From a283e690bcd83029b57c07978eecca0c517d083f Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Tue, 19 Jun 2018 11:20:08 -0700
Subject: [PATCH] wip, link repr coloring
---
src/mol-geo/representation/structure/utils.ts | 24 +++++--
.../structure/visual/element-point.ts | 2 +-
.../structure/visual/element-sphere.ts | 11 +--
.../visual/intra-unit-link-cylinder.ts | 9 ++-
src/mol-geo/theme/structure/color/chain-id.ts | 72 +++++++++++++++++--
.../theme/structure/color/element-index.ts | 5 +-
.../theme/structure/color/element-symbol.ts | 8 +--
src/mol-geo/theme/structure/color/index.ts | 5 +-
src/mol-geo/util/color-data.ts | 15 ++--
9 files changed, 103 insertions(+), 48 deletions(-)
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index f49793aa3..17aae12e0 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -13,7 +13,7 @@ import { createUniformSize, SizeData } from '../../util/size-data';
import { physicalSizeData, getPhysicalRadius } from '../../theme/structure/size/physical';
import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
-import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
+import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdElementColorData } from '../../theme/structure/color';
import { ValueCell, defaults } from 'mol-util';
import { Mesh } from '../../shape/mesh';
import { RuntimeContext } from 'mol-task';
@@ -34,21 +34,33 @@ export function createTransforms({ units }: Unit.SymmetryGroup, transforms?: Val
return transforms ? ValueCell.update(transforms, array) : ValueCell.create(array)
}
-export function createColors(group: Unit.SymmetryGroup, vertexMap: VertexMap, props: ColorTheme, colorData?: ColorData) {
+export function createColors(group: Unit.SymmetryGroup, elementCount: number, props: ColorTheme, colorData?: ColorData) {
switch (props.name) {
case 'atom-index':
- return elementIndexColorData({ group, vertexMap }, colorData)
+ return elementIndexColorData({ group, elementCount }, colorData)
case 'chain-id':
- return chainIdColorData({ group, vertexMap }, colorData)
+ return chainIdElementColorData({ group, elementCount }, colorData)
case 'element-symbol':
- return elementSymbolColorData({ group, vertexMap }, colorData)
+ return elementSymbolColorData({ group, elementCount }, colorData)
case 'instance-index':
- return instanceIndexColorData({ group, vertexMap }, colorData)
+ return instanceIndexColorData({ group, elementCount }, colorData)
case 'uniform':
return createUniformColor(props, colorData)
}
}
+// export function createLinkColors(group: Unit.SymmetryGroup, props: ColorTheme, colorData?: ColorData): ColorData {
+// switch (props.name) {
+// case 'atom-index':
+// case 'chain-id':
+// case 'element-symbol':
+// case 'instance-index':
+// return chainIdLinkColorData({ group, vertexMap }, colorData)
+// case 'uniform':
+// return createUniformColor(props, colorData)
+// }
+// }
+
export function createSizes(group: Unit.SymmetryGroup, vertexMap: VertexMap, props: SizeTheme): SizeData {
switch (props.name) {
case 'uniform':
diff --git a/src/mol-geo/representation/structure/visual/element-point.ts b/src/mol-geo/representation/structure/visual/element-point.ts
index bca8c3e37..2f487719c 100644
--- a/src/mol-geo/representation/structure/visual/element-point.ts
+++ b/src/mol-geo/representation/structure/visual/element-point.ts
@@ -85,7 +85,7 @@ export default function PointVisual(): UnitsVisual<PointProps> {
const transforms = createTransforms(group)
if (ctx.shouldUpdate) await ctx.update('Computing point colors');
- const color = createColors(group, vertexMap, colorTheme)
+ const color = createColors(group, elementCount, colorTheme)
if (ctx.shouldUpdate) await ctx.update('Computing point sizes');
const size = createSizes(group, vertexMap, sizeTheme)
diff --git a/src/mol-geo/representation/structure/visual/element-sphere.ts b/src/mol-geo/representation/structure/visual/element-sphere.ts
index 78ced5e32..d3b059276 100644
--- a/src/mol-geo/representation/structure/visual/element-sphere.ts
+++ b/src/mol-geo/representation/structure/visual/element-sphere.ts
@@ -12,7 +12,6 @@ import { Unit, Element } from 'mol-model/structure';
import { DefaultStructureProps, UnitsVisual } from '../index';
import { RuntimeContext } from 'mol-task'
import { createTransforms, createColors, createElementSphereMesh, markElement, getElementRadius } from '../utils';
-import VertexMap from '../../../shape/vertex-map';
import { deepEqual, defaults } from 'mol-util';
import { fillSerial } from 'mol-gl/renderable/util';
import { RenderableState, MeshValues } from 'mol-gl/renderable';
@@ -39,7 +38,6 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
let currentProps: typeof DefaultElementSphereProps
let mesh: Mesh
let currentGroup: Unit.SymmetryGroup
- let vertexMap: VertexMap
return {
renderObjects,
@@ -56,14 +54,12 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
const radius = getElementRadius(unit, sizeTheme)
mesh = await createElementSphereMesh(ctx, unit, radius, detail, mesh)
- // console.log(mesh)
- vertexMap = VertexMap.fromMesh(mesh)
if (ctx.shouldUpdate) await ctx.update('Computing spacefill transforms');
const transforms = createTransforms(group)
if (ctx.shouldUpdate) await ctx.update('Computing spacefill colors');
- const color = createColors(group, vertexMap, colorTheme)
+ const color = createColors(group, elementCount, colorTheme)
if (ctx.shouldUpdate) await ctx.update('Computing spacefill marks');
const marker = createMarkers(instanceCount * elementCount)
@@ -109,8 +105,6 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
const radius = getElementRadius(unit, newProps.sizeTheme)
mesh = await createElementSphereMesh(ctx, unit, radius, newProps.detail, mesh)
ValueCell.update(spheres.values.drawCount, mesh.triangleCount * 3)
- // TODO update in-place
- vertexMap = VertexMap.fromMesh(mesh)
updateColor = true
}
@@ -119,8 +113,9 @@ export function ElementSphereVisual(): UnitsVisual<ElementSphereProps> {
}
if (updateColor) {
+ const elementCount = currentGroup.elements.length
if (ctx.shouldUpdate) await ctx.update('Computing spacefill colors');
- createColors(currentGroup, vertexMap, newProps.colorTheme, spheres.values)
+ createColors(currentGroup, elementCount, newProps.colorTheme, spheres.values)
}
ValueCell.updateIfChanged(spheres.values.uAlpha, newProps.alpha)
diff --git a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
index 983840d79..4d221dfbc 100644
--- a/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
+++ b/src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts
@@ -21,11 +21,12 @@ import { Mesh } from '../../../shape/mesh';
import { PickingId } from '../../../util/picking';
import { MeshBuilder } from '../../../shape/mesh-builder';
import { Vec3, Mat4 } from 'mol-math/linear-algebra';
-import { createUniformColor } from '../../../util/color-data';
+// import { createUniformColor } from '../../../util/color-data';
import { defaults } from 'mol-util';
import { Loci, isEveryLoci, EmptyLoci } from 'mol-model/loci';
import { MarkerAction, applyMarkerAction, createMarkers, MarkerData } from '../../../util/marker-data';
import { SizeTheme } from '../../../theme';
+import { chainIdLinkColorData } from '../../../theme/structure/color/chain-id';
async function createLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, mesh?: Mesh) {
if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)
@@ -102,14 +103,12 @@ export function IntraUnitLinkVisual(): UnitsVisual<IntraUnitLinkProps> {
mesh = await createLinkCylinderMesh(ctx, unit)
- // console.log(mesh)
- // vertexMap = VertexMap.fromMesh(mesh)
-
if (ctx.shouldUpdate) await ctx.update('Computing link transforms');
const transforms = createTransforms(group)
if (ctx.shouldUpdate) await ctx.update('Computing link colors');
- const color = createUniformColor({ value: 0xFF0000 })
+ // const color = createUniformColor({ value: 0xFF0000 })
+ const color = chainIdLinkColorData({ group, elementCount })
if (ctx.shouldUpdate) await ctx.update('Computing link marks');
const marker = createMarkers(instanceCount * elementCount)
diff --git a/src/mol-geo/theme/structure/color/chain-id.ts b/src/mol-geo/theme/structure/color/chain-id.ts
index b6de2bc05..4c4b9687f 100644
--- a/src/mol-geo/theme/structure/color/chain-id.ts
+++ b/src/mol-geo/theme/structure/color/chain-id.ts
@@ -7,7 +7,7 @@
import { Unit, Queries, Element } from 'mol-model/structure';
import { StructureColorDataProps } from '.';
-import { createAttributeOrElementColor, ColorData } from '../../../util/color-data';
+import { ColorData, createElementColor } from '../../../util/color-data';
import { ColorScale } from 'mol-util/color';
import { Column } from 'mol-data/db';
@@ -38,8 +38,8 @@ function createChainIdMap(unit: Unit) {
return { map, count: index }
}
-export function chainIdColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units, elements }, vertexMap } = props
+export function chainIdColorData(props: StructureColorDataProps, locationFn: (l: Element.Location, renderElementIdx: number) => void, colorData?: ColorData) {
+ const { group: { units }, elementCount } = props
const unit = units[0]
const { map, count } = createChainIdMap(unit)
@@ -52,16 +52,74 @@ export function chainIdColorData(props: StructureColorDataProps, colorData?: Col
asym_id = Queries.props.chain.label_asym_id
} else if (Unit.isCoarse(unit)) {
asym_id = Queries.props.coarse.asym_id
+ } else {
+ throw new Error('unhandled unit kind')
}
const l = Element.Location()
l.unit = unit
- return createAttributeOrElementColor(vertexMap, {
- colorFn: (elementIdx: number) => {
- l.element = elements[elementIdx]
+ // return createAttributeOrElementColor(vertexMap, {
+ // colorFn: (renderElementIdx: number) => {
+ // locationFn(l, renderElementIdx)
+ // console.log(l.element, asym_id(l))
+ // return scale.color(map.get(asym_id(l)) || 0)
+ // },
+ // vertexMap
+ // }, colorData)
+ return createElementColor({
+ colorFn: (renderElementIdx: number) => {
+ locationFn(l, renderElementIdx)
return scale.color(map.get(asym_id(l)) || 0)
},
- vertexMap
+ elementCount
}, colorData)
+}
+
+export function chainIdElementColorData(props: StructureColorDataProps, colorData?: ColorData) {
+ const elements = props.group.units[0].elements
+ function locationFn(l: Element.Location, renderElementIdx: number) {
+ l.element = elements[renderElementIdx]
+ }
+ return chainIdColorData(props, locationFn, colorData)
+ // const { group: { units, elements }, vertexMap } = props
+ // const unit = units[0]
+
+ // const { map, count } = createChainIdMap(unit)
+
+ // const domain = [ 0, count - 1 ]
+ // const scale = ColorScale.create({ domain })
+
+ // let asym_id: Element.Property<string>
+ // if (Unit.isAtomic(unit)) {
+ // asym_id = Queries.props.chain.label_asym_id
+ // } else if (Unit.isCoarse(unit)) {
+ // asym_id = Queries.props.coarse.asym_id
+ // }
+
+ // const l = Element.Location()
+ // l.unit = unit
+
+ // return createAttributeOrElementColor(vertexMap, {
+ // colorFn: (elementIdx: number) => {
+ // l.element = elements[elementIdx]
+ // return scale.color(map.get(asym_id(l)) || 0)
+ // },
+ // vertexMap
+ // }, colorData)
+}
+
+export function chainIdLinkColorData(props: StructureColorDataProps, colorData?: ColorData) {
+ const { group: { units } } = props
+ const elements = props.group.units[0].elements
+ const links = (units[0] as Unit.Atomic).links
+ // const { edgeCount, a, b } = links
+ const { a } = links
+
+ function locationFn(l: Element.Location, renderElementIdx: number) {
+ const aI = elements[a[renderElementIdx]]
+ // const bI = elements[b[renderElementIdx]];
+ l.element = aI
+ }
+ return chainIdColorData(props, locationFn, colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-index.ts b/src/mol-geo/theme/structure/color/element-index.ts
index 7b5de65a4..510e0a4d5 100644
--- a/src/mol-geo/theme/structure/color/element-index.ts
+++ b/src/mol-geo/theme/structure/color/element-index.ts
@@ -9,15 +9,14 @@ import { StructureColorDataProps } from '.';
import { createElementInstanceColor, ColorData } from '../../../util/color-data';
export function elementIndexColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units, elements }, vertexMap } = props
+ const { group: { units }, elementCount } = props
const instanceCount = units.length
- const elementCount = elements.length
const domain = [ 0, instanceCount * elementCount - 1 ]
const scale = ColorScale.create({ domain })
return createElementInstanceColor({
colorFn: (instanceIdx, elementIdx) => scale.color(instanceIdx * elementCount + elementIdx),
instanceCount,
- vertexMap
+ elementCount
}, colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/element-symbol.ts b/src/mol-geo/theme/structure/color/element-symbol.ts
index b9a493a41..eebb514d9 100644
--- a/src/mol-geo/theme/structure/color/element-symbol.ts
+++ b/src/mol-geo/theme/structure/color/element-symbol.ts
@@ -7,7 +7,7 @@
import { ElementSymbol } from 'mol-model/structure/model/types';
import { Color } from 'mol-util/color';
import { StructureColorDataProps } from '.';
-import { createAttributeOrElementColor, ColorData } from '../../../util/color-data';
+import { createElementColor, ColorData } from '../../../util/color-data';
// from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
export const ElementSymbolColors: { [k: string]: Color } = {
@@ -22,13 +22,13 @@ export function elementSymbolColor(element: ElementSymbol): Color {
}
export function elementSymbolColorData(props: StructureColorDataProps, colorData?: ColorData) {
- const { group: { units, elements }, vertexMap } = props
+ const { group: { units, elements }, elementCount } = props
const { type_symbol } = units[0].model.atomicHierarchy.atoms
- return createAttributeOrElementColor(vertexMap, {
+ return createElementColor({
colorFn: (elementIdx: number) => {
const e = elements[elementIdx]
return elementSymbolColor(type_symbol.value(e))
},
- vertexMap
+ elementCount
}, colorData)
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/color/index.ts b/src/mol-geo/theme/structure/color/index.ts
index 9e0d0318d..41645f276 100644
--- a/src/mol-geo/theme/structure/color/index.ts
+++ b/src/mol-geo/theme/structure/color/index.ts
@@ -5,14 +5,13 @@
*/
import { Unit } from 'mol-model/structure';
-import VertexMap from '../../../shape/vertex-map';
export interface StructureColorDataProps {
group: Unit.SymmetryGroup,
- vertexMap: VertexMap
+ elementCount: number
}
export { elementIndexColorData } from './element-index'
-export { chainIdColorData } from './chain-id'
+export { chainIdElementColorData } 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/util/color-data.ts b/src/mol-geo/util/color-data.ts
index aadc34027..4aa569851 100644
--- a/src/mol-geo/util/color-data.ts
+++ b/src/mol-geo/util/color-data.ts
@@ -120,13 +120,12 @@ export function createInstanceColor(props: InstanceColorProps, colorData?: Color
export interface ElementColorProps {
colorFn: (elementIdx: number) => Color
- vertexMap: VertexMap
+ elementCount: number
}
/** Creates color texture with color for each element (i.e. shared across instances/units) */
export function createElementColor(props: ElementColorProps, colorData?: ColorData): ColorData {
- const { colorFn, vertexMap } = props
- const elementCount = vertexMap.offsetCount - 1
+ const { colorFn, elementCount } = props
const colors = colorData && colorData.tColor.ref.value.array.length >= elementCount * 3 ? colorData.tColor.ref.value : createTextureImage(elementCount, 3)
for (let i = 0, il = elementCount; i < il; ++i) {
Color.toArray(colorFn(i), colors.array, i * 3)
@@ -137,13 +136,12 @@ export function createElementColor(props: ElementColorProps, colorData?: ColorDa
export interface ElementInstanceColorProps {
colorFn: (instanceIdx: number, elementIdx: number) => Color
instanceCount: number,
- vertexMap: VertexMap
+ elementCount: number
}
/** Creates color texture with color for each element instance (i.e. for each unit) */
export function createElementInstanceColor(props: ElementInstanceColorProps, colorData?: ColorData): ColorData {
- const { colorFn, instanceCount, vertexMap } = props
- const elementCount = vertexMap.offsetCount - 1
+ const { colorFn, instanceCount, elementCount } = props
const count = instanceCount * elementCount
const colors = colorData && colorData.tColor.ref.value.array.length >= count * 3 ? colorData.tColor.ref.value : createTextureImage(count, 3)
let colorOffset = 0
@@ -154,9 +152,4 @@ export function createElementInstanceColor(props: ElementInstanceColorProps, col
}
}
return createTextureColor(colors, 'elementInstance', colorData)
-}
-
-/** Create color attribute or texture, depending on the vertexMap */
-export function createAttributeOrElementColor(vertexMap: VertexMap, props: AttributeColorProps, colorData?: ColorData) {
- return vertexMap.idCount < 4 * vertexMap.offsetCount ? createAttributeColor(props, colorData) : createElementColor(props, colorData)
}
\ No newline at end of file
--
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