molstar 3.0.0-dev.2 → 3.0.0-dev.6

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

@@ -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>
  */
@@ -10,43 +10,46 @@ var mol_plugin_ui_1 = require("../../mol-plugin-ui");
 var spec_1 = require("../../mol-plugin-ui/spec");
 var commands_1 = require("../../mol-plugin/commands");
 var assets_1 = require("../../mol-util/assets");
+var color_1 = require("../../mol-util/color");
 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 } }
-        },
-        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 }]
+            }
         }
     }
 };
@@ -57,24 +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;

package/lib/commonjs/extensions/alpha-orbitals/transforms.js

@@ -179,7 +179,6 @@ exports.CreateOrbitalRepresentation3D = objects_1.PluginStateTransform.BuiltIn({
     from: objects_1.PluginStateObject.Volume.Data,
     to: objects_1.PluginStateObject.Volume.Representation3D,
     params: {
-        directVolume: param_definition_1.ParamDefinition.Boolean(false),
         relativeIsovalue: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
         kind: param_definition_1.ParamDefinition.Select('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
         color: param_definition_1.ParamDefinition.Color(names_1.ColorNames.blue),
@@ -252,19 +251,7 @@ function volumeParams(plugin, volume, params) {
     if (!isovalues)
         throw new Error('Isovalues are not computed.');
     var value = isovalues[params.kind];
-    return (0, volume_representation_params_1.createVolumeRepresentationParams)(plugin, volume.data, params.directVolume ? {
-        type: 'direct-volume',
-        typeParams: {
-            alpha: params.alpha,
-            renderMode: {
-                name: 'isosurface',
-                params: { isoValue: { kind: 'absolute', absoluteValue: (value !== null && value !== void 0 ? value : 1000) * params.relativeIsovalue }, singleLayer: false }
-            },
-            xrayShaded: params.xrayShaded
-        },
-        color: 'uniform',
-        colorParams: { value: params.color }
-    } : {
+    return (0, volume_representation_params_1.createVolumeRepresentationParams)(plugin, volume.data, {
         type: 'isosurface',
         typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value !== null && value !== void 0 ? value : 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded, tryUseGpu: params.tryUseGpu },
         color: 'uniform',

package/lib/commonjs/extensions/anvil/behavior.d.ts

@@ -30,6 +30,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     material: PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>;
     sectorOpacity: number;
     doubleSided: boolean;
@@ -37,6 +38,8 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
 }>>;
 export declare const MembraneOrientationPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;

package/lib/commonjs/extensions/anvil/representation.d.ts

@@ -18,11 +18,14 @@ declare const BilayerPlanesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type BilayerPlanesParams = typeof BilayerPlanesParams;
@@ -39,6 +42,7 @@ declare const BilayerRimsParams: {
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type BilayerRimsParams = typeof BilayerRimsParams;
@@ -56,6 +60,7 @@ export declare const MembraneOrientationParams: {
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
     sectorOpacity: PD.Numeric;
     doubleSided: PD.BooleanParam;
@@ -63,6 +68,8 @@ export declare const MembraneOrientationParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
 };
 export declare type MembraneOrientationParams = typeof MembraneOrientationParams;
 export declare type MembraneOrientationProps = PD.Values<MembraneOrientationParams>;
@@ -79,6 +86,7 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
     sectorOpacity: PD.Numeric;
     doubleSided: PD.BooleanParam;
@@ -86,6 +94,8 @@ export declare function getMembraneOrientationParams(ctx: ThemeRegistryContext,
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
 };
 export declare type MembraneOrientationRepresentation = StructureRepresentation<MembraneOrientationParams>;
 export declare function MembraneOrientationRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MembraneOrientationParams>): MembraneOrientationRepresentation;
@@ -102,6 +112,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
     sectorOpacity: PD.Numeric;
     doubleSided: PD.BooleanParam;
@@ -109,5 +120,7 @@ export declare const MembraneOrientationRepresentationProvider: StructureReprese
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
 }, "membrane-orientation">;
 export {};

package/lib/commonjs/extensions/cellpack/representation.d.ts

@@ -44,10 +44,13 @@ export declare const MBParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type MBParams = typeof MBParams;

package/lib/commonjs/extensions/dnatco/confal-pyramids/representation.d.ts

@@ -17,11 +17,14 @@ export declare const ConfalPyramidsParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type ConfalPyramidsParams = typeof ConfalPyramidsParams;
@@ -33,11 +36,14 @@ export declare function getConfalPyramidsParams(ctx: ThemeRegistryContext, struc
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type ConfalPyramidsRepresentation = StructureRepresentation<ConfalPyramidsParams>;
@@ -50,10 +56,13 @@ export declare const ConfalPyramidsRepresentationProvider: StructureRepresentati
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 }, "confal-pyramids">;

package/lib/commonjs/extensions/geo-export/obj-exporter.js

@@ -140,7 +140,7 @@ var ObjExporter = /** @class */ (function (_super) {
                             color = ObjExporter.getColor(v, geoData, interpolatedColors, interpolatedOverpaint);
                             color_1.Color.toArray(color, quantizedColors, i);
                         }
-                        ObjExporter.quantizeColors(quantizedColors, mesh.vertexCount);
+                        ObjExporter.quantizeColors(quantizedColors, vertexCount);
                         // face
                         for (i = 0; i < drawCount; i += 3) {
                             color = color_1.Color.fromArray(quantizedColors, i);

package/lib/commonjs/extensions/geo-export/usdz-exporter.js

@@ -133,7 +133,7 @@ var UsdzExporter = /** @class */ (function (_super) {
                                             color = UsdzExporter.getColor(v, geoData, interpolatedColors, interpolatedOverpaint);
                                             color_1.Color.toArray(color, quantizedColors, i);
                                         }
-                                        UsdzExporter.quantizeColors(quantizedColors, mesh.vertexCount);
+                                        UsdzExporter.quantizeColors(quantizedColors, vertexCount);
                                         faceIndicesByMaterial = new Map();
                                         for (i = 0; i < drawCount; i += 3) {
                                             color = color_1.Color.fromArray(quantizedColors, i);

package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts

@@ -0,0 +1,68 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state/builder/structure/representation-preset';
+export declare const MAQualityAssessment: import("../../../mol-state/transformer").StateTransformer<PluginBehavior.Category, PluginBehavior.Behavior, {
+    autoAttach: boolean;
+    showTooltip: boolean;
+}>;
+export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: PD.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+    };
+    representations: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+} | {
+    components: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+}>;
+export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
+    ignoreHydrogens: boolean | undefined;
+    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    theme: PD.Normalize<{
+        globalName: any;
+        carbonColor: any;
+        symmetryColor: any;
+        focus: any;
+    }> | undefined;
+}, {
+    components?: undefined;
+    representations?: undefined;
+} | {
+    components: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+    };
+    representations: {
+        polymer: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+} | {
+    components: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
+        branched: undefined;
+    };
+    representations: {
+        all: import("../../../mol-state").StateObjectSelector<import("../../../mol-plugin-state/objects").PluginStateObject.Molecule.Structure.Representation3D, import("../../../mol-state/transformer").StateTransformer<import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, import("../../../mol-state/object").StateObject<any, import("../../../mol-state/object").StateObject.Type<any>>, any>>;
+    };
+}>;