molstar
Version:
A comprehensive macromolecular library.
301 lines • 20.9 kB
JavaScript
;
/**
* Copyright (c) 2018-2020 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.AddTrajectory = exports.EnableStructureCustomProps = exports.EnableModelCustomProps = exports.UpdateTrajectory = exports.DownloadStructure = exports.PdbDownloadProvider = void 0;
var tslib_1 = require("tslib");
var mol_state_1 = require("../../mol-state");
var mol_task_1 = require("../../mol-task");
var param_definition_1 = require("../../mol-util/param-definition");
var representation_preset_1 = require("../builder/structure/representation-preset");
var trajectory_1 = require("../formats/trajectory");
var root_structure_1 = require("../helpers/root-structure");
var objects_1 = require("../objects");
var transforms_1 = require("../transforms");
var model_1 = require("../transforms/model");
var assets_1 = require("../../mol-util/assets");
var config_1 = require("../../mol-plugin/config");
var DownloadModelRepresentationOptions = function (plugin) { return param_definition_1.ParamDefinition.Group({
type: root_structure_1.RootStructureDefinition.getParams(void 0, 'auto').type,
representation: param_definition_1.ParamDefinition.Select(representation_preset_1.PresetStructureRepresentations.auto.id, plugin.builders.structure.representation.getPresets().map(function (p) { return [p.id, p.display.name, p.display.group]; }), { description: 'Which representation preset to use.' }),
representationParams: param_definition_1.ParamDefinition.Group(representation_preset_1.StructureRepresentationPresetProvider.CommonParams, { isHidden: true }),
asTrajectory: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
}, { isExpanded: false }); };
exports.PdbDownloadProvider = {
'rcsb': param_definition_1.ParamDefinition.Group({
encoding: param_definition_1.ParamDefinition.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']]),
}, { label: 'RCSB PDB', isFlat: true }),
'pdbe': param_definition_1.ParamDefinition.Group({
variant: param_definition_1.ParamDefinition.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']]),
}, { label: 'PDBe', isFlat: true }),
};
var DownloadStructure = mol_state_1.StateAction.build({
from: objects_1.PluginStateObject.Root,
display: { name: 'Download Structure', description: 'Load a structure from the provided source and create its representation.' },
params: function (_, plugin) {
var options = DownloadModelRepresentationOptions(plugin);
var defaultPdbProvider = plugin.config.get(config_1.PluginConfig.Download.DefaultPdbProvider) || 'pdbe';
return {
source: param_definition_1.ParamDefinition.MappedStatic('pdb', {
'pdb': param_definition_1.ParamDefinition.Group({
provider: param_definition_1.ParamDefinition.Group({
id: param_definition_1.ParamDefinition.Text('1tqn', { label: 'PDB Id(s)', description: 'One or more comma/space separated PDB ids.' }),
server: param_definition_1.ParamDefinition.MappedStatic(defaultPdbProvider, exports.PdbDownloadProvider),
}, { pivot: 'id' }),
options: options
}, { isFlat: true, label: 'PDB' }),
'pdb-dev': param_definition_1.ParamDefinition.Group({
provider: param_definition_1.ParamDefinition.Group({
id: param_definition_1.ParamDefinition.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
encoding: param_definition_1.ParamDefinition.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']]),
}, { pivot: 'id' }),
options: options
}, { isFlat: true, label: 'PDBDEV' }),
'swissmodel': param_definition_1.ParamDefinition.Group({
id: param_definition_1.ParamDefinition.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
options: options
}, { isFlat: true, label: 'SWISS-MODEL', description: 'Loads the best homology model or experimental structure' }),
'pubchem': param_definition_1.ParamDefinition.Group({
id: param_definition_1.ParamDefinition.Text('2244,2245', { label: 'PubChem ID', description: 'One or more comma/space separated IDs.' }),
options: options
}, { isFlat: true, label: 'PubChem', description: 'Loads 3D conformer from PubChem.' }),
'url': param_definition_1.ParamDefinition.Group({
url: param_definition_1.ParamDefinition.Url(''),
format: param_definition_1.ParamDefinition.Select('mmcif', param_definition_1.ParamDefinition.arrayToOptions(trajectory_1.BuiltInTrajectoryFormats.map(function (f) { return f[0]; }), function (f) { return f; })),
isBinary: param_definition_1.ParamDefinition.Boolean(false),
options: options
}, { isFlat: true, label: 'URL' })
})
};
}
})(function (_a, plugin) {
var params = _a.params, state = _a.state;
return mol_task_1.Task.create('Download Structure', function (ctx) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
var src, downloadParams, asTrajectory, format, representationPreset, showUnitcell, structure;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
plugin.behaviors.layout.leftPanelTabName.next('data');
src = params.source;
asTrajectory = false, format = 'mmcif';
switch (src.name) {
case 'url':
downloadParams = [{ url: src.params.url, isBinary: src.params.isBinary }];
format = src.params.format;
break;
case 'pdb':
downloadParams = src.params.provider.server.name === 'pdbe'
? src.params.provider.server.params.variant === 'updated'
? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/" + id.toLowerCase() + "_updated.cif"; }, function (id) { return "PDBe: " + id + " (updated cif)"; }, false)
: src.params.provider.server.params.variant === 'updated-bcif'
? getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/entry-files/download/" + id.toLowerCase() + ".bcif"; }, function (id) { return "PDBe: " + id + " (updated cif)"; }, true)
: getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/" + id.toLowerCase() + ".cif"; }, function (id) { return "PDBe: " + id + " (cif)"; }, false)
: src.params.provider.server.params.encoding === 'cif'
? getDownloadParams(src.params.provider.id, function (id) { return "https://files.rcsb.org/download/" + id.toUpperCase() + ".cif"; }, function (id) { return "RCSB: " + id + " (cif)"; }, false)
: getDownloadParams(src.params.provider.id, function (id) { return "https://models.rcsb.org/" + id.toUpperCase() + ".bcif"; }, function (id) { return "RCSB: " + id + " (bcif)"; }, true);
asTrajectory = !!src.params.options.asTrajectory;
break;
case 'pdb-dev':
downloadParams = getDownloadParams(src.params.provider.id, function (id) {
var nId = id.toUpperCase().startsWith('PDBDEV_') ? id : "PDBDEV_" + id.padStart(8, '0');
return src.params.provider.encoding === 'bcif'
? "https://pdb-dev.wwpdb.org/bcif/" + nId.toUpperCase() + ".bcif"
: "https://pdb-dev.wwpdb.org/cif/" + nId.toUpperCase() + ".cif";
}, function (id) { return id.toUpperCase().startsWith('PDBDEV_') ? id : "PDBDEV_" + id.padStart(8, '0'); }, src.params.provider.encoding === 'bcif');
asTrajectory = !!src.params.options.asTrajectory;
break;
case 'swissmodel':
downloadParams = getDownloadParams(src.params.id, function (id) { return "https://swissmodel.expasy.org/repository/uniprot/" + id.toUpperCase() + ".pdb"; }, function (id) { return "SWISS-MODEL: " + id; }, false);
asTrajectory = !!src.params.options.asTrajectory;
format = 'pdb';
break;
case 'pubchem':
downloadParams = getDownloadParams(src.params.id, function (id) { return "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/" + id.trim() + "/record/SDF/?record_type=3d"; }, function (id) { return "PubChem: " + id; }, false);
asTrajectory = !!src.params.options.asTrajectory;
format = 'mol';
break;
default: throw new Error(src.name + " not supported.");
}
representationPreset = params.source.params.options.representation || representation_preset_1.PresetStructureRepresentations.auto.id;
showUnitcell = representationPreset !== representation_preset_1.PresetStructureRepresentations.empty.id;
structure = src.params.options.type.name === 'auto' ? void 0 : src.params.options.type;
return [4 /*yield*/, state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
var blob, trajectory, _i, downloadParams_1, download, data, trajectory;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
if (!(downloadParams.length > 0 && asTrajectory)) return [3 /*break*/, 4];
return [4 /*yield*/, plugin.builders.data.downloadBlob({
sources: downloadParams.map(function (src, i) { return ({ id: '' + i, url: src.url, isBinary: src.isBinary }); }),
maxConcurrency: 6
}, { state: { isGhost: true } })];
case 1:
blob = _a.sent();
return [4 /*yield*/, plugin.builders.structure.parseTrajectory(blob, { formats: downloadParams.map(function (_, i) { return ({ id: '' + i, format: 'cif' }); }) })];
case 2:
trajectory = _a.sent();
return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
structure: structure,
showUnitcell: showUnitcell,
representationPreset: representationPreset,
representationPresetParams: params.source.params.options.representationParams
})];
case 3:
_a.sent();
return [3 /*break*/, 10];
case 4:
_i = 0, downloadParams_1 = downloadParams;
_a.label = 5;
case 5:
if (!(_i < downloadParams_1.length)) return [3 /*break*/, 10];
download = downloadParams_1[_i];
return [4 /*yield*/, plugin.builders.data.download(download, { state: { isGhost: true } })];
case 6:
data = _a.sent();
return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, format)];
case 7:
trajectory = _a.sent();
return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
structure: structure,
showUnitcell: showUnitcell,
representationPreset: representationPreset,
representationPresetParams: params.source.params.options.representationParams
})];
case 8:
_a.sent();
_a.label = 9;
case 9:
_i++;
return [3 /*break*/, 5];
case 10: return [2 /*return*/];
}
});
}); }).runInContext(ctx)];
case 1:
_a.sent();
return [2 /*return*/];
}
});
}); });
});
exports.DownloadStructure = DownloadStructure;
function getDownloadParams(src, url, label, isBinary) {
var ids = src.split(/[,\s]/).map(function (id) { return id.trim(); }).filter(function (id) { return !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)); });
var ret = [];
for (var _i = 0, ids_1 = ids; _i < ids_1.length; _i++) {
var id = ids_1[_i];
ret.push({ url: assets_1.Asset.Url(url(id)), isBinary: isBinary, label: label(id) });
}
return ret;
}
exports.UpdateTrajectory = mol_state_1.StateAction.build({
display: { name: 'Update Trajectory' },
params: {
action: param_definition_1.ParamDefinition.Select('advance', [['advance', 'Advance'], ['reset', 'Reset']]),
by: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Numeric(1, { min: -1, max: 1, step: 1 }))
}
})(function (_a) {
var params = _a.params, state = _a.state;
var models = state.selectQ(function (q) { return q.ofTransformer(transforms_1.StateTransforms.Model.ModelFromTrajectory); });
var update = state.build();
if (params.action === 'reset') {
for (var _i = 0, models_1 = models; _i < models_1.length; _i++) {
var m = models_1[_i];
update.to(m).update({ modelIndex: 0 });
}
}
else {
var _loop_1 = function (m) {
var parent_1 = mol_state_1.StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, objects_1.PluginStateObject.Molecule.Trajectory);
if (!parent_1 || !parent_1.obj)
return "continue";
var traj = parent_1.obj;
update.to(m).update(function (old) {
var modelIndex = (old.modelIndex + params.by) % traj.data.frameCount;
if (modelIndex < 0)
modelIndex += traj.data.frameCount;
return { modelIndex: modelIndex };
});
};
for (var _b = 0, models_2 = models; _b < models_2.length; _b++) {
var m = models_2[_b];
_loop_1(m);
}
}
return state.updateTree(update);
});
exports.EnableModelCustomProps = mol_state_1.StateAction.build({
display: { name: 'Custom Model Properties', description: 'Enable parameters for custom properties of the model.' },
from: objects_1.PluginStateObject.Molecule.Model,
params: function (a, ctx) {
return ctx.customModelProperties.getParams(a === null || a === void 0 ? void 0 : a.data);
},
isApplicable: function (a, t, ctx) {
return t.transformer !== model_1.CustomModelProperties;
}
})(function (_a, ctx) {
var ref = _a.ref, params = _a.params;
return ctx.builders.structure.insertModelProperties(ref, params);
});
exports.EnableStructureCustomProps = mol_state_1.StateAction.build({
display: { name: 'Custom Structure Properties', description: 'Enable parameters for custom properties of the structure.' },
from: objects_1.PluginStateObject.Molecule.Structure,
params: function (a, ctx) {
return ctx.customStructureProperties.getParams(a === null || a === void 0 ? void 0 : a.data);
},
isApplicable: function (a, t, ctx) {
return t.transformer !== model_1.CustomStructureProperties;
}
})(function (_a, ctx) {
var ref = _a.ref, params = _a.params;
return ctx.builders.structure.insertStructureProperties(ref, params);
});
exports.AddTrajectory = mol_state_1.StateAction.build({
display: { name: 'Add Trajectory', description: 'Add trajectory from existing model/topology and coordinates.' },
from: objects_1.PluginStateObject.Root,
params: function (a, ctx) {
var state = ctx.state.data;
var models = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Model); }), true), state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Topology); }), true);
var modelOptions = models.map(function (t) { return [t.transform.ref, t.obj.label]; });
var coords = state.selectQ(function (q) { return q.rootsOfType(objects_1.PluginStateObject.Molecule.Coordinates); });
var coordOptions = coords.map(function (c) { return [c.transform.ref, c.obj.label]; });
return {
model: param_definition_1.ParamDefinition.Select(modelOptions.length ? modelOptions[0][0] : '', modelOptions),
coordinates: param_definition_1.ParamDefinition.Select(coordOptions.length ? coordOptions[0][0] : '', coordOptions)
};
}
})(function (_a, ctx) {
var params = _a.params, state = _a.state;
return mol_task_1.Task.create('Add Trajectory', function (taskCtx) {
return state.transaction(function () { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
var dependsOn, model, structure;
return (0, tslib_1.__generator)(this, function (_a) {
switch (_a.label) {
case 0:
dependsOn = [params.model, params.coordinates];
model = state.build().toRoot()
.apply(model_1.TrajectoryFromModelAndCoordinates, {
modelRef: params.model,
coordinatesRef: params.coordinates
}, { dependsOn: dependsOn })
.apply(transforms_1.StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
return [4 /*yield*/, state.updateTree(model).runInContext(taskCtx)];
case 1:
_a.sent();
return [4 /*yield*/, ctx.builders.structure.createStructure(model.selector)];
case 2:
structure = _a.sent();
return [4 /*yield*/, ctx.builders.structure.representation.applyPreset(structure, 'auto')];
case 3:
_a.sent();
return [2 /*return*/];
}
});
}); }).runInContext(taskCtx);
});
});
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