added residue-name color-scheme

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

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': {},

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 {

src/mol-view/theme/color/residue-name.ts

+/**
+ * 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 ]]))
+    }
+}
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