trajectory, 'default');
}
exports.MmcifProvider = {
label: 'mmCIF',
description: 'mmCIF',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['cif', 'mmcif', 'mcif'],
binaryExtensions: ['bcif'],
isApplicable: (info, data) => {
if (info.ext === 'mmcif' || info.ext === 'mcif')
return true;
// assume undetermined cif/bcif files are mmCIF
if (info.ext === 'cif' || info.ext === 'bcif')
return (0, provider_1.guessCifVariant)(info, data) === -1;
return false;
},
parse: async (plugin, data, params) => {
var _a, _b;
const state = plugin.state.data;
const cif = state.build().to(data)
.apply(transforms_1.StateTransforms.Data.ParseCif, void 0, { state: { isGhost: true } });
const trajectory = await cif
.apply(transforms_1.StateTransforms.Model.TrajectoryFromMmCif, void 0, { tags: params === null || params === void 0 ? void 0 : params.trajectoryTags })
.commit({ revertOnError: true });
if ((((_b = (_a = cif.selector.cell) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data.blocks.length) || 0) > 1) {
plugin.state.data.updateCellState(cif.ref, { isGhost: false });
}
return { trajectory };
},
visuals: defaultVisuals
};
exports.CifCoreProvider = {
label: 'cifCore',
description: 'CIF Core',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['cif'],
isApplicable: (info, data) => {
if (info.ext === 'cif')
return (0, provider_1.guessCifVariant)(info, data) === 'coreCif';
return false;
},
parse: async (plugin, data, params) => {
var _a, _b;
const state = plugin.state.data;
const cif = state.build().to(data)
.apply(transforms_1.StateTransforms.Data.ParseCif, void 0, { state: { isGhost: true } });
const trajectory = await cif
.apply(transforms_1.StateTransforms.Model.TrajectoryFromCifCore, void 0, { tags: params === null || params === void 0 ? void 0 : params.trajectoryTags })
.commit({ revertOnError: true });
if ((((_b = (_a = cif.selector.cell) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data.blocks.length) || 0) > 1) {
plugin.state.data.updateCellState(cif.ref, { isGhost: false });
}
return { trajectory };
},
visuals: defaultVisuals
};
function directTrajectory(transformer, transformerParams) {
return async (plugin, data, params) => {
const state = plugin.state.data;
const trajectory = await state.build().to(data)
.apply(transformer, transformerParams, { tags: params === null || params === void 0 ? void 0 : params.trajectoryTags })
.commit({ revertOnError: true });
return { trajectory };
};
}
exports.PdbProvider = {
label: 'PDB',
description: 'PDB',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['pdb', 'ent'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromPDB),
visuals: defaultVisuals
};
exports.PdbqtProvider = {
label: 'PDBQT',
description: 'PDBQT',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['pdbqt'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromPDB, { isPdbqt: true }),
visuals: defaultVisuals
};
exports.XyzProvider = {
label: 'XYZ',
description: 'XYZ',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['xyz'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromXYZ),
visuals: defaultVisuals
};
exports.LammpsDataProvider = {
label: 'Lammps Data',
description: 'Lammps Data',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['data'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromLammpsData),
visuals: defaultVisuals
};
exports.LammpsTrajectoryDataProvider = {
label: 'Lammps Trajectory Data',
description: 'Lammps Trajectory Data',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['lammpstrj'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromLammpsTrajData),
visuals: defaultVisuals
};
exports.GroProvider = {
label: 'GRO',
description: 'GRO',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['gro'],
binaryExtensions: [],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromGRO),
visuals: defaultVisuals
};
exports.MolProvider = {
label: 'MOL',
description: 'MOL',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['mol'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromMOL),
visuals: defaultVisuals
};
exports.SdfProvider = {
label: 'SDF',
description: 'SDF',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['sdf', 'sd'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromSDF),
visuals: defaultVisuals
};
exports.Mol2Provider = {
label: 'MOL2',
description: 'MOL2',
category: exports.TrajectoryFormatCategory,
stringExtensions: ['mol2'],
parse: directTrajectory(transforms_1.StateTransforms.Model.TrajectoryFromMOL2),
visuals: defaultVisuals
};
exports.BuiltInTrajectoryFormats = [
['mmcif', exports.MmcifProvider],
['cifCore', exports.CifCoreProvider],
['pdb', exports.PdbProvider],
['pdbqt', exports.PdbqtProvider],
['gro', exports.GroProvider],
['xyz', exports.XyzProvider],
['lammps_data', exports.LammpsDataProvider],
['lammps_traj_data', exports.LammpsTrajectoryDataProvider],
['mol', exports.MolProvider],
['sdf', exports.SdfProvider],
['mol2', exports.Mol2Provider],
];