molstar 3.44.0 → 3.45.0

package/lib/extensions/mvs/components/annotation-label/representation.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -8,6 +8,7 @@ import { Representation } from '../../../../mol-repr/representation';
 import { ComplexRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../../../../mol-repr/structure/representation';
 import { MarkerAction } from '../../../../mol-util/marker-action';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { isMVSStructure } from '../is-mvs-model-prop';
 import { MVSAnnotationLabelTextParams, MVSAnnotationLabelTextVisual } from './visual';
 /** Components of "MVS Annotation Label" representation */
 var MVSAnnotationLabelVisuals = {
@@ -29,5 +30,5 @@ export var MVSAnnotationLabelRepresentationProvider = StructureRepresentationPro
     defaultValues: PD.getDefaultValues(MVSAnnotationLabelParams),
     defaultColorTheme: { name: 'uniform' }, // this ain't workin
     defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; },
+    isApplicable: function (structure) { return structure.elementCount > 0 && isMVSStructure(structure); },
 });

package/lib/extensions/mvs/components/annotation-prop.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */

package/lib/extensions/mvs/components/annotation-prop.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -45,7 +45,7 @@ export var MVSAnnotationsParams = {
 };
 /** Provider for custom model property "Annotations" */
 export var MVSAnnotationsProvider = CustomModelProperty.createProvider({
-    label: 'Annotations',
+    label: 'MVS Annotations',
     descriptor: CustomPropertyDescriptor({
         name: 'mvs-annotations',
     }),

package/lib/extensions/mvs/components/custom-label/representation.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */

package/lib/extensions/mvs/components/custom-label/representation.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -8,6 +8,7 @@ import { Representation } from '../../../../mol-repr/representation';
 import { ComplexRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../../../../mol-repr/structure/representation';
 import { MarkerAction } from '../../../../mol-util/marker-action';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
+import { isMVSStructure } from '../is-mvs-model-prop';
 import { CustomLabelTextParams, CustomLabelTextVisual } from './visual';
 /** Components of "Custom Label" representation */
 var CustomLabelVisuals = {
@@ -22,12 +23,12 @@ export function CustomLabelRepresentation(ctx, getParams) {
 /** A thingy that is needed to register representation type "Custom Label", allowing user-defined labels at at user-defined positions */
 export var CustomLabelRepresentationProvider = StructureRepresentationProvider({
     name: 'mvs-custom-label',
-    label: 'Custom Label',
+    label: 'MVS Custom Label',
     description: 'Displays labels with custom text',
     factory: CustomLabelRepresentation,
     getParams: function () { return CustomLabelParams; },
     defaultValues: PD.getDefaultValues(CustomLabelParams),
     defaultColorTheme: { name: 'uniform' },
     defaultSizeTheme: { name: 'physical' },
-    isApplicable: function (structure) { return structure.elementCount > 0; }
+    isApplicable: function (structure) { return structure.elementCount > 0 && isMVSStructure(structure); },
 });

package/lib/extensions/mvs/components/custom-tooltips-prop.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */

package/lib/extensions/mvs/components/custom-tooltips-prop.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -18,7 +18,7 @@ export var CustomTooltipsParams = {
 };
 /** Provider for custom structure property "CustomTooltips" */
 export var CustomTooltipsProvider = CustomStructureProperty.createProvider({
-    label: 'Custom Tooltips',
+    label: 'MVS Custom Tooltips',
     descriptor: CustomPropertyDescriptor({
         name: 'mvs-custom-tooltips',
     }),

package/lib/extensions/mvs/components/is-mvs-model-prop.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { Model, Structure } from '../../../mol-model/structure';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+/** Parameter definition for custom model property "Is MVS" */
+export type IsMVSModelParams = typeof IsMVSModelParams;
+export declare const IsMVSModelParams: {
+    isMvs: PD.BooleanParam;
+};
+/** Parameter values for custom model property "Is MVS" */
+export type IsMVSModelProps = PD.Values<IsMVSModelParams>;
+/** Provider for custom model property "Is MVS" */
+export declare const IsMVSModelProvider: CustomModelProperty.Provider<IsMVSModelParams, {}>;
+/** Decide if the model is flagged as managed by MolViewSpec */
+export declare function isMVSModel(model: Model): boolean;
+/** Decide if the structure is flagged as managed by MolViewSpec */
+export declare function isMVSStructure(structure: Structure): boolean;

package/lib/extensions/mvs/components/is-mvs-model-prop.js

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Adam Midlik <midlik@gmail.com>
+ */
+import { __awaiter, __generator } from "tslib";
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+export var IsMVSModelParams = {
+    isMvs: PD.Boolean(false, { description: 'Flag this model as managed by MolViewSpec and enable MolViewSpec features' }),
+};
+/** Provider for custom model property "Is MVS" */
+export var IsMVSModelProvider = CustomModelProperty.createProvider({
+    label: 'MVS',
+    descriptor: CustomPropertyDescriptor({
+        name: 'mvs-is-mvs-model',
+    }),
+    type: 'static',
+    defaultParams: IsMVSModelParams,
+    getParams: function (data) { return IsMVSModelParams; },
+    isApplicable: function (data) { return true; },
+    obtain: function (ctx, data, props) { return __awaiter(void 0, void 0, void 0, function () { return __generator(this, function (_a) {
+        return [2 /*return*/, ({ value: {} })];
+    }); }); },
+});
+/** Decide if the model is flagged as managed by MolViewSpec */
+export function isMVSModel(model) {
+    var _a;
+    return !!((_a = IsMVSModelProvider.props(model)) === null || _a === void 0 ? void 0 : _a.isMvs);
+}
+/** Decide if the structure is flagged as managed by MolViewSpec */
+export function isMVSStructure(structure) {
+    return structure.models.some(isMVSModel);
+}

package/lib/extensions/mvs/components/multilayer-color-theme.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */

package/lib/extensions/mvs/components/multilayer-color-theme.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -9,6 +9,7 @@ import { Color } from '../../../mol-util/color';
 import { ColorNames } from '../../../mol-util/color/names';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { stringToWords } from '../../../mol-util/string';
+import { isMVSStructure } from './is-mvs-model-prop';
 import { ElementSet, SelectorParams, isSelectorAll } from './selector';
 /** Special value that can be used as color with null-like semantic (i.e. "no color provided").
  * By some lucky coincidence, Mol* treats -1 as white. */
@@ -117,11 +118,11 @@ export var MultilayerColorThemeName = 'mvs-multilayer';
 export function makeMultilayerColorThemeProvider(colorThemeRegistry) {
     return {
         name: MultilayerColorThemeName,
-        label: 'Multi-layer',
+        label: 'MVS Multi-layer',
         category: ColorTheme.Category.Misc,
         factory: function (ctx, props) { return makeMultilayerColorTheme(ctx, props, colorThemeRegistry); },
         getParams: function (ctx) { return makeMultilayerColorThemeParams(colorThemeRegistry, ctx); },
         defaultValues: DefaultMultilayerColorThemeProps,
-        isApplicable: function (ctx) { return true; },
+        isApplicable: function (ctx) { return !!ctx.structure && isMVSStructure(ctx.structure); },
     };
 }

package/lib/extensions/mvs/load.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */

package/lib/extensions/mvs/load.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  */
@@ -14,6 +14,7 @@ import { MVSAnnotationStructureComponent } from './components/annotation-structu
 import { MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-prop';
 import { CustomLabelRepresentationProvider } from './components/custom-label/representation';
 import { CustomTooltipsProvider } from './components/custom-tooltips-prop';
+import { IsMVSModelProvider } from './components/is-mvs-model-prop';
 import { UpdateTarget, collectAnnotationReferences, collectAnnotationTooltips, collectInlineLabels, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, loadTree, makeNearestReprMap, prettyNameFromSelector, representationProps, structureProps, transformProps } from './load-helpers';
 import { validateTree } from './tree/generic/tree-schema';
 import { convertMvsToMolstar, mvsSanityCheck } from './tree/molstar/conversion';
@@ -138,10 +139,12 @@ var MolstarLoadingActions = {
         });
         UpdateTarget.apply(model, CustomModelProperties, {
             properties: (_a = {},
+                _a[IsMVSModelProvider.descriptor.name] = { isMvs: true },
                 _a[MVSAnnotationsProvider.descriptor.name] = { annotations: annotations },
                 _a),
             autoAttach: [
-                MVSAnnotationsProvider.descriptor.name
+                IsMVSModelProvider.descriptor.name,
+                MVSAnnotationsProvider.descriptor.name,
             ],
         });
         return model;

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

@@ -28,7 +28,7 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean | "inverted";
-    transparentBackfaces: string;
+    transparentBackfaces: "on" | "off" | "opaque";
     bumpFrequency: number;
     bumpAmplitude: number;
     alpha: number;

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

@@ -16,7 +16,7 @@ export declare const AssemblySymmetryParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/extensions/rcsb/graphql/types.d.ts

@@ -522,7 +522,9 @@ export type CoreAssembly = {
     readonly pdbx_struct_oper_list?: Maybe<ReadonlyArray<Maybe<PdbxStructOperList>>>;
     /** Get a list of polymer entity instances (chains) that constitute this assembly. */
     readonly polymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CorePolymerEntityInstance>>>;
+    readonly rcsb_assembly_annotation?: Maybe<ReadonlyArray<Maybe<RcsbAssemblyAnnotation>>>;
     readonly rcsb_assembly_container_identifiers: RcsbAssemblyContainerIdentifiers;
+    readonly rcsb_assembly_feature?: Maybe<ReadonlyArray<Maybe<RcsbAssemblyFeature>>>;
     readonly rcsb_assembly_info?: Maybe<RcsbAssemblyInfo>;
     /**
      * A unique identifier for each object in this assembly container formed by
@@ -1226,8 +1228,15 @@ export type DrugbankInfo = {
     readonly description?: Maybe<Scalars['String']['output']>;
     /** The DrugBank drug categories. */
     readonly drug_categories?: Maybe<ReadonlyArray<Maybe<Scalars['String']['output']>>>;
-    /** The DrugBank drug drug groups. */
+    /**
+     * The DrugBank drug groups determine their drug development status.
+     *
+     * Allowable values:
+     * approved, experimental, illicit, investigational, nutraceutical, vet_approved, withdrawn
+     *
+     */
     readonly drug_groups?: Maybe<ReadonlyArray<Maybe<Scalars['String']['output']>>>;
+    readonly drug_products?: Maybe<ReadonlyArray<Maybe<DrugbankInfoDrugProducts>>>;
     /** The DrugBank accession code */
     readonly drugbank_id: Scalars['String']['output'];
     /**
@@ -1259,6 +1268,56 @@ export type DrugbankInfo = {
     /** DrugBank drug name synonyms. */
     readonly synonyms?: Maybe<ReadonlyArray<Maybe<Scalars['String']['output']>>>;
 };
+export type DrugbankInfoDrugProducts = {
+    /**
+     * Indicates whether this drug has been approved by the regulating government.
+     *
+     * Allowable values:
+     * N, Y
+     *
+     */
+    readonly approved?: Maybe<Scalars['String']['output']>;
+    /**
+     * The country where this commercially available drug has been approved.
+     *
+     * Allowable values:
+     * Canada, EU, US
+     *
+     */
+    readonly country?: Maybe<Scalars['String']['output']>;
+    /**
+     * The ending date for market approval.
+     *
+     * Examples:
+     * 2003-07-30
+     *
+     */
+    readonly ended_marketing_on?: Maybe<Scalars['Date']['output']>;
+    /**
+     * The proprietary name(s) provided by the manufacturer for any commercially available products containing this drug.
+     *
+     * Examples:
+     * Hivid Tab 0.375mg
+     *
+     */
+    readonly name?: Maybe<Scalars['String']['output']>;
+    /**
+     * Source of this product information. For example, a value of DPD indicates this information was retrieved from the Canadian Drug Product Database.
+     *
+     * Allowable values:
+     * DPD, EMA, FDA NDC
+     *
+     */
+    readonly source?: Maybe<Scalars['String']['output']>;
+    /**
+     * The starting date for market approval.
+     *
+     * Examples:
+     * 1992-12-31
+     *
+     */
+    readonly started_marketing_on?: Maybe<Scalars['Date']['output']>;
+};
 export type DrugbankTarget = {
     /** The type of target interaction. */
     readonly interaction_type?: Maybe<Scalars['String']['output']>;
@@ -6438,6 +6497,46 @@ export type RcsbAccessionInfo = {
      */
     readonly status_code?: Maybe<Scalars['String']['output']>;
 };
+export type RcsbAssemblyAnnotation = {
+    readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbAssemblyAnnotationAdditionalProperties>>>;
+    /** An identifier for the annotation. */
+    readonly annotation_id?: Maybe<Scalars['String']['output']>;
+    /** Identifies the version of the annotation assignment. */
+    readonly assignment_version?: Maybe<Scalars['String']['output']>;
+    /** A description for the annotation. */
+    readonly description?: Maybe<Scalars['String']['output']>;
+    /** A name for the annotation. */
+    readonly name?: Maybe<Scalars['String']['output']>;
+    /**
+     * Code identifying the individual, organization or program that
+     *  assigned the annotation.
+     *
+     * Examples:
+     * MCSA
+     *
+     */
+    readonly provenance_source?: Maybe<Scalars['String']['output']>;
+    /**
+     * A type or category of the annotation.
+     *
+     * Allowable values:
+     * MCSA
+     *
+     */
+    readonly type?: Maybe<Scalars['String']['output']>;
+};
+export type RcsbAssemblyAnnotationAdditionalProperties = {
+    /**
+     * The additional property name.
+     *
+     * Allowable values:
+     * MCSA_MOTIF_COMPATIBILITY
+     *
+     */
+    readonly name?: Maybe<Scalars['String']['output']>;
+    /** The value(s) of the additional property. */
+    readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']['output']>>>;
+};
 export type RcsbAssemblyContainerIdentifiers = {
     /**
      * Assembly identifier for the container.
@@ -6461,6 +6560,66 @@ export type RcsbAssemblyContainerIdentifiers = {
      */
     readonly rcsb_id?: Maybe<Scalars['String']['output']>;
 };
+export type RcsbAssemblyFeature = {
+    readonly additional_properties?: Maybe<ReadonlyArray<Maybe<RcsbAssemblyFeatureAdditionalProperties>>>;
+    /** Identifies the version of the feature assignment. */
+    readonly assignment_version?: Maybe<Scalars['String']['output']>;
+    /** A description for the feature. */
+    readonly description?: Maybe<Scalars['String']['output']>;
+    /** An identifier for the feature. */
+    readonly feature_id?: Maybe<Scalars['String']['output']>;
+    /** This container groups together chain-level identifiers of the assigned features. */
+    readonly feature_positions?: Maybe<ReadonlyArray<Maybe<RcsbAssemblyFeatureFeaturePositions>>>;
+    /** A name for the feature. */
+    readonly name?: Maybe<Scalars['String']['output']>;
+    /**
+     * Code identifying the individual, organization or program that
+     *  assigned the feature.
+     *
+     * Examples:
+     * MCSA
+     *
+     */
+    readonly provenance_source?: Maybe<Scalars['String']['output']>;
+    /**
+     * A type or category of the feature.
+     *
+     * Allowable values:
+     * MCSA
+     *
+     */
+    readonly type?: Maybe<Scalars['String']['output']>;
+};
+export type RcsbAssemblyFeatureAdditionalProperties = {
+    /**
+     * The additional property name.
+     *
+     * Allowable values:
+     * MCSA_MOTIF_COMPATIBILITY
+     *
+     */
+    readonly name?: Maybe<Scalars['String']['output']>;
+    /** The value(s) of the additional property. */
+    readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']['output']>>>;
+};
+export type RcsbAssemblyFeatureFeaturePositions = {
+    /**
+     * An identifier of polymer chain (label_asym_id) corresponding to the feature assignment.
+     *
+     * Examples:
+     * A, B
+     *
+     */
+    readonly asym_id: Scalars['String']['output'];
+    /** An identifier for the monomer at which this segment of the feature begins. */
+    readonly beg_seq_id: Scalars['Int']['output'];
+    /** An identifier for the monomer at which this segment of the feature ends. */
+    readonly end_seq_id?: Maybe<Scalars['Int']['output']>;
+    /** Identifies the list of operations from the category pdbx_struct_oper_list. One item in array per operator applied. The order follows how operators are applied. */
+    readonly struct_oper_list: ReadonlyArray<Maybe<Scalars['String']['output']>>;
+    /** The value(s) of the feature over the monomer segment. */
+    readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']['output']>>>;
+};
 export type RcsbAssemblyInfo = {
     /** Entity identifier for the container. */
     readonly assembly_id?: Maybe<Scalars['String']['output']>;

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

@@ -24,6 +24,7 @@ export declare const IntraUnitClashParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -31,7 +32,7 @@ export declare const IntraUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -68,6 +69,7 @@ export declare const InterUnitClashParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -75,7 +77,7 @@ export declare const InterUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -114,13 +116,14 @@ export declare const ClashesParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -158,13 +161,14 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -203,13 +207,14 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
+    colorMode: PD.Select<"default" | "interpolate">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.Select<boolean | "inverted">;
-    transparentBackfaces: PD.Select<string>;
+    transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -24,7 +24,7 @@ export declare const HandleHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean | "inverted";
-        transparentBackfaces: string;
+        transparentBackfaces: "on" | "off" | "opaque";
         bumpFrequency: number;
         bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";

package/lib/mol-geo/geometry/color-data.d.ts

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { ValueCell } from '../../mol-util';
 import { TextureImage } from '../../mol-gl/renderable/util';

package/lib/mol-geo/geometry/color-data.js

@@ -3,6 +3,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { ValueCell } from '../../mol-util';
 import { createTextureImage } from '../../mol-gl/renderable/util';
@@ -129,24 +130,30 @@ function createInstanceColor(locationIt, color, colorData) {
 }
 /** Creates color texture with color for each group (i.e. shared across instances) */
 function createGroupColor(locationIt, color, colorData) {
-    var groupCount = locationIt.groupCount;
-    var colors = createTextureImage(Math.max(1, groupCount), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
+    var groupCount = locationIt.groupCount, hasLocation2 = locationIt.hasLocation2;
+    var colors = createTextureImage(Math.max(1, groupCount * (hasLocation2 ? 2 : 1)), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
     locationIt.reset();
+    var indexMultiplier = hasLocation2 ? 6 : 3;
     while (locationIt.hasNext && !locationIt.isNextNewInstance) {
-        var _a = locationIt.move(), location_2 = _a.location, isSecondary = _a.isSecondary, groupIndex = _a.groupIndex;
-        Color.toArray(color(location_2, isSecondary), colors.array, groupIndex * 3);
+        var _a = locationIt.move(), location_2 = _a.location, location2 = _a.location2, isSecondary = _a.isSecondary, groupIndex = _a.groupIndex;
+        Color.toArray(color(location_2, isSecondary), colors.array, groupIndex * indexMultiplier);
+        if (hasLocation2)
+            Color.toArray(color(location2, isSecondary), colors.array, groupIndex * indexMultiplier + 3);
     }
     return createTextureColor(colors, 'group', colorData);
 }
 /** Creates color texture with color for each group in each instance */
 function createGroupInstanceColor(locationIt, color, colorData) {
-    var groupCount = locationIt.groupCount, instanceCount = locationIt.instanceCount;
-    var count = instanceCount * groupCount;
+    var groupCount = locationIt.groupCount, instanceCount = locationIt.instanceCount, hasLocation2 = locationIt.hasLocation2;
+    var count = instanceCount * groupCount * (hasLocation2 ? 2 : 1);
     var colors = createTextureImage(Math.max(1, count), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
     locationIt.reset();
+    var indexMultiplier = hasLocation2 ? 6 : 3;
     while (locationIt.hasNext) {
-        var _a = locationIt.move(), location_3 = _a.location, isSecondary = _a.isSecondary, index = _a.index;
-        Color.toArray(color(location_3, isSecondary), colors.array, index * 3);
+        var _a = locationIt.move(), location_3 = _a.location, location2 = _a.location2, isSecondary = _a.isSecondary, index = _a.index;
+        Color.toArray(color(location_3, isSecondary), colors.array, index * indexMultiplier);
+        if (hasLocation2)
+            Color.toArray(color(location2, isSecondary), colors.array, index * indexMultiplier + 3);
     }
     return createTextureColor(colors, 'groupInstance', colorData);
 }

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

@@ -7,9 +7,15 @@
 import { Cylinders } from './cylinders';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 export interface CylindersBuilder {
-    add(startX: number, startY: number, startZ: number, endX: number, endY: number, endZ: number, radiusScale: number, topCap: boolean, bottomCap: boolean, group: number): void;
-    addFixedCountDashes(start: Vec3, end: Vec3, segmentCount: number, radiusScale: number, topCap: boolean, bottomCap: boolean, stubCap: boolean, group: number): void;
-    addFixedLengthDashes(start: Vec3, end: Vec3, segmentLength: number, radiusScale: number, topCap: boolean, bottomCap: boolean, group: number): void;
+    /**
+     * @param colorMode - controls if and how theme colors are interpolated
+     * - for colorMode between 0 and 1 use colorMode to interpolate
+     * - for colorMode == 2 do nothing, i.e., use given theme color
+     * - for colorMode == 3 use position on cylinder axis to interpolate
+     */
+    add(startX: number, startY: number, startZ: number, endX: number, endY: number, endZ: number, radiusScale: number, topCap: boolean, bottomCap: boolean, colorMode: number, group: number): void;
+    addFixedCountDashes(start: Vec3, end: Vec3, segmentCount: number, radiusScale: number, topCap: boolean, bottomCap: boolean, stubCap: boolean, interpolate: boolean, group: number): void;
+    addFixedLengthDashes(start: Vec3, end: Vec3, segmentLength: number, radiusScale: number, topCap: boolean, bottomCap: boolean, interpolate: boolean, group: number): void;
     getCylinders(): Cylinders;
 }
 export declare namespace CylindersBuilder {