From b31e58d821de573a68e8b7981272b3d7591581ff Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 20 Nov 2018 15:24:33 -0800
Subject: [PATCH] added polymer-id color scheme, removed model.asymIdSerialMap
---
.../structure/model/formats/mmcif.ts | 20 ----
src/mol-model/structure/model/model.ts | 2 -
.../structure/representation/cartoon.ts | 2 +-
.../representation/molecular-surface.ts | 2 +-
src/mol-theme/color.ts | 2 +
src/mol-theme/color/chain-id.ts | 25 +++--
src/mol-theme/color/polymer-id.ts | 104 ++++++++++++++++++
7 files changed, 126 insertions(+), 31 deletions(-)
create mode 100644 src/mol-theme/color/polymer-id.ts
diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 155a94777..31c4dfc1e 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -88,24 +88,6 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
return { parentId, details };
}
-function getAsymIdSerialMap(format: mmCIF_Format): ReadonlyMap<string, number> {
- const data = format.data.struct_asym;
- const map = new Map<string, number>();
- let serial = 0
-
- const id = data.id
- const count = data._rowCount
- for (let i = 0; i < count; ++i) {
- const _id = id.value(i)
- if (!map.has(_id)) {
- map.set(_id, serial)
- serial += 1
- }
- }
-
- return map;
-}
-
function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
const map = new Map<string, ChemicalComponent>();
const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
@@ -150,7 +132,6 @@ function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap
export interface FormatData {
modifiedResidues: Model['properties']['modifiedResidues']
- asymIdSerialMap: Model['properties']['asymIdSerialMap']
chemicalComponentMap: Model['properties']['chemicalComponentMap']
saccharideComponentMap: Model['properties']['saccharideComponentMap']
}
@@ -158,7 +139,6 @@ export interface FormatData {
function getFormatData(format: mmCIF_Format): FormatData {
return {
modifiedResidues: getModifiedResidueNameMap(format),
- asymIdSerialMap: getAsymIdSerialMap(format),
chemicalComponentMap: getChemicalComponentMap(format),
saccharideComponentMap: getSaccharideComponentMap(format)
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 1eaad6e45..a9442fc94 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -47,8 +47,6 @@ export interface Model extends Readonly<{
parentId: ReadonlyMap<string, string>,
details: ReadonlyMap<string, string>
}>,
- /** maps asym id to unique serial number */
- readonly asymIdSerialMap: ReadonlyMap<string, number>
/** maps residue name to `ChemicalComponent` data */
readonly chemicalComponentMap: ChemicalComponentMap
/** maps residue name to `SaccharideComponent` data */
diff --git a/src/mol-repr/structure/representation/cartoon.ts b/src/mol-repr/structure/representation/cartoon.ts
index ccb54f933..4d21933e8 100644
--- a/src/mol-repr/structure/representation/cartoon.ts
+++ b/src/mol-repr/structure/representation/cartoon.ts
@@ -31,7 +31,7 @@ export const CartoonParams = {
...NucleotideBlockParams,
...PolymerDirectionParams,
sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
- colorTheme: PD.Mapped('polymer-index', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
+ colorTheme: PD.Mapped('polymer-id', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
visuals: PD.MultiSelect<CartoonVisualName>(['polymer-trace', 'polymer-gap', 'nucleotide-block'], CartoonVisualOptions),
}
PD.getDefaultValues(CartoonParams).colorTheme.name
diff --git a/src/mol-repr/structure/representation/molecular-surface.ts b/src/mol-repr/structure/representation/molecular-surface.ts
index cdf89b914..71ac6eb26 100644
--- a/src/mol-repr/structure/representation/molecular-surface.ts
+++ b/src/mol-repr/structure/representation/molecular-surface.ts
@@ -27,7 +27,7 @@ export const MolecularSurfaceParams = {
...GaussianSurfaceParams,
...GaussianWireframeParams,
...GaussianDensityVolumeParams,
- colorTheme: PD.Mapped('polymer-index', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
+ colorTheme: PD.Mapped('polymer-id', BuiltInColorThemeOptions, getBuiltInColorThemeParams),
visuals: PD.MultiSelect<MolecularSurfaceVisualName>(['gaussian-surface'], MolecularSurfaceVisualOptions),
}
PD.getDefaultValues(MolecularSurfaceParams).colorTheme.name
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index 31c5b3fd5..52d9608cf 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -17,6 +17,7 @@ import { CrossLinkColorThemeProvider } from './color/cross-link';
import { ElementIndexColorThemeProvider } from './color/element-index';
import { ElementSymbolColorThemeProvider } from './color/element-symbol';
import { MoleculeTypeColorThemeProvider } from './color/molecule-type';
+import { PolymerIdColorThemeProvider } from './color/polymer-id';
import { PolymerIndexColorThemeProvider } from './color/polymer-index';
import { ResidueNameColorThemeProvider } from './color/residue-name';
import { SecondaryStructureColorThemeProvider } from './color/secondary-structure';
@@ -96,6 +97,7 @@ export const BuiltInColorThemes = {
'element-index': ElementIndexColorThemeProvider,
'element-symbol': ElementSymbolColorThemeProvider,
'molecule-type': MoleculeTypeColorThemeProvider,
+ 'polymer-id': PolymerIdColorThemeProvider,
'polymer-index': PolymerIndexColorThemeProvider,
'residue-name': ResidueNameColorThemeProvider,
'secondary-structure': SecondaryStructureColorThemeProvider,
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index 2983ce357..0d90464d8 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -12,6 +12,7 @@ import { ColorTheme, LocationColor } from '../color';
import { ParamDefinition as PD } from 'mol-util/param-definition'
import { ThemeDataContext } from 'mol-theme/theme';
import { ColorListOptions, ColorListName } from 'mol-util/color/scale';
+import { Column } from 'mol-data/db';
const DefaultColor = Color(0xCCCCCC)
const Description = 'Gives every chain a color based on its `asym_id` value.'
@@ -34,6 +35,17 @@ function getAsymId(unit: Unit): StructureElement.Property<string> {
}
}
+function addAsymIds(map: Map<string, number>, data: Column<string>) {
+ let j = map.size
+ for (let o = 0, ol = data.rowCount; o < ol; ++o) {
+ const k = data.value(o)
+ if (!map.has(k)) {
+ map.set(k, j)
+ j += 1
+ }
+ }
+}
+
export function ChainIdColorTheme(ctx: ThemeDataContext, props: ChainIdColorThemeProps): ColorTheme<ChainIdColorThemeProps> {
let color: LocationColor
const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
@@ -42,14 +54,13 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: ChainIdColorThem
const l = StructureElement.create()
const { models } = ctx.structure
const asymIdSerialMap = new Map<string, number>()
- let j = 0
for (let i = 0, il = models.length; i <il; ++i) {
- models[i].properties.asymIdSerialMap.forEach((v, k) => {
- if (!asymIdSerialMap.has(k)) {
- asymIdSerialMap.set(k, j)
- j += 1
- }
- })
+ const m = models[i]
+ addAsymIds(asymIdSerialMap, m.atomicHierarchy.chains.label_asym_id)
+ if (m.coarseHierarchy.isDefined) {
+ addAsymIds(asymIdSerialMap, m.coarseHierarchy.spheres.asym_id)
+ addAsymIds(asymIdSerialMap, m.coarseHierarchy.gaussians.asym_id)
+ }
}
scale.setDomain(0, asymIdSerialMap.size - 1)
const scaleColor = scale.color
diff --git a/src/mol-theme/color/polymer-id.ts b/src/mol-theme/color/polymer-id.ts
new file mode 100644
index 000000000..c543ca7e0
--- /dev/null
+++ b/src/mol-theme/color/polymer-id.ts
@@ -0,0 +1,104 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, StructureProperties, StructureElement, Link } from 'mol-model/structure';
+
+import { ColorScale, Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorTheme, LocationColor } from '../color';
+import { ParamDefinition as PD } from 'mol-util/param-definition'
+import { ThemeDataContext } from 'mol-theme/theme';
+import { ColorListOptions, ColorListName } from 'mol-util/color/scale';
+import { Column } from 'mol-data/db';
+import { Entities } from 'mol-model/structure/model/properties/common';
+
+const DefaultColor = Color(0xCCCCCC)
+const Description = 'Gives every polymer chain a color based on its `asym_id` value.'
+
+export const PolymerIdColorThemeParams = {
+ list: PD.Select<ColorListName>('RdYlBu', ColorListOptions),
+}
+export function getPolymerIdColorThemeParams(ctx: ThemeDataContext) {
+ return PolymerIdColorThemeParams // TODO return copy
+}
+export type PolymerIdColorThemeProps = PD.Values<typeof PolymerIdColorThemeParams>
+
+function getAsymId(unit: Unit): StructureElement.Property<string> {
+ switch (unit.kind) {
+ case Unit.Kind.Atomic:
+ return StructureProperties.chain.label_asym_id
+ case Unit.Kind.Spheres:
+ case Unit.Kind.Gaussians:
+ return StructureProperties.coarse.asym_id
+ }
+}
+
+function addPolymerAsymIds(map: Map<string, number>, asymId: Column<string>, entityId: Column<string>, entities: Entities) {
+ let j = map.size
+ for (let o = 0, ol = asymId.rowCount; o < ol; ++o) {
+ const e = entityId.value(o)
+ const eI = entities.getEntityIndex(e)
+ if (entities.data.type.value(eI) === 'polymer') {
+ const k = asymId.value(o)
+ if (!map.has(k)) {
+ map.set(k, j)
+ j += 1
+ }
+ }
+ }
+}
+
+export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PolymerIdColorThemeProps): ColorTheme<PolymerIdColorThemeProps> {
+ let color: LocationColor
+ const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
+
+ if (ctx.structure) {
+ const l = StructureElement.create()
+ const { models } = ctx.structure
+ const polymerAsymIdSerialMap = new Map<string, number>()
+ for (let i = 0, il = models.length; i <il; ++i) {
+ for (let i = 0, il = models.length; i <il; ++i) {
+ const m = models[i]
+ addPolymerAsymIds(polymerAsymIdSerialMap, m.atomicHierarchy.chains.label_asym_id, m.atomicHierarchy.chains.label_entity_id, m.entities)
+ if (m.coarseHierarchy.isDefined) {
+ addPolymerAsymIds(polymerAsymIdSerialMap, m.coarseHierarchy.spheres.asym_id, m.coarseHierarchy.spheres.entity_id, m.entities)
+ addPolymerAsymIds(polymerAsymIdSerialMap, m.coarseHierarchy.gaussians.asym_id, m.coarseHierarchy.spheres.entity_id, m.entities)
+ }
+ }
+ }
+ scale.setDomain(0, polymerAsymIdSerialMap.size - 1)
+ const scaleColor = scale.color
+
+ color = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ const asym_id = getAsymId(location.unit)
+ return scaleColor(polymerAsymIdSerialMap.get(asym_id(location)) || 0)
+ } else if (Link.isLocation(location)) {
+ const asym_id = getAsymId(location.aUnit)
+ l.unit = location.aUnit
+ l.element = location.aUnit.elements[location.aIndex]
+ return scaleColor(polymerAsymIdSerialMap.get(asym_id(l)) || 0)
+ }
+ return DefaultColor
+ }
+ } else {
+ color = () => DefaultColor
+ }
+
+ return {
+ granularity: 'group',
+ color,
+ props,
+ description: Description,
+ legend: scale ? scale.legend : undefined
+ }
+}
+
+export const PolymerIdColorThemeProvider: ColorTheme.Provider<typeof PolymerIdColorThemeParams> = {
+ label: 'Polymer Id',
+ factory: PolymerIdColorTheme,
+ getParams: getPolymerIdColorThemeParams
+}
\ No newline at end of file
--
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