molstar 3.0.0-dev.3 → 3.0.0-dev.7

package/lib/mol-plugin/util/viewport-screenshot.d.ts

@@ -37,10 +37,17 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            bumpFrequency: number;
+            bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             material: PD.Normalize<{
                 metalness: number;
                 roughness: number;
+                bumpiness: number;
+            }>;
+            clip: PD.Normalize<{
+                variant: any;
+                objects: any;
             }>;
         }>, "on">>;
     };
@@ -62,10 +69,17 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 flipSided: boolean;
                 flatShaded: boolean;
                 xrayShaded: boolean;
+                bumpFrequency: number;
+                bumpAmplitude: number;
                 quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
                 material: PD.Normalize<{
                     metalness: number;
                     roughness: number;
+                    bumpiness: number;
+                }>;
+                clip: PD.Normalize<{
+                    variant: any;
+                    objects: any;
                 }>;
             }>, "on">>;
         }>>;
@@ -95,10 +109,17 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flipSided: boolean;
             flatShaded: boolean;
             xrayShaded: boolean;
+            bumpFrequency: number;
+            bumpAmplitude: number;
             quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             material: PD.Normalize<{
                 metalness: number;
                 roughness: number;
+                bumpiness: number;
+            }>;
+            clip: PD.Normalize<{
+                variant: any;
+                objects: any;
             }>;
         }>, "on">>;
     }>;

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.0.0-dev.3';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1638685340455);
+export var PLUGIN_VERSION = '3.0.0-dev.7';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1640068825049);

package/lib/mol-plugin-state/actions/structure.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -36,6 +36,12 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
     }>, "swissmodel"> | PD.NamedParams<PD.Normalize<{
         id: any;
         options: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
     }>, "pubchem">;
 }>>;
 export declare const UpdateTrajectory: StateAction<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, void, PD.Normalize<{

package/lib/mol-plugin-state/actions/structure.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -16,15 +16,19 @@ import { StateTransforms } from '../transforms';
 import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
 import { Asset } from '../../mol-util/assets';
 import { PluginConfig } from '../../mol-plugin/config';
-var DownloadModelRepresentationOptions = function (plugin) { return PD.Group({
-    type: RootStructureDefinition.getParams(void 0, 'auto').type,
-    representation: PD.Select(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: PD.Group(StructureRepresentationPresetProvider.CommonParams, { isHidden: true }),
-    asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
-}, { isExpanded: false }); };
+import { getFileInfo } from '../../mol-util/file-info';
+var DownloadModelRepresentationOptions = function (plugin) {
+    var representationDefault = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+    return PD.Group({
+        type: RootStructureDefinition.getParams(void 0, 'auto').type,
+        representation: PD.Select(representationDefault, plugin.builders.structure.representation.getPresets().map(function (p) { return [p.id, p.display.name, p.display.group]; }), { description: 'Which representation preset to use.' }),
+        representationParams: PD.Group(StructureRepresentationPresetProvider.CommonParams, { isHidden: true }),
+        asTrajectory: PD.Optional(PD.Boolean(false, { description: 'Load all entries into a single trajectory.' }))
+    }, { isExpanded: false });
+};
 export var PdbDownloadProvider = {
     'rcsb': PD.Group({
-        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']]),
+        encoding: PD.Select('bcif', PD.arrayToOptions(['cif', 'bcif'])),
     }, { label: 'RCSB PDB', isFlat: true }),
     'pdbe': PD.Group({
         variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']]),
@@ -49,7 +53,7 @@ var DownloadStructure = StateAction.build({
                 'pdb-dev': PD.Group({
                     provider: PD.Group({
                         id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
-                        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']]),
+                        encoding: PD.Select('bcif', PD.arrayToOptions(['cif', 'bcif'])),
                     }, { pivot: 'id' }),
                     options: options
                 }, { isFlat: true, label: 'PDBDEV' }),
@@ -57,6 +61,14 @@ var DownloadStructure = StateAction.build({
                     id: PD.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' }),
+                'alphafolddb': PD.Group({
+                    id: PD.Text('Q8W3K0', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
+                    options: options
+                }, { isFlat: true, label: 'AlphaFold DB', description: 'Loads the predicted model if available' }),
+                'modelarchive': PD.Group({
+                    id: PD.Text('ma-bak-cepc-0003', { label: 'Accession Code(s)', description: 'One or more comma/space separated ACs.' }),
+                    options: options
+                }, { isFlat: true, label: 'Model Archive' }),
                 'pubchem': PD.Group({
                     id: PD.Text('2244,2245', { label: 'PubChem ID', description: 'One or more comma/space separated IDs.' }),
                     options: options
@@ -73,58 +85,99 @@ var DownloadStructure = StateAction.build({
 })(function (_a, plugin) {
     var params = _a.params, state = _a.state;
     return Task.create('Download Structure', function (ctx) { return __awaiter(void 0, void 0, void 0, function () {
-        var src, downloadParams, asTrajectory, format, representationPreset, showUnitcell, structure;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
+        var src, downloadParams, asTrajectory, format, _a, representationPreset, showUnitcell, structure;
+        return __generator(this, function (_b) {
+            switch (_b.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/".concat(id.toLowerCase(), "_updated.cif"); }, function (id) { return "PDBe: ".concat(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/".concat(id.toLowerCase(), ".bcif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, true)
-                                        : getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBe: ".concat(id, " (cif)"); }, false)
-                                : src.params.provider.server.params.encoding === 'cif'
-                                    ? getDownloadParams(src.params.provider.id, function (id) { return "https://files.rcsb.org/download/".concat(id.toUpperCase(), ".cif"); }, function (id) { return "RCSB: ".concat(id, " (cif)"); }, false)
-                                    : getDownloadParams(src.params.provider.id, function (id) { return "https://models.rcsb.org/".concat(id.toUpperCase(), ".bcif"); }, function (id) { return "RCSB: ".concat(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_".concat(id.padStart(8, '0'));
-                                return src.params.provider.encoding === 'bcif'
-                                    ? "https://pdb-dev.wwpdb.org/bcif/".concat(nId.toUpperCase(), ".bcif")
-                                    : "https://pdb-dev.wwpdb.org/cif/".concat(nId.toUpperCase(), ".cif");
-                            }, function (id) { return id.toUpperCase().startsWith('PDBDEV_') ? id : "PDBDEV_".concat(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/".concat(id.toUpperCase(), ".pdb"); }, function (id) { return "SWISS-MODEL: ".concat(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/".concat(id.trim(), "/record/SDF/?record_type=3d"); }, function (id) { return "PubChem: ".concat(id); }, false);
-                            asTrajectory = !!src.params.options.asTrajectory;
-                            format = 'mol';
-                            break;
-                        default: throw new Error("".concat(src.name, " not supported."));
+                    _a = src.name;
+                    switch (_a) {
+                        case 'url': return [3 /*break*/, 1];
+                        case 'pdb': return [3 /*break*/, 2];
+                        case 'pdb-dev': return [3 /*break*/, 4];
+                        case 'swissmodel': return [3 /*break*/, 6];
+                        case 'alphafolddb': return [3 /*break*/, 8];
+                        case 'modelarchive': return [3 /*break*/, 10];
+                        case 'pubchem': return [3 /*break*/, 12];
                     }
-                    representationPreset = params.source.params.options.representation || PresetStructureRepresentations.auto.id;
+                    return [3 /*break*/, 14];
+                case 1:
+                    downloadParams = [{ url: src.params.url, isBinary: src.params.isBinary }];
+                    format = src.params.format;
+                    return [3 /*break*/, 15];
+                case 2: return [4 /*yield*/, (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/".concat(id.toLowerCase(), "_updated.cif"); }, function (id) { return "PDBe: ".concat(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/".concat(id.toLowerCase(), ".bcif"); }, function (id) { return "PDBe: ".concat(id, " (updated cif)"); }, true)
+                                : getDownloadParams(src.params.provider.id, function (id) { return "https://www.ebi.ac.uk/pdbe/static/entry/".concat(id.toLowerCase(), ".cif"); }, function (id) { return "PDBe: ".concat(id, " (cif)"); }, false)
+                        : src.params.provider.server.params.encoding === 'cif'
+                            ? getDownloadParams(src.params.provider.id, function (id) { return "https://files.rcsb.org/download/".concat(id.toUpperCase(), ".cif"); }, function (id) { return "RCSB: ".concat(id, " (cif)"); }, false)
+                            : getDownloadParams(src.params.provider.id, function (id) { return "https://models.rcsb.org/".concat(id.toUpperCase(), ".bcif"); }, function (id) { return "RCSB: ".concat(id, " (bcif)"); }, true))];
+                case 3:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    return [3 /*break*/, 15];
+                case 4: return [4 /*yield*/, getDownloadParams(src.params.provider.id, function (id) {
+                        var nId = id.toUpperCase().startsWith('PDBDEV_') ? id : "PDBDEV_".concat(id.padStart(8, '0'));
+                        return src.params.provider.encoding === 'bcif'
+                            ? "https://pdb-dev.wwpdb.org/bcif/".concat(nId.toUpperCase(), ".bcif")
+                            : "https://pdb-dev.wwpdb.org/cif/".concat(nId.toUpperCase(), ".cif");
+                    }, function (id) { return id.toUpperCase().startsWith('PDBDEV_') ? id : "PDBDEV_".concat(id.padStart(8, '0')); }, src.params.provider.encoding === 'bcif')];
+                case 5:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    return [3 /*break*/, 15];
+                case 6: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return "https://swissmodel.expasy.org/repository/uniprot/".concat(id.toUpperCase(), ".pdb"); }, function (id) { return "SWISS-MODEL: ".concat(id); }, false)];
+                case 7:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    format = 'pdb';
+                    return [3 /*break*/, 15];
+                case 8: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return __awaiter(void 0, void 0, void 0, function () {
+                        var url, info;
+                        return __generator(this, function (_a) {
+                            switch (_a.label) {
+                                case 0:
+                                    url = "https://www.alphafold.ebi.ac.uk/api/prediction/".concat(id.toUpperCase());
+                                    return [4 /*yield*/, plugin.runTask(plugin.fetch({ url: url, type: 'json' }))];
+                                case 1:
+                                    info = _a.sent();
+                                    if (Array.isArray(info) && info.length > 0)
+                                        return [2 /*return*/, info[0].cifUrl];
+                                    throw new Error("No AlphaFold DB entry for '".concat(id, "'"));
+                            }
+                        });
+                    }); }, function (id) { return "AlphaFold DB: ".concat(id); }, false)];
+                case 9:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    format = 'mmcif';
+                    return [3 /*break*/, 15];
+                case 10: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return "https://www.modelarchive.org/doi/10.5452/".concat(id.toLowerCase(), ".cif"); }, function (id) { return "Model Archive: ".concat(id); }, false)];
+                case 11:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    format = 'mmcif';
+                    return [3 /*break*/, 15];
+                case 12: return [4 /*yield*/, getDownloadParams(src.params.id, function (id) { return "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/CID/".concat(id.trim(), "/record/SDF/?record_type=3d"); }, function (id) { return "PubChem: ".concat(id); }, false)];
+                case 13:
+                    downloadParams = _b.sent();
+                    asTrajectory = !!src.params.options.asTrajectory;
+                    format = 'mol';
+                    return [3 /*break*/, 15];
+                case 14: throw new Error("".concat(src.name, " not supported."));
+                case 15:
+                    representationPreset = params.source.params.options.representation || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
                     showUnitcell = representationPreset !== PresetStructureRepresentations.empty.id;
                     structure = src.params.options.type.name === 'auto' ? void 0 : src.params.options.type;
                     return [4 /*yield*/, state.transaction(function () { return __awaiter(void 0, void 0, void 0, function () {
-                            var blob, trajectory, _i, downloadParams_1, download, data, trajectory;
-                            return __generator(this, function (_a) {
-                                switch (_a.label) {
+                            var blob, trajectory, _i, downloadParams_1, download, data, provider, trajectory;
+                            var _a;
+                            return __generator(this, function (_b) {
+                                switch (_b.label) {
                                     case 0:
                                         if (!(downloadParams.length > 0 && asTrajectory)) return [3 /*break*/, 4];
                                         return [4 /*yield*/, plugin.builders.data.downloadBlob({
@@ -132,10 +185,10 @@ var DownloadStructure = StateAction.build({
                                                 maxConcurrency: 6
                                             }, { state: { isGhost: true } })];
                                     case 1:
-                                        blob = _a.sent();
+                                        blob = _b.sent();
                                         return [4 /*yield*/, plugin.builders.structure.parseTrajectory(blob, { formats: downloadParams.map(function (_, i) { return ({ id: '' + i, format: 'cif' }); }) })];
                                     case 2:
-                                        trajectory = _a.sent();
+                                        trajectory = _b.sent();
                                         return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
                                                 structure: structure,
                                                 showUnitcell: showUnitcell,
@@ -143,20 +196,25 @@ var DownloadStructure = StateAction.build({
                                                 representationPresetParams: params.source.params.options.representationParams
                                             })];
                                     case 3:
-                                        _a.sent();
+                                        _b.sent();
                                         return [3 /*break*/, 10];
                                     case 4:
                                         _i = 0, downloadParams_1 = downloadParams;
-                                        _a.label = 5;
+                                        _b.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)];
+                                        data = _b.sent();
+                                        provider = format === 'auto'
+                                            ? plugin.dataFormats.auto(getFileInfo(Asset.getUrl(download.url)), (_a = data.cell) === null || _a === void 0 ? void 0 : _a.obj)
+                                            : plugin.dataFormats.get(format);
+                                        if (!provider)
+                                            throw new Error('unknown file format');
+                                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, provider)];
                                     case 7:
-                                        trajectory = _a.sent();
+                                        trajectory = _b.sent();
                                         return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
                                                 structure: structure,
                                                 showUnitcell: showUnitcell,
@@ -164,8 +222,8 @@ var DownloadStructure = StateAction.build({
                                                 representationPresetParams: params.source.params.options.representationParams
                                             })];
                                     case 8:
-                                        _a.sent();
-                                        _a.label = 9;
+                                        _b.sent();
+                                        _b.label = 9;
                                     case 9:
                                         _i++;
                                         return [3 /*break*/, 5];
@@ -173,26 +231,46 @@ var DownloadStructure = StateAction.build({
                                 }
                             });
                         }); }).runInContext(ctx)];
-                case 1:
-                    _a.sent();
+                case 16:
+                    _b.sent();
                     return [2 /*return*/];
             }
         });
     }); });
 });
 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]*$/.test(id)); });
-    var ret = [];
-    for (var _i = 0, ids_1 = ids; _i < ids_1.length; _i++) {
-        var id = ids_1[_i];
-        ret.push({ url: Asset.Url(url(id)), isBinary: isBinary, label: label(id) });
-    }
-    return ret;
+    return __awaiter(this, void 0, void 0, function () {
+        var ids, ret, _i, ids_1, id, _a, _b, _c, _d;
+        var _e;
+        return __generator(this, function (_f) {
+            switch (_f.label) {
+                case 0:
+                    ids = src.split(/[,\s]/).map(function (id) { return id.trim(); }).filter(function (id) { return !!id && (id.length >= 4 || /^[1-9][0-9]*$/.test(id)); });
+                    ret = [];
+                    _i = 0, ids_1 = ids;
+                    _f.label = 1;
+                case 1:
+                    if (!(_i < ids_1.length)) return [3 /*break*/, 4];
+                    id = ids_1[_i];
+                    _b = (_a = ret).push;
+                    _e = {};
+                    _d = (_c = Asset).Url;
+                    return [4 /*yield*/, url(id)];
+                case 2:
+                    _b.apply(_a, [(_e.url = _d.apply(_c, [_f.sent()]), _e.isBinary = isBinary, _e.label = label(id), _e)]);
+                    _f.label = 3;
+                case 3:
+                    _i++;
+                    return [3 /*break*/, 1];
+                case 4: return [2 /*return*/, ret];
+            }
+        });
+    });
 }
 export var UpdateTrajectory = StateAction.build({
     display: { name: 'Update Trajectory' },
     params: {
-        action: PD.Select('advance', [['advance', 'Advance'], ['reset', 'Reset']]),
+        action: PD.Select('advance', PD.arrayToOptions(['advance', 'reset'])),
         by: PD.Optional(PD.Numeric(1, { min: -1, max: 1, step: 1 }))
     }
 })(function (_a) {