From 44b8f5c19dc97b70ac6cfa6769d9f1a26c60229a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 18 Sep 2018 09:37:23 -0700
Subject: [PATCH] added molecule-type color scheme
---
src/mol-view/theme/color.ts | 3 ++
src/mol-view/theme/color/molecule-type.ts | 59 +++++++++++++++++++++++
2 files changed, 62 insertions(+)
create mode 100644 src/mol-view/theme/color/molecule-type.ts
diff --git a/src/mol-view/theme/color.ts b/src/mol-view/theme/color.ts
index 6f0cecf67..a9ca94485 100644
--- a/src/mol-view/theme/color.ts
+++ b/src/mol-view/theme/color.ts
@@ -21,6 +21,7 @@ import { CustomColorTheme } from './color/custom';
import { ResidueNameColorTheme } from './color/residue-name';
import { SequenceIdColorTheme } from './color/sequence-id';
import { SecondaryStructureColorTheme } from './color/secondary-structure';
+import { MoleculeTypeColorTheme } from './color/molecule-type';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -57,6 +58,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
case 'custom': return CustomColorTheme(props)
case 'element-index': return ElementIndexColorTheme(props)
case 'element-symbol': return ElementSymbolColorTheme(props)
+ case 'molecule-type': return MoleculeTypeColorTheme(props)
case 'residue-name': return ResidueNameColorTheme(props)
case 'secondary-structure': return SecondaryStructureColorTheme(props)
case 'sequence-id': return SequenceIdColorTheme(props)
@@ -84,6 +86,7 @@ export const ColorThemeInfo = {
'custom': {},
'element-index': {},
'element-symbol': {},
+ 'molecule-type': {},
'residue-name': {},
'secondary-structure': {},
'sequence-id': {},
diff --git a/src/mol-view/theme/color/molecule-type.ts b/src/mol-view/theme/color/molecule-type.ts
new file mode 100644
index 000000000..f2be520fe
--- /dev/null
+++ b/src/mol-view/theme/color/molecule-type.ts
@@ -0,0 +1,59 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Color, ColorMap } from 'mol-util/color';
+import { StructureElement, Unit, Link, ElementIndex } from 'mol-model/structure';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps, ColorTheme, TableLegend } from '../color';
+import { MoleculeType } from 'mol-model/structure/model/types';
+import { getElementMoleculeType } from 'mol-model/structure/util';
+
+const MoleculeTypeColors = ColorMap({
+ water: 0x386cb0,
+ ion: 0xf0027f,
+ protein: 0xbeaed4,
+ RNA: 0xfdc086,
+ DNA: 0xbf5b17,
+ PNA: 0x42A49A,
+ saccharide: 0x7fc97f,
+})
+
+const DefaultMoleculeTypeColor = Color(0xffff99)
+const Description = 'Assigns a color based on the molecule type of a residue.'
+
+export function moleculeTypeColor(unit: Unit, element: ElementIndex): Color {
+ const moleculeType = getElementMoleculeType(unit, element)
+ switch (moleculeType) {
+ case MoleculeType.water: return MoleculeTypeColors.water
+ case MoleculeType.ion: return MoleculeTypeColors.ion
+ case MoleculeType.protein: return MoleculeTypeColors.protein
+ case MoleculeType.RNA: return MoleculeTypeColors.RNA
+ case MoleculeType.DNA: return MoleculeTypeColors.DNA
+ case MoleculeType.PNA: return MoleculeTypeColors.PNA
+ case MoleculeType.saccharide: return MoleculeTypeColors.saccharide
+ }
+ return DefaultMoleculeTypeColor
+}
+
+export function MoleculeTypeColorTheme(props: ColorThemeProps): ColorTheme {
+ function color(location: Location): Color {
+ if (StructureElement.isLocation(location)) {
+ return moleculeTypeColor(location.unit, location.element)
+ } else if (Link.isLocation(location)) {
+ return moleculeTypeColor(location.aUnit, location.aUnit.elements[location.aIndex])
+ }
+ return DefaultMoleculeTypeColor
+ }
+
+ return {
+ granularity: 'group',
+ color,
+ description: Description,
+ legend: TableLegend(Object.keys(MoleculeTypeColors).map(name => {
+ return [name, (MoleculeTypeColors as any)[name] as Color] as [string, Color]
+ }).concat([[ 'Other/unknown', DefaultMoleculeTypeColor ]]))
+ }
+}
\ No newline at end of file
--
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