molstar 3.0.0-dev.7 → 3.0.1

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

@@ -1,31 +1,39 @@
 /**
- * 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>
  */
-import { __assign } from "tslib";
 import { Color, ColorMap } from '../../mol-util/color';
 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';
+import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
 export var ElementSymbolColors = ColorMap({
     'H': 0xFFFFFF, 'D': 0xFFFFC0, 'T': 0xFFFFA0, 'HE': 0xD9FFFF, 'LI': 0xCC80FF, 'BE': 0xC2FF00, 'B': 0xFFB5B5, 'C': 0x909090, 'N': 0x3050F8, 'O': 0xFF0D0D, 'F': 0x90E050, 'NE': 0xB3E3F5, 'NA': 0xAB5CF2, 'MG': 0x8AFF00, 'AL': 0xBFA6A6, 'SI': 0xF0C8A0, 'P': 0xFF8000, 'S': 0xFFFF30, 'CL': 0x1FF01F, 'AR': 0x80D1E3, 'K': 0x8F40D4, 'CA': 0x3DFF00, 'SC': 0xE6E6E6, 'TI': 0xBFC2C7, 'V': 0xA6A6AB, 'CR': 0x8A99C7, 'MN': 0x9C7AC7, 'FE': 0xE06633, 'CO': 0xF090A0, 'NI': 0x50D050, 'CU': 0xC88033, 'ZN': 0x7D80B0, 'GA': 0xC28F8F, 'GE': 0x668F8F, 'AS': 0xBD80E3, 'SE': 0xFFA100, 'BR': 0xA62929, 'KR': 0x5CB8D1, 'RB': 0x702EB0, 'SR': 0x00FF00, 'Y': 0x94FFFF, 'ZR': 0x94E0E0, 'NB': 0x73C2C9, 'MO': 0x54B5B5, 'TC': 0x3B9E9E, 'RU': 0x248F8F, 'RH': 0x0A7D8C, 'PD': 0x006985, 'AG': 0xC0C0C0, 'CD': 0xFFD98F, 'IN': 0xA67573, 'SN': 0x668080, 'SB': 0x9E63B5, 'TE': 0xD47A00, 'I': 0x940094, 'XE': 0x940094, 'CS': 0x57178F, 'BA': 0x00C900, 'LA': 0x70D4FF, 'CE': 0xFFFFC7, 'PR': 0xD9FFC7, 'ND': 0xC7FFC7, 'PM': 0xA3FFC7, 'SM': 0x8FFFC7, 'EU': 0x61FFC7, 'GD': 0x45FFC7, 'TB': 0x30FFC7, 'DY': 0x1FFFC7, 'HO': 0x00FF9C, 'ER': 0x00E675, 'TM': 0x00D452, 'YB': 0x00BF38, 'LU': 0x00AB24, 'HF': 0x4DC2FF, 'TA': 0x4DA6FF, 'W': 0x2194D6, 'RE': 0x267DAB, 'OS': 0x266696, 'IR': 0x175487, 'PT': 0xD0D0E0, 'AU': 0xFFD123, 'HG': 0xB8B8D0, 'TL': 0xA6544D, 'PB': 0x575961, 'BI': 0x9E4FB5, 'PO': 0xAB5C00, 'AT': 0x754F45, 'RN': 0x428296, 'FR': 0x420066, 'RA': 0x007D00, 'AC': 0x70ABFA, 'TH': 0x00BAFF, 'PA': 0x00A1FF, 'U': 0x008FFF, 'NP': 0x0080FF, 'PU': 0x006BFF, 'AM': 0x545CF2, 'CM': 0x785CE3, 'BK': 0x8A4FE3, 'CF': 0xA136D4, 'ES': 0xB31FD4, 'FM': 0xB31FBA, 'MD': 0xB30DA6, 'NO': 0xBD0D87, 'LR': 0xC70066, 'RF': 0xCC0059, 'DB': 0xD1004F, 'SG': 0xD90045, 'BH': 0xE00038, 'HS': 0xE6002E, 'MT': 0xEB0026, 'DS': 0xFFFFFF, 'RG': 0xFFFFFF, 'CN': 0xFFFFFF, 'UUT': 0xFFFFFF, 'FL': 0xFFFFFF, 'UUP': 0xFFFFFF, 'LV': 0xFFFFFF, 'UUH': 0xFFFFFF
 });
 var DefaultElementSymbolColor = Color(0xFFFFFF);
 var Description = 'Assigns a color to every atom according to its chemical element.';
-// TODO generalise `carbonColor` param to all themes?
 export var ElementSymbolColorThemeParams = {
     carbonColor: PD.MappedStatic('chain-id', {
-        'chain-id': PD.Group(__assign({}, ChainIdColorThemeParams)),
-        'operator-name': PD.Group(__assign({}, OperatorNameColorThemeParams)),
-        'element-symbol': PD.Group({})
+        'chain-id': PD.Group(ChainIdColorThemeParams),
+        'entity-id': PD.Group(EntityIdColorThemeParams),
+        'entity-source': PD.Group(EntitySourceColorThemeParams),
+        'operator-name': PD.Group(OperatorNameColorThemeParams),
+        'element-symbol': PD.EmptyGroup()
     }, { 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
@@ -35,12 +43,14 @@ export function elementSymbolColor(colorMap, element) {
     return c === undefined ? DefaultElementSymbolColor : c;
 }
 export function ElementSymbolColorTheme(ctx, props) {
-    var colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
-    var carbonColor = props.carbonColor.name === 'chain-id'
-        ? ChainIdColorTheme(ctx, props.carbonColor.params).color
-        : props.carbonColor.name === 'operator-name'
-            ? OperatorNameColorTheme(ctx, props.carbonColor.params).color
-            : undefined;
+    var colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
+    var pcc = props.carbonColor;
+    var carbonColor = pcc.name === 'chain-id' ? ChainIdColorTheme(ctx, pcc.params).color :
+        pcc.name === 'entity-id' ? EntityIdColorTheme(ctx, pcc.params).color :
+            pcc.name === 'entity-source' ? EntitySourceColorTheme(ctx, pcc.params).color :
+                pcc.name === 'operator-name' ? OperatorNameColorTheme(ctx, pcc.params).color :
+                    pcc.name === 'element-symbol' ? undefined :
+                        assertUnreachable(pcc);
     function elementColor(element, location) {
         return (carbonColor && element === 'C')
             ? carbonColor(location, false)
@@ -70,8 +80,8 @@ 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 +28,33 @@ function getEntityIdSerialMap(structure) {
             if (!map.has(k))
                 map.set(k, map.size);
         }
+        var coarseHierarchy = structure.models[i].coarseHierarchy;
+        if (coarseHierarchy.isDefined) {
+            var spheres_entity_id = 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 = 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 +68,17 @@ 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<{
+        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">;
 };
 export declare type IllustrativeColorThemeParams = typeof IllustrativeColorThemeParams;
 export declare function getIllustrativeColorThemeParams(ctx: ThemeDataContext): {
+    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">;
 };
 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]]))
     };
 }

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>;