diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index a2c2417686935eb95a0ea3385591d38e0f8ba0f5..5d49660e57af6b6b08dd31a2b7253b7f31e7edb7 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -27,6 +27,7 @@ import { UnitIndexColorThemeProvider } from './color/unit-index';
import { ScaleLegend } from 'mol-util/color/scale';
import { TableLegend } from 'mol-util/color/tables';
import { UncertaintyColorThemeProvider } from './color/uncertainty';
+import { GeneColorThemeProvider } from './color/gene';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -73,6 +74,7 @@ export const BuiltInColorThemes = {
'cross-link': CrossLinkColorThemeProvider,
'element-index': ElementIndexColorThemeProvider,
'element-symbol': ElementSymbolColorThemeProvider,
+ 'gene': GeneColorThemeProvider,
'molecule-type': MoleculeTypeColorThemeProvider,
'polymer-id': PolymerIdColorThemeProvider,
'polymer-index': PolymerIndexColorThemeProvider,
diff --git a/src/mol-theme/color/chain-id.ts b/src/mol-theme/color/chain-id.ts
index 6167f4a6d1e258c4129b8b9439578cbb5ffca1e1..46629e03e925f6481011a9bd175b918cfca2b88e 100644
--- a/src/mol-theme/color/chain-id.ts
+++ b/src/mol-theme/color/chain-id.ts
@@ -51,6 +51,7 @@ export function ChainIdColorTheme(ctx: ThemeDataContext, props: PD.Values<ChainI
const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
if (ctx.structure) {
+ // TODO same asym ids in different models should get different color
const l = StructureElement.create()
const { models } = ctx.structure
const asymIdSerialMap = new Map<string, number>()
diff --git a/src/mol-theme/color/gene.ts b/src/mol-theme/color/gene.ts
new file mode 100644
index 0000000000000000000000000000000000000000..1f0110e846f700fdb7e0a3e01319248d35b0b585
--- /dev/null
+++ b/src/mol-theme/color/gene.ts
@@ -0,0 +1,127 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { 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 { NumberArray } from 'mol-util/type-helpers';
+
+const DefaultColor = Color(0xCCCCCC)
+const Description = 'Gives ranges of a polymer chain a color based on the gene (or linker/terminal extension) it originates from.'
+
+export const GeneColorThemeParams = {
+ list: PD.ColorScale<ColorListName>('RedYellowBlue', ColorListOptions),
+}
+export type GeneColorThemeParams = typeof GeneColorThemeParams
+export function getGeneColorThemeParams(ctx: ThemeDataContext) {
+ return GeneColorThemeParams // TODO return copy
+}
+
+function modelEntityKey(modelIndex: number, entityId: string) {
+ return `${modelIndex}|${entityId}`
+}
+
+function addGene(geneSerialMap: Map<string, number>, geneNames: string[], beg: number, end: number, seqToSrcGen: NumberArray) {
+ const gene = geneNames.map(s => s.toUpperCase()).sort().join(',')
+ let geneIndex = 0 // serial no starting from 1
+ if (gene === '') {
+ geneIndex = geneSerialMap.size + 1
+ geneSerialMap.set(`UNKNOWN${geneIndex}`, geneIndex)
+ } else if (geneSerialMap.has(gene)) {
+ geneIndex = geneSerialMap.get(gene)!
+ } else {
+ geneIndex = geneSerialMap.size + 1
+ geneSerialMap.set(gene, geneIndex)
+ }
+ for (let i = beg, il = end; i <= il; ++i) {
+ seqToSrcGen[i - 1] = geneIndex
+ }
+}
+
+export function GeneColorTheme(ctx: ThemeDataContext, props: PD.Values<GeneColorThemeParams>): ColorTheme<GeneColorThemeParams> {
+ let color: LocationColor
+ const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
+ const { structure } = ctx
+
+ if (structure) {
+ const l = StructureElement.create()
+ const { models } = structure
+ const seqToSrcGenByModelEntity = new Map<string, NumberArray>()
+ const geneSerialMap = new Map<string, number>() // serial no starting from 1
+ for (let i = 0, il = models.length; i <il; ++i) {
+ const m = models[i]
+ if (m.sourceData.kind !== 'mmCIF') continue
+ const { entity_src_gen } = m.sourceData.data
+
+ const { entity_id, pdbx_beg_seq_num, pdbx_end_seq_num, pdbx_gene_src_gene } = entity_src_gen
+ for (let j = 0, jl = entity_src_gen._rowCount; j < jl; ++j) {
+ const entityId = entity_id.value(j)
+ const k = modelEntityKey(i, entityId)
+ if (!seqToSrcGenByModelEntity.has(k)) {
+ const entityIndex = m.entities.getEntityIndex(entityId)
+ const seq = m.sequence.sequences[entityIndex].sequence
+ const seqLength = seq.sequence.length
+ const seqToGene = new Int16Array(seqLength)
+ addGene(geneSerialMap, pdbx_gene_src_gene.value(j), pdbx_beg_seq_num.value(j), pdbx_end_seq_num.value(j), seqToGene)
+ seqToSrcGenByModelEntity.set(k, seqToGene)
+ } else {
+ const seqToGene = seqToSrcGenByModelEntity.get(k)!
+ addGene(geneSerialMap, pdbx_gene_src_gene.value(j), pdbx_beg_seq_num.value(j), pdbx_end_seq_num.value(j), seqToGene)
+ seqToSrcGenByModelEntity.set(k, seqToGene)
+ }
+ }
+ }
+ scale.setDomain(1, geneSerialMap.size)
+ const scaleColor = scale.color
+
+ const getGeneColor = (location: StructureElement) => {
+ const modelIndex = structure.models.indexOf(location.unit.model)
+ const entityId = StructureProperties.entity.id(location)
+ const k = modelEntityKey(modelIndex, entityId)
+ const seqToGene = seqToSrcGenByModelEntity.get(k)
+ if (seqToGene) {
+ // minus 1 to convert seqId to array index
+ return scaleColor(seqToGene[StructureProperties.residue.label_seq_id(location) - 1])
+ } else {
+ return DefaultColor
+ }
+ }
+
+ color = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ return getGeneColor(location)
+ } else if (Link.isLocation(location)) {
+ l.unit = location.aUnit
+ l.element = location.aUnit.elements[location.aIndex]
+ return getGeneColor(l)
+ }
+ return DefaultColor
+ }
+ } else {
+ color = () => DefaultColor
+ }
+
+ return {
+ factory: GeneColorTheme,
+ granularity: 'group',
+ color,
+ props,
+ description: Description,
+ legend: scale ? scale.legend : undefined
+ }
+}
+
+export const GeneColorThemeProvider: ColorTheme.Provider<GeneColorThemeParams> = {
+ label: 'Gene',
+ factory: GeneColorTheme,
+ getParams: getGeneColorThemeParams,
+ defaultValues: PD.getDefaultValues(GeneColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}
\ No newline at end of file
diff --git a/src/mol-theme/color/polymer-id.ts b/src/mol-theme/color/polymer-id.ts
index a19c84d6423ed18670f47fbaf3864e73e43b20b0..f97def2d4c011ad40c5ee6952bd649e60fc382d1 100644
--- a/src/mol-theme/color/polymer-id.ts
+++ b/src/mol-theme/color/polymer-id.ts
@@ -56,17 +56,16 @@ export function PolymerIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Poly
const scale = ColorScale.create({ listOrName: props.list, minLabel: 'Start', maxLabel: 'End' })
if (ctx.structure) {
+ // TODO same asym ids in different models should get different color
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)
- }
+ 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)