diff --git a/data/mmcif-field-names.csv b/data/mmcif-field-names.csv
index f05f299f39864c70572447630a3bf934951ef3cc..137c35a8cdcf492b237cbd5eab50c3a44da46e16 100644
--- a/data/mmcif-field-names.csv
+++ b/data/mmcif-field-names.csv
@@ -93,12 +93,24 @@ entity_poly_seq.hetero
entity_src_gen.entity_id
entity_src_gen.pdbx_src_id
-entity_src_gen.pdbx_alt_source_flag
-entity_src_gen.pdbx_seq_type
+entity_src_gen.pdbx_alt_source_flag
+entity_src_gen.pdbx_seq_type
entity_src_gen.pdbx_beg_seq_num
entity_src_gen.pdbx_end_seq_num
entity_src_gen.pdbx_gene_src_gene
+entity_src_nat.entity_id
+entity_src_nat.pdbx_src_id
+entity_src_nat.pdbx_alt_source_flag
+entity_src_nat.pdbx_beg_seq_num
+entity_src_nat.pdbx_end_seq_num
+
+pdbx_entity_src_syn.entity_id
+pdbx_entity_src_syn.pdbx_src_id
+pdbx_entity_src_syn.pdbx_alt_source_flag
+pdbx_entity_src_syn.pdbx_beg_seq_num
+pdbx_entity_src_syn.pdbx_end_seq_num
+
pdbx_entity_branch.entity_id
pdbx_entity_branch.type
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 39d20bcd83d4312a874eb2598fe6132005316e87..dc6c7747ae0f7c4de6a86bd4d4669857cfe24ece 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.309, IHM 0.141, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.310, IHM 0.141, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -1964,6 +1964,40 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the ENTITY_SRC_NAT category record details of
+ * the source from which the entity was obtained in cases
+ * where the entity was isolated directly from a natural tissue.
+ */
+ entity_src_nat: {
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
+ entity_id: str,
+ /**
+ * This data item is an ordinal identifier for entity_src_nat data records.
+ */
+ pdbx_src_id: int,
+ /**
+ * This data item identifies cases in which an alternative source
+ * modeled.
+ */
+ pdbx_alt_source_flag: Aliased<'sample' | 'model'>(str),
+ /**
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
+ */
+ pdbx_beg_seq_num: int,
+ /**
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
+ */
+ pdbx_end_seq_num: int,
+ },
/**
* Data items in the ENTITY_SRC_GEN category record details of
* the source from which the entity was obtained in cases
@@ -2010,6 +2044,39 @@ export const mmCIF_Schema = {
*/
pdbx_end_seq_num: int,
},
+ /**
+ * The data items in category PDBX_ENTITY_SRC_SYN record the source details
+ * about chemically synthesized molecules.
+ */
+ pdbx_entity_src_syn: {
+ /**
+ * This data item is a pointer to _entity.id in the ENTITY category.
+ */
+ entity_id: str,
+ /**
+ * This data item is an ordinal identifier for pdbx_entity_src_syn data records.
+ */
+ pdbx_src_id: int,
+ /**
+ * This data item identifies cases in which an alternative source
+ * modeled.
+ */
+ pdbx_alt_source_flag: Aliased<'sample' | 'model'>(str),
+ /**
+ * The beginning polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
+ */
+ pdbx_beg_seq_num: int,
+ /**
+ * The ending polymer sequence position for the polymer section corresponding
+ * to this source.
+ *
+ * A reference to the sequence position in the entity_poly category.
+ */
+ pdbx_end_seq_num: int,
+ },
/**
* Data items in the PDBX_ENTITY_DESCRIPTOR category provide
* string descriptors of entity chemical structure.
diff --git a/src/mol-theme/color.ts b/src/mol-theme/color.ts
index b82996be6a92aa90ee0bd5101e55c1ca462fb3a2..bab8e130c4fbb0ce67bf44413004a83d355dbfad 100644
--- a/src/mol-theme/color.ts
+++ b/src/mol-theme/color.ts
@@ -27,7 +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';
+import { EntitySourceColorThemeProvider } from './color/entity-source';
import { IllustrativeColorThemeProvider } from './color/illustrative';
import { HydrophobicityColorThemeProvider } from './color/hydrophobicity';
@@ -76,7 +76,7 @@ export const BuiltInColorThemes = {
'cross-link': CrossLinkColorThemeProvider,
'element-index': ElementIndexColorThemeProvider,
'element-symbol': ElementSymbolColorThemeProvider,
- 'gene': GeneColorThemeProvider,
+ 'entity-source': EntitySourceColorThemeProvider,
'hydrophobicity': HydrophobicityColorThemeProvider,
'illustrative': IllustrativeColorThemeProvider,
'molecule-type': MoleculeTypeColorThemeProvider,
diff --git a/src/mol-theme/color/entity-source.ts b/src/mol-theme/color/entity-source.ts
new file mode 100644
index 0000000000000000000000000000000000000000..828f0b824a957d4d49f7f172ab388cc9b302f565
--- /dev/null
+++ b/src/mol-theme/color/entity-source.ts
@@ -0,0 +1,143 @@
+/**
+ * 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, Model } 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 { Table, Column } from 'mol-data/db';
+import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
+
+const DefaultColor = Color(0xCCCCCC)
+const Description = 'Gives ranges of a polymer chain a color based on the entity source it originates from. Genes get the same color per entity'
+
+export const EntitySourceColorThemeParams = {
+ list: PD.ColorScale<ColorListName>('RedYellowBlue', ColorListOptions),
+}
+export type EntitySourceColorThemeParams = typeof EntitySourceColorThemeParams
+export function getEntitySourceColorThemeParams(ctx: ThemeDataContext) {
+ return EntitySourceColorThemeParams // TODO return copy
+}
+
+function modelEntityKey(modelIndex: number, entityId: string) {
+ return `${modelIndex}|${entityId}`
+}
+
+type EntitySrc = Table<{
+ entity_id: mmCIF_Schema['entity_src_gen']['entity_id'],
+ pdbx_src_id: mmCIF_Schema['entity_src_gen']['pdbx_src_id'],
+ pdbx_beg_seq_num: mmCIF_Schema['entity_src_gen']['pdbx_beg_seq_num'],
+ pdbx_end_seq_num: mmCIF_Schema['entity_src_gen']['pdbx_end_seq_num'],
+}>
+type GeneSrcGene = Column<mmCIF_Schema['entity_src_gen']['pdbx_gene_src_gene']['T']>
+
+function srcKey(modelIndex: number, entityId: string, srcId: number, gene: string) {
+ return `${modelIndex}|${entityId}|${gene ? gene : srcId}`
+}
+
+function addSrc(seqToSrcByModelEntity: Map<string, Int16Array>, srcKeySerialMap: Map<string, number>, modelIndex: number, model: Model, entity_src: EntitySrc, gene_src_gene?: GeneSrcGene) {
+ const { entity_id, pdbx_src_id, pdbx_beg_seq_num, pdbx_end_seq_num } = entity_src
+ for (let j = 0, jl = entity_src._rowCount; j < jl; ++j) {
+ const entityId = entity_id.value(j)
+ const mK = modelEntityKey(modelIndex, entityId)
+ let seqToSrc: Int16Array
+ if (!seqToSrcByModelEntity.has(mK)) {
+ const entityIndex = model.entities.getEntityIndex(entityId)
+ const seq = model.sequence.sequences[entityIndex].sequence
+ seqToSrc = new Int16Array(seq.sequence.length)
+ seqToSrcByModelEntity.set(mK, seqToSrc)
+ } else {
+ seqToSrc = seqToSrcByModelEntity.get(mK)!
+ }
+ const sK = srcKey(modelIndex, entityId, pdbx_src_id.value(j), gene_src_gene ? gene_src_gene.value(j).join(',') : '')
+
+ // may not be given (= 0) indicating src is for the whole seq
+ const beg = pdbx_beg_seq_num.valueKind(j) === Column.ValueKind.Present ? pdbx_beg_seq_num.value(j) : 1
+ const end = pdbx_end_seq_num.valueKind(j) === Column.ValueKind.Present ? pdbx_end_seq_num.value(j) : seqToSrc.length
+
+ let srcIndex: number // serial no starting from 1
+ if (srcKeySerialMap.has(sK)) {
+ srcIndex = srcKeySerialMap.get(sK)!
+ } else {
+ srcIndex = srcKeySerialMap.size + 1
+ srcKeySerialMap.set(sK, srcIndex)
+ }
+ // set src index
+ for (let i = beg, il = end; i <= il; ++i) {
+ seqToSrc[i - 1] = srcIndex
+ }
+ }
+}
+
+export function EntitySourceColorTheme(ctx: ThemeDataContext, props: PD.Values<EntitySourceColorThemeParams>): ColorTheme<EntitySourceColorThemeParams> {
+ 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 seqToSrcByModelEntity = new Map<string, Int16Array>()
+ const srcKeySerialMap = 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, entity_src_nat, pdbx_entity_src_syn } = m.sourceData.data
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_gen, entity_src_gen.pdbx_gene_src_gene)
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, entity_src_nat)
+ addSrc(seqToSrcByModelEntity, srcKeySerialMap, i, m, pdbx_entity_src_syn)
+ }
+ scale.setDomain(1, srcKeySerialMap.size)
+ const scaleColor = scale.color
+
+ const getSrcColor = (location: StructureElement) => {
+ const modelIndex = structure.models.indexOf(location.unit.model)
+ const entityId = StructureProperties.entity.id(location)
+ const mK = modelEntityKey(modelIndex, entityId)
+ const seqToSrc = seqToSrcByModelEntity.get(mK)
+ if (seqToSrc) {
+ // minus 1 to convert seqId to array index
+ return scaleColor(seqToSrc[StructureProperties.residue.label_seq_id(location) - 1])
+ } else {
+ return DefaultColor
+ }
+ }
+
+ color = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ return getSrcColor(location)
+ } else if (Link.isLocation(location)) {
+ l.unit = location.aUnit
+ l.element = location.aUnit.elements[location.aIndex]
+ return getSrcColor(l)
+ }
+ return DefaultColor
+ }
+ } else {
+ color = () => DefaultColor
+ }
+
+ return {
+ factory: EntitySourceColorTheme,
+ granularity: 'group',
+ color,
+ props,
+ description: Description,
+ legend: scale ? scale.legend : undefined
+ }
+}
+
+export const EntitySourceColorThemeProvider: ColorTheme.Provider<EntitySourceColorThemeParams> = {
+ label: 'Entity Source',
+ factory: EntitySourceColorTheme,
+ getParams: getEntitySourceColorThemeParams,
+ defaultValues: PD.getDefaultValues(EntitySourceColorThemeParams),
+ isApplicable: (ctx: ThemeDataContext) => !!ctx.structure
+}
\ No newline at end of file
diff --git a/src/mol-theme/color/gene.ts b/src/mol-theme/color/gene.ts
deleted file mode 100644
index 1f0110e846f700fdb7e0a3e01319248d35b0b585..0000000000000000000000000000000000000000
--- a/src/mol-theme/color/gene.ts
+++ /dev/null
@@ -1,127 +0,0 @@
-/**
- * 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