molstar 3.0.0 → 3.0.1

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

@@ -12,7 +12,7 @@ export declare const MAQualityAssessment: import("../../../mol-state/transformer
 }>;
 export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -40,7 +40,7 @@ export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPreset
 }>;
 export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -27,7 +27,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
     material: PD.Normalize<{
         metalness: number;
         roughness: number;
@@ -43,11 +43,11 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
 }>>;
 export declare const AssemblySymmetryPresetParams: {
     ignoreHydrogens: PD.Base<boolean | undefined>;
-    quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
+    quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
     theme: PD.Base<PD.Normalize<{
-        globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        globalName: "element-index" | "element-symbol" | "uniform" | "entity-id" | "chain-id" | "entity-source" | "operator-name" | "atom-id" | "carbohydrate-symbol" | "hydrophobicity" | "molecule-type" | "illustrative" | "model-index" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | "volume-value" | undefined;
         carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        symmetryColor: "element-index" | "element-symbol" | "uniform" | "entity-id" | "chain-id" | "entity-source" | "operator-name" | "atom-id" | "carbohydrate-symbol" | "hydrophobicity" | "molecule-type" | "illustrative" | "model-index" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | "volume-value" | undefined;
         focus: PD.Normalize<{
             name: any;
             params: any;
@@ -56,7 +56,7 @@ export declare const AssemblySymmetryPresetParams: {
 };
 export declare const AssemblySymmetryPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/color.d.ts

@@ -17,7 +17,7 @@ export declare const AssemblySymmetryClusterColorThemeParams: {
         minSampleCount: number;
     }>, "generate"> | PD.NamedParams<PD.Normalize<{
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "colors">>;
@@ -33,7 +33,7 @@ export declare function getAssemblySymmetryClusterColorThemeParams(ctx: ThemeDat
         minSampleCount: number;
     }>, "generate"> | PD.NamedParams<PD.Normalize<{
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "colors">>;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts

@@ -19,7 +19,7 @@ export declare const AssemblySymmetryParams: {
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;

package/lib/commonjs/extensions/rcsb/validation-report/behavior.d.ts

@@ -12,7 +12,7 @@ export declare const RCSBValidationReport: import("../../../mol-state/transforme
 }>;
 export declare const ValidationReportGeometryQualityPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -48,7 +48,7 @@ export declare const ValidationReportGeometryQualityPreset: StructureRepresentat
 }>;
 export declare const ValidationReportDensityFitPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;
@@ -76,7 +76,7 @@ export declare const ValidationReportDensityFitPreset: StructureRepresentationPr
 }>;
 export declare const ValidationReportRandomCoilIndexPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
-    quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
+    quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
         carbonColor: any;

package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts

@@ -34,7 +34,7 @@ export declare const IntraUnitClashParams: {
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
@@ -76,7 +76,7 @@ export declare const InterUnitClashParams: {
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
@@ -119,7 +119,7 @@ export declare const ClashesParams: {
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
@@ -161,7 +161,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
@@ -204,7 +204,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;

package/lib/commonjs/mol-canvas3d/canvas3d.d.ts

@@ -58,12 +58,12 @@ export declare const Canvas3DParams: {
         sampleLevel: number;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
-        occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
+        occlusion: PD.NamedParams<PD.Normalize<{
             samples: any;
             radius: any;
             bias: any;
             blurKernelSize: any;
-        }>, "on">;
+        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">;
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;
@@ -210,12 +210,12 @@ export declare const DefaultCanvas3DParams: PD.Values<{
         sampleLevel: number;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
-        occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
+        occlusion: PD.NamedParams<PD.Normalize<{
             samples: any;
             radius: any;
             bias: any;
             blurKernelSize: any;
-        }>, "on">;
+        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">;
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;

package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts

@@ -24,7 +24,7 @@ export declare const CameraHelperParams: {
         xrayShaded: boolean;
         bumpFrequency: number;
         bumpAmplitude: number;
-        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
         material: PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts

@@ -26,7 +26,7 @@ export declare const HandleHelperParams: {
         xrayShaded: boolean;
         bumpFrequency: number;
         bumpAmplitude: number;
-        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
         material: PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-canvas3d/helper/interaction-events.js

@@ -89,7 +89,7 @@ var Canvas3dInteractionHelper = /** @class */ (function () {
     Canvas3dInteractionHelper.prototype.identify = function (e, t) {
         var xyChanged = this.startX !== this.endX || this.startY !== this.endY;
         if (e === 2 /* Drag */) {
-            if (xyChanged && !representation_1.Representation.Loci.isEmpty(this.prevLoci)) {
+            if (xyChanged && !this.outsideViewport(this.startX, this.startY)) {
                 this.events.drag.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, pageStart: linear_algebra_1.Vec2.create(this.startX, this.startY), pageEnd: linear_algebra_1.Vec2.create(this.endX, this.endY) });
                 this.startX = this.endX;
                 this.startY = this.endY;

package/lib/commonjs/mol-canvas3d/passes/draw.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>

package/lib/commonjs/mol-canvas3d/passes/draw.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -228,11 +228,11 @@ var DrawPass = /** @class */ (function () {
             var markingDepthTest = props.marking.ghostEdgeStrength < 1;
             if (markingDepthTest) {
                 this.marking.depthTarget.bind();
-                renderer.clear(false);
+                renderer.clear(false, true);
                 renderer.renderMarkingDepth(scene.primitives, camera, null);
             }
             this.marking.maskTarget.bind();
-            renderer.clear(false);
+            renderer.clear(false, true);
             renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
             this.marking.update(props.marking);
             this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);

package/lib/commonjs/mol-canvas3d/passes/image.d.ts

@@ -18,12 +18,12 @@ export declare const ImageParams: {
         sampleLevel: number;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
-        occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
+        occlusion: PD.NamedParams<PD.Normalize<{
             samples: any;
             radius: any;
             bias: any;
             blurKernelSize: any;
-        }>, "on">;
+        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">;
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;

package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts

@@ -11,12 +11,12 @@ import { DrawPass } from './draw';
 import { ICamera } from '../../mol-canvas3d/camera';
 import { Color } from '../../mol-util/color';
 export declare const PostprocessingParams: {
-    occlusion: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
+    occlusion: PD.Mapped<PD.NamedParams<PD.Normalize<{
         samples: number;
         radius: number;
         bias: number;
         blurKernelSize: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
     outline: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         scale: number;
         threshold: number;

package/lib/commonjs/mol-geo/geometry/base.d.ts

@@ -23,13 +23,13 @@ export declare const VisualQualityInfo: {
     lowest: {};
 };
 export declare type VisualQuality = keyof typeof VisualQualityInfo;
-export declare const VisualQualityNames: ("auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest")[];
-export declare const VisualQualityOptions: ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string][];
+export declare const VisualQualityNames: ("custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest")[];
+export declare const VisualQualityOptions: ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string][];
 export declare const ColorSmoothingParams: {
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
 };
 export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
 export declare function hasColorSmoothingProp(props: PD.Values<any>): props is PD.Values<ColorSmoothingParams>;
@@ -43,7 +43,7 @@ export declare namespace BaseGeometry {
     const CustomQualityParamInfo: PD.Info;
     const Params: {
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts

@@ -46,10 +46,10 @@ export declare namespace Cylinders {
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
-            metalness: number; /** Number of cylinders */
-            roughness: number;
+            metalness: number;
+            roughness: number; /** Number of cylinders */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts

@@ -39,7 +39,7 @@ export declare namespace DirectVolume {
         stepsPerCell: PD.Numeric;
         jumpLength: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/image/image.d.ts

@@ -16,7 +16,7 @@ export declare const InterpolationTypes: {
     bspline: string;
 };
 export declare type InterpolationTypes = keyof typeof InterpolationTypes;
-export declare const InterpolationTypeNames: ("nearest" | "bspline" | "catmulrom" | "mitchell")[];
+export declare const InterpolationTypeNames: ("nearest" | "catmulrom" | "mitchell" | "bspline")[];
 export { Image };
 interface Image {
     readonly kind: 'image';
@@ -31,9 +31,9 @@ declare namespace Image {
     function create(imageTexture: TextureImage<Uint8Array>, corners: Float32Array, groupTexture: TextureImage<Uint8Array>, image?: Image): Image;
     function createEmpty(image?: Image): Image;
     const Params: {
-        interpolation: PD.Select<"nearest" | "bspline" | "catmulrom" | "mitchell">;
+        interpolation: PD.Select<"nearest" | "catmulrom" | "mitchell" | "bspline">;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts

@@ -40,11 +40,10 @@ export declare namespace Lines {
         sizeFactor: PD.Numeric;
         lineSizeAttenuation: PD.BooleanParam;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
-            /** Number of lines */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts

@@ -65,7 +65,7 @@ export declare namespace Mesh {
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/points/points.d.ts

@@ -34,16 +34,16 @@ export declare namespace Points {
         fuzzy: string;
     };
     type StyleTypes = keyof typeof StyleTypes;
-    const StyleTypeNames: ("circle" | "square" | "fuzzy")[];
+    const StyleTypeNames: ("fuzzy" | "square" | "circle")[];
     const Params: {
         sizeFactor: PD.Numeric;
         pointSizeAttenuation: PD.BooleanParam;
-        pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
+        pointStyle: PD.Select<"fuzzy" | "square" | "circle">;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
-            roughness: number;
+            roughness: number; /** Number of vertices in the point cloud */
             bumpiness: number;
         }>>;
         clip: PD.Group<PD.Normalize<{

package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts

@@ -37,7 +37,7 @@ export declare namespace Spheres {
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/text/text.d.ts

@@ -59,7 +59,7 @@ export declare namespace Text {
         fontVariant: PD.Select<import("./font-atlas").FontVariant>;
         fontWeight: PD.Select<import("./font-atlas").FontWeight>;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-geo/geometry/texture-mesh/texture-mesh.d.ts

@@ -48,7 +48,7 @@ export declare namespace TextureMesh {
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
-        quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+        quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;

package/lib/commonjs/mol-gl/renderer.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,7 +37,7 @@ export declare const enum MarkingType {
 interface Renderer {
     readonly stats: RendererStats;
     readonly props: Readonly<RendererProps>;
-    clear: (toBackgroundColor: boolean) => void;
+    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void;
     clearDepth: () => void;
     update: (camera: ICamera) => void;
     renderPick: (group: Scene.Group, camera: ICamera, variant: GraphicsRenderVariant, depthTexture: Texture | null, pickType: PickType) => void;

package/lib/commonjs/mol-gl/renderer.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -382,12 +382,12 @@ var Renderer;
             }
         };
         return {
-            clear: function (toBackgroundColor) {
+            clear: function (toBackgroundColor, ignoreTransparentBackground) {
                 state.enable(gl.SCISSOR_TEST);
                 state.enable(gl.DEPTH_TEST);
                 state.colorMask(true, true, true, true);
                 state.depthMask(true);
-                if (transparentBackground) {
+                if (transparentBackground && !ignoreTransparentBackground) {
                     state.clearColor(0, 0, 0, 0);
                 }
                 else if (toBackgroundColor) {

package/lib/commonjs/mol-gl/scene.d.ts

@@ -31,6 +31,6 @@ declare namespace Scene {
     interface Group extends Object3D {
         readonly renderables: ReadonlyArray<GraphicsRenderable>;
     }
-    function create(ctx: WebGLContext, variants?: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[]): Scene;
+    function create(ctx: WebGLContext, variants?: ("colorBlended" | "colorWboit" | "pick" | "depth" | "marking")[]): Scene;
 }
 export { Scene };

package/lib/commonjs/mol-model/loci.d.ts

@@ -54,56 +54,56 @@ declare namespace Loci {
     export function getPrincipalAxes(loci: Loci): PrincipalAxes | undefined;
     const Granularity: {
         element: (loci: Loci) => Loci;
-        residue: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        residue: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chain: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        chain: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        entity: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        entity: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        model: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        model: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        operator: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        operator: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        structure: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        structure: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci;
-        elementInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        elementInstances: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        residueInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        residueInstances: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
-        chainInstances: (loci: Loci) => StructureElement.Loci | Structure.Loci | Bond.Loci | Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
+        chainInstances: (loci: Loci) => Volume.Loci | Volume.Isosurface.Loci | Volume.Cell.Loci | {
             kind: "every-loci";
-        } | {
+        } | StructureElement.Loci | Structure.Loci | Bond.Loci | {
             kind: "empty-loci";
         } | DataLoci<unknown, unknown> | Shape.Loci | ShapeGroup.Loci;
     };
     export type Granularity = keyof typeof Granularity;
-    export const GranularityOptions: ["element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances", string][];
+    export const GranularityOptions: ["residue" | "entity" | "element" | "chain" | "model" | "operator" | "structure" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "element" | "operator" | "residue" | "entity" | "model" | "structure" | "chain" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): "residue" | "entity" | "element" | "chain" | "model" | "operator" | "structure" | "elementInstances" | "residueInstances" | "chainInstances";
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies

package/lib/commonjs/mol-model/shape/shape.d.ts

@@ -38,7 +38,7 @@ export declare namespace Shape {
     function getTheme(shape: Shape): Theme;
     function groupIterator(shape: Shape): LocationIterator;
     function createTransform(transforms: Mat4[], transformData?: TransformData): TransformData;
-    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"text" | "image" | "points" | "spheres" | "cylinders" | "lines" | "mesh" | "direct-volume" | "texture-mesh">;
+    function createRenderObject<G extends Geometry>(shape: Shape<G>, props: PD.Values<Geometry.Params<G>>): import("../../mol-gl/render-object").GraphicsRenderObject<"mesh" | "points" | "spheres" | "cylinders" | "text" | "lines" | "direct-volume" | "image" | "texture-mesh">;
     interface Loci {
         readonly kind: 'shape-loci';
         readonly shape: Shape;

package/lib/commonjs/mol-model/structure/model/properties/coarse/hierarchy.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>