molstar 4.3.0 → 4.4.1

package/lib/extensions/mvs/tree/mvs/mvs-builder.d.ts

@@ -96,7 +96,6 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -152,7 +151,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -172,7 +170,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -192,7 +189,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -280,7 +276,6 @@ declare class _Base<TKind extends MVSKind> {
             };
             component_from_source: {
                 field_values: import("../generic/params-schema").OptionalField<string[] | null>;
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -336,7 +331,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             color_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -356,7 +350,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             label_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;
@@ -376,7 +369,6 @@ declare class _Base<TKind extends MVSKind> {
                 field_name: import("../generic/params-schema").OptionalField<string>;
             };
             tooltip_from_source: {
-                /** Add a 'camera' node and return builder pointing to the root. 'camera' node instructs to set the camera position and orientation. */
                 schema: import("../generic/params-schema").RequiredField<"atom" | "residue" | "entity" | "chain" | "whole_structure" | "auth_chain" | "auth_residue" | "residue_range" | "auth_residue_range" | "auth_atom" | "all_atomic">;
                 block_header: import("../generic/params-schema").OptionalField<string | null>;
                 block_index: import("../generic/params-schema").OptionalField<number>;

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

@@ -31,6 +31,7 @@ export declare const IntraUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -80,6 +81,7 @@ export declare const InterUnitClashParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -130,6 +132,7 @@ export declare const ClashesParams: {
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -179,6 +182,7 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
@@ -229,6 +233,7 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
+    celShaded: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
     transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;

package/lib/extensions/sb-ncbr/tunnels/data-model.d.ts

@@ -104,18 +104,18 @@ declare const TunnelStateObject_base: {
         tunnel: Tunnel;
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             tunnel: Tunnel;
         };
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{
         tunnel: Tunnel;
     }, PluginStateObject.TypeInfo>;
 };
@@ -126,18 +126,18 @@ declare const TunnelsStateObject_base: {
         tunnels: Tunnel[];
     }, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: {
             tunnels: Tunnel[];
         };
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../../mol-state").StateObject<any, import("../../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../../mol-state").StateObject<{
+    is(obj?: import("../../../mol-state").StateObject): obj is import("../../../mol-state").StateObject<{
         tunnels: Tunnel[];
     }, PluginStateObject.TypeInfo>;
 };

package/lib/extensions/volumes-and-segmentations/entry-root.d.ts

@@ -37,16 +37,16 @@ export declare namespace VolsegEntryParamValues {
 declare const VolsegEntry_base: {
     new (data: VolsegEntryData, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: VolsegEntryData;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<VolsegEntryData, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<VolsegEntryData, PluginStateObject.TypeInfo>;
 };
 export declare class VolsegEntry extends VolsegEntry_base {
 }

package/lib/extensions/volumes-and-segmentations/entry-state.d.ts

@@ -39,12 +39,12 @@ declare const VolsegState_base: {
         }>>;
     }>, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: PD.Values<{
             volumeType: PD.Select<"off" | "direct-volume" | "isosurface">;
             volumeIsovalueKind: PD.Select<string>;
@@ -61,7 +61,7 @@ declare const VolsegState_base: {
         }>;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<PD.Values<{
+    is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<PD.Values<{
         volumeType: PD.Select<"off" | "direct-volume" | "isosurface">;
         volumeIsovalueKind: PD.Select<string>;
         volumeIsovalueValue: PD.Numeric;

package/lib/extensions/volumes-and-segmentations/global-state.d.ts

@@ -16,16 +16,16 @@ export type VolsegGlobalStateParamValues = PD.Values<typeof VolsegGlobalStatePar
 declare const VolsegGlobalState_base: {
     new (data: VolsegGlobalStateData, props?: {
         label: string;
-        description?: string | undefined;
+        description?: string;
     } | undefined): {
         id: import("../../mol-util").UUID;
         type: PluginStateObject.TypeInfo;
         label: string;
-        description?: string | undefined;
+        description?: string;
         data: VolsegGlobalStateData;
     };
     type: PluginStateObject.TypeInfo;
-    is(obj?: import("../../mol-state").StateObject<any, import("../../mol-state").StateObject.Type<any>> | undefined): obj is import("../../mol-state").StateObject<VolsegGlobalStateData, PluginStateObject.TypeInfo>;
+    is(obj?: import("../../mol-state").StateObject): obj is import("../../mol-state").StateObject<VolsegGlobalStateData, PluginStateObject.TypeInfo>;
 };
 export declare class VolsegGlobalState extends VolsegGlobalState_base {
 }

package/lib/extensions/volumes-and-segmentations/ui.d.ts

@@ -3,7 +3,6 @@
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
-/// <reference types="react" />
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 import { VolsegEntry } from './entry-root';
 import { VolsegGlobalStateData } from './global-state';

package/lib/extensions/zenodo/ui.d.ts

@@ -3,7 +3,6 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-/// <reference types="react" />
 import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
 import { PluginContext } from '../../mol-plugin/context';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';

package/lib/mol-canvas3d/camera/transition.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */

package/lib/mol-canvas3d/camera/transition.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -68,19 +68,36 @@ class CameraTransitionManager {
     }
 }
 (function (CameraTransitionManager) {
-    const _rot = Quat.identity();
+    const _rotUp = Quat.identity();
+    const _rotDist = Quat.identity();
+    const _sourcePosition = Vec3();
+    const _targetPosition = Vec3();
     function defaultTransition(out, t, source, target) {
         Camera.copySnapshot(out, target);
         // Rotate up
-        Quat.slerp(_rot, Quat.Identity, Quat.rotationTo(_rot, source.up, target.up), t);
-        Vec3.transformQuat(out.up, source.up, _rot);
+        Quat.slerp(_rotUp, Quat.Identity, Quat.rotationTo(_rotUp, source.up, target.up), t);
+        Vec3.transformQuat(out.up, source.up, _rotUp);
         // Lerp target, position & radius
         Vec3.lerp(out.target, source.target, target.target, t);
-        Vec3.lerp(out.position, source.position, target.position, t);
+        // Interpolate distance
+        const distSource = Vec3.distance(source.target, source.position);
+        const distTarget = Vec3.distance(target.target, target.position);
+        const dist = lerp(distSource, distTarget, t);
+        // Rotate between source and targer direction
+        Vec3.sub(_sourcePosition, source.position, source.target);
+        Vec3.normalize(_sourcePosition, _sourcePosition);
+        Vec3.sub(_targetPosition, target.position, target.target);
+        Vec3.normalize(_targetPosition, _targetPosition);
+        Quat.rotationTo(_rotDist, _sourcePosition, _targetPosition);
+        Quat.slerp(_rotDist, Quat.Identity, _rotDist, t);
+        Vec3.transformQuat(_sourcePosition, _sourcePosition, _rotDist);
+        Vec3.scale(_sourcePosition, _sourcePosition, dist);
+        Vec3.add(out.position, out.target, _sourcePosition);
+        // Interpolate radius
         out.radius = lerp(source.radius, target.radius, t);
         // TODO take change of `clipFar` into account
         out.radiusMax = lerp(source.radiusMax, target.radiusMax, t);
-        // Lerp fov & fog
+        // Interpolate fov & fog
         out.fov = lerp(source.fov, target.fov, t);
         out.fog = lerp(source.fog, target.fog, t);
     }

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

@@ -64,6 +64,7 @@ export declare const Canvas3DParams: {
         mode: string;
         sampleLevel: number;
         reduceFlicker: boolean;
+        reuseOcclusion: boolean;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
         occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
@@ -72,6 +73,7 @@ export declare const Canvas3DParams: {
             radius: any;
             bias: any;
             blurKernelSize: any;
+            blurDepthBias: any;
             resolutionScale: any;
             color: any;
         }>, "on">;
@@ -148,6 +150,7 @@ export declare const Canvas3DParams: {
         dimStrength: number;
         markerPriority: number;
         xrayEdgeFalloff: number;
+        celSteps: number;
         exposure: number;
         light: PD.Normalize<{
             inclination: number;
@@ -231,6 +234,7 @@ export declare const Canvas3DParams: {
             doubleSided: any;
             flipSided: any;
             flatShaded: any;
+            celShaded: any;
             xrayShaded: any;
             transparentBackfaces: any;
             bumpFrequency: any;
@@ -287,6 +291,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
         mode: string;
         sampleLevel: number;
         reduceFlicker: boolean;
+        reuseOcclusion: boolean;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
         occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
@@ -295,6 +300,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             radius: any;
             bias: any;
             blurKernelSize: any;
+            blurDepthBias: any;
             resolutionScale: any;
             color: any;
         }>, "on">;
@@ -371,6 +377,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
         dimStrength: number;
         markerPriority: number;
         xrayEdgeFalloff: number;
+        celSteps: number;
         exposure: number;
         light: PD.Normalize<{
             inclination: number;
@@ -454,6 +461,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             doubleSided: any;
             flipSided: any;
             flatShaded: any;
+            celShaded: any;
             xrayShaded: any;
             transparentBackfaces: any;
             bumpFrequency: any;
@@ -496,7 +504,7 @@ interface Canvas3DContext {
 }
 declare namespace Canvas3DContext {
     const DefaultAttribs: {
-        powerPreference: WebGLPowerPreference | undefined;
+        powerPreference: WebGLContextAttributes["powerPreference"];
         failIfMajorPerformanceCaveat: boolean;
         /** true by default to avoid issues with Safari (Jan 2021) */
         antialias: boolean;

package/lib/mol-canvas3d/helper/bounding-sphere-helper.d.ts

@@ -27,11 +27,6 @@ export declare class BoundingSphereHelper {
     syncVisibility(): void;
     clear(): void;
     get isEnabled(): boolean;
-    get props(): Readonly<PD.Values<{
-        sceneBoundingSpheres: PD.BooleanParam;
-        visibleSceneBoundingSpheres: PD.BooleanParam;
-        objectBoundingSpheres: PD.BooleanParam;
-        instanceBoundingSpheres: PD.BooleanParam;
-    }>>;
+    get props(): Readonly<DebugHelperProps>;
     setProps(props: Partial<DebugHelperProps>): void;
 }

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

@@ -23,6 +23,7 @@ export declare const HandleHelperParams: {
         doubleSided: boolean;
         flipSided: boolean;
         flatShaded: boolean;
+        celShaded: boolean;
         xrayShaded: boolean | "inverted";
         transparentBackfaces: "on" | "off" | "opaque";
         bumpFrequency: number;

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

@@ -32,6 +32,7 @@ export declare const HelperParams: {
             doubleSided: any;
             flipSided: any;
             flatShaded: any;
+            celShaded: any;
             xrayShaded: any;
             transparentBackfaces: any;
             bumpFrequency: any;
@@ -70,6 +71,7 @@ export declare const DefaultHelperProps: PD.Values<{
             doubleSided: any;
             flipSided: any;
             flatShaded: any;
+            celShaded: any;
             xrayShaded: any;
             transparentBackfaces: any;
             bumpFrequency: any;

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

@@ -19,6 +19,7 @@ export declare const ImageParams: {
         mode: string;
         sampleLevel: number;
         reduceFlicker: boolean;
+        reuseOcclusion: boolean;
     }>>;
     postprocessing: PD.Group<PD.Normalize<{
         occlusion: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
@@ -27,6 +28,7 @@ export declare const ImageParams: {
             radius: any;
             bias: any;
             blurKernelSize: any;
+            blurDepthBias: any;
             resolutionScale: any;
             color: any;
         }>, "on">;

package/lib/mol-canvas3d/passes/multi-sample.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -18,6 +18,7 @@ export declare const MultiSampleParams: {
     mode: PD.Select<string>;
     sampleLevel: PD.Numeric;
     reduceFlicker: PD.BooleanParam;
+    reuseOcclusion: PD.BooleanParam;
 };
 export type MultiSampleProps = PD.Values<typeof MultiSampleParams>;
 type Props = {

package/lib/mol-canvas3d/passes/multi-sample.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,6 +37,7 @@ export const MultiSampleParams = {
     mode: PD.Select('temporal', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
     sampleLevel: PD.Numeric(2, { min: 0, max: 5, step: 1 }, { description: 'Take level^2 samples.' }),
     reduceFlicker: PD.Boolean(true, { description: 'Reduce flicker in "temporal" mode.' }),
+    reuseOcclusion: PD.Boolean(true, { description: 'Reuse occlusion data. It is faster but has some artefacts.' }),
 };
 export class MultiSamplePass {
     static isEnabled(props) {
@@ -114,7 +115,7 @@ export class MultiSamplePass {
             const sampleWeight = baseSampleWeight + roundingRange * uniformCenteredDistribution;
             ValueCell.update(compose.values.uWeight, sampleWeight);
             // render scene
-            if (i === 0) {
+            if (i === 0 || !props.multiSample.reuseOcclusion) {
                 drawPass.postprocessing.setOcclusionOffset(0, 0);
             }
             else {
@@ -193,7 +194,7 @@ export class MultiSamplePass {
                 Camera.setViewOffset(camera.viewOffset, width, height, offset[0], offset[1], width, height);
                 camera.update();
                 // render scene
-                if (sampleIndex === 0) {
+                if (sampleIndex === 0 || !props.multiSample.reuseOcclusion) {
                     drawPass.postprocessing.setOcclusionOffset(0, 0);
                 }
                 else {

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

@@ -45,6 +45,7 @@ export declare const PostprocessingParams: {
         radius: number;
         bias: number;
         blurKernelSize: number;
+        blurDepthBias: number;
         resolutionScale: number;
         color: Color;
     }>, "on">>;

package/lib/mol-canvas3d/passes/postprocessing.js

@@ -155,6 +155,7 @@ const SsaoBlurSchema = {
     uTexSize: UniformSpec('v2'),
     uKernel: UniformSpec('f[]'),
     dOcclusionKernelSize: DefineSpec('number'),
+    uBlurDepthBias: UniformSpec('f'),
     uBlurDirectionX: UniformSpec('f'),
     uBlurDirectionY: UniformSpec('f'),
     uInvProjection: UniformSpec('m4'),
@@ -170,6 +171,7 @@ function getSsaoBlurRenderable(ctx, ssaoDepthTexture, direction) {
         uTexSize: ValueCell.create(Vec2.create(ssaoDepthTexture.getWidth(), ssaoDepthTexture.getHeight())),
         uKernel: ValueCell.create(getBlurKernel(15)),
         dOcclusionKernelSize: ValueCell.create(15),
+        uBlurDepthBias: ValueCell.create(0.5),
         uBlurDirectionX: ValueCell.create(direction === 'horizontal' ? 1 : 0),
         uBlurDirectionY: ValueCell.create(direction === 'vertical' ? 1 : 0),
         uInvProjection: ValueCell.create(Mat4.identity()),
@@ -292,6 +294,7 @@ export const PostprocessingParams = {
             radius: PD.Numeric(5, { min: 0, max: 20, step: 0.1 }, { description: 'Final occlusion radius is 2^x', hideIf: p => (p === null || p === void 0 ? void 0 : p.multiScale.name) === 'on' }),
             bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
             blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+            blurDepthBias: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
             resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
             color: PD.Color(Color(0x000000)),
         }),
@@ -480,6 +483,8 @@ export class PostprocessingPass {
             ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.uFar, camera.far);
             ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uInvProjection, invProjection);
             ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uInvProjection, invProjection);
+            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uBlurDepthBias, props.occlusion.params.blurDepthBias);
+            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uBlurDepthBias, props.occlusion.params.blurDepthBias);
             if (this.ssaoBlurFirstPassRenderable.values.dOrthographic.ref.value !== orthographic) {
                 needsUpdateSsaoBlur = true;
                 ValueCell.update(this.ssaoBlurFirstPassRenderable.values.dOrthographic, orthographic);

package/lib/mol-data/db/column.d.ts

@@ -137,7 +137,7 @@ declare namespace Column {
     function view<T>(column: Column<T>, indices: ArrayLike<number>, checkIndentity?: boolean): Column<T>;
     /** A map of the 1st occurence of each value. */
     function createFirstIndexMap<T>(column: Column<T>): Map<T, number>;
-    function createIndexer<T, R extends number = number>(column: Column<T>): (e: T) => R;
+    function createIndexer<T, R extends number = number>(column: Column<T>): ((e: T) => R);
     function mapToArray<T, S>(column: Column<T>, f: (v: T) => S, ctor?: ArrayCtor<S>): ArrayLike<S>;
     function areEqual<T>(a: Column<T>, b: Column<T>): boolean;
     function indicesOf<T>(c: Column<T>, test: (e: T) => boolean): number[];

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

@@ -24,7 +24,7 @@ export declare const VisualQualityInfo: {
     lowest: {};
 };
 export type VisualQuality = keyof typeof VisualQualityInfo;
-export declare const VisualQualityNames: ("auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest")[];
+export declare const VisualQualityNames: VisualQuality[];
 export declare const VisualQualityOptions: ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string][];
 export declare const ColorSmoothingParams: {
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{

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

@@ -50,6 +50,7 @@ export declare namespace Cylinders {
         sizeAspectRatio: PD.Numeric;
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
+        celShaded: PD.BooleanParam;
         xrayShaded: PD.Select<boolean | "inverted">;
         transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
         solidInterior: PD.BooleanParam;

package/lib/mol-geo/geometry/cylinders/cylinders.js

@@ -117,6 +117,7 @@ export var Cylinders;
         sizeAspectRatio: PD.Numeric(1, { min: 0, max: 3, step: 0.01 }),
         doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
+        celShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], BaseGeometry.ShadingCategory),
         transparentBackfaces: PD.Select('off', PD.arrayToOptions(['off', 'on', 'opaque']), BaseGeometry.ShadingCategory),
         solidInterior: PD.Boolean(true, BaseGeometry.ShadingCategory),
@@ -199,6 +200,7 @@ export var Cylinders;
             uSizeFactor: ValueCell.create(props.sizeFactor * props.sizeAspectRatio),
             uDoubleSided: ValueCell.create(props.doubleSided),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
+            dCelShaded: ValueCell.create(props.celShaded),
             dXrayShaded: ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'),
             dTransparentBackfaces: ValueCell.create(props.transparentBackfaces),
             dSolidInterior: ValueCell.create(props.solidInterior),
@@ -217,6 +219,7 @@ export var Cylinders;
         ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor * props.sizeAspectRatio);
         ValueCell.updateIfChanged(values.uDoubleSided, props.doubleSided);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
+        ValueCell.updateIfChanged(values.dCelShaded, props.celShaded);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off');
         ValueCell.updateIfChanged(values.dTransparentBackfaces, props.transparentBackfaces);
         ValueCell.updateIfChanged(values.dSolidInterior, props.solidInterior);

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

@@ -34,6 +34,7 @@ export declare namespace DirectVolume {
     function createEmpty(directVolume?: DirectVolume): DirectVolume;
     const Params: {
         ignoreLight: PD.BooleanParam;
+        celShaded: PD.BooleanParam;
         xrayShaded: PD.Select<boolean | "inverted">;
         controlPoints: PD.LineGraph;
         stepsPerCell: PD.Numeric;

package/lib/mol-geo/geometry/direct-volume/direct-volume.js

@@ -110,6 +110,7 @@ export var DirectVolume;
     DirectVolume.Params = {
         ...BaseGeometry.Params,
         ignoreLight: PD.Boolean(false, BaseGeometry.ShadingCategory),
+        celShaded: PD.Boolean(false, BaseGeometry.ShadingCategory),
         xrayShaded: PD.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], BaseGeometry.ShadingCategory),
         controlPoints: PD.LineGraph([
             Vec2.create(0.19, 0.0), Vec2.create(0.2, 0.05), Vec2.create(0.25, 0.05), Vec2.create(0.26, 0.0),
@@ -215,6 +216,7 @@ export var DirectVolume;
             dPackedGroup: directVolume.packedGroup,
             dAxisOrder: ValueCell.create(directVolume.axisOrder.ref.value.join('')),
             dIgnoreLight: ValueCell.create(props.ignoreLight),
+            dCelShaded: ValueCell.create(props.celShaded),
             dXrayShaded: ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'),
         };
     }
@@ -226,6 +228,7 @@ export var DirectVolume;
     function updateValues(values, props) {
         BaseGeometry.updateValues(values, props);
         ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
+        ValueCell.updateIfChanged(values.dCelShaded, props.celShaded);
         ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off');
         const controlPoints = getControlPointsFromVec2Array(props.controlPoints);
         createTransferFunctionTexture(controlPoints, values.tTransferTex);

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

@@ -16,7 +16,7 @@ export declare const InterpolationTypes: {
     bspline: string;
 };
 export type InterpolationTypes = keyof typeof InterpolationTypes;
-export declare const InterpolationTypeNames: ("nearest" | "bspline" | "catmulrom" | "mitchell")[];
+export declare const InterpolationTypeNames: InterpolationTypes[];
 export { Image };
 interface Image {
     readonly kind: 'image';

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

@@ -63,6 +63,7 @@ export declare namespace Mesh {
         flipSided: PD.BooleanParam;
         flatShaded: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
+        celShaded: PD.BooleanParam;
         xrayShaded: PD.Select<boolean | "inverted">;
         transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
         bumpFrequency: PD.Numeric;