molstar 3.44.0 → 3.45.0

package/lib/commonjs/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+     * approved, experimental, illicit, investigational, nutraceutical, vet_approved, withdrawn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/commonjs/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/commonjs/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/commonjs/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/commonjs/mol-geo/geometry/color-data.js

@@ -4,6 +4,7 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createGridColor = exports.createTextureColor = exports.createValueColor = exports.createColors = void 0;
@@ -135,24 +136,30 @@ 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 = (0, util_1.createTextureImage)(Math.max(1, groupCount), 3, Uint8Array, colorData && colorData.tColor.ref.value.array);
+    var groupCount = locationIt.groupCount, hasLocation2 = locationIt.hasLocation2;
+    var colors = (0, util_1.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_3 = _a.location, isSecondary = _a.isSecondary, groupIndex = _a.groupIndex;
-        color_1.Color.toArray(color(location_3, isSecondary), colors.array, groupIndex * 3);
+        var _a = locationIt.move(), location_3 = _a.location, location2 = _a.location2, isSecondary = _a.isSecondary, groupIndex = _a.groupIndex;
+        color_1.Color.toArray(color(location_3, isSecondary), colors.array, groupIndex * indexMultiplier);
+        if (hasLocation2)
+            color_1.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 = (0, util_1.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_4 = _a.location, isSecondary = _a.isSecondary, index = _a.index;
-        color_1.Color.toArray(color(location_4, isSecondary), colors.array, index * 3);
+        var _a = locationIt.move(), location_4 = _a.location, location2 = _a.location2, isSecondary = _a.isSecondary, index = _a.index;
+        color_1.Color.toArray(color(location_4, isSecondary), colors.array, index * indexMultiplier);
+        if (hasLocation2)
+            color_1.Color.toArray(color(location2, isSecondary), colors.array, index * indexMultiplier + 3);
     }
     return createTextureColor(colors, 'groupInstance', colorData);
 }

package/lib/commonjs/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 {

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

@@ -26,20 +26,23 @@ var CylindersBuilder;
         var ends = util_1.ChunkedArray.create(Float32Array, 3, chunkSize, cylinders ? cylinders.endBuffer.ref.value : initialCount);
         var scales = util_1.ChunkedArray.create(Float32Array, 1, chunkSize, cylinders ? cylinders.scaleBuffer.ref.value : initialCount);
         var caps = util_1.ChunkedArray.create(Float32Array, 1, chunkSize, cylinders ? cylinders.capBuffer.ref.value : initialCount);
-        var add = function (startX, startY, startZ, endX, endY, endZ, radiusScale, topCap, bottomCap, group) {
+        var colorModes = util_1.ChunkedArray.create(Float32Array, 1, chunkSize, cylinders ? cylinders.colorModeBuffer.ref.value : initialCount);
+        var add = function (startX, startY, startZ, endX, endY, endZ, radiusScale, topCap, bottomCap, colorMode, group) {
             for (var i = 0; i < 6; ++i) {
                 caAdd3(starts, startX, startY, startZ);
                 caAdd3(ends, endX, endY, endZ);
                 caAdd(groups, group);
                 caAdd(scales, radiusScale);
                 caAdd(caps, (topCap ? 1 : 0) + (bottomCap ? 2 : 0));
+                caAdd(colorModes, colorMode);
             }
         };
-        var addFixedCountDashes = function (start, end, segmentCount, radiusScale, topCap, bottomCap, stubCap, group) {
+        var addFixedCountDashes = function (start, end, segmentCount, radiusScale, topCap, bottomCap, stubCap, interpolate, group) {
             var d = linear_algebra_1.Vec3.distance(start, end);
             var isOdd = segmentCount % 2 !== 0;
             var s = Math.floor((segmentCount + 1) / 2);
             var step = d / (segmentCount + 0.5);
+            var colorMode = 2.0;
             linear_algebra_1.Vec3.setMagnitude(tmpDir, linear_algebra_1.Vec3.sub(tmpDir, end, start), step);
             linear_algebra_1.Vec3.copy(tmpVecA, start);
             for (var j = 0; j < s; ++j) {
@@ -52,16 +55,19 @@ var CylindersBuilder;
                 else {
                     linear_algebra_1.Vec3.add(tmpVecB, tmpVecA, tmpDir);
                 }
-                add(tmpVecA[0], tmpVecA[1], tmpVecA[2], tmpVecB[0], tmpVecB[1], tmpVecB[2], radiusScale, topCap, bottomCap, group);
+                if (interpolate) {
+                    colorMode = linear_algebra_1.Vec3.distance(start, tmpVecB) / (d * 2);
+                }
+                add(tmpVecA[0], tmpVecA[1], tmpVecA[2], tmpVecB[0], tmpVecB[1], tmpVecB[2], radiusScale, topCap, bottomCap, colorMode, group);
                 linear_algebra_1.Vec3.add(tmpVecA, tmpVecA, tmpDir);
             }
         };
         return {
             add: add,
             addFixedCountDashes: addFixedCountDashes,
-            addFixedLengthDashes: function (start, end, segmentLength, radiusScale, topCap, bottomCap, group) {
+            addFixedLengthDashes: function (start, end, segmentLength, radiusScale, topCap, bottomCap, interpolate, group) {
                 var d = linear_algebra_1.Vec3.distance(start, end);
-                addFixedCountDashes(start, end, d / segmentLength, radiusScale, topCap, bottomCap, true, group);
+                addFixedCountDashes(start, end, d / segmentLength, radiusScale, topCap, bottomCap, true, interpolate, group);
             },
             getCylinders: function () {
                 var cylinderCount = groups.elementCount / 6;
@@ -70,11 +76,12 @@ var CylindersBuilder;
                 var eb = util_1.ChunkedArray.compact(ends, true);
                 var ab = util_1.ChunkedArray.compact(scales, true);
                 var cb = util_1.ChunkedArray.compact(caps, true);
+                var cmb = util_1.ChunkedArray.compact(colorModes, true);
                 var mb = cylinders && cylinderCount <= cylinders.cylinderCount ? cylinders.mappingBuffer.ref.value : new Float32Array(cylinderCount * 18);
                 var ib = cylinders && cylinderCount <= cylinders.cylinderCount ? cylinders.indexBuffer.ref.value : new Uint32Array(cylinderCount * 12);
                 if (!cylinders || cylinderCount > cylinders.cylinderCount)
                     fillMappingAndIndices(cylinderCount, mb, ib);
-                return cylinders_1.Cylinders.create(mb, ib, gb, sb, eb, ab, cb, cylinderCount, cylinders);
+                return cylinders_1.Cylinders.create(mb, ib, gb, sb, eb, ab, cb, cmb, cylinderCount, cylinders);
             }
         };
     }

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

@@ -2,6 +2,7 @@
  * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { ValueCell } from '../../../mol-util';
 import { Mat4 } from '../../../mol-math/linear-algebra';
@@ -27,6 +28,13 @@ export interface Cylinders {
     readonly scaleBuffer: ValueCell<Float32Array>;
     /** Cylinder cap buffer as array of cap flags wrapped in a value cell */
     readonly capBuffer: ValueCell<Float32Array>;
+    /**
+     * Cylinder colorMode buffer as array of coloring modes flags wrapped in a value cell
+     * - 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
+     */
+    readonly colorModeBuffer: ValueCell<Float32Array>;
     /** Bounding sphere of the cylinders */
     readonly boundingSphere: Sphere3D;
     /** Maps group ids to cylinder indices */
@@ -34,7 +42,7 @@ export interface Cylinders {
     setBoundingSphere(boundingSphere: Sphere3D): void;
 }
 export declare namespace Cylinders {
-    function create(mappings: Float32Array, indices: Uint32Array, groups: Float32Array, starts: Float32Array, ends: Float32Array, scales: Float32Array, caps: Float32Array, cylinderCount: number, cylinders?: Cylinders): Cylinders;
+    function create(mappings: Float32Array, indices: Uint32Array, groups: Float32Array, starts: Float32Array, ends: Float32Array, scales: Float32Array, caps: Float32Array, colorModes: Float32Array, cylinderCount: number, cylinders?: Cylinders): Cylinders;
     function createEmpty(cylinders?: Cylinders): Cylinders;
     function transform(cylinders: Cylinders, t: Mat4): void;
     const Params: {
@@ -43,10 +51,11 @@ export declare namespace Cylinders {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.Select<boolean | "inverted">;
-        transparentBackfaces: PD.Select<string>;
+        transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
         solidInterior: PD.BooleanParam;
         bumpFrequency: PD.Numeric;
         bumpAmplitude: PD.Numeric;
+        colorMode: PD.Select<"default" | "interpolate">;
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{

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

@@ -3,6 +3,7 @@
  * Copyright (c) 2020-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.Cylinders = void 0;
@@ -25,10 +26,10 @@ var clipping_data_1 = require("../clipping-data");
 var substance_data_1 = require("../substance-data");
 var Cylinders;
 (function (Cylinders) {
-    function create(mappings, indices, groups, starts, ends, scales, caps, cylinderCount, cylinders) {
+    function create(mappings, indices, groups, starts, ends, scales, caps, colorModes, cylinderCount, cylinders) {
         return cylinders ?
-            update(mappings, indices, groups, starts, ends, scales, caps, cylinderCount, cylinders) :
-            fromArrays(mappings, indices, groups, starts, ends, scales, caps, cylinderCount);
+            update(mappings, indices, groups, starts, ends, scales, caps, colorModes, cylinderCount, cylinders) :
+            fromArrays(mappings, indices, groups, starts, ends, scales, caps, colorModes, cylinderCount);
     }
     Cylinders.create = create;
     function createEmpty(cylinders) {
@@ -39,16 +40,17 @@ var Cylinders;
         var eb = cylinders ? cylinders.endBuffer.ref.value : new Float32Array(0);
         var ab = cylinders ? cylinders.scaleBuffer.ref.value : new Float32Array(0);
         var cb = cylinders ? cylinders.capBuffer.ref.value : new Float32Array(0);
-        return create(mb, ib, gb, sb, eb, ab, cb, 0, cylinders);
+        var cmb = cylinders ? cylinders.colorModeBuffer.ref.value : new Float32Array(0);
+        return create(mb, ib, gb, sb, eb, ab, cb, cmb, 0, cylinders);
     }
     Cylinders.createEmpty = createEmpty;
     function hashCode(cylinders) {
         return (0, util_3.hashFnv32a)([
             cylinders.cylinderCount, cylinders.mappingBuffer.ref.version, cylinders.indexBuffer.ref.version,
-            cylinders.groupBuffer.ref.version, cylinders.startBuffer.ref.version, cylinders.endBuffer.ref.version, cylinders.scaleBuffer.ref.version, cylinders.capBuffer.ref.version
+            cylinders.groupBuffer.ref.version, cylinders.startBuffer.ref.version, cylinders.endBuffer.ref.version, cylinders.scaleBuffer.ref.version, cylinders.capBuffer.ref.version, cylinders.colorModeBuffer.ref.version
         ]);
     }
-    function fromArrays(mappings, indices, groups, starts, ends, scales, caps, cylinderCount) {
+    function fromArrays(mappings, indices, groups, starts, ends, scales, caps, colorModes, cylinderCount) {
         var boundingSphere = (0, geometry_1.Sphere3D)();
         var groupMapping;
         var currentHash = -1;
@@ -63,6 +65,7 @@ var Cylinders;
             endBuffer: mol_util_1.ValueCell.create(ends),
             scaleBuffer: mol_util_1.ValueCell.create(scales),
             capBuffer: mol_util_1.ValueCell.create(caps),
+            colorModeBuffer: mol_util_1.ValueCell.create(colorModes),
             get boundingSphere() {
                 var newHash = hashCode(cylinders);
                 if (newHash !== currentHash) {
@@ -87,7 +90,7 @@ var Cylinders;
         };
         return cylinders;
     }
-    function update(mappings, indices, groups, starts, ends, scales, caps, cylinderCount, cylinders) {
+    function update(mappings, indices, groups, starts, ends, scales, caps, colorModes, cylinderCount, cylinders) {
         if (cylinderCount > cylinders.cylinderCount) {
             mol_util_1.ValueCell.update(cylinders.mappingBuffer, mappings);
             mol_util_1.ValueCell.update(cylinders.indexBuffer, indices);
@@ -98,6 +101,7 @@ var Cylinders;
         mol_util_1.ValueCell.update(cylinders.endBuffer, ends);
         mol_util_1.ValueCell.update(cylinders.scaleBuffer, scales);
         mol_util_1.ValueCell.update(cylinders.capBuffer, caps);
+        mol_util_1.ValueCell.update(cylinders.colorModeBuffer, colorModes);
         return cylinders;
     }
     function transform(cylinders, t) {
@@ -110,7 +114,7 @@ var Cylinders;
     }
     Cylinders.transform = transform;
     //
-    Cylinders.Params = tslib_1.__assign(tslib_1.__assign({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], base_1.BaseGeometry.ShadingCategory), transparentBackfaces: param_definition_1.ParamDefinition.Select('off', param_definition_1.ParamDefinition.arrayToOptions(['off', 'on', 'opaque']), base_1.BaseGeometry.ShadingCategory), solidInterior: param_definition_1.ParamDefinition.Boolean(true, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
+    Cylinders.Params = tslib_1.__assign(tslib_1.__assign({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Select(false, [[false, 'Off'], [true, 'On'], ['inverted', 'Inverted']], base_1.BaseGeometry.ShadingCategory), transparentBackfaces: param_definition_1.ParamDefinition.Select('off', param_definition_1.ParamDefinition.arrayToOptions(['off', 'on', 'opaque']), base_1.BaseGeometry.ShadingCategory), solidInterior: param_definition_1.ParamDefinition.Boolean(true, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), colorMode: param_definition_1.ParamDefinition.Select('default', param_definition_1.ParamDefinition.arrayToOptions(['default', 'interpolate']), base_1.BaseGeometry.ShadingCategory) });
     Cylinders.Utils = {
         Params: Cylinders.Params,
         createEmpty: createEmpty,
@@ -158,7 +162,7 @@ var Cylinders;
         var padding = (0, size_data_1.getMaxSize)(size) * props.sizeFactor;
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount, 0);
-        return tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ dGeometryType: mol_util_1.ValueCell.create('cylinders'), aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'), dTransparentBackfaces: mol_util_1.ValueCell.create(props.transparentBackfaces), dSolidInterior: mol_util_1.ValueCell.create(props.solidInterior), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
+        return tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({ dGeometryType: mol_util_1.ValueCell.create('cylinders'), aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, aColorMode: cylinders.colorModeBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), uDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded === 'inverted' ? 'inverted' : props.xrayShaded === true ? 'on' : 'off'), dTransparentBackfaces: mol_util_1.ValueCell.create(props.transparentBackfaces), dSolidInterior: mol_util_1.ValueCell.create(props.solidInterior), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), dDualColor: mol_util_1.ValueCell.create(props.colorMode === 'interpolate') });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -175,6 +179,7 @@ var Cylinders;
         mol_util_1.ValueCell.updateIfChanged(values.dSolidInterior, props.solidInterior);
         mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
         mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
+        mol_util_1.ValueCell.updateIfChanged(values.dDualColor, props.colorMode === 'interpolate');
     }
     function updateBoundingSphere(values, cylinders) {
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);

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

@@ -64,7 +64,7 @@ export declare namespace Mesh {
         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/commonjs/mol-geo/geometry/spheres/spheres.d.ts

@@ -38,7 +38,7 @@ export declare namespace Spheres {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.Select<boolean | "inverted">;
-        transparentBackfaces: PD.Select<string>;
+        transparentBackfaces: PD.Select<"on" | "off" | "opaque">;
         solidInterior: PD.BooleanParam;
         clipPrimitive: PD.BooleanParam;
         approximate: PD.BooleanParam;

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

@@ -48,7 +48,7 @@ export declare namespace TextureMesh {
         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/commonjs/mol-geo/util/location-iterator.d.ts

@@ -2,12 +2,14 @@
  * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 import { Iterator } from '../../mol-data';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { Location } from '../../mol-model/location';
 export interface LocationValue {
     location: Location;
+    location2: Location;
     index: number;
     groupIndex: number;
     instanceIndex: number;
@@ -21,6 +23,7 @@ export interface LocationIterator extends Iterator<LocationValue> {
     readonly count: number;
     readonly stride: number;
     readonly nonInstanceable: boolean;
+    readonly hasLocation2: boolean;
     move(): LocationValue;
     reset(): void;
     skipInstance(): void;
@@ -28,7 +31,7 @@ export interface LocationIterator extends Iterator<LocationValue> {
 }
 type LocationGetter = (groupIndex: number, instanceIndex: number) => Location;
 type IsSecondaryGetter = (groupIndex: number, instanceIndex: number) => boolean;
-export declare function LocationIterator(groupCount: number, instanceCount: number, stride: number, getLocation: LocationGetter, nonInstanceable?: boolean, isSecondary?: IsSecondaryGetter): LocationIterator;
+export declare function LocationIterator(groupCount: number, instanceCount: number, stride: number, getLocation: LocationGetter, nonInstanceable?: boolean, isSecondary?: IsSecondaryGetter, getLocation2?: LocationGetter): LocationIterator;
 /** A position Location */
 export interface PositionLocation {
     readonly kind: 'position-location';