diff --git a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
index dcf176ba3d1fef8188b3b2886be11e7d46beb4c6..82387af83fe0a284eebadd7a38b129219606807e 100644
--- a/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
+++ b/src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts
@@ -54,11 +54,11 @@ async function createNucleotideBlockMesh(ctx: RuntimeContext, unit: Unit, struct
while (residueIt.hasNext) {
const { index: residueIndex } = residueIt.move();
- const cc = chemicalComponentMap.get(label_comp_id.value(residueIndex))
+ let compId = label_comp_id.value(residueIndex)
+ const cc = chemicalComponentMap.get(compId)
const moleculeType = cc ? cc.moleculeType : MoleculeType.unknown
if (isNucleic(moleculeType)) {
- let compId = label_comp_id.value(residueIndex)
const parentId = modifiedResidues.parentId.get(compId)
if (parentId !== undefined) compId = parentId
let idx1 = -1, idx2 = -1, idx3 = -1, idx4 = -1, idx5 = -1, idx6 = -1
diff --git a/src/mol-view/theme/color.ts b/src/mol-view/theme/color.ts
index 7b1f0e4d2f6275d31d13506303a5a512db649a1a..aac704dd314321c5bc8b169fb036348db8e74378 100644
--- a/src/mol-view/theme/color.ts
+++ b/src/mol-view/theme/color.ts
@@ -7,6 +7,7 @@
import { Color } from 'mol-util/color';
import { Structure } from 'mol-model/structure';
import { Location } from 'mol-model/location';
+import { ColorType } from 'mol-geo/util/color-data';
import { ElementIndexColorTheme } from './color/element-index';
import { CarbohydrateSymbolColorTheme } from './color/carbohydrate-symbol';
@@ -17,7 +18,7 @@ import { UniformColorTheme } from './color/uniform';
import { CrossLinkColorTheme } from './color/cross-link';
import { ShapeGroupColorTheme } from './color/shape-group';
import { CustomColorTheme } from './color/custom';
-import { ColorType } from 'mol-geo/util/color-data';
+import { ResidueNameColorTheme } from './color/residue-name';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -53,6 +54,7 @@ export function ColorTheme(props: ColorThemeProps): ColorTheme {
case 'cross-link': return CrossLinkColorTheme(props)
case 'chain-id': return ChainIdColorTheme(props)
case 'element-symbol': return ElementSymbolColorTheme(props)
+ case 'residue-name': return ResidueNameColorTheme(props)
case 'unit-index': return UnitIndexColorTheme(props)
case 'uniform': return UniformColorTheme(props)
case 'shape-group': return ShapeGroupColorTheme(props)
@@ -77,6 +79,7 @@ export const ColorThemeInfo = {
'cross-link': {},
'chain-id': {},
'element-symbol': {},
+ 'residue-name': {},
'unit-index': {},
'uniform': {},
'shape-group': {},
diff --git a/src/mol-view/theme/color/element-symbol.ts b/src/mol-view/theme/color/element-symbol.ts
index c73ae2d46280e1491535b2d6d79c98a328760d49..e382f14d87f48d496faaa8eb2c0e794bbc04aa5c 100644
--- a/src/mol-view/theme/color/element-symbol.ts
+++ b/src/mol-view/theme/color/element-symbol.ts
@@ -20,7 +20,7 @@ const Description = 'Assigns a color to every atom according to its chemical ele
export function elementSymbolColor(element: ElementSymbol): Color {
const c = (ElementSymbolColors as { [k: string]: Color })[element];
- return c === void 0 ? DefaultElementSymbolColor : c
+ return c === undefined ? DefaultElementSymbolColor : c
}
export function ElementSymbolColorTheme(props: ColorThemeProps): ColorTheme {
diff --git a/src/mol-view/theme/color/residue-name.ts b/src/mol-view/theme/color/residue-name.ts
new file mode 100644
index 0000000000000000000000000000000000000000..02f2425fbc446cc9ca174ae743073b9b047c2501
--- /dev/null
+++ b/src/mol-view/theme/color/residue-name.ts
@@ -0,0 +1,115 @@
+/**
+ * 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';
+
+// protein colors from Jmol http://jmol.sourceforge.net/jscolors/
+const ResidueNameColors = ColorMap({
+ // standard amino acids
+ 'ALA': 0x8CFF8C,
+ 'ARG': 0x00007C,
+ 'ASN': 0xFF7C70,
+ 'ASP': 0xA00042,
+ 'CYS': 0xFFFF70,
+ 'GLN': 0xFF4C4C,
+ 'GLU': 0x660000,
+ 'GLY': 0xEEEEEE,
+ 'HIS': 0x7070FF,
+ 'ILE': 0x004C00,
+ 'LEU': 0x455E45,
+ 'LYS': 0x4747B8,
+ 'MET': 0xB8A042,
+ 'PHE': 0x534C52,
+ 'PRO': 0x525252,
+ 'SER': 0xFF7042,
+ 'THR': 0xB84C00,
+ 'TRP': 0x4F4600,
+ 'TYR': 0x8C704C,
+ 'VAL': 0xFF8CFF,
+
+ // rna bases
+ 'A': 0xDC143C, // Crimson Red
+ 'G': 0x32CD32, // Lime Green
+ 'I': 0x9ACD32, // Yellow Green
+ 'C': 0xFFD700, // Gold Yellow
+ 'T': 0x4169E1, // Royal Blue
+ 'U': 0x40E0D0, // Turquoise Cyan
+
+ // dna bases
+ 'DA': 0xDC143C,
+ 'DG': 0x32CD32,
+ 'DI': 0x9ACD32,
+ 'DC': 0xFFD700,
+ 'DT': 0x4169E1,
+ 'DU': 0x40E0D0,
+
+ // peptide bases
+ 'APN': 0xDC143C,
+ 'GPN': 0x32CD32,
+ 'CPN': 0xFFD700,
+ 'TPN': 0x4169E1,
+})
+
+const DefaultResidueNameColor = Color(0xFF00FF)
+const Description = 'Assigns a color to every residue according to its name.'
+
+export function residueNameColor(residueName: string): Color {
+ const c = (ResidueNameColors as { [k: string]: Color })[residueName];
+ return c === undefined ? DefaultResidueNameColor : c
+}
+
+function getAtomicCompId(unit: Unit.Atomic, element: ElementIndex) {
+ const { modifiedResidues } = unit.model.properties
+ const compId = unit.model.atomicHierarchy.residues.auth_comp_id.value(unit.residueIndex[element])
+ const parentId = modifiedResidues.parentId.get(compId)
+ return parentId === undefined ? compId : parentId
+}
+
+function getCoarseCompId(unit: Unit.Spheres | Unit.Gaussians, element: ElementIndex) {
+ const seqIdBegin = unit.coarseElements.seq_id_begin.value(element)
+ const seqIdEnd = unit.coarseElements.seq_id_end.value(element)
+ if (seqIdBegin === seqIdEnd) {
+ const { modifiedResidues } = unit.model.properties
+ const entityKey = unit.coarseElements.entityKey[element]
+ const seq = unit.model.sequence.byEntityKey[entityKey]
+ let compId = seq.compId.value(seqIdBegin - 1) // 1-indexed
+ const parentId = modifiedResidues.parentId.get(compId)
+ return parentId === undefined ? compId : parentId
+ }
+}
+
+export function ResidueNameColorTheme(props: ColorThemeProps): ColorTheme {
+ function color(location: Location): Color {
+ if (StructureElement.isLocation(location)) {
+ if (Unit.isAtomic(location.unit)) {
+ return residueNameColor(getAtomicCompId(location.unit, location.element))
+ } else {
+ const compId = getCoarseCompId(location.unit, location.element)
+ if (compId) return residueNameColor(compId)
+ }
+ } else if (Link.isLocation(location)) {
+ if (Unit.isAtomic(location.aUnit)) {
+ return residueNameColor(getAtomicCompId(location.aUnit, location.aUnit.elements[location.aIndex]))
+ } else {
+ const compId = getCoarseCompId(location.aUnit, location.aUnit.elements[location.aIndex])
+ if (compId) return residueNameColor(compId)
+ }
+ }
+ return DefaultResidueNameColor
+ }
+
+ return {
+ granularity: 'group',
+ color,
+ description: Description,
+ legend: TableLegend(Object.keys(ResidueNameColors).map(name => {
+ return [name, (ResidueNameColors as any)[name] as Color] as [string, Color]
+ }).concat([[ 'Unknown', DefaultResidueNameColor ]]))
+ }
+}
\ No newline at end of file