From 32e2552c082a8b8126b1ef171d0fea8be63a6a39 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 15 Aug 2018 17:57:20 -0700
Subject: [PATCH] rudimentary cross-link color scheme
---
src/mol-view/stage.ts | 2 +-
src/mol-view/theme/color.ts | 5 ++-
src/mol-view/theme/color/cross-link.ts | 48 ++++++++++++++++++++++++++
3 files changed, 53 insertions(+), 2 deletions(-)
create mode 100644 src/mol-view/theme/color/cross-link.ts
diff --git a/src/mol-view/stage.ts b/src/mol-view/stage.ts
index e13d439a5..910b8b39b 100644
--- a/src/mol-view/stage.ts
+++ b/src/mol-view/stage.ts
@@ -36,7 +36,7 @@ const ballAndStickProps: Partial<BallAndStickProps> = {
const distanceRestraintProps: Partial<DistanceRestraintProps> = {
doubleSided: true,
- colorTheme: { name: 'chain-id' },
+ colorTheme: { name: 'cross-link' },
sizeTheme: { name: 'uniform', value: 0.6 },
quality: 'auto',
useFog: false
diff --git a/src/mol-view/theme/color.ts b/src/mol-view/theme/color.ts
index f7ef557a5..ba8fec56a 100644
--- a/src/mol-view/theme/color.ts
+++ b/src/mol-view/theme/color.ts
@@ -14,6 +14,7 @@ import { ChainIdColorTheme } from './color/chain-id';
import { ElementSymbolColorTheme } from './color/element-symbol';
import { UnitIndexColorTheme } from './color/unit-index';
import { UniformColorTheme } from './color/uniform';
+import { CrossLinkColorTheme } from './color/cross-link';
export interface ColorTheme {
kind: ColorType
@@ -24,6 +25,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
switch (props.name) {
case 'element-index': return ElementIndexColorTheme(props)
case 'carbohydrate-symbol': return CarbohydrateSymbolColorTheme(props)
+ case 'cross-link': return CrossLinkColorTheme(props)
case 'chain-id': return ChainIdColorTheme(props)
case 'element-symbol': return ElementSymbolColorTheme(props)
case 'unit-index': return UnitIndexColorTheme(props)
@@ -32,7 +34,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
}
export interface ColorThemeProps {
- name: 'element-index' | 'chain-id'| 'unit-index' | 'uniform' | 'carbohydrate-symbol' | 'element-symbol'
+ name: ColorThemeName
domain?: [number, number]
value?: Color
structure?: Structure
@@ -41,6 +43,7 @@ export interface ColorThemeProps {
export const ColorThemeInfo = {
'element-index': {},
'carbohydrate-symbol': {},
+ 'cross-link': {},
'chain-id': {},
'element-symbol': {},
'unit-index': {},
diff --git a/src/mol-view/theme/color/cross-link.ts b/src/mol-view/theme/color/cross-link.ts
new file mode 100644
index 000000000..891b14eb3
--- /dev/null
+++ b/src/mol-view/theme/color/cross-link.ts
@@ -0,0 +1,48 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Link } from 'mol-model/structure';
+
+import { Color, ColorScale, ColorBrewer } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps, ColorTheme } from '../color';
+import { LocationColor } from 'mol-geo/util/color-data';
+import { Vec3 } from 'mol-math/linear-algebra';
+
+const DefaultColor = 0xCCCCCC;
+
+const distVecA = Vec3.zero(), distVecB = Vec3.zero()
+function linkDistance(link: Link.Location) {
+ link.aUnit.conformation.position(link.aIndex, distVecA)
+ link.bUnit.conformation.position(link.bIndex, distVecB)
+ return Vec3.distance(distVecA, distVecB)
+}
+
+export function CrossLinkColorTheme(props: ColorThemeProps): ColorTheme {
+ let colorFn: LocationColor
+
+ if (props.structure) {
+ const crosslinks = props.structure.crossLinkRestraints
+ const scale = ColorScale.create({ domain: [ -10, 10 ], colors: ColorBrewer.RdYlBu })
+
+ colorFn = (location: Location): Color => {
+ if (Link.isLocation(location)) {
+ const pairs = crosslinks.getPairs(location.aIndex, location.aUnit, location.bIndex, location.bUnit)
+ if (pairs) {
+ return scale.color(linkDistance(location) - pairs[0].distanceThreshold)
+ }
+ }
+ return DefaultColor
+ }
+ } else {
+ colorFn = () => DefaultColor
+ }
+
+ return {
+ kind: 'element',
+ color: colorFn
+ }
+}
\ No newline at end of file
--
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