molstar 3.0.0-dev.9 → 3.1.0

package/lib/mol-theme/color/illustrative.js

@@ -1,23 +1,42 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-import { __assign } from "tslib";
 import { Color } from '../../mol-util/color';
 import { StructureElement, Unit, Bond } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
+import { UniformColorTheme, UniformColorThemeParams } from './uniform';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
+import { MoleculeTypeColorTheme, MoleculeTypeColorThemeParams } from './molecule-type';
+import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
 var DefaultIllustrativeColor = Color(0xEEEEEE);
-var Description = "Assigns an illustrative color that gives every chain a unique color with lighter carbons (inspired by David Goodsell's Molecule of the Month style).";
-export var IllustrativeColorThemeParams = __assign(__assign({}, ChainIdColorThemeParams), { carbonLightness: PD.Numeric(0.8, { min: -6, max: 6, step: 0.1 }) });
+var Description = "Assigns an illustrative color that gives every chain a color based on the choosen style but with lighter carbons (inspired by David Goodsell's Molecule of the Month style).";
+export var IllustrativeColorThemeParams = {
+    style: PD.MappedStatic('entity-id', {
+        uniform: PD.Group(UniformColorThemeParams),
+        'chain-id': PD.Group(ChainIdColorThemeParams),
+        'entity-id': PD.Group(EntityIdColorThemeParams),
+        'entity-source': PD.Group(EntitySourceColorThemeParams),
+        'molecule-type': PD.Group(MoleculeTypeColorThemeParams),
+    }),
+    carbonLightness: PD.Numeric(0.8, { min: -6, max: 6, step: 0.1 })
+};
 export function getIllustrativeColorThemeParams(ctx) {
-    return IllustrativeColorThemeParams; // TODO return copy
+    var params = PD.clone(IllustrativeColorThemeParams);
+    return params;
 }
 export function IllustrativeColorTheme(ctx, props) {
-    var _a = ChainIdColorTheme(ctx, props), chainIdColor = _a.color, legend = _a.legend;
+    var _a = props.style.name === 'uniform' ? UniformColorTheme(ctx, props.style.params) :
+        props.style.name === 'chain-id' ? ChainIdColorTheme(ctx, props.style.params) :
+            props.style.name === 'entity-id' ? EntityIdColorTheme(ctx, props.style.params) :
+                props.style.name === 'entity-source' ? EntitySourceColorTheme(ctx, props.style.params) :
+                    props.style.name === 'molecule-type' ? MoleculeTypeColorTheme(ctx, props.style.params) :
+                        assertUnreachable(props.style), styleColor = _a.color, legend = _a.legend;
     function illustrativeColor(location, typeSymbol) {
-        var baseColor = chainIdColor(location, false);
+        var baseColor = styleColor(location, false);
         return typeSymbol === 'C' ? Color.lighten(baseColor, props.carbonLightness) : baseColor;
     }
     function color(location) {

package/lib/mol-theme/color/molecule-type.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -21,11 +21,29 @@ export declare type MoleculeTypeColors = typeof MoleculeTypeColors;
 export declare const MoleculeTypeColorThemeParams: {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        water: Color;
+        ion: Color;
+        protein: Color;
+        RNA: Color;
+        DNA: Color;
+        PNA: Color;
+        saccharide: Color;
+    }>, "custom">>;
 };
 export declare type MoleculeTypeColorThemeParams = typeof MoleculeTypeColorThemeParams;
 export declare function getMoleculeTypeColorThemeParams(ctx: ThemeDataContext): {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        water: Color;
+        ion: Color;
+        protein: Color;
+        RNA: Color;
+        DNA: Color;
+        PNA: Color;
+        saccharide: Color;
+    }>, "custom">>;
 };
 export declare function moleculeTypeColor(colorMap: MoleculeTypeColors, unit: Unit, element: ElementIndex): Color;
 export declare function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<MoleculeTypeColorThemeParams>): ColorTheme<MoleculeTypeColorThemeParams>;

package/lib/mol-theme/color/molecule-type.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,6 +9,7 @@ import { getElementMoleculeType } from '../../mol-model/structure/util';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 export var MoleculeTypeColors = ColorMap({
     water: 0x386cb0,
     ion: 0xf0027f,
@@ -22,7 +23,11 @@ var DefaultMoleculeTypeColor = Color(0xffff99);
 var Description = 'Assigns a color based on the molecule type of a residue.';
 export var MoleculeTypeColorThemeParams = {
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(MoleculeTypeColors))
+    })
 };
 export function getMoleculeTypeColorThemeParams(ctx) {
     return MoleculeTypeColorThemeParams; // TODO return copy
@@ -41,7 +46,7 @@ export function moleculeTypeColor(colorMap, unit, element) {
     return DefaultMoleculeTypeColor;
 }
 export function MoleculeTypeColorTheme(ctx, props) {
-    var colorMap = getAdjustedColorMap(MoleculeTypeColors, props.saturation, props.lightness);
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? MoleculeTypeColors : props.colors.params, props.saturation, props.lightness);
     function color(location) {
         if (StructureElement.Location.is(location)) {
             return moleculeTypeColor(colorMap, location.unit, location.element);
@@ -57,8 +62,8 @@ export function MoleculeTypeColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: TableLegend(Object.keys(MoleculeTypeColors).map(function (name) {
-            return [name, MoleculeTypeColors[name]];
+        legend: TableLegend(Object.keys(colorMap).map(function (name) {
+            return [name, colorMap[name]];
         }).concat([['Other/unknown', DefaultMoleculeTypeColor]]))
     };
 }

package/lib/mol-theme/color/residue-name.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -49,11 +49,87 @@ export declare type ResidueNameColors = typeof ResidueNameColors;
 export declare const ResidueNameColorThemeParams: {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        ALA: Color;
+        ARG: Color;
+        ASN: Color;
+        ASP: Color;
+        CYS: Color;
+        GLN: Color;
+        GLU: Color;
+        GLY: Color;
+        HIS: Color;
+        ILE: Color;
+        LEU: Color;
+        LYS: Color;
+        MET: Color;
+        PHE: Color;
+        PRO: Color;
+        SER: Color;
+        THR: Color;
+        TRP: Color;
+        TYR: Color;
+        VAL: Color;
+        A: Color;
+        G: Color;
+        I: Color;
+        C: Color;
+        T: Color;
+        U: Color;
+        DA: Color;
+        DG: Color;
+        DI: Color;
+        DC: Color;
+        DT: Color;
+        DU: Color;
+        APN: Color;
+        GPN: Color;
+        CPN: Color;
+        TPN: Color;
+    }>, "custom">>;
 };
 export declare type ResidueNameColorThemeParams = typeof ResidueNameColorThemeParams;
 export declare function getResidueNameColorThemeParams(ctx: ThemeDataContext): {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        ALA: Color;
+        ARG: Color;
+        ASN: Color;
+        ASP: Color;
+        CYS: Color;
+        GLN: Color;
+        GLU: Color;
+        GLY: Color;
+        HIS: Color;
+        ILE: Color;
+        LEU: Color;
+        LYS: Color;
+        MET: Color;
+        PHE: Color;
+        PRO: Color;
+        SER: Color;
+        THR: Color;
+        TRP: Color;
+        TYR: Color;
+        VAL: Color;
+        A: Color;
+        G: Color;
+        I: Color;
+        C: Color;
+        T: Color;
+        U: Color;
+        DA: Color;
+        DG: Color;
+        DI: Color;
+        DC: Color;
+        DT: Color;
+        DU: Color;
+        APN: Color;
+        GPN: Color;
+        CPN: Color;
+        TPN: Color;
+    }>, "custom">>;
 };
 export declare function residueNameColor(colorMap: ResidueNameColors, residueName: string): Color;
 export declare function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<ResidueNameColorThemeParams>): ColorTheme<ResidueNameColorThemeParams>;

package/lib/mol-theme/color/residue-name.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,6 +8,7 @@ import { StructureElement, Unit, Bond } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 // protein colors from Jmol http://jmol.sourceforge.net/jscolors/
 export var ResidueNameColors = ColorMap({
     // standard amino acids
@@ -55,7 +56,11 @@ var DefaultResidueNameColor = Color(0xFF00FF);
 var Description = 'Assigns a color to every residue according to its name.';
 export var ResidueNameColorThemeParams = {
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ResidueNameColors))
+    })
 };
 export function getResidueNameColorThemeParams(ctx) {
     return ResidueNameColorThemeParams; // TODO return copy
@@ -77,7 +82,7 @@ export function residueNameColor(colorMap, residueName) {
     return c === undefined ? DefaultResidueNameColor : c;
 }
 export function ResidueNameColorTheme(ctx, props) {
-    var colorMap = getAdjustedColorMap(ResidueNameColors, props.saturation, props.lightness);
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ResidueNameColors : props.colors.params, props.saturation, props.lightness);
     function color(location) {
         if (StructureElement.Location.is(location)) {
             if (Unit.isAtomic(location.unit)) {
@@ -110,8 +115,8 @@ export function ResidueNameColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: TableLegend(Object.keys(ResidueNameColors).map(function (name) {
-            return [name, ResidueNameColors[name]];
+        legend: TableLegend(Object.keys(colorMap).map(function (name) {
+            return [name, colorMap[name]];
         }).concat([['Unknown', DefaultResidueNameColor]]))
     };
 }

package/lib/mol-theme/color/secondary-structure.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -26,11 +26,37 @@ export declare type SecondaryStructureColors = typeof SecondaryStructureColors;
 export declare const SecondaryStructureColorThemeParams: {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        alphaHelix: Color;
+        threeTenHelix: Color;
+        piHelix: Color;
+        betaTurn: Color;
+        betaStrand: Color;
+        coil: Color;
+        bend: Color;
+        turn: Color;
+        dna: Color;
+        rna: Color;
+        carbohydrate: Color;
+    }>, "custom">>;
 };
 export declare type SecondaryStructureColorThemeParams = typeof SecondaryStructureColorThemeParams;
 export declare function getSecondaryStructureColorThemeParams(ctx: ThemeDataContext): {
     saturation: PD.Numeric;
     lightness: PD.Numeric;
+    colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+        alphaHelix: Color;
+        threeTenHelix: Color;
+        piHelix: Color;
+        betaTurn: Color;
+        betaStrand: Color;
+        coil: Color;
+        bend: Color;
+        turn: Color;
+        dna: Color;
+        rna: Color;
+        carbohydrate: Color;
+    }>, "custom">>;
 };
 export declare function secondaryStructureColor(colorMap: SecondaryStructureColors, unit: Unit, element: ElementIndex, computedSecondaryStructure?: SecondaryStructureValue): Color;
 export declare function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Values<SecondaryStructureColorThemeParams>): ColorTheme<SecondaryStructureColorThemeParams>;

package/lib/mol-theme/color/secondary-structure.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,6 +11,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { TableLegend } from '../../mol-util/legend';
 import { SecondaryStructureProvider } from '../../mol-model-props/computed/secondary-structure';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { hash2 } from '../../mol-data/util';
 // from Jmol http://jmol.sourceforge.net/jscolors/ (shapely)
 var SecondaryStructureColors = ColorMap({
@@ -30,7 +31,11 @@ var DefaultSecondaryStructureColor = Color(0x808080);
 var Description = 'Assigns a color based on the type of secondary structure and basic molecule type.';
 export var SecondaryStructureColorThemeParams = {
     saturation: PD.Numeric(-1, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(SecondaryStructureColors))
+    })
 };
 export function getSecondaryStructureColorThemeParams(ctx) {
     return SecondaryStructureColorThemeParams; // TODO return copy
@@ -80,7 +85,7 @@ export function secondaryStructureColor(colorMap, unit, element, computedSeconda
 export function SecondaryStructureColorTheme(ctx, props) {
     var computedSecondaryStructure = ctx.structure && SecondaryStructureProvider.get(ctx.structure);
     var contextHash = computedSecondaryStructure ? hash2(computedSecondaryStructure.id, computedSecondaryStructure.version) : -1;
-    var colorMap = getAdjustedColorMap(SecondaryStructureColors, props.saturation, props.lightness);
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? SecondaryStructureColors : props.colors.params, props.saturation, props.lightness);
     function color(location) {
         if (StructureElement.Location.is(location)) {
             return secondaryStructureColor(colorMap, location.unit, location.element, computedSecondaryStructure === null || computedSecondaryStructure === void 0 ? void 0 : computedSecondaryStructure.value);
@@ -98,8 +103,8 @@ export function SecondaryStructureColorTheme(ctx, props) {
         props: props,
         contextHash: contextHash,
         description: Description,
-        legend: TableLegend(Object.keys(SecondaryStructureColors).map(function (name) {
-            return [name, SecondaryStructureColors[name]];
+        legend: TableLegend(Object.keys(colorMap).map(function (name) {
+            return [name, colorMap[name]];
         }).concat([['Other', DefaultSecondaryStructureColor]]))
     };
 }

package/lib/mol-theme/color.d.ts

@@ -125,9 +125,152 @@ declare namespace ColorTheme {
                 }>, "generate"> | PD.NamedParams<PD.Normalize<{
                     list: any;
                 }>, "colors">;
-            }>, "operator-name">>;
+            }>, "operator-name"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-source">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;
+            colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                H: Color;
+                D: Color;
+                T: Color;
+                HE: Color;
+                LI: Color;
+                BE: Color;
+                B: Color;
+                C: Color;
+                N: Color;
+                O: Color;
+                F: Color;
+                NE: Color;
+                NA: Color;
+                MG: Color;
+                AL: Color;
+                SI: Color;
+                P: Color;
+                S: Color;
+                CL: Color;
+                AR: Color;
+                K: Color;
+                CA: Color;
+                SC: Color;
+                TI: Color;
+                V: Color;
+                CR: Color;
+                MN: Color;
+                FE: Color;
+                CO: Color;
+                NI: Color;
+                CU: Color;
+                ZN: Color;
+                GA: Color;
+                GE: Color;
+                AS: Color;
+                SE: Color;
+                BR: Color;
+                KR: Color;
+                RB: Color;
+                SR: Color;
+                Y: Color;
+                ZR: Color;
+                NB: Color;
+                MO: Color;
+                TC: Color;
+                RU: Color;
+                RH: Color;
+                PD: Color;
+                AG: Color;
+                CD: Color;
+                IN: Color;
+                SN: Color;
+                SB: Color;
+                TE: Color;
+                I: Color;
+                XE: Color;
+                CS: Color;
+                BA: Color;
+                LA: Color;
+                CE: Color;
+                PR: Color;
+                ND: Color;
+                PM: Color;
+                SM: Color;
+                EU: Color;
+                GD: Color;
+                TB: Color;
+                DY: Color;
+                HO: Color;
+                ER: Color;
+                TM: Color;
+                YB: Color;
+                LU: Color;
+                HF: Color;
+                TA: Color;
+                W: Color;
+                RE: Color;
+                OS: Color;
+                IR: Color;
+                PT: Color;
+                AU: Color;
+                HG: Color;
+                TL: Color;
+                PB: Color;
+                BI: Color;
+                PO: Color;
+                AT: Color;
+                RN: Color;
+                FR: Color;
+                RA: Color;
+                AC: Color;
+                TH: Color;
+                PA: Color;
+                U: Color;
+                NP: Color;
+                PU: Color;
+                AM: Color;
+                CM: Color;
+                BK: Color;
+                CF: Color;
+                ES: Color;
+                FM: Color;
+                MD: Color;
+                NO: Color;
+                LR: Color;
+                RF: Color;
+                DB: Color;
+                SG: Color;
+                BH: Color;
+                HS: Color;
+                MT: Color;
+                DS: Color;
+                RG: Color;
+                CN: Color;
+                UUT: Color;
+                FL: Color;
+                UUP: Color;
+                LV: Color;
+                UUH: Color;
+            }>, "custom">>;
         }, "element-symbol">;
         'entity-id': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
@@ -164,21 +307,56 @@ declare namespace ColorTheme {
             scale: PD.Select<"DGwif" | "DGwoct" | "Oct-IF">;
         }, "hydrophobicity">;
         illustrative: Provider<{
+            style: PD.Mapped<PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+                asymId: "label" | "auth";
+            }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-id"> | PD.NamedParams<PD.Normalize<{
+                palette: PD.NamedParams<PD.Normalize<{
+                    maxCount: any;
+                    hue: any;
+                    chroma: any;
+                    luminance: any;
+                    clusteringStepCount: any;
+                    minSampleCount: any;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
+            }>, "entity-source"> | PD.NamedParams<PD.Normalize<{
+                value: Color;
+            }>, "uniform"> | PD.NamedParams<PD.Normalize<{
+                saturation: number;
+                lightness: number;
+                colors: PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                    water: any;
+                    ion: any;
+                    protein: any;
+                    RNA: any;
+                    DNA: any;
+                    PNA: any;
+                    saccharide: any;
+                }>, "custom">;
+            }>, "molecule-type">>;
             carbonLightness: PD.Numeric;
-            palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
-                maxCount: number;
-                hue: [number, number];
-                chroma: [number, number];
-                luminance: [number, number];
-                clusteringStepCount: number;
-                minSampleCount: number;
-            }>, "generate"> | PD.NamedParams<PD.Normalize<{
-                list: {
-                    kind: "set" | "interpolate";
-                    colors: import("../mol-util/color/color").ColorListEntry[];
-                };
-            }>, "colors">>;
-            asymId: PD.Select<"label" | "auth">;
         }, "illustrative">;
         'model-index': Provider<{
             palette: PD.Mapped<PD.NamedParams<PD.Normalize<{
@@ -198,6 +376,15 @@ declare namespace ColorTheme {
         'molecule-type': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
+            colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                water: Color;
+                ion: Color;
+                protein: Color;
+                RNA: Color;
+                DNA: Color;
+                PNA: Color;
+                saccharide: Color;
+            }>, "custom">>;
         }, "molecule-type">;
         occupancy: Provider<{
             domain: PD.Interval;
@@ -270,10 +457,61 @@ declare namespace ColorTheme {
         'residue-name': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
+            colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                ALA: Color;
+                ARG: Color;
+                ASN: Color;
+                ASP: Color;
+                CYS: Color;
+                GLN: Color;
+                GLU: Color;
+                GLY: Color;
+                HIS: Color;
+                ILE: Color;
+                LEU: Color;
+                LYS: Color;
+                MET: Color;
+                PHE: Color;
+                PRO: Color;
+                SER: Color;
+                THR: Color;
+                TRP: Color;
+                TYR: Color;
+                VAL: Color;
+                A: Color;
+                G: Color;
+                I: Color;
+                C: Color;
+                T: Color;
+                U: Color;
+                DA: Color;
+                DG: Color;
+                DI: Color;
+                DC: Color;
+                DT: Color;
+                DU: Color;
+                APN: Color;
+                GPN: Color;
+                CPN: Color;
+                TPN: Color;
+            }>, "custom">>;
         }, "residue-name">;
         'secondary-structure': Provider<{
             saturation: PD.Numeric;
             lightness: PD.Numeric;
+            colors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "default"> | PD.NamedParams<PD.Normalize<{
+                alphaHelix: Color;
+                threeTenHelix: Color;
+                piHelix: Color;
+                betaTurn: Color;
+                betaStrand: Color;
+                coil: Color;
+                bend: Color;
+                turn: Color;
+                dna: Color;
+                rna: Color;
+                carbohydrate: Color;
+            }>, "custom">>;
         }, "secondary-structure">;
         'sequence-id': Provider<{
             list: PD.ColorList;

package/lib/mol-util/color/color.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */