molstar 3.3.1 → 3.6.0

package/lib/commonjs/apps/viewer/app.d.ts

@@ -7,7 +7,8 @@
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
@@ -21,7 +22,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -179,23 +180,23 @@ export interface LoadTrajectoryParams {
     } | {
         kind: 'topology-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
         isBinary?: boolean;
     } | {
         kind: 'topology-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInTopologyFormat;
     };
     modelLabel?: string;
     coordinates: {
         kind: 'coordinates-url';
         url: string;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
         isBinary?: boolean;
     } | {
         kind: 'coordinates-data';
         data: string | number[] | ArrayBuffer | Uint8Array;
-        format: BuildInStructureFormat;
+        format: BuiltInCoordinatesFormat;
     };
     coordinatesLabel?: string;
     preset?: keyof PresetTrajectoryHierarchy;

package/lib/commonjs/apps/viewer/app.js

@@ -20,6 +20,7 @@ var model_export_1 = require("../../extensions/model-export");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
+var zenodo_1 = require("../../extensions/zenodo");
 var volume_1 = require("../../mol-model/volume");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
 var volume_2 = require("../../mol-plugin-state/actions/volume");
@@ -27,7 +28,7 @@ var representation_preset_1 = require("../../mol-plugin-state/builder/structure/
 var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
 var model_1 = require("../../mol-plugin-state/transforms/model");
-var mol_plugin_ui_1 = require("../../mol-plugin-ui");
+var react18_1 = require("../../mol-plugin-ui/react18");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
@@ -56,6 +57,7 @@ var Extensions = {
     '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),
 };
 var DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -93,9 +95,9 @@ var Viewer = /** @class */ (function () {
     Viewer.create = function (elementOrId, options) {
         var _a;
         if (options === void 0) { options = {}; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var definedOptions, _i, _b, p, o, defaultSpec, spec, element, plugin;
-            return (0, tslib_1.__generator)(this, function (_c) {
+            return tslib_1.__generator(this, function (_c) {
                 switch (_c.label) {
                     case 0:
                         definedOptions = {};
@@ -106,12 +108,12 @@ var Viewer = /** @class */ (function () {
                             if (options[p] !== void 0)
                                 definedOptions[p] = options[p];
                         }
-                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), definedOptions);
+                        o = tslib_1.__assign(tslib_1.__assign({}, DefaultViewerOptions), definedOptions);
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
                         spec = {
                             actions: defaultSpec.actions,
-                            behaviors: (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
-                            animations: (0, tslib_1.__spreadArray)([], defaultSpec.animations || [], true),
+                            behaviors: tslib_1.__spreadArray(tslib_1.__spreadArray([], defaultSpec.behaviors, true), o.extensions.map(function (e) { return Extensions[e]; }), true),
+                            animations: tslib_1.__spreadArray([], defaultSpec.animations || [], true),
                             customParamEditors: defaultSpec.customParamEditors,
                             customFormats: o === null || o === void 0 ? void 0 : o.customFormats,
                             layout: {
@@ -127,7 +129,7 @@ var Viewer = /** @class */ (function () {
                                     }
                                 },
                             },
-                            components: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec.components), { controls: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.controls), { top: o.layoutShowSequence ? undefined : 'none', bottom: o.layoutShowLog ? undefined : 'none', left: o.layoutShowLeftPanel ? undefined : 'none' }), remoteState: o.layoutShowRemoteState ? 'default' : 'none' }),
+                            components: tslib_1.__assign(tslib_1.__assign({}, defaultSpec.components), { controls: tslib_1.__assign(tslib_1.__assign({}, (_a = defaultSpec.components) === null || _a === void 0 ? void 0 : _a.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],
@@ -154,7 +156,7 @@ var Viewer = /** @class */ (function () {
                             : elementOrId;
                         if (!element)
                             throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(element, spec, {
+                        return [4 /*yield*/, (0, react18_1.createPluginUI)(element, spec, {
                                 onBeforeUIRender: function (plugin) {
                                     // the preset needs to be added before the UI renders otherwise
                                     // "Download Structure" wont be able to pick it up
@@ -186,7 +188,7 @@ var Viewer = /** @class */ (function () {
                     url: assets_1.Asset.Url(url),
                     format: format,
                     isBinary: isBinary,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
                 }
             }
         }));
@@ -194,9 +196,9 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadAllModelsOrAssemblyFromUrl = function (url, format, isBinary, options) {
         if (format === void 0) { format = 'mmcif'; }
         if (isBinary === void 0) { isBinary = false; }
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, data, trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0:
                         plugin = this.plugin;
@@ -215,9 +217,9 @@ var Viewer = /** @class */ (function () {
         });
     };
     Viewer.prototype.loadStructureFromData = function (data, format, options) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var _data, trajectory;
-            return (0, tslib_1.__generator)(this, function (_a) {
+            return tslib_1.__generator(this, function (_a) {
                 switch (_a.label) {
                     case 0: return [4 /*yield*/, this.plugin.builders.data.rawData({ data: data, label: options === null || options === void 0 ? void 0 : options.dataLabel })];
                     case 1:
@@ -247,7 +249,7 @@ var Viewer = /** @class */ (function () {
                             params: structure_1.PdbDownloadProvider[provider].defaultValue
                         }
                     },
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representationParams: options === null || options === void 0 ? void 0 : options.representationParams }),
                 }
             }
         }));
@@ -290,7 +292,7 @@ var Viewer = /** @class */ (function () {
                 name: 'alphafolddb',
                 params: {
                     id: afdb,
-                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
+                    options: tslib_1.__assign(tslib_1.__assign({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
                 }
             }
         }));
@@ -348,10 +350,10 @@ var Viewer = /** @class */ (function () {
      */
     Viewer.prototype.loadVolumeFromUrl = function (_a, isovalues, options) {
         var url = _a.url, format = _a.format, isBinary = _a.isBinary;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, update;
             var _this = this;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 plugin = this.plugin;
                 if (!plugin.dataFormats.get(format)) {
                     throw new Error("Unknown density format: ".concat(format));
@@ -363,14 +365,14 @@ var Viewer = /** @class */ (function () {
                         format: format,
                         entryId: options === null || options === void 0 ? void 0 : options.entryId,
                         isBinary: isBinary,
-                        isovalues: isovalues.map(function (v) { return ((0, tslib_1.__assign)({ alpha: 1, volumeIndex: 0 }, v)); })
+                        isovalues: isovalues.map(function (v) { return (tslib_1.__assign({ alpha: 1, volumeIndex: 0 }, v)); })
                     });
                     return [2 /*return*/, update.commit()];
                 }
-                return [2 /*return*/, plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+                return [2 /*return*/, plugin.dataTransaction(function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
                         var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
-                        return (0, tslib_1.__generator)(this, function (_e) {
+                        return tslib_1.__generator(this, function (_e) {
                             switch (_e.label) {
                                 case 0: return [4 /*yield*/, plugin.builders.data.download({ url: url, isBinary: isBinary }, { state: { isGhost: true } })];
                                 case 1:
@@ -415,9 +417,9 @@ var Viewer = /** @class */ (function () {
      */
     Viewer.prototype.loadTrajectory = function (params) {
         var _a, _b;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var plugin, model, coords, data, _c, trajectory_1, data, _d, provider, data, _e, provider, trajectory, preset;
-            return (0, tslib_1.__generator)(this, function (_f) {
+            return tslib_1.__generator(this, function (_f) {
                 switch (_f.label) {
                     case 0:
                         plugin = this.plugin;
@@ -508,9 +510,9 @@ exports.ViewerAutoPreset = (0, representation_preset_1.StructureRepresentationPr
     params: function () { return representation_preset_1.StructureRepresentationPresetProvider.CommonParams; },
     apply: function (ref, params, plugin) {
         var _a;
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+        return tslib_1.__awaiter(this, void 0, void 0, function () {
             var structureCell, structure;
-            return (0, tslib_1.__generator)(this, function (_b) {
+            return tslib_1.__generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);

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

@@ -11,4 +11,4 @@ require("./embedded.html");
 require("./favicon.ico");
 require("./index.html");
 require('mol-plugin-ui/skin/light.scss');
-(0, tslib_1.__exportStar)(require("./app"), exports);
+tslib_1.__exportStar(require("./app"), exports);

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

@@ -7,10 +7,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var util_1 = (0, tslib_1.__importDefault)(require("util"));
-var fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var path = tslib_1.__importStar(require("path"));
+var util_1 = tslib_1.__importDefault(require("util"));
+var fs_1 = tslib_1.__importDefault(require("fs"));
 require('util.promisify').shim();
 var writeFile = util_1.default.promisify(fs_1.default.writeFile);
 var util_2 = require("./util");
@@ -32,9 +32,9 @@ function writeIonNamesFile(filePath, ionNames) {
 }
 function run(out, forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ccd, ionNames;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, util_2.ensureDataAvailable)(forceDownload)];
                 case 1:

package/lib/commonjs/cli/chem-comp-dict/create-saccharides.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export {};

package/lib/commonjs/cli/chem-comp-dict/create-saccharides.js

@@ -0,0 +1,69 @@
+#!/usr/bin/env node
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+var tslib_1 = require("tslib");
+var argparse = tslib_1.__importStar(require("argparse"));
+var path = tslib_1.__importStar(require("path"));
+var util_1 = tslib_1.__importDefault(require("util"));
+var fs_1 = tslib_1.__importDefault(require("fs"));
+require('util.promisify').shim();
+var writeFile = util_1.default.promisify(fs_1.default.writeFile);
+var util_2 = require("./util");
+function extractSaccharideNames(ccd) {
+    var saccharideNames = [];
+    for (var k in ccd) {
+        var chem_comp = ccd[k].chem_comp;
+        var type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push('UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+    'SQD');
+    return saccharideNames;
+}
+function writeSaccharideNamesFile(filePath, ionNames) {
+    var output = "/**\n * Copyright (c) 2022 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/cli/chem-comp-dict/create-saccharides\n */\n\nexport const SaccharideNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
+    writeFile(filePath, output);
+}
+function run(out, forceDownload) {
+    if (forceDownload === void 0) { forceDownload = false; }
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var ccd, saccharideNames;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, util_2.ensureDataAvailable)(forceDownload)];
+                case 1:
+                    _a.sent();
+                    return [4 /*yield*/, (0, util_2.readCCD)()];
+                case 2:
+                    ccd = _a.sent();
+                    saccharideNames = extractSaccharideNames(ccd);
+                    if (!fs_1.default.existsSync(path.dirname(out))) {
+                        fs_1.default.mkdirSync(path.dirname(out));
+                    }
+                    writeSaccharideNamesFile(out, saccharideNames);
+                    return [2 /*return*/];
+            }
+        });
+    });
+}
+var parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+var args = parser.parse_args();
+run(args.out, args.forceDownload);

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

@@ -7,10 +7,10 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var util = (0, tslib_1.__importStar)(require("util"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
+var argparse = tslib_1.__importStar(require("argparse"));
+var util = tslib_1.__importStar(require("util"));
+var path = tslib_1.__importStar(require("path"));
+var fs = tslib_1.__importStar(require("fs"));
 require('util.promisify').shim();
 var writeFile = util.promisify(fs.writeFile);
 var db_1 = require("../../mol-data/db");
@@ -103,7 +103,7 @@ function checkAddingAtomsFromPVCD(pvcd) {
     }
 }
 function createBonds(ccd, pvcd, atomsRequested) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function addBonds(compId, ccb, protonationVariant) {
             for (var i = 0, il = ccb._rowCount; i < il; ++i) {
                 var atomId1 = ccb.atom_id_1.value(i);
@@ -122,7 +122,7 @@ function createBonds(ccd, pvcd, atomsRequested) {
             }
         }
         var ccbSet, comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant, k, _a, chem_comp, chem_comp_bond, parentIds, i, il, k, _b, chem_comp, chem_comp_bond, bondTable, bondDatabase;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             ccbSet = new Set();
             comp_id = [];
             atom_id_1 = [];
@@ -223,9 +223,9 @@ function createAtoms(ccd, pvcd) {
 function run(out, binary, forceDownload, ccaOut) {
     if (binary === void 0) { binary = false; }
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ccd, pvcd, _a, bonds, atoms, ccbCif, ccaCif;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, (0, util_1.ensureDataAvailable)(forceDownload)];
                 case 1:

package/lib/commonjs/cli/chem-comp-dict/util.d.ts

@@ -16,7 +16,7 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -26,12 +26,12 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -47,9 +47,9 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -57,13 +57,13 @@ export declare function readCCD(): Promise<import("../../mol-data/db").DatabaseC
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };
@@ -84,7 +84,7 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         name: import("../../mol-data/db/column").Column.Schema.Str;
         one_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
         three_letter_code: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking">;
         pdbx_synonyms: import("../../mol-data/db/column").Column.Schema.List<string>;
         pdbx_type: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ambiguous_flag: import("../../mol-data/db/column").Column.Schema.Str;
@@ -94,12 +94,12 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_model_coordinates_db_code: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_ideal_coordinates_details: import("../../mol-data/db/column").Column.Schema.Str;
-        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_ideal_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_model_coordinates_missing_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         pdbx_initial_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_modified_date: import("../../mol-data/db/column").Column.Schema.Str;
         pdbx_release_status: import("../../mol-data/db/column").Column.Schema.Aliased<"REL" | "HOLD" | "HPUB" | "OBS" | "DEL" | "REF_ONLY">;
-        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "EBI" | "PDBE" | "PDBJ" | "PDBC">;
+        pdbx_processing_site: import("../../mol-data/db/column").Column.Schema.Aliased<"RCSB" | "PDBE" | "PDBJ" | "PDBC" | "EBI">;
     };
     chem_comp_atom: {
         alt_atom_id: import("../../mol-data/db/column").Column.Schema.Str;
@@ -115,9 +115,9 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         pdbx_model_Cartn_x_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_y_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
         pdbx_model_Cartn_z_ideal: import("../../mol-data/db/column").Column.Schema.Coordinate;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "R" | "S">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
-        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"s" | "r" | "n">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
+        pdbx_leaving_atom_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     chem_comp_bond: {
         atom_id_1: import("../../mol-data/db/column").Column.Schema.Str;
@@ -125,13 +125,13 @@ export declare function readPVCD(): Promise<import("../../mol-data/db").Database
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         value_order: import("../../mol-data/db/column").Column.Schema.Aliased<"sing" | "doub" | "trip" | "quad" | "arom" | "poly" | "delo" | "pi">;
         pdbx_ordinal: import("../../mol-data/db/column").Column.Schema.Int;
-        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "E" | "Z">;
-        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        pdbx_stereo_config: import("../../mol-data/db/column").Column.Schema.Aliased<"z" | "n" | "e">;
+        pdbx_aromatic_flag: import("../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
     };
     pdbx_chem_comp_descriptor: {
         comp_id: import("../../mol-data/db/column").Column.Schema.Str;
         descriptor: import("../../mol-data/db/column").Column.Schema.Str;
-        type: import("../../mol-data/db/column").Column.Schema.Aliased<"SMILES_CANNONICAL" | "SMILES_CANONICAL" | "SMILES" | "InChI" | "InChI_MAIN" | "InChI_MAIN_FORMULA" | "InChI_MAIN_CONNECT" | "InChI_MAIN_HATOM" | "InChI_CHARGE" | "InChI_STEREO" | "InChI_ISOTOPE" | "InChI_FIXEDH" | "InChI_RECONNECT" | "InChIKey">;
+        type: import("../../mol-data/db/column").Column.Schema.Aliased<"smiles_cannonical" | "smiles_canonical" | "smiles" | "inchi" | "inchi_main" | "inchi_main_formula" | "inchi_main_connect" | "inchi_main_hatom" | "inchi_charge" | "inchi_stereo" | "inchi_isotope" | "inchi_fixedh" | "inchi_reconnect" | "inchikey">;
         program: import("../../mol-data/db/column").Column.Schema.Str;
         program_version: import("../../mol-data/db/column").Column.Schema.Str;
     };

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

@@ -7,11 +7,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getEncodedCif = exports.readPVCD = exports.readCCD = exports.readFileAsCollection = exports.ensureDataAvailable = exports.ensureAvailable = void 0;
 var tslib_1 = require("tslib");
-var util = (0, tslib_1.__importStar)(require("util"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var zlib = (0, tslib_1.__importStar)(require("zlib"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
+var util = tslib_1.__importStar(require("util"));
+var path = tslib_1.__importStar(require("path"));
+var fs = tslib_1.__importStar(require("fs"));
+var zlib = tslib_1.__importStar(require("zlib"));
+var node_fetch_1 = tslib_1.__importDefault(require("node-fetch"));
 require('util.promisify').shim();
 var readFile = util.promisify(fs.readFile);
 var writeFile = util.promisify(fs.writeFile);
@@ -21,9 +21,9 @@ var cif_2 = require("../../mol-io/writer/cif");
 var ccd_1 = require("../../mol-io/reader/cif/schema/ccd");
 function ensureAvailable(path, url, forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var data, _a, _b, _c, _d, _e, _f;
-        return (0, tslib_1.__generator)(this, function (_g) {
+        return tslib_1.__generator(this, function (_g) {
             switch (_g.label) {
                 case 0:
                     if (!(forceDownload || !fs.existsSync(path))) return [3 /*break*/, 8];
@@ -62,8 +62,8 @@ function ensureAvailable(path, url, forceDownload) {
 exports.ensureAvailable = ensureAvailable;
 function ensureDataAvailable(forceDownload) {
     if (forceDownload === void 0) { forceDownload = false; }
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureAvailable(CCD_PATH, CCD_URL, forceDownload)];
                 case 1:
@@ -78,9 +78,9 @@ function ensureDataAvailable(forceDownload) {
 }
 exports.ensureDataAvailable = ensureDataAvailable;
 function readFileAsCollection(path, schema) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var parsed, _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     _a = parseCif;
@@ -95,25 +95,25 @@ function readFileAsCollection(path, schema) {
 }
 exports.readFileAsCollection = readFileAsCollection;
 function readCCD() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, readFileAsCollection(CCD_PATH, ccd_1.CCD_Schema)];
         });
     });
 }
 exports.readCCD = readCCD;
 function readPVCD() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, readFileAsCollection(PVCD_PATH, ccd_1.CCD_Schema)];
         });
     });
 }
 exports.readPVCD = readPVCD;
 function parseCif(data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     comp = cif_1.CIF.parse(data);