molstar 3.0.0-dev.9 → 3.0.0

package/lib/mol-theme/color/element-symbol.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>
  */
@@ -157,6 +157,127 @@ export declare const ElementSymbolColorThemeParams: {
     }>, "operator-name">>;
     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">>;
 };
 export declare type ElementSymbolColorThemeParams = typeof ElementSymbolColorThemeParams;
 export declare function getElementSymbolColorThemeParams(ctx: ThemeDataContext): {
@@ -186,6 +307,127 @@ export declare function getElementSymbolColorThemeParams(ctx: ThemeDataContext):
     }>, "operator-name">>;
     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">>;
 };
 export declare function elementSymbolColor(colorMap: ElementSymbolColors, element: ElementSymbol): Color;
 export declare function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams>;

package/lib/mol-theme/color/element-symbol.js

@@ -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>
  */
@@ -9,6 +9,7 @@ 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';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
 import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
@@ -25,7 +26,11 @@ export var ElementSymbolColorThemeParams = {
         'element-symbol': PD.Group({})
     }, { description: 'Use chain-id coloring for carbon atoms.' }),
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ElementSymbolColors))
+    })
 };
 export function getElementSymbolColorThemeParams(ctx) {
     return ElementSymbolColorThemeParams; // TODO return copy
@@ -35,7 +40,7 @@ export function elementSymbolColor(colorMap, element) {
     return c === undefined ? DefaultElementSymbolColor : c;
 }
 export function ElementSymbolColorTheme(ctx, props) {
-    var colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
     var carbonColor = props.carbonColor.name === 'chain-id'
         ? ChainIdColorTheme(ctx, props.carbonColor.params).color
         : props.carbonColor.name === 'operator-name'
@@ -70,8 +75,8 @@ export function ElementSymbolColorTheme(ctx, props) {
         color: color,
         props: props,
         description: Description,
-        legend: TableLegend(Object.keys(ElementSymbolColors).map(function (name) {
-            return [name, ElementSymbolColors[name]];
+        legend: TableLegend(Object.keys(colorMap).map(function (name) {
+            return [name, colorMap[name]];
         }))
     };
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-theme/color/entity-id.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -28,9 +28,30 @@ function getEntityIdSerialMap(structure) {
             if (!map.has(k))
                 map.set(k, map.size);
         }
+        var spheres_entity_id = structure.models[i].coarseHierarchy.spheres.entity_id;
+        for (var j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+            var k = key(spheres_entity_id.value(j), i);
+            if (!map.has(k))
+                map.set(k, map.size);
+        }
+        var gaussians_entity_id = structure.models[i].coarseHierarchy.gaussians.entity_id;
+        for (var j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+            var k = key(gaussians_entity_id.value(j), i);
+            if (!map.has(k))
+                map.set(k, map.size);
+        }
     }
     return map;
 }
+function getEntityId(location) {
+    switch (location.unit.kind) {
+        case 0 /* Atomic */:
+            return StructureProperties.chain.label_entity_id(location);
+        case 1 /* Spheres */:
+        case 2 /* Gaussians */:
+            return StructureProperties.coarse.entity_id(location);
+    }
+}
 export function EntityIdColorTheme(ctx, props) {
     var color;
     var legend;
@@ -44,17 +65,17 @@ export function EntityIdColorTheme(ctx, props) {
         color = function (location) {
             var serial = undefined;
             if (StructureElement.Location.is(location)) {
-                var atomId = StructureProperties.chain.label_entity_id(location);
+                var entityId = getEntityId(location);
                 var modelIndex = location.structure.models.indexOf(location.unit.model);
-                var k = key(atomId, modelIndex);
+                var k = key(entityId, modelIndex);
                 serial = entityIdSerialMap_1.get(k);
             }
             else if (Bond.isLocation(location)) {
                 l_1.unit = location.aUnit;
                 l_1.element = location.aUnit.elements[location.aIndex];
-                var atomId = StructureProperties.chain.label_entity_id(l_1);
+                var entityId = getEntityId(l_1);
                 var modelIndex = l_1.structure.models.indexOf(l_1.unit.model);
-                var k = key(atomId, modelIndex);
+                var k = key(entityId, modelIndex);
                 serial = entityIdSerialMap_1.get(k);
             }
             return serial === undefined ? DefaultColor : palette_1.color(serial);

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

@@ -1,45 +1,116 @@
 /**
- * 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 { Color } from '../../mol-util/color';
 import { ColorTheme } from '../color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 export declare const IllustrativeColorThemeParams: {
+    style: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        value: Color;
+    }>, "uniform"> | 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<{
+        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"> | 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<{
+        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">>;
     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">;
 };
 export declare type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams;
 export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext): {
+    style: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        value: Color;
+    }>, "uniform"> | 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<{
+        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"> | 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<{
+        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">>;
     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">;
 };
 export declare function IllustrativeColorTheme(ctx: ThemeDataContext, props: PD.Values<IllustrativeColorThemeParams>): ColorTheme<IllustrativeColorThemeParams>;
 export declare const IllustrativeColorThemeProvider: ColorTheme.Provider<IllustrativeColorThemeParams, 'illustrative'>;

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]]))
     };
 }