molstar 3.0.0-dev.4 → 3.0.0-dev.8

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

@@ -6,18 +6,22 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
+exports.ViewerAutoPreset = exports.Viewer = exports.setProductionMode = exports.setDebugMode = exports.version = void 0;
 var tslib_1 = require("tslib");
 var behavior_1 = require("../../extensions/anvil/behavior");
 var cellpack_1 = require("../../extensions/cellpack");
 var dnatco_1 = require("../../extensions/dnatco");
 var format_1 = require("../../extensions/g3d/format");
 var geo_export_1 = require("../../extensions/geo-export");
+var behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
+var behavior_3 = require("../../extensions/model-archive/quality-assessment/behavior");
+var prop_1 = require("../../extensions/model-archive/quality-assessment/prop");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
 var volume_1 = require("../../mol-plugin-state/actions/volume");
+var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
 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");
@@ -26,6 +30,7 @@ var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var config_1 = require("../../mol-plugin/config");
 var spec_2 = require("../../mol-plugin/spec");
+var mol_state_1 = require("../../mol-state");
 var assets_1 = require("../../mol-util/assets");
 require("../../mol-util/polyfill");
 var type_helpers_1 = require("../../mol-util/type-helpers");
@@ -50,7 +55,8 @@ var Extensions = {
     'anvil-membrane-orientation': spec_2.PluginSpec.Behavior(behavior_1.ANVILMembraneOrientation),
     'g3d': spec_2.PluginSpec.Behavior(format_1.G3DFormat),
     'mp4-export': spec_2.PluginSpec.Behavior(mp4_export_1.Mp4Export),
-    'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport)
+    'geo-export': spec_2.PluginSpec.Behavior(geo_export_1.GeometryExport),
+    'ma-quality-assessment': spec_2.PluginSpec.Behavior(behavior_2.MAQualityAssessment),
 };
 var DefaultViewerOptions = {
     customFormats: CustomFormats,
@@ -69,6 +75,7 @@ var DefaultViewerOptions = {
     pickScale: config_1.PluginConfig.General.PickScale.defaultValue,
     pickPadding: config_1.PluginConfig.General.PickPadding.defaultValue,
     enableWboit: config_1.PluginConfig.General.EnableWboit.defaultValue,
+    preferWebgl1: config_1.PluginConfig.General.PreferWebGl1.defaultValue,
     viewportShowExpand: config_1.PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowControls: config_1.PluginConfig.Viewport.ShowControls.defaultValue,
     viewportShowSettings: config_1.PluginConfig.Viewport.ShowSettings.defaultValue,
@@ -81,57 +88,79 @@ var DefaultViewerOptions = {
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
 };
 var Viewer = /** @class */ (function () {
-    function Viewer(elementOrId, options) {
-        if (options === void 0) { options = {}; }
-        var _a;
-        var o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
-        var defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-        var 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),
-            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: (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' }),
-            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.PickPadding, o.pickPadding],
-                [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
-                [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.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]
-            ]
-        };
-        var element = typeof elementOrId === 'string'
-            ? document.getElementById(elementOrId)
-            : elementOrId;
-        if (!element)
-            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(element, spec);
+    function Viewer(plugin) {
+        this.plugin = plugin;
     }
+    Viewer.create = function (elementOrId, options) {
+        var _a;
+        if (options === void 0) { options = {}; }
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var o, defaultSpec, spec, element, plugin;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        o = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, DefaultViewerOptions), options);
+                        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),
+                            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: (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' }),
+                            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.PickPadding, o.pickPadding],
+                                [config_1.PluginConfig.General.EnableWboit, o.enableWboit],
+                                [config_1.PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+                                [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.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],
+                            ]
+                        };
+                        element = typeof elementOrId === 'string'
+                            ? document.getElementById(elementOrId)
+                            : 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, {
+                                onBeforeUIRender: function (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);
+                                }
+                            })];
+                    case 1:
+                        plugin = _b.sent();
+                        return [2 /*return*/, new Viewer(plugin)];
+                }
+            });
+        });
+    };
     Viewer.prototype.setRemoteSnapshot = function (id) {
         var url = "".concat(this.plugin.config.get(config_1.PluginConfig.State.CurrentServer), "/get/").concat(id);
         return commands_1.PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
@@ -247,6 +276,30 @@ var Viewer = /** @class */ (function () {
             }
         }));
     };
+    Viewer.prototype.loadAlphaFoldDb = function (afdb) {
+        var 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: {
+                    id: afdb,
+                    options: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, params.source.params.options), { representation: 'preset-structure-representation-ma-quality-assessment-plddt' }),
+                }
+            }
+        }));
+    };
+    Viewer.prototype.loadModelArchive = function (id) {
+        var 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: id,
+                    options: params.source.params.options,
+                }
+            }
+        }));
+    };
     /**
      * @example Load X-ray density from volume server
         viewer.loadVolumeFromUrl({
@@ -433,4 +486,40 @@ var Viewer = /** @class */ (function () {
     return Viewer;
 }());
 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: function (a) {
+        return (!!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); }) ||
+            !!a.data.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); }));
+    },
+    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 () {
+            var structureCell, structure;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+                        structure = (_a = structureCell === null || structureCell === void 0 ? void 0 : structureCell.obj) === null || _a === void 0 ? void 0 : _a.data;
+                        if (!structureCell || !structure)
+                            return [2 /*return*/, {}];
+                        if (!!!structure.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'pLDDT'); })) return [3 /*break*/, 2];
+                        return [4 /*yield*/, behavior_3.QualityAssessmentPLDDTPreset.apply(ref, params, plugin)];
+                    case 1: return [2 /*return*/, _b.sent()];
+                    case 2:
+                        if (!!!structure.models.some(function (m) { return prop_1.QualityAssessment.isApplicable(m, 'qmean'); })) return [3 /*break*/, 4];
+                        return [4 /*yield*/, behavior_3.QualityAssessmentQmeanPreset.apply(ref, params, plugin)];
+                    case 3: return [2 /*return*/, _b.sent()];
+                    case 4: return [4 /*yield*/, representation_preset_1.PresetStructureRepresentations.auto.apply(ref, params, plugin)];
+                    case 5: return [2 /*return*/, _b.sent()];
+                }
+            });
+        });
+    }
+});
 //# sourceMappingURL=index.js.map

package/lib/commonjs/cli/cifschema/index.d.ts

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

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

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,7 +25,7 @@ function getDicNamespace(block) {
 function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImportPath, addAliases) {
     if (typescript === void 0) { typescript = false; }
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var mmcifDic, ihmDic, carbBranchDic, carbCompDic, mmcifDicVersion, ihmDicVersion, carbDicVersion, version, frames, schema;
+        var mmcifDic, ihmDic, maDic, mmcifDicVersion, ihmDicVersion, maDicVersion, version, frames, schema;
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ensureMmcifDicAvailable()];
@@ -44,30 +44,22 @@ function runGenerateSchemaMmcif(name, fieldNamesPath, typescript, out, moldbImpo
                     ihmDic = _a.sent();
                     if (ihmDic.isError)
                         throw ihmDic;
-                    return [4 /*yield*/, ensureCarbBranchDicAvailable()];
+                    return [4 /*yield*/, ensureMaDicAvailable()];
                 case 5:
                     _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run()];
+                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(MA_DIC_PATH, 'utf8')).run()];
                 case 6:
-                    carbBranchDic = _a.sent();
-                    if (carbBranchDic.isError)
-                        throw carbBranchDic;
-                    return [4 /*yield*/, ensureCarbCompDicAvailable()];
-                case 7:
-                    _a.sent();
-                    return [4 /*yield*/, (0, parser_2.parseCifText)(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run()];
-                case 8:
-                    carbCompDic = _a.sent();
-                    if (carbCompDic.isError)
-                        throw carbCompDic;
+                    maDic = _a.sent();
+                    if (maDic.isError)
+                        throw maDic;
                     mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
                     ihmDicVersion = getDicVersion(ihmDic.result.blocks[0]);
-                    carbDicVersion = 'draft';
-                    version = "Dictionary versions: mmCIF ".concat(mmcifDicVersion, ", IHM ").concat(ihmDicVersion, ", CARB ").concat(carbDicVersion, ".");
-                    frames = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__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);
+                    maDicVersion = getDicVersion(maDic.result.blocks[0]);
+                    version = "Dictionary versions: mmCIF ".concat(mmcifDicVersion, ", IHM ").concat(ihmDicVersion, ", MA ").concat(maDicVersion, ".");
+                    frames = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], mmcifDic.result.blocks[0].saveFrames, true), ihmDic.result.blocks[0].saveFrames, true), maDic.result.blocks[0].saveFrames, true);
                     schema = (0, cif_dic_1.generateSchema)(frames);
                     return [4 /*yield*/, runGenerateSchema(name, version, schema, fieldNamesPath, typescript, out, moldbImportPath, addAliases)];
-                case 9:
+                case 7:
                     _a.sent();
                     return [2 /*return*/];
             }
@@ -251,20 +243,10 @@ function ensureIhmDicAvailable() {
         }
     }); });
 }
-function ensureCarbBranchDicAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-        switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureDicAvailable(CARB_BRANCH_DIC_PATH, CARB_BRANCH_DIC_URL)];
-            case 1:
-                _a.sent();
-                return [2 /*return*/];
-        }
-    }); });
-}
-function ensureCarbCompDicAvailable() {
+function ensureMaDicAvailable() {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
         switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureDicAvailable(CARB_COMP_DIC_PATH, CARB_COMP_DIC_URL)];
+            case 0: return [4 /*yield*/, ensureDicAvailable(MA_DIC_PATH, MA_DIC_URL)];
             case 1:
                 _a.sent();
                 return [2 /*return*/];
@@ -321,10 +303,8 @@ 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 = "".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 = "".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 = "".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 MA_DIC_PATH = "".concat(DIC_DIR, "/ma-extension.dic");
+var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/MA-dictionary/master/mmcif_ma.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 = "".concat(DIC_DIR, "/templ_enum.cif");

package/lib/commonjs/examples/alpha-orbitals/index.js

@@ -24,7 +24,7 @@ require('mol-plugin-ui/skin/light.scss');
 var AlphaOrbitalsExample = /** @class */ (function () {
     function AlphaOrbitalsExample() {
         this.params = new rxjs_1.BehaviorSubject({});
-        this.state = new rxjs_1.BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+        this.state = new rxjs_1.BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: true });
         this.selectors = void 0;
         this.basis = void 0;
         this.currentParams = (0, tslib_1.__assign)({}, this.state.value);
@@ -38,7 +38,7 @@ var AlphaOrbitalsExample = /** @class */ (function () {
                     case 0:
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
                         _b = this;
-                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginAsync)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec), { layout: {
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, defaultSpec), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false
@@ -150,12 +150,11 @@ var AlphaOrbitalsExample = /** @class */ (function () {
         return {
             alpha: 0.85,
             color: color,
-            directVolume: this.state.value.gpuSurface,
             kind: kind,
             relativeIsovalue: this.state.value.isoValue,
             pickable: false,
             xrayShaded: true,
-            tryUseGpu: false
+            tryUseGpu: true
         };
     };
     AlphaOrbitalsExample.prototype.load = function (input) {

package/lib/commonjs/examples/basic-wrapper/index.js

@@ -180,18 +180,30 @@ var BasicWrapper = /** @class */ (function () {
         };
     }
     BasicWrapper.prototype.init = function (target) {
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var _a;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    }
+                                }, components: {
+                                    remoteState: 'none'
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(coloring_1.StripedResidues.colorThemeProvider);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(custom_theme_1.CustomColorThemeProvider);
+                        this.plugin.managers.lociLabels.addProvider(coloring_1.StripedResidues.labelProvider);
+                        this.plugin.customModelProperties.register(coloring_1.StripedResidues.propertyProvider, true);
+                        return [2 /*return*/];
                 }
-            }, components: {
-                remoteState: 'none'
-            } }));
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(coloring_1.StripedResidues.colorThemeProvider);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(custom_theme_1.CustomColorThemeProvider);
-        this.plugin.managers.lociLabels.addProvider(coloring_1.StripedResidues.labelProvider);
-        this.plugin.customModelProperties.register(coloring_1.StripedResidues.propertyProvider, true);
+            });
+        });
     };
     BasicWrapper.prototype.load = function (_a) {
         var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? false : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d;

package/lib/commonjs/examples/lighting/index.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/examples/lighting/index.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -15,39 +15,41 @@ require("./index.html");
 require('mol-plugin-ui/skin/light.scss');
 var Canvas3DPresets = {
     illustrative: {
-        multiSample: {
-            mode: 'temporal'
-        },
-        postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.1, color: (0, color_1.Color)(0x000000) } }
-        },
-        renderer: {
-            style: { name: 'flat', params: {} }
+        canvas3d: {
+            postprocessing: {
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: (0, color_1.Color)(0x000000) } }
+            },
+            renderer: {
+                ambientIntensity: 1.0,
+                light: []
+            }
         }
     },
     occlusion: {
-        multiSample: {
-            mode: 'temporal'
-        },
-        postprocessing: {
-            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
-            outline: { name: 'off', params: {} }
-        },
-        renderer: {
-            style: { name: 'matte', params: {} }
+        canvas3d: {
+            postprocessing: {
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                outline: { name: 'off', params: {} }
+            },
+            renderer: {
+                ambientIntensity: 0.4,
+                light: [{ inclination: 180, azimuth: 0, color: color_1.Color.fromNormalizedRgb(1.0, 1.0, 1.0),
+                        intensity: 0.6 }]
+            }
         }
     },
     standard: {
-        multiSample: {
-            mode: 'off'
-        },
-        postprocessing: {
-            occlusion: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} }
-        },
-        renderer: {
-            style: { name: 'matte', params: {} }
+        canvas3d: {
+            postprocessing: {
+                occlusion: { name: 'off', params: {} },
+                outline: { name: 'off', params: {} }
+            },
+            renderer: {
+                ambientIntensity: 0.4,
+                light: [{ inclination: 180, azimuth: 0, color: color_1.Color.fromNormalizedRgb(1.0, 1.0, 1.0),
+                        intensity: 0.6 }]
+            }
         }
     }
 };
@@ -58,24 +60,38 @@ var LightingDemo = /** @class */ (function () {
         this.preset = 'illustrative';
     }
     LightingDemo.prototype.init = function (target) {
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
-                },
-            }, components: {
-                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
-            } }));
-        this.setPreset('illustrative');
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var _a;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    },
+                                }, components: {
+                                    controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        this.setPreset('illustrative');
+                        return [2 /*return*/];
+                }
+            });
+        });
     };
     LightingDemo.prototype.setPreset = function (preset) {
         var _a;
         var props = Canvas3DPresets[preset];
-        if (((_a = props.postprocessing.occlusion) === null || _a === void 0 ? void 0 : _a.name) === 'on') {
-            props.postprocessing.occlusion.params.radius = this.radius;
-            props.postprocessing.occlusion.params.bias = this.bias;
+        if (((_a = props.canvas3d.postprocessing.occlusion) === null || _a === void 0 ? void 0 : _a.name) === 'on') {
+            props.canvas3d.postprocessing.occlusion.params.radius = this.radius;
+            props.canvas3d.postprocessing.occlusion.params.bias = this.bias;
         }
-        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, props), { multiSample: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.canvas3d.props.multiSample), props.multiSample), renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.canvas3d.props.renderer), props.renderer), postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.canvas3d.props.postprocessing), props.postprocessing) }) });
+        commands_1.PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, props), { renderer: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.canvas3d.props.renderer), props.canvas3d.renderer), postprocessing: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, this.plugin.canvas3d.props.postprocessing), props.canvas3d.postprocessing) })
+        });
     };
     LightingDemo.prototype.load = function (_a, radius, bias) {
         var url = _a.url, _b = _a.format, format = _b === void 0 ? 'mmcif' : _b, _c = _a.isBinary, isBinary = _c === void 0 ? true : _c, _d = _a.assemblyId, assemblyId = _d === void 0 ? '' : _d;

package/lib/commonjs/examples/proteopedia-wrapper/index.js

@@ -235,21 +235,33 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         };
     }
     MolStarProteopediaWrapper.prototype.init = function (target, options) {
-        this.plugin = (0, mol_plugin_ui_1.createPlugin)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
-                model_index_1.AnimateModelIndex
-            ], layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
+        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            var _a, customColoring;
+            return (0, tslib_1.__generator)(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, (0, mol_plugin_ui_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, (0, spec_1.DefaultPluginUISpec)()), { animations: [
+                                    model_index_1.AnimateModelIndex
+                                ], layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    }
+                                }, components: {
+                                    remoteState: 'none'
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        customColoring = (0, coloring_1.createProteopediaCustomTheme)((options && options.customColorList) || []);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(annotation_1.EvolutionaryConservation.colorThemeProvider);
+                        this.plugin.managers.lociLabels.addProvider(annotation_1.EvolutionaryConservation.labelProvider);
+                        this.plugin.customModelProperties.register(annotation_1.EvolutionaryConservation.propertyProvider, true);
+                        return [2 /*return*/];
                 }
-            }, components: {
-                remoteState: 'none'
-            } }));
-        var customColoring = (0, coloring_1.createProteopediaCustomTheme)((options && options.customColorList) || []);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(annotation_1.EvolutionaryConservation.colorThemeProvider);
-        this.plugin.managers.lociLabels.addProvider(annotation_1.EvolutionaryConservation.labelProvider);
-        this.plugin.customModelProperties.register(annotation_1.EvolutionaryConservation.propertyProvider, true);
+            });
+        });
     };
     Object.defineProperty(MolStarProteopediaWrapper.prototype, "state", {
         get: function () {

package/lib/commonjs/extensions/alpha-orbitals/transforms.d.ts

@@ -72,7 +72,6 @@ export declare const CreateOrbitalDensityVolume: StateTransformer<BasisAndOrbita
     }>, "on">;
 }>>;
 export declare const CreateOrbitalRepresentation3D: StateTransformer<PluginStateObject.Volume.Data, PluginStateObject.Volume.Representation3D, PD.Normalize<{
-    directVolume: boolean;
     relativeIsovalue: number;
     kind: "negative" | "positive";
     color: import("../../mol-util/color").Color;