molstar 3.0.0-dev.0 → 3.0.0-dev.10

package/lib/commonjs/mol-util/{float-packing.js → number-packing.js}

@@ -1,25 +1,16 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.unpackRGBAToDepth = exports.decodeFloatRGB = exports.encodeFloatRGBtoArray = exports.decodeFloatLog = exports.encodeFloatLog = void 0;
+exports.unpackRGBAToDepth = exports.unpackRGBToInt = exports.packIntToRGBArray = void 0;
 var interpolate_1 = require("../mol-math/interpolate");
-var approx_1 = require("../mol-math/approx");
 var linear_algebra_1 = require("../mol-math/linear-algebra");
-var maxFloat = 10000.0; // NOTE same constant is set in shaders
-var floatLogFactor = (0, approx_1.fasterLog)(maxFloat + 1);
-/** encode float logarithmically */
-function encodeFloatLog(value) { return (0, approx_1.fasterLog)(value + 1) / floatLogFactor; }
-exports.encodeFloatLog = encodeFloatLog;
-/** decode logarithmically encoded float */
-function decodeFloatLog(value) { return (0, approx_1.fasterExp)(value * floatLogFactor) - 1; }
-exports.decodeFloatLog = decodeFloatLog;
-/** encode float as rgb triplet into array at offset */
-function encodeFloatRGBtoArray(value, array, offset) {
-    value = (0, interpolate_1.clamp)(value, 0, 16777216 - 1) + 1;
+/** encode positive integer as rgb byte triplet into array at offset */
+function packIntToRGBArray(value, array, offset) {
+    value = (0, interpolate_1.clamp)(Math.round(value), 0, 16777216 - 1) + 1;
     array[offset + 2] = value % 256;
     value = Math.floor(value / 256);
     array[offset + 1] = value % 256;
@@ -27,12 +18,12 @@ function encodeFloatRGBtoArray(value, array, offset) {
     array[offset] = value % 256;
     return array;
 }
-exports.encodeFloatRGBtoArray = encodeFloatRGBtoArray;
-/** decode float encoded as rgb triplet */
-function decodeFloatRGB(r, g, b) {
+exports.packIntToRGBArray = packIntToRGBArray;
+/** decode positive integer encoded as rgb byte triplet */
+function unpackRGBToInt(r, g, b) {
     return (Math.floor(r) * 256 * 256 + Math.floor(g) * 256 + Math.floor(b)) - 1;
 }
-exports.decodeFloatRGB = decodeFloatRGB;
+exports.unpackRGBToInt = unpackRGBToInt;
 var UnpackDownscale = 255 / 256; // 0..1 -> fraction (excluding 1)
 var PackFactors = linear_algebra_1.Vec3.create(256 * 256 * 256, 256 * 256, 256);
 var UnpackFactors = linear_algebra_1.Vec4.create(UnpackDownscale / PackFactors[0], UnpackDownscale / PackFactors[1], UnpackDownscale / PackFactors[2], UnpackDownscale / 1);
@@ -42,4 +33,4 @@ function unpackRGBAToDepth(r, g, b, a) {
     return linear_algebra_1.Vec4.dot(tmpDepthRGBA, UnpackFactors);
 }
 exports.unpackRGBAToDepth = unpackRGBAToDepth;
-//# sourceMappingURL=float-packing.js.map
+//# sourceMappingURL=number-packing.js.map

package/lib/commonjs/mol-util/param-definition.d.ts

@@ -165,6 +165,7 @@ export declare namespace ParamDefinition {
     export interface Group<T> extends Base<T> {
         type: 'group';
         params: Params;
+        presets?: Select<T>['options'];
         isExpanded?: boolean;
         isFlat?: boolean;
         pivot?: keyof T;
@@ -174,6 +175,7 @@ export declare namespace ParamDefinition {
         isFlat?: boolean;
         customDefault?: any;
         pivot?: keyof T;
+        presets?: Select<T>['options'];
     }): Group<Normalize<T>>;
     export function EmptyGroup(info?: Info): Group<Normalize<unknown>>;
     export interface NamedParams<T = any, K = string> {

package/lib/commonjs/mol-util/param-definition.js

@@ -150,6 +150,8 @@ var ParamDefinition;
     ParamDefinition.LineGraph = LineGraph;
     function Group(params, info) {
         var ret = setInfo({ type: 'group', defaultValue: (info === null || info === void 0 ? void 0 : info.customDefault) || getDefaultValues(params), params: params }, info);
+        if (info === null || info === void 0 ? void 0 : info.presets)
+            ret.presets = info.presets;
         if (info === null || info === void 0 ? void 0 : info.isExpanded)
             ret.isExpanded = info.isExpanded;
         if (info === null || info === void 0 ? void 0 : info.isFlat)

package/lib/examples/alpha-orbitals/index.html

@@ -57,5 +57,6 @@
         <script>
             AlphaOrbitalsExample.init('app')
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

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

@@ -8,7 +8,7 @@ import { BehaviorSubject } from 'rxjs';
 import { debounceTime, skip } from 'rxjs/operators';
 import { CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
 import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
-import { createPluginAsync } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginConfig } from '../../mol-plugin/config';
@@ -21,7 +21,7 @@ require('mol-plugin-ui/skin/light.scss');
 var AlphaOrbitalsExample = /** @class */ (function () {
     function AlphaOrbitalsExample() {
         this.params = new BehaviorSubject({});
-        this.state = new BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+        this.state = new BehaviorSubject({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: true });
         this.selectors = void 0;
         this.basis = void 0;
         this.currentParams = __assign({}, this.state.value);
@@ -35,7 +35,7 @@ var AlphaOrbitalsExample = /** @class */ (function () {
                     case 0:
                         defaultSpec = DefaultPluginUISpec();
                         _b = this;
-                        return [4 /*yield*/, createPluginAsync(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, defaultSpec), { layout: {
+                        return [4 /*yield*/, createPluginUI(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, defaultSpec), { layout: {
                                     initial: {
                                         isExpanded: false,
                                         showControls: false
@@ -147,12 +147,11 @@ 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/examples/basic-wrapper/index.html

@@ -69,8 +69,9 @@
             $('format').value = format;
             $('format').onchange = function (e) { format = e.target.value; }
 
-            BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
-            BasicMolStarWrapper.setBackground(0xffffff);
+            BasicMolStarWrapper.init('app' /** or document.getElementById('app') */).then(() => {
+                BasicMolStarWrapper.setBackground(0xffffff);
+            });
 
             addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
             addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));

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

@@ -8,7 +8,7 @@ import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { EmptyLoci } from '../../mol-model/loci';
 import { StructureSelection } from '../../mol-model/structure';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
-import { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { Script } from '../../mol-script/script';
@@ -178,18 +178,30 @@ var BasicWrapper = /** @class */ (function () {
         };
     }
     BasicWrapper.prototype.init = function (target) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
+        return __awaiter(this, void 0, void 0, function () {
+            var _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, createPluginUI(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    }
+                                }, components: {
+                                    remoteState: 'none'
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(CustomColorThemeProvider);
+                        this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider);
+                        this.plugin.customModelProperties.register(StripedResidues.propertyProvider, true);
+                        return [2 /*return*/];
                 }
-            }, components: {
-                remoteState: 'none'
-            } }));
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(StripedResidues.colorThemeProvider);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(CustomColorThemeProvider);
-        this.plugin.managers.lociLabels.addProvider(StripedResidues.labelProvider);
-        this.plugin.customModelProperties.register(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;
@@ -230,13 +242,17 @@ var BasicWrapper = /** @class */ (function () {
     BasicWrapper.prototype.toggleSpin = function () {
         if (!this.plugin.canvas3d)
             return;
+        var trackball = this.plugin.canvas3d.props.trackball;
         PluginCommands.Canvas3D.SetSettings(this.plugin, {
-            settings: function (props) {
-                props.trackball.spin = !props.trackball.spin;
+            settings: {
+                trackball: __assign(__assign({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
             }
         });
-        if (!this.plugin.canvas3d.props.trackball.spin)
+        if (this.plugin.canvas3d.props.trackball.animate.name !== 'spin') {
             PluginCommands.Camera.Reset(this.plugin, {});
+        }
     };
     BasicWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

package/lib/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/examples/lighting/index.html

@@ -45,8 +45,9 @@
         <div id='controls'></div>
         <div id="app"></div>
         <script>
-            LightingDemo.init('app')
-            LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
+            LightingDemo.init('app').then(() => {
+                LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3);
+            });
 
             addHeader('Example PDB IDs');
             addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
@@ -83,5 +84,6 @@
                 $('controls').appendChild(h);
             }
         </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
     </body>
 </html>

package/lib/examples/lighting/index.js

@@ -1,50 +1,53 @@
 /**
- * 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>
  */
 import { __assign, __awaiter, __generator } from "tslib";
-import { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import './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: 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.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.fromNormalizedRgb(1.0, 1.0, 1.0),
+                        intensity: 0.6 }]
+            }
         }
     }
 };
@@ -55,24 +58,38 @@ var LightingDemo = /** @class */ (function () {
         this.preset = 'illustrative';
     }
     LightingDemo.prototype.init = function (target) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
-                },
-            }, components: {
-                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' }
-            } }));
-        this.setPreset('illustrative');
+        return __awaiter(this, void 0, void 0, function () {
+            var _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, createPluginUI(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, 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;
         }
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: __assign(__assign({}, props), { multiSample: __assign(__assign({}, this.plugin.canvas3d.props.multiSample), props.multiSample), renderer: __assign(__assign({}, this.plugin.canvas3d.props.renderer), props.renderer), postprocessing: __assign(__assign({}, this.plugin.canvas3d.props.postprocessing), props.postprocessing) }) });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: __assign(__assign({}, props), { renderer: __assign(__assign({}, this.plugin.canvas3d.props.renderer), props.canvas3d.renderer), postprocessing: __assign(__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/examples/proteopedia-wrapper/index.html

@@ -103,10 +103,11 @@
 
             PluginWrapper.init('app' /** or document.getElementById('app') */, {
                 customColorList: CustomColors
+            }).then(() => {
+                PluginWrapper.setBackground(0xffffff);
+                loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+                PluginWrapper.toggleSpin();
             });
-            PluginWrapper.setBackground(0xffffff);
-            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
-            PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
                 console.log('Model Info', info);

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

@@ -9,7 +9,7 @@ import { DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { createPlugin } from '../../mol-plugin-ui';
+import { createPluginUI } from '../../mol-plugin-ui';
 import { DefaultPluginUISpec } from '../../mol-plugin-ui/spec';
 import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { PluginCommands } from '../../mol-plugin/commands';
@@ -233,21 +233,33 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         };
     }
     MolStarProteopediaWrapper.prototype.init = function (target, options) {
-        this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { animations: [
-                AnimateModelIndex
-            ], layout: {
-                initial: {
-                    isExpanded: false,
-                    showControls: false
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, customColoring;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = this;
+                        return [4 /*yield*/, createPluginUI(typeof target === 'string' ? document.getElementById(target) : target, __assign(__assign({}, DefaultPluginUISpec()), { animations: [
+                                    AnimateModelIndex
+                                ], layout: {
+                                    initial: {
+                                        isExpanded: false,
+                                        showControls: false
+                                    }
+                                }, components: {
+                                    remoteState: 'none'
+                                } }))];
+                    case 1:
+                        _a.plugin = _b.sent();
+                        customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
+                        this.plugin.representation.structure.themes.colorThemeRegistry.add(EvolutionaryConservation.colorThemeProvider);
+                        this.plugin.managers.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
+                        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider, true);
+                        return [2 /*return*/];
                 }
-            }, components: {
-                remoteState: 'none'
-            } }));
-        var customColoring = createProteopediaCustomTheme((options && options.customColorList) || []);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(customColoring);
-        this.plugin.representation.structure.themes.colorThemeRegistry.add(EvolutionaryConservation.colorThemeProvider);
-        this.plugin.managers.lociLabels.addProvider(EvolutionaryConservation.labelProvider);
-        this.plugin.customModelProperties.register(EvolutionaryConservation.propertyProvider, true);
+            });
+        });
     };
     Object.defineProperty(MolStarProteopediaWrapper.prototype, "state", {
         get: function () {
@@ -465,7 +477,13 @@ var MolStarProteopediaWrapper = /** @class */ (function () {
         if (!this.plugin.canvas3d)
             return;
         var trackball = this.plugin.canvas3d.props.trackball;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: __assign(__assign({}, trackball), { spin: !trackball.spin }) } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, {
+            settings: {
+                trackball: __assign(__assign({}, trackball), { animate: trackball.animate.name === 'spin'
+                        ? { name: 'off', params: {} }
+                        : { name: 'spin', params: { speed: 1 } } })
+            }
+        });
     };
     MolStarProteopediaWrapper.prototype.animateModelIndexTargetFps = function () {
         return Math.max(1, this.animate.modelIndex.targetFps | 0);

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

@@ -176,7 +176,6 @@ export var CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
     from: PluginStateObject.Volume.Data,
     to: PluginStateObject.Volume.Representation3D,
     params: {
-        directVolume: PD.Boolean(false),
         relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
         kind: PD.Select('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
         color: PD.Color(ColorNames.blue),
@@ -249,19 +248,7 @@ function volumeParams(plugin, volume, params) {
     if (!isovalues)
         throw new Error('Isovalues are not computed.');
     var value = isovalues[params.kind];
-    return 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 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/extensions/anvil/behavior.d.ts

@@ -27,13 +27,23 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     sizeFactor: number;
     alpha: number;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
-    material: import("../../mol-util/material").Material;
+    material: PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>;
+    clip: PD.Normalize<{
+        variant: any;
+        objects: any;
+    }>;
     sectorOpacity: number;
     doubleSided: boolean;
     flipSided: boolean;
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
 }>>;
 export declare const MembraneOrientationPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;