added occupancy color theme

src/mol-theme/color.ts

@@ -31,6 +31,7 @@ import { EntitySourceColorThemeProvider } from './color/entity-source';
 import { IllustrativeColorThemeProvider } from './color/illustrative';
 import { HydrophobicityColorThemeProvider } from './color/hydrophobicity';
 import { ModelIndexColorThemeProvider } from './color/model-index';
+import { OccupancyColorThemeProvider } from './color/occupancy';
 
 export type LocationColor = (location: Location, isSecondary: boolean) => Color
 
@@ -82,6 +83,7 @@ export const BuiltInColorThemes = {
     'illustrative': IllustrativeColorThemeProvider,
     'model-index': ModelIndexColorThemeProvider,
     'molecule-type': MoleculeTypeColorThemeProvider,
+    'occupancy': OccupancyColorThemeProvider,
     'polymer-id': PolymerIdColorThemeProvider,
     'polymer-index': PolymerIndexColorThemeProvider,
     'residue-name': ResidueNameColorThemeProvider,

src/mol-theme/color/occupancy.ts

@@ -0,0 +1,67 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Color, ColorScale } from '../../mol-util/color';
+import { StructureElement, Unit, Link, ElementIndex } from '../../mol-model/structure';
+import { Location } from '../../mol-model/location';
+import { ColorTheme } from '../color';
+import { ParamDefinition as PD } from '../../mol-util/param-definition'
+import { ThemeDataContext } from '../theme';
+import { ColorListName, ColorListOptionsScale } from '../../mol-util/color/lists';
+
+const DefaultOccupancyColor = Color(0xCCCCCC)
+const Description = `Assigns a color based on the occupancy of an atom.`
+
+export const OccupancyColorThemeParams = {
+    domain: PD.Interval([0, 1]),
+    list: PD.ColorList<ColorListName>('purples', ColorListOptionsScale),
+}
+export type OccupancyColorThemeParams = typeof OccupancyColorThemeParams
+export function getOccupancyColorThemeParams(ctx: ThemeDataContext) {
+    return OccupancyColorThemeParams // TODO return copy
+}
+
+export function getOccupancy(unit: Unit, element: ElementIndex): number {
+    if (Unit.isAtomic(unit)) {
+        return unit.model.atomicConformation.occupancy.value(element)
+    } else {
+        return 0
+    }
+}
+
+export function OccupancyColorTheme(ctx: ThemeDataContext, props: PD.Values<OccupancyColorThemeParams>): ColorTheme<OccupancyColorThemeParams> {
+    const scale = ColorScale.create({
+        reverse: false,
+        domain: props.domain,
+        listOrName: props.list,
+    })
+
+    function color(location: Location): Color {
+        if (StructureElement.Location.is(location)) {
+            return scale.color(getOccupancy(location.unit, location.element))
+        } else if (Link.isLocation(location)) {
+            return scale.color(getOccupancy(location.aUnit, location.aUnit.elements[location.aIndex]))
+        }
+        return DefaultOccupancyColor
+    }
+
+    return {
+        factory: OccupancyColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        description: Description,
+        legend: scale ? scale.legend : undefined
+    }
+}
+
+export const OccupancyColorThemeProvider: ColorTheme.Provider<OccupancyColorThemeParams> = {
+    label: 'Occupancy',
+    factory: OccupancyColorTheme,
+    getParams: getOccupancyColorThemeParams,
+    defaultValues: PD.getDefaultValues(OccupancyColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}