From d7cc97d4cb2c88f9a73de0454797a4dd247d01cd Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Mon, 23 Apr 2018 11:44:02 -0700
Subject: [PATCH] wip, coloring
---
src/apps/render-test/state.ts | 8 +--
src/mol-geo/representation/structure/point.ts | 2 +-
.../representation/structure/spacefill.ts | 2 +-
src/mol-geo/representation/structure/utils.ts | 30 ++++-------
src/mol-geo/theme/index.ts | 2 +-
.../theme/structure/color/atom-index.ts | 24 +++++++++
src/mol-geo/theme/structure/color/chain-id.ts | 51 +++++++++++++++++++
.../color/{element.ts => element-symbol.ts} | 0
src/mol-geo/theme/structure/color/index.ts | 7 ++-
.../theme/structure/color/instance-index.ts | 21 ++++++++
src/mol-geo/theme/structure/size/index.ts | 4 +-
11 files changed, 123 insertions(+), 28 deletions(-)
create mode 100644 src/mol-geo/theme/structure/color/atom-index.ts
create mode 100644 src/mol-geo/theme/structure/color/chain-id.ts
rename src/mol-geo/theme/structure/color/{element.ts => element-symbol.ts} (100%)
create mode 100644 src/mol-geo/theme/structure/color/instance-index.ts
diff --git a/src/apps/render-test/state.ts b/src/apps/render-test/state.ts
index 212a941cb..e7cb9fab2 100644
--- a/src/apps/render-test/state.ts
+++ b/src/apps/render-test/state.ts
@@ -49,7 +49,8 @@ export default class State {
const structPointRepr = StructureRepresentation(Point)
const pointProps: PointProps = {
- colorTheme: { name: 'uniform', value: 0xFF4411 },
+ // colorTheme: { name: 'uniform', value: 0xFF4411 },
+ colorTheme: { name: 'chain-id' },
sizeTheme: { name: 'uniform', value: 0.1 }
}
await Run(structPointRepr.create(struct, pointProps), log, 100)
@@ -59,9 +60,10 @@ export default class State {
const spacefillProps: SpacefillProps = {
detail: 1,
// colorTheme: { name: 'uniform', value: 0xFF4411 },
- // colorTheme: { name: 'instance-id' },
+ // colorTheme: { name: 'instance-index' },
// colorTheme: { name: 'element-symbol' },
- colorTheme: { name: 'atom-id' },
+ // colorTheme: { name: 'atom-index' },
+ colorTheme: { name: 'chain-id' },
}
await Run(structSpacefillRepr.create(struct, spacefillProps), log, 100)
structSpacefillRepr.renderObjects.forEach(viewer.add)
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index 0555750a0..8735c23d8 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -19,7 +19,7 @@ import { ColorTheme, SizeTheme } from '../../theme';
import { createTransforms, createColors, createSizes } from './utils';
export const DefaultPointProps = {
- colorTheme: { name: 'instance-id' } as ColorTheme,
+ colorTheme: { name: 'instance-index' } as ColorTheme,
sizeTheme: { name: 'vdw' } as SizeTheme
}
export type PointProps = Partial<typeof DefaultPointProps>
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 2cdc6d5e8..5778ecee6 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -21,7 +21,7 @@ import VertexMap from '../../shape/vertex-map';
export const DefaultSpacefillProps = {
detail: 0,
- colorTheme: { name: 'instance-id' } as ColorTheme,
+ colorTheme: { name: 'instance-index' } as ColorTheme,
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index a0eb47202..a7a1d1587 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -7,14 +7,12 @@
import { Unit, ElementGroup } from 'mol-model/structure';
import { Mat4 } from 'mol-math/linear-algebra'
-import { ColorScale } from 'mol-util/color';
-import { createUniformColor, createInstanceColor, createElementInstanceColor } from '../../util/color-data';
+import { createUniformColor } from '../../util/color-data';
import { createUniformSize } from '../../util/size-data';
import { vdwSizeData } from '../../theme/structure/size/vdw';
import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
-import { elementSymbolColorData } from '../../theme/structure/color/element';
-import { OrderedSet } from 'mol-data/int';
+import { atomIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
export function createTransforms(units: ReadonlyArray<Unit>) {
const unitCount = units.length
@@ -26,25 +24,17 @@ export function createTransforms(units: ReadonlyArray<Unit>) {
}
export function createColors(units: ReadonlyArray<Unit>, elementGroup: ElementGroup, vertexMap: VertexMap, props: ColorTheme) {
- const instanceCount = units.length
- const elementCount = OrderedSet.size(elementGroup.elements)
switch (props.name) {
- case 'uniform':
- return createUniformColor(props)
- case 'instance-id':
- const instanceDomain = props.domain ? props.domain : [ 0, instanceCount - 1 ]
- const instanceScale = ColorScale.create({ domain: instanceDomain })
- return createInstanceColor({ colorFn: instanceScale.color, instanceCount })
- case 'atom-id':
- const atomDomain = props.domain ? props.domain : [ 0, instanceCount * elementCount - 1 ]
- const atomScale = ColorScale.create({ domain: atomDomain })
- return createElementInstanceColor({
- colorFn: (unitIdx, elementIdx) => atomScale.color(unitIdx * elementCount + elementIdx),
- instanceCount,
- vertexMap
- })
+ case 'atom-index':
+ return atomIndexColorData({ units, elementGroup, vertexMap })
+ case 'chain-id':
+ return chainIdColorData({ units, elementGroup, vertexMap })
case 'element-symbol':
return elementSymbolColorData({ units, elementGroup, vertexMap })
+ case 'instance-index':
+ return instanceIndexColorData({ units, elementGroup, vertexMap })
+ case 'uniform':
+ return createUniformColor(props)
}
}
diff --git a/src/mol-geo/theme/index.ts b/src/mol-geo/theme/index.ts
index 70eaa22d9..452ff76ed 100644
--- a/src/mol-geo/theme/index.ts
+++ b/src/mol-geo/theme/index.ts
@@ -12,7 +12,7 @@ export interface UniformColorTheme {
}
export interface ScaleColorTheme {
- name: 'instance-id' | 'element-symbol' | 'atom-id'
+ name: 'atom-index' | 'chain-id' | 'element-symbol' | 'instance-index'
domain?: [number, number]
}
diff --git a/src/mol-geo/theme/structure/color/atom-index.ts b/src/mol-geo/theme/structure/color/atom-index.ts
new file mode 100644
index 000000000..1bd61c99a
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/atom-index.ts
@@ -0,0 +1,24 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorScale } from 'mol-util/color';
+import { StructureColorDataProps } from '.';
+import { OrderedSet } from 'mol-data/int';
+import { createElementInstanceColor } from '../../../util/color-data';
+
+export function atomIndexColorData(props: StructureColorDataProps) {
+ const { units, elementGroup, vertexMap } = props
+ const instanceCount = units.length
+ const elementCount = OrderedSet.size(elementGroup.elements)
+
+ const domain = [ 0, instanceCount * elementCount - 1 ]
+ const scale = ColorScale.create({ domain })
+ return createElementInstanceColor({
+ colorFn: (instanceIdx, elementIdx) => scale.color(instanceIdx * elementCount + elementIdx),
+ instanceCount,
+ vertexMap
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
new file mode 100644
index 000000000..a6bd36b1a
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -0,0 +1,51 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ElementGroup, Model } from 'mol-model/structure';
+
+import { StructureColorDataProps } from '.';
+import { createAttributeOrElementColor } from '../../../util/color-data';
+import { ColorScale } from 'mol-util/color';
+
+function createChainIdMap(model: Model) {
+ const { chains } = model.hierarchy
+ const { label_asym_id } = chains
+
+ const map = new Map<string, number>()
+ let index = 0
+
+ for (let i = 0, il = chains._rowCount; i < il; ++i) {
+ const chainId = label_asym_id.value(i)
+ if (map.get(chainId) === undefined) {
+ map.set(chainId, index)
+ index += 1
+ }
+ }
+ return { map, count: index }
+}
+
+export function chainIdColorData(props: StructureColorDataProps) {
+ const { units, elementGroup, vertexMap } = props
+ const unit = units[0]
+
+ const { chains, chainSegments } = unit.model.hierarchy
+ const { label_asym_id } = chains
+ const { map, count } = createChainIdMap(unit.model)
+
+ const domain = [ 0, count - 1 ]
+ const scale = ColorScale.create({ domain })
+
+ return createAttributeOrElementColor(vertexMap, {
+ colorFn: (elementIdx: number) => {
+ const aI = ElementGroup.getAt(elementGroup, elementIdx);
+ const cI = chainSegments.segmentMap[aI]
+ const chainId = label_asym_id.value(cI)
+
+ return scale.color(map.get(chainId) || 0)
+ },
+ vertexMap
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
similarity index 100%
rename from src/mol-geo/theme/structure/color/element.ts
rename to src/mol-geo/theme/structure/color/element-symbol.ts
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 35b994ba9..435874109 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -11,4 +11,9 @@ export interface StructureColorDataProps {
units: ReadonlyArray<Unit>,
elementGroup: ElementGroup,
vertexMap: VertexMap
-}
\ No newline at end of file
+}
+
+export { atomIndexColorData } from './atom-index'
+export { chainIdColorData } from './chain-id'
+export { elementSymbolColorData } from './element-symbol'
+export { instanceIndexColorData } from './instance-index'
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/instance-index.ts b/src/mol-geo/theme/structure/color/instance-index.ts
new file mode 100644
index 000000000..bd7d6f577
--- /dev/null
+++ b/src/mol-geo/theme/structure/color/instance-index.ts
@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ColorScale } from 'mol-util/color';
+import { StructureColorDataProps } from '.';
+import { createInstanceColor } from '../../../util/color-data';
+
+export function instanceIndexColorData(props: StructureColorDataProps) {
+ const { units } = props
+ const instanceCount = units.length
+
+ const domain = [ 0, instanceCount - 1 ]
+ const scale = ColorScale.create({ domain })
+ return createInstanceColor({
+ colorFn: scale.color,
+ instanceCount
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/index.ts b/src/mol-geo/theme/structure/size/index.ts
index 775c3c0d7..b178ad42b 100644
--- a/src/mol-geo/theme/structure/size/index.ts
+++ b/src/mol-geo/theme/structure/size/index.ts
@@ -11,4 +11,6 @@ export interface StructureSizeDataProps {
units: ReadonlyArray<Unit>,
elementGroup: ElementGroup,
vertexMap: VertexMap
-}
\ No newline at end of file
+}
+
+export { vdwSizeData } from './vdw'
\ No newline at end of file
--
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