molstar 2.3.5 → 2.3.9

package/lib/apps/viewer/index.js

@@ -9,14 +9,15 @@ import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { CellPack } from '../../extensions/cellpack';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
-import { Mp4Export } from '../../extensions/mp4-export';
 import { GeometryExport } from '../../extensions/geo-export';
+import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { TrajectoryFromModelAndCoordinates } from '../../mol-plugin-state/transforms/model';
 import { createPlugin } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -56,6 +57,7 @@ var DefaultViewerOptions = {
     layoutShowLog: true,
     layoutShowLeftPanel: true,
     collapseLeftPanel: false,
+    collapseRightPanel: false,
     disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
     pixelScale: PluginConfig.General.PixelScale.defaultValue,
     pickScale: PluginConfig.General.PickScale.defaultValue,
@@ -92,7 +94,7 @@ var Viewer = /** @class */ (function () {
                     regionState: {
                         bottom: 'full',
                         left: o.collapseLeftPanel ? 'collapsed' : 'full',
-                        right: 'full',
+                        right: o.collapseRightPanel ? 'hidden' : 'full',
                         top: 'full',
                     }
                 },
@@ -121,11 +123,11 @@ var Viewer = /** @class */ (function () {
             ? document.getElementById(elementOrId)
             : elementOrId;
         if (!element)
-            throw new Error("Could not get element with id '" + elementOrId + "'");
+            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
         this.plugin = createPlugin(element, spec);
     }
     Viewer.prototype.setRemoteSnapshot = function (id) {
-        var url = this.plugin.config.get(PluginConfig.State.CurrentServer) + "/get/" + id;
+        var url = "".concat(this.plugin.config.get(PluginConfig.State.CurrentServer), "/get/").concat(id);
         return PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
     };
     Viewer.prototype.loadSnapshotFromUrl = function (url, type) {
@@ -286,7 +288,7 @@ var Viewer = /** @class */ (function () {
             return __generator(this, function (_b) {
                 plugin = this.plugin;
                 if (!plugin.dataFormats.get(format)) {
-                    throw new Error("Unknown density format: " + format);
+                    throw new Error("Unknown density format: ".concat(format));
                 }
                 if (options === null || options === void 0 ? void 0 : options.isLazy) {
                     update = this.plugin.build();
@@ -335,6 +337,90 @@ var Viewer = /** @class */ (function () {
             });
         });
     };
+    /**
+     * @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'
+     *  });
+     */
+    Viewer.prototype.loadTrajectory = function (params) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function () {
+            var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
+            return __generator(this, function (_f) {
+                switch (_f.label) {
+                    case 0:
+                        plugin = this.plugin;
+                        if (!(params.model.kind === 'model-data' || params.model.kind === 'model-url')) return [3 /*break*/, 7];
+                        if (!(params.model.kind === 'model-data')) return [3 /*break*/, 2];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })];
+                    case 1:
+                        _c = _f.sent();
+                        return [3 /*break*/, 4];
+                    case 2: return [4 /*yield*/, plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel })];
+                    case 3:
+                        _c = _f.sent();
+                        _f.label = 4;
+                    case 4:
+                        data = _c;
+                        return [4 /*yield*/, plugin.builders.structure.parseTrajectory(data, (_a = params.model.format) !== null && _a !== void 0 ? _a : 'mmcif')];
+                    case 5:
+                        trajectory_1 = _f.sent();
+                        return [4 /*yield*/, plugin.builders.structure.createModel(trajectory_1)];
+                    case 6:
+                        model = _f.sent();
+                        return [3 /*break*/, 13];
+                    case 7:
+                        if (!(params.model.kind === 'topology-data')) return [3 /*break*/, 9];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.model.data, label: params.modelLabel })];
+                    case 8:
+                        _d = _f.sent();
+                        return [3 /*break*/, 11];
+                    case 9: return [4 /*yield*/, plugin.builders.data.download({ url: params.model.url, isBinary: params.model.isBinary, label: params.modelLabel })];
+                    case 10:
+                        _d = _f.sent();
+                        _f.label = 11;
+                    case 11:
+                        data = _d;
+                        provider = plugin.dataFormats.get(params.model.format);
+                        return [4 /*yield*/, provider.parse(plugin, data)];
+                    case 12:
+                        model = _f.sent();
+                        _f.label = 13;
+                    case 13:
+                        if (!(params.coordinates.kind === 'coordinates-data')) return [3 /*break*/, 15];
+                        return [4 /*yield*/, plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })];
+                    case 14:
+                        _e = _f.sent();
+                        return [3 /*break*/, 17];
+                    case 15: return [4 /*yield*/, plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel })];
+                    case 16:
+                        _e = _f.sent();
+                        _f.label = 17;
+                    case 17:
+                        data = _e;
+                        provider = plugin.dataFormats.get(params.coordinates.format);
+                        return [4 /*yield*/, provider.parse(plugin, data)];
+                    case 18:
+                        coords = _f.sent();
+                        return [4 /*yield*/, plugin.build().toRoot()
+                                .apply(TrajectoryFromModelAndCoordinates, {
+                                modelRef: model.ref,
+                                coordinatesRef: coords.ref
+                            }, { dependsOn: [model.ref, coords.ref] })
+                                .commit()];
+                    case 19:
+                        trajectory = _f.sent();
+                        return [4 /*yield*/, plugin.builders.structure.hierarchy.applyPreset(trajectory, (_b = params.preset) !== null && _b !== void 0 ? _b : 'default')];
+                    case 20:
+                        preset = _f.sent();
+                        return [2 /*return*/, { model: model, coords: coords, preset: preset }];
+                }
+            });
+        });
+    };
     Viewer.prototype.handleResize = function () {
         this.plugin.layout.events.updated.next(void 0);
     };

package/lib/apps/viewer/index.js.map

@@ -1 +1 @@
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package/lib/cli/chem-comp-dict/create-ions.js

@@ -25,7 +25,7 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(" + JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ') + ");\n";
+    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
     writeFile(filePath, output);
 }
 function run(out, forceDownload) {

package/lib/cli/chem-comp-dict/create-ions.js.map

@@ -1 +1 @@
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+{"version":3,"file":"create-ions.js","sourceRoot":"","sources":["../../../src/cli/chem-comp-dict/create-ions.ts"],"names":[],"mappings":";AACA;;;;GAIG;;AAEH,OAAO,KAAK,QAAQ,MAAM,UAAU,CAAC;AACrC,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,IAAI,MAAM,MAAM,CAAC;AACxB,OAAO,EAAE,MAAM,IAAI,CAAC;AACpB,OAAO,CAAC,gBAAgB,CAAC,CAAC,IAAI,EAAE,CAAC;AACjC,IAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;AAI/C,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAC;AAEtD,SAAS,eAAe,CAAC,GAAmC;IACxD,IAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,IAAM,CAAC,IAAI,GAAG,EAAE;QACT,IAAA,SAAS,GAAK,GAAG,CAAC,CAAC,CAAC,UAAX,CAAY;QAC7B,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;YACxD,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;SACxC;KACJ;IACD,yDAAyD;IACzD,QAAQ,CAAC,IAAI,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IAC5B,OAAO,QAAQ,CAAC;AACpB,CAAC;AAED,SAAS,iBAAiB,CAAC,QAAgB,EAAE,QAAkB;IAC3D,IAAM,MAAM,GAAG,+RAQe,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,IAAI,CAAC,SAChG,CAAC;IACE,SAAS,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;AAChC,CAAC;AAED,SAAe,GAAG,CAAC,GAAW,EAAE,aAAqB;IAArB,8BAAA,EAAA,qBAAqB;;;;;wBACjD,qBAAM,mBAAmB,CAAC,aAAa,CAAC,EAAA;;oBAAxC,SAAwC,CAAC;oBAC7B,qBAAM,OAAO,EAAE,EAAA;;oBAArB,GAAG,GAAG,SAAe;oBACrB,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;oBACtC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE;wBACnC,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC;qBACnC;oBACD,iBAAiB,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;;;;;CACpC;AAED,IAAM,MAAM,GAAG,IAAI,QAAQ,CAAC,cAAc,CAAC;IACvC,QAAQ,EAAE,IAAI;IACd,WAAW,EAAE,qCAAqC;CACrD,CAAC,CAAC;AACH,MAAM,CAAC,YAAY,CAAC,KAAK,EAAE;IACvB,IAAI,EAAE,6BAA6B;CACtC,CAAC,CAAC;AACH,MAAM,CAAC,YAAY,CAAC,iBAAiB,EAAE,IAAI,EAAE;IACzC,MAAM,EAAE,YAAY;IACpB,IAAI,EAAE,iCAAiC;CAC1C,CAAC,CAAC;AAKH,IAAM,IAAI,GAAS,MAAM,CAAC,UAAU,EAAE,CAAC;AAEvC,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,aAAa,CAAC,CAAC"}

package/lib/cli/chem-comp-dict/create-table.js

@@ -18,10 +18,10 @@ import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-
 import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
 import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 function ccbKey(compId, atomId1, atomId2) {
-    return atomId1 < atomId2 ? compId + ":" + atomId1 + "-" + atomId2 : compId + ":" + atomId2 + "-" + atomId1;
+    return atomId1 < atomId2 ? "".concat(compId, ":").concat(atomId1, "-").concat(atomId2) : "".concat(compId, ":").concat(atomId2, "-").concat(atomId1);
 }
 function ccaKey(compId, atomId) {
-    return compId + ":" + atomId;
+    return "".concat(compId, ":").concat(atomId);
 }
 function addChemCompBondToSet(set, ccb) {
     for (var i = 0, il = ccb._rowCount; i < il; ++i) {
@@ -66,7 +66,7 @@ function checkAddingBondsFromPVCD(pvcd) {
                     extraBonds.forEach(function (bk) {
                         var _a = bk.split('|'), a1 = _a[0], a2 = _a[1];
                         if (entryAtoms.has(a1) && entryAtoms.has(a2)) {
-                            console.error("Adding all PVCD bonds would wrongly add bond " + bk + " for " + k);
+                            console.error("Adding all PVCD bonds would wrongly add bond ".concat(bk, " for ").concat(k));
                         }
                     });
                 };

package/lib/cli/chem-comp-dict/create-table.js.map

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package/lib/cli/chem-comp-dict/util.js

@@ -24,7 +24,7 @@ export function ensureAvailable(path, url, forceDownload) {
             switch (_g.label) {
                 case 0:
                     if (!(forceDownload || !fs.existsSync(path))) return [3 /*break*/, 8];
-                    console.log("downloading " + url + "...");
+                    console.log("downloading ".concat(url, "..."));
                     return [4 /*yield*/, fetch(url)];
                 case 1:
                     data = _g.sent();
@@ -49,7 +49,7 @@ export function ensureAvailable(path, url, forceDownload) {
                     _g.sent();
                     _g.label = 7;
                 case 7:
-                    console.log("done downloading " + url);
+                    console.log("done downloading ".concat(url));
                     _g.label = 8;
                 case 8: return [2 /*return*/];
             }

package/lib/cli/chem-comp-dict/util.js.map

@@ -1 +1 @@
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package/lib/cli/cif2bcif/converter.js

@@ -14,8 +14,8 @@ import { Progress, Task } from '../../mol-task';
 import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-cif';
 import { Category } from '../../mol-io/writer/cif/encoder';
 function showProgress(p) {
-    process.stdout.write("\r" + new Array(80).join(' '));
-    process.stdout.write("\r" + Progress.format(p));
+    process.stdout.write("\r".concat(new Array(80).join(' ')));
+    process.stdout.write("\r".concat(Progress.format(p)));
 }
 var readFileAsync = util.promisify(fs.readFile);
 var unzipAsync = util.promisify(zlib.unzip);

package/lib/cli/cif2bcif/converter.js.map

@@ -1 +1 @@
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package/lib/cli/cifschema/index.js

@@ -61,7 +61,7 @@ function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImpo
                     mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
                     ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
                     carbDicVersion = 'draft';
-                    version = "Dictionary versions: mmCIF " + mmcifDicVersion + ", IHM " + ihmDicVersion + ", CARB " + carbDicVersion + ".";
+                    version = "Dictionary versions: mmCIF ".concat(mmcifDicVersion, ", IHM ").concat(ihmDicVersion, ", CARB ").concat(carbDicVersion, ".");
                     frames = __spreadArray(__spreadArray(__spreadArray(__spreadArray([], mmcifDic.result.blocks[0].saveFrames, true), ihmDic.result.blocks[0].saveFrames, true), carbBranchDic.result.blocks[0].saveFrames, true), carbCompDic.result.blocks[0].saveFrames, true);
                     schema = generateSchema(frames);
                     return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
@@ -87,7 +87,7 @@ function runGenerateSchemaCifCore(name, fieldNamesPath, typescript, out, moldbIm
                     if (cifCoreDic.isError)
                         throw cifCoreDic;
                     cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
-                    version = "Dictionary versions: CifCore " + cifCoreDicVersion + ".";
+                    version = "Dictionary versions: CifCore ".concat(cifCoreDicVersion, ".");
                     frames = __spreadArray([], cifCoreDic.result.blocks[0].saveFrames, true);
                     return [4 /*yield*/, resolveImports(frames, DIC_DIR)];
                 case 3:
@@ -156,7 +156,7 @@ function runGenerateSchemaDic(name, dicPath, fieldNamesPath, typescript, out, mo
                         throw dic;
                     dicVersion = getDicVersion(dic.result.blocks[0]);
                     dicName = getDicNamespace(dic.result.blocks[0]);
-                    version = "Dictionary versions: " + dicName + " " + dicVersion + ".";
+                    version = "Dictionary versions: ".concat(dicName, " ").concat(dicVersion, ".");
                     frames = __spreadArray([], dic.result.blocks[0].saveFrames, true);
                     return [4 /*yield*/, resolveImports(frames, path.dirname(dicPath))];
                 case 2:
@@ -295,7 +295,7 @@ function ensureDicAvailable(dicPath, dicUrl) {
                 case 0:
                     if (!(FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath))) return [3 /*break*/, 3];
                     name_1 = dicUrl.substr(dicUrl.lastIndexOf('/') + 1);
-                    console.log("downloading " + name_1 + "...");
+                    console.log("downloading ".concat(name_1, "..."));
                     return [4 /*yield*/, fetch(dicUrl)];
                 case 1:
                     data = _d.sent();
@@ -307,7 +307,7 @@ function ensureDicAvailable(dicPath, dicUrl) {
                     return [4 /*yield*/, data.text()];
                 case 2:
                     _b.apply(_a, _c.concat([_d.sent()]));
-                    console.log("done downloading " + name_1);
+                    console.log("done downloading ".concat(name_1));
                     _d.label = 3;
                 case 3: return [2 /*return*/];
             }
@@ -315,19 +315,19 @@ function ensureDicAvailable(dicPath, dicUrl) {
     });
 }
 var DIC_DIR = path.resolve(__dirname, '../../../../build/dics/');
-var MMCIF_DIC_PATH = DIC_DIR + "/mmcif_pdbx_v50.dic";
+var MMCIF_DIC_PATH = "".concat(DIC_DIR, "/mmcif_pdbx_v50.dic");
 var MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
-var IHM_DIC_PATH = DIC_DIR + "/ihm-extension.dic";
+var IHM_DIC_PATH = "".concat(DIC_DIR, "/ihm-extension.dic");
 var IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
-var CARB_BRANCH_DIC_PATH = DIC_DIR + "/entity_branch-extension.dic";
+var CARB_BRANCH_DIC_PATH = "".concat(DIC_DIR, "/entity_branch-extension.dic");
 var CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic';
-var CARB_COMP_DIC_PATH = DIC_DIR + "/chem_comp-extension.dic";
+var CARB_COMP_DIC_PATH = "".concat(DIC_DIR, "/chem_comp-extension.dic");
 var CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.dic';
-var CIF_CORE_DIC_PATH = DIC_DIR + "/cif_core.dic";
+var CIF_CORE_DIC_PATH = "".concat(DIC_DIR, "/cif_core.dic");
 var CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
-var CIF_CORE_ENUM_PATH = DIC_DIR + "/templ_enum.cif";
+var CIF_CORE_ENUM_PATH = "".concat(DIC_DIR, "/templ_enum.cif");
 var CIF_CORE_ENUM_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_enum.cif';
-var CIF_CORE_ATTR_PATH = DIC_DIR + "/templ_attr.cif";
+var CIF_CORE_ATTR_PATH = "".concat(DIC_DIR, "/templ_attr.cif");
 var CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';
 var parser = new argparse.ArgumentParser({
     add_help: true,

package/lib/cli/cifschema/index.js.map

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