gene color scheme

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,

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>()

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
+}

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)