From 0e040d77446b232130cd84b2438d67278d82e8b8 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 10 Sep 2019 15:31:57 -0700
Subject: [PATCH] added occupancy color theme
---
src/mol-theme/color.ts | 2 +
src/mol-theme/color/occupancy.ts | 67 ++++++++++++++++++++++++++++++++
2 files changed, 69 insertions(+)
create mode 100644 src/mol-theme/color/occupancy.ts
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 29ea80857..18edc8457 100644
--- a/src/mol-theme/color.ts
+++ b/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,
diff --git a/src/mol-theme/color/occupancy.ts b/src/mol-theme/color/occupancy.ts
new file mode 100644
index 000000000..3f315c5c2
--- /dev/null
+++ b/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
+}
\ No newline at end of file
--
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