molstar
Version:
A comprehensive macromolecular library.
569 lines (568 loc) • 31.3 kB
JavaScript
"use strict";
/**
* Copyright (c) 2018-2025 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 Neli Fonseca <neli@ebi.ac.uk>
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.PluginExtensions = exports.ViewerAutoPreset = exports.Viewer = exports.ExtensionMap = exports.isTimingMode = exports.isDebugMode = exports.isProductionMode = exports.setTimingMode = exports.setProductionMode = exports.setDebugMode = exports.consoleStats = exports.version = void 0;
const behavior_1 = require("../../extensions/anvil/behavior");
const backgrounds_1 = require("../../extensions/backgrounds");
const dnatco_1 = require("../../extensions/dnatco");
const format_1 = require("../../extensions/g3d/format");
const geo_export_1 = require("../../extensions/geo-export");
const behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
const prop_1 = require("../../extensions/model-archive/quality-assessment/prop");
const model_export_1 = require("../../extensions/model-export");
const mp4_export_1 = require("../../extensions/mp4-export");
const behavior_3 = require("../../extensions/mvs/behavior");
const formats_1 = require("../../extensions/mvs/components/formats");
const load_1 = require("../../extensions/mvs/load");
const mvs_data_1 = require("../../extensions/mvs/mvs-data");
const pdbe_1 = require("../../extensions/pdbe");
const rcsb_1 = require("../../extensions/rcsb");
const assembly_symmetry_1 = require("../../extensions/assembly-symmetry");
const sb_ncbr_1 = require("../../extensions/sb-ncbr");
const behavior_4 = require("../../extensions/wwpdb/ccd/behavior");
const struct_conn_1 = require("../../extensions/wwpdb/struct-conn");
const zenodo_1 = require("../../extensions/zenodo");
const volume_1 = require("../../mol-model/volume");
const structure_1 = require("../../mol-plugin-state/actions/structure");
const volume_2 = require("../../mol-plugin-state/actions/volume");
const representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
const volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
const transforms_1 = require("../../mol-plugin-state/transforms");
const model_1 = require("../../mol-plugin-state/transforms/model");
const mol_plugin_ui_1 = require("../../mol-plugin-ui");
const react18_1 = require("../../mol-plugin-ui/react18");
const spec_1 = require("../../mol-plugin-ui/spec");
const commands_1 = require("../../mol-plugin/commands");
const config_1 = require("../../mol-plugin/config");
const spec_2 = require("../../mol-plugin/spec");
const mol_state_1 = require("../../mol-state");
const mol_task_1 = require("../../mol-task");
const assets_1 = require("../../mol-util/assets");
const color_1 = require("../../mol-util/color");
require("../../mol-util/polyfill");
const type_helpers_1 = require("../../mol-util/type-helpers");
const file_1 = require("../../mol-plugin-state/actions/file");
const string_like_1 = require("../../mol-io/common/string-like");
var version_1 = require("../../mol-plugin/version");
Object.defineProperty(exports, "version", { enumerable: true, get: function () { return version_1.PLUGIN_VERSION; } });
var debug_1 = require("../../mol-util/debug");
Object.defineProperty(exports, "consoleStats", { enumerable: true, get: function () { return debug_1.consoleStats; } });
Object.defineProperty(exports, "setDebugMode", { enumerable: true, get: function () { return debug_1.setDebugMode; } });
Object.defineProperty(exports, "setProductionMode", { enumerable: true, get: function () { return debug_1.setProductionMode; } });
Object.defineProperty(exports, "setTimingMode", { enumerable: true, get: function () { return debug_1.setTimingMode; } });
Object.defineProperty(exports, "isProductionMode", { enumerable: true, get: function () { return debug_1.isProductionMode; } });
Object.defineProperty(exports, "isDebugMode", { enumerable: true, get: function () { return debug_1.isDebugMode; } });
Object.defineProperty(exports, "isTimingMode", { enumerable: true, get: function () { return debug_1.isTimingMode; } });
const CustomFormats = [
['g3d', format_1.G3dProvider]
];
exports.ExtensionMap = {
'backgrounds': spec_2.PluginSpec.Behavior(backgrounds_1.Backgrounds),
'dnatco-ntcs': spec_2.PluginSpec.Behavior(dnatco_1.DnatcoNtCs),
'pdbe-structure-quality-report': spec_2.PluginSpec.Behavior(pdbe_1.PDBeStructureQualityReport),
'assembly-symmetry': spec_2.PluginSpec.Behavior(assembly_symmetry_1.AssemblySymmetry),
'rcsb-validation-report': spec_2.PluginSpec.Behavior(rcsb_1.RCSBValidationReport),
'anvil-membrane-orientation': spec_2.PluginSpec.Behavior(behavior_1.ANVILMembraneOrientation),
'g3d': spec_2.PluginSpec.Behavior(format_1.G3DFormat),
'model-export': spec_2.PluginSpec.Behavior(model_export_1.ModelExport),
'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
'zenodo-import': spec_2.PluginSpec.Behavior(zenodo_1.ZenodoImport),
'sb-ncbr-partial-charges': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrPartialCharges),
'wwpdb-chemical-component-dictionary': spec_2.PluginSpec.Behavior(behavior_4.wwPDBChemicalComponentDictionary),
'mvs': spec_2.PluginSpec.Behavior(behavior_3.MolViewSpec),
'tunnels': spec_2.PluginSpec.Behavior(sb_ncbr_1.SbNcbrTunnels),
};
const DefaultViewerOptions = {
customFormats: CustomFormats,
extensions: (0, type_helpers_1.ObjectKeys)(exports.ExtensionMap),
disabledExtensions: [],
layoutIsExpanded: true,
layoutShowControls: true,
layoutShowRemoteState: true,
layoutControlsDisplay: 'reactive',
layoutShowSequence: true,
layoutShowLog: true,
layoutShowLeftPanel: true,
collapseLeftPanel: false,
collapseRightPanel: false,
disableAntialiasing: config_1.PluginConfig.General.DisableAntialiasing.defaultValue,
pixelScale: config_1.PluginConfig.General.PixelScale.defaultValue,
pickScale: config_1.PluginConfig.General.PickScale.defaultValue,
transparency: config_1.PluginConfig.General.Transparency.defaultValue,
preferWebgl1: config_1.PluginConfig.General.PreferWebGl1.defaultValue,
allowMajorPerformanceCaveat: config_1.PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
powerPreference: config_1.PluginConfig.General.PowerPreference.defaultValue,
resolutionMode: config_1.PluginConfig.General.ResolutionMode.defaultValue,
illumination: false,
viewportShowExpand: config_1.PluginConfig.Viewport.ShowExpand.defaultValue,
viewportShowControls: config_1.PluginConfig.Viewport.ShowControls.defaultValue,
viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
viewportShowSelectionMode: config_1.PluginConfig.Viewport.ShowSelectionMode.defaultValue,
viewportShowAnimation: config_1.PluginConfig.Viewport.ShowAnimation.defaultValue,
viewportShowTrajectoryControls: config_1.PluginConfig.Viewport.ShowTrajectoryControls.defaultValue,
pluginStateServer: config_1.PluginConfig.State.DefaultServer.defaultValue,
volumeStreamingServer: config_1.PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
volumeStreamingDisabled: !config_1.PluginConfig.VolumeStreaming.Enabled.defaultValue,
pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
saccharideCompIdMapType: 'default',
rcsbAssemblySymmetryDefaultServerType: assembly_symmetry_1.AssemblySymmetryConfig.DefaultServerType.defaultValue,
rcsbAssemblySymmetryDefaultServerUrl: assembly_symmetry_1.AssemblySymmetryConfig.DefaultServerUrl.defaultValue,
rcsbAssemblySymmetryApplyColors: assembly_symmetry_1.AssemblySymmetryConfig.ApplyColors.defaultValue,
config: [],
};
class Viewer {
constructor(plugin) {
this.plugin = plugin;
}
static async create(elementOrId, options = {}) {
var _a, _b, _c, _d;
const definedOptions = {};
// filter for defined properies only so the default values
// are property applied
for (const p of Object.keys(options)) {
if (options[p] !== void 0)
definedOptions[p] = options[p];
}
const o = { ...DefaultViewerOptions, ...definedOptions };
const defaultSpec = (0, spec_1.DefaultPluginUISpec)();
const disabledExtension = new Set((_a = o.disabledExtensions) !== null && _a !== void 0 ? _a : []);
const spec = {
actions: defaultSpec.actions,
behaviors: [
...defaultSpec.behaviors,
...o.extensions.filter(e => !disabledExtension.has(e)).map(e => exports.ExtensionMap[e]),
],
animations: [...defaultSpec.animations || []],
customParamEditors: defaultSpec.customParamEditors,
customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
layout: {
initial: {
isExpanded: o.layoutIsExpanded,
showControls: o.layoutShowControls,
controlsDisplay: o.layoutControlsDisplay,
regionState: {
bottom: 'full',
left: o.collapseLeftPanel ? 'collapsed' : 'full',
right: o.collapseRightPanel ? 'hidden' : 'full',
top: 'full',
}
},
},
components: {
...defaultSpec.components,
controls: {
...(_b = defaultSpec.components) === null || _b === void 0 ? void 0 : _b.controls,
top: o.layoutShowSequence ? undefined : 'none',
bottom: o.layoutShowLog ? undefined : 'none',
left: o.layoutShowLeftPanel ? undefined : 'none',
},
remoteState: o.layoutShowRemoteState ? 'default' : 'none',
},
config: [
[config_1.PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
[config_1.PluginConfig.General.PixelScale, o.pixelScale],
[config_1.PluginConfig.General.PickScale, o.pickScale],
[config_1.PluginConfig.General.Transparency, o.transparency],
[config_1.PluginConfig.General.PreferWebGl1, o.preferWebgl1],
[config_1.PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
[config_1.PluginConfig.General.PowerPreference, o.powerPreference],
[config_1.PluginConfig.General.ResolutionMode, o.resolutionMode],
[config_1.PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
[config_1.PluginConfig.Viewport.ShowControls, o.viewportShowControls],
[config_1.PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
[config_1.PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
[config_1.PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
[config_1.PluginConfig.Viewport.ShowTrajectoryControls, o.viewportShowTrajectoryControls],
[config_1.PluginConfig.State.DefaultServer, o.pluginStateServer],
[config_1.PluginConfig.State.CurrentServer, o.pluginStateServer],
[config_1.PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
[config_1.PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
[config_1.PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
[config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
[config_1.PluginConfig.Structure.DefaultRepresentationPreset, exports.ViewerAutoPreset.id],
[config_1.PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
[assembly_symmetry_1.AssemblySymmetryConfig.DefaultServerType, o.rcsbAssemblySymmetryDefaultServerType],
[assembly_symmetry_1.AssemblySymmetryConfig.DefaultServerUrl, o.rcsbAssemblySymmetryDefaultServerUrl],
[assembly_symmetry_1.AssemblySymmetryConfig.ApplyColors, o.rcsbAssemblySymmetryApplyColors],
...((_c = o.config) !== null && _c !== void 0 ? _c : []),
]
};
const element = typeof elementOrId === 'string'
? document.getElementById(elementOrId)
: elementOrId;
if (!element)
throw new Error(`Could not get element with id '${elementOrId}'`);
const plugin = await (0, mol_plugin_ui_1.createPluginUI)({
target: element,
spec,
render: react18_1.renderReact18,
onBeforeUIRender: plugin => {
// the preset needs to be added before the UI renders otherwise
// "Download Structure" wont be able to pick it up
plugin.builders.structure.representation.registerPreset(exports.ViewerAutoPreset);
}
});
(_d = plugin.canvas3d) === null || _d === void 0 ? void 0 : _d.setProps({ illumination: { enabled: o.illumination } });
return new Viewer(plugin);
}
setRemoteSnapshot(id) {
const url = `${this.plugin.config.get(config_1.PluginConfig.State.CurrentServer)}/get/${id}`;
return commands_1.PluginCommands.State.Snapshots.Fetch(this.plugin, { url });
}
loadSnapshotFromUrl(url, type) {
return commands_1.PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
}
loadStructureFromUrl(url, format = 'mmcif', isBinary = false, options) {
const params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
source: {
name: 'url',
params: {
url: assets_1.Asset.Url(url),
format: format,
isBinary,
label: options === null || options === void 0 ? void 0 : options.label,
options: { ...params.source.params.options, representationParams: options === null || options === void 0 ? void 0 : options.representationParams },
}
}
}));
}
async loadAllModelsOrAssemblyFromUrl(url, format = 'mmcif', isBinary = false, options) {
const plugin = this.plugin;
const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options === null || options === void 0 ? void 0 : options.representationParams });
}
async loadStructureFromData(data, format, options) {
const _data = await this.plugin.builders.data.rawData({ data, label: options === null || options === void 0 ? void 0 : options.dataLabel });
const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
}
loadPdb(pdb, options) {
const params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
const provider = this.plugin.config.get(config_1.PluginConfig.Download.DefaultPdbProvider);
return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
source: {
name: 'pdb',
params: {
provider: {
id: pdb,
server: {
name: provider,
params: structure_1.PdbDownloadProvider[provider].defaultValue
}
},
options: { ...params.source.params.options, representationParams: options === null || options === void 0 ? void 0 : options.representationParams },
}
}
}));
}
/**
* @deprecated Scheduled for removal in v5. Use {@link loadPdbIhm | loadPdbIhm(pdbIhm: string)} instead.
*/
loadPdbDev(pdbDev) {
return this.loadPdbIhm(pdbDev);
}
loadPdbIhm(pdbIhm) {
const params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
source: {
name: 'pdb-ihm',
params: {
provider: {
id: pdbIhm,
encoding: 'bcif',
},
options: params.source.params.options,
}
}
}));
}
loadEmdb(emdb, options) {
var _a;
const provider = this.plugin.config.get(config_1.PluginConfig.Download.DefaultEmdbProvider);
return this.plugin.runTask(this.plugin.state.data.applyAction(volume_2.DownloadDensity, {
source: {
name: 'pdb-emd-ds',
params: {
provider: {
id: emdb,
server: provider,
},
detail: (_a = options === null || options === void 0 ? void 0 : options.detail) !== null && _a !== void 0 ? _a : 3,
}
}
}));
}
loadAlphaFoldDb(afdb) {
const params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
source: {
name: 'alphafolddb',
params: {
provider: {
id: afdb,
encoding: 'bcif'
},
options: {
...params.source.params.options,
representation: 'preset-structure-representation-ma-quality-assessment-plddt'
},
}
}
}));
}
loadModelArchive(id) {
const params = structure_1.DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj, this.plugin);
return this.plugin.runTask(this.plugin.state.data.applyAction(structure_1.DownloadStructure, {
source: {
name: 'modelarchive',
params: {
id,
options: params.source.params.options,
}
}
}));
}
/**
* @example Load X-ray density from volume server
viewer.loadVolumeFromUrl({
url: 'https://www.ebi.ac.uk/pdbe/densities/x-ray/1tqn/cell?detail=3',
format: 'dscif',
isBinary: true
}, [{
type: 'relative',
value: 1.5,
color: 0x3362B2
}, {
type: 'relative',
value: 3,
color: 0x33BB33,
volumeIndex: 1
}, {
type: 'relative',
value: -3,
color: 0xBB3333,
volumeIndex: 1
}], {
entryId: ['2FO-FC', 'FO-FC'],
isLazy: true
});
* *********************
* @example Load EM density from volume server
viewer.loadVolumeFromUrl({
url: 'https://maps.rcsb.org/em/emd-30210/cell?detail=6',
format: 'dscif',
isBinary: true
}, [{
type: 'relative',
value: 1,
color: 0x3377aa
}], {
entryId: 'EMD-30210',
isLazy: true
});
*/
async loadVolumeFromUrl({ url, format, isBinary }, isovalues, options) {
const plugin = this.plugin;
if (!plugin.dataFormats.get(format)) {
throw new Error(`Unknown density format: ${format}`);
}
if (options === null || options === void 0 ? void 0 : options.isLazy) {
const update = this.plugin.build();
update.toRoot().apply(transforms_1.StateTransforms.Data.LazyVolume, {
url,
format,
entryId: options === null || options === void 0 ? void 0 : options.entryId,
isBinary,
isovalues: isovalues.map(v => ({ alpha: 1, volumeIndex: 0, ...v }))
});
return update.commit();
}
return plugin.dataTransaction(async () => {
var _a, _b, _c, _d;
const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
const parsed = await plugin.dataFormats.get(format).parse(plugin, data, { entryId: options === null || options === void 0 ? void 0 : options.entryId });
const firstVolume = (parsed.volume || parsed.volumes[0]);
if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
throw new Error('Failed to parse any volume.');
const repr = plugin.build();
for (const iso of isovalues) {
const volume = (_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume;
const volumeData = volume.cell.obj.data;
repr
.to(volume)
.apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.plugin, firstVolume.data, {
type: 'isosurface',
typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: volume_1.Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
color: 'uniform',
colorParams: { value: iso.color }
}));
}
await repr.commit();
});
}
loadFullResolutionEMDBMap(emdbId, options) {
const plugin = this.plugin;
const numericId = parseInt(emdbId.toUpperCase().replace('EMD-', ''));
const url = `https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-${numericId}/map/emd_${numericId}.map.gz`;
return plugin.dataTransaction(async () => {
var _a, _b, _c;
const data = await plugin.build().toRoot()
.apply(transforms_1.StateTransforms.Data.Download, { url, isBinary: true, label: emdbId }, { state: { isGhost: true } })
.apply(transforms_1.StateTransforms.Data.DeflateData)
.commit();
const parsed = await plugin.dataFormats.get('ccp4').parse(plugin, data, { entryId: emdbId });
const firstVolume = (parsed.volume || parsed.volumes[0]);
if (!(firstVolume === null || firstVolume === void 0 ? void 0 : firstVolume.isOk))
throw new Error('Failed to parse any volume.');
const volume = (_b = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[0]) !== null && _b !== void 0 ? _b : parsed.volume;
await plugin.build()
.to(volume)
.apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.plugin, firstVolume.data, {
type: 'isosurface',
typeParams: { alpha: 1, isoValue: options.isoValue },
color: 'uniform',
colorParams: { value: (_c = options.color) !== null && _c !== void 0 ? _c : (0, color_1.Color)(0x33BB33) }
}))
.commit();
});
}
/**
* @example
* viewer.loadTrajectory({
* model: { kind: 'model-url', url: 'villin.gro', format: 'gro' },
* coordinates: { kind: 'coordinates-url', url: 'villin.xtc', format: 'xtc', isBinary: true },
* preset: 'all-models' // or 'default'
* });
*/
async loadTrajectory(params) {
var _a, _b;
const plugin = this.plugin;
let model;
if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
const data = params.model.kind === 'model-data'
? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
: await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
const trajectory = await plugin.builders.structure.parseTrajectory(data, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif');
model = await plugin.builders.structure.createModel(trajectory);
}
else {
const data = params.model.kind === 'topology-data'
? await plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })
: await plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel });
const provider = plugin.dataFormats.get(params.model.format);
const parsed = await provider.parse(plugin, data);
model = parsed.topology;
}
const data = params.coordinates.kind === 'coordinates-data'
? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
: await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
const provider = plugin.dataFormats.get(params.coordinates.format);
const coords = await provider.parse(plugin, data);
const trajectory = await plugin.build().toRoot()
.apply(model_1.TrajectoryFromModelAndCoordinates, {
modelRef: model.ref,
coordinatesRef: coords.ref
}, { dependsOn: [model.ref, coords.ref] })
.commit();
const preset = await plugin.builders.structure.hierarchy.applyPreset(trajectory, (_b = params.preset) !== null && _b !== void 0 ? _b : 'default');
return { model, coords, preset };
}
async loadMvsFromUrl(url, format, options) {
if (format === 'mvsj') {
const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'string' }));
const mvsData = mvs_data_1.MVSData.fromMVSJ(string_like_1.StringLike.toString(data));
await (0, load_1.loadMVS)(this.plugin, mvsData, { sanityChecks: true, sourceUrl: url, ...options });
}
else if (format === 'mvsx') {
const data = await this.plugin.runTask(this.plugin.fetch({ url, type: 'binary' }));
await this.plugin.runTask(mol_task_1.Task.create('Load MVSX file', async (ctx) => {
const parsed = await (0, formats_1.loadMVSX)(this.plugin, ctx, data);
await (0, load_1.loadMVS)(this.plugin, parsed.mvsData, { sanityChecks: true, sourceUrl: parsed.sourceUrl, ...options });
}));
}
else {
throw new Error(`Unknown MolViewSpec format: ${format}`);
}
}
/** Load MolViewSpec from `data`.
* If `format` is 'mvsj', `data` must be a string or a Uint8Array containing a UTF8-encoded string.
* If `format` is 'mvsx', `data` must be a Uint8Array or a string containing base64-encoded binary data prefixed with 'base64,'. */
loadMvsData(data, format, options) {
return (0, formats_1.loadMVSData)(this.plugin, data, format, options);
}
loadFiles(files) {
const sessions = files.filter(f => {
const fn = f.name.toLowerCase();
return fn.endsWith('.molx') || fn.endsWith('.molj');
});
if (sessions.length > 0) {
return commands_1.PluginCommands.State.Snapshots.OpenFile(this.plugin, { file: sessions[0] });
}
else {
return this.plugin.runTask(this.plugin.state.data.applyAction(file_1.OpenFiles, {
files: files.map(f => assets_1.Asset.File(f)),
format: { name: 'auto', params: {} },
visuals: true
}));
}
}
handleResize() {
this.plugin.layout.events.updated.next(void 0);
}
dispose() {
this.plugin.dispose();
}
}
exports.Viewer = Viewer;
exports.ViewerAutoPreset = (0, representation_preset_1.StructureRepresentationPresetProvider)({
id: 'preset-structure-representation-viewer-auto',
display: {
name: 'Automatic (w/ Annotation)', group: 'Annotation',
description: 'Show standard automatic representation but colored by quality assessment (if available in the model).'
},
isApplicable(a) {
return (!!a.data.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'pLDDT')) ||
!!a.data.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'qmean')));
},
params: () => representation_preset_1.StructureRepresentationPresetProvider.CommonParams,
async apply(ref, params, plugin) {
var _a;
const structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
const structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
if (!structureCell || !structure)
return {};
if (!!structure.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'pLDDT'))) {
return await behavior_2.QualityAssessmentPLDDTPreset.apply(ref, params, plugin);
}
else if (!!structure.models.some(m => prop_1.QualityAssessment.isApplicable(m, 'qmean'))) {
return await behavior_2.QualityAssessmentQmeanPreset.apply(ref, params, plugin);
}
else if (!!structure.models.some(m => sb_ncbr_1.SbNcbrPartialChargesPropertyProvider.isApplicable(m))) {
return await sb_ncbr_1.SbNcbrPartialChargesPreset.apply(ref, params, plugin);
}
else {
return await representation_preset_1.PresetStructureRepresentations.auto.apply(ref, params, plugin);
}
}
});
exports.PluginExtensions = {
wwPDBStructConn: struct_conn_1.wwPDBStructConnExtensionFunctions,
mvs: { MVSData: mvs_data_1.MVSData, loadMVS: load_1.loadMVS, loadMVSData: formats_1.loadMVSData },
modelArchive: {
qualityAssessment: {
config: behavior_2.MAQualityAssessmentConfig
}
}
};