diff --git a/src/apps/canvas/component/structure-representation.tsx b/src/apps/canvas/component/structure-representation.tsx
index 13cc8cac48dfe6179a956df3cc56147a5d33c513..4cc29f75c99100dc55dbcefd2073afe7e0500d05 100644
--- a/src/apps/canvas/component/structure-representation.tsx
+++ b/src/apps/canvas/component/structure-representation.tsx
@@ -220,8 +220,8 @@ export class StructureRepresentationComponent extends React.Component<StructureR
background: `linear-gradient(to right, ${ct.legend.colors.map(c => Color.toStyle(c)).join(', ')})`
}}
>
- <span style={{float: 'left', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.min}</span>
- <span style={{float: 'right', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.max}</span>
+ <span style={{float: 'left', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.minLabel}</span>
+ <span style={{float: 'right', padding: '6px', color: 'white', fontWeight: 'bold', backgroundColor: 'rgba(0, 0, 0, 0.2)'}}>{ct.legend.maxLabel}</span>
</div>
: ct.legend && ct.legend.kind === 'table-legend'
? <div>
diff --git a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
index e4b98c009cfe449ea2bd183a5280b6c564fcff9c..37bfc18d317b5c96c015f13bda2c9c15bafbb37b 100644
--- a/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-geo/representation/structure/visual/util/polymer/trace-iterator.ts
@@ -11,7 +11,7 @@ import Iterator from 'mol-data/iterator';
import { Vec3 } from 'mol-math/linear-algebra';
import SortedRanges from 'mol-data/int/sorted-ranges';
import { CoarseSphereConformation, CoarseGaussianConformation } from 'mol-model/structure/model/properties/coarse';
-import { getMoleculeType, getElementIndexForAtomRole } from 'mol-model/structure/util';
+import { getAtomicMoleculeType, getElementIndexForAtomRole } from 'mol-model/structure/util';
import { getPolymerRanges } from '../polymer';
/**
@@ -165,7 +165,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
value.first = residueIndex === this.residueSegmentMin
value.last = residueIndex === this.residueSegmentMax
value.secStrucChange = this.unit.model.properties.secondaryStructure.key[residueIndex] !== this.unit.model.properties.secondaryStructure.key[residueIndex + 1]
- value.moleculeType = getMoleculeType(this.unit.model, residueIndex)
+ value.moleculeType = getAtomicMoleculeType(this.unit.model, residueIndex)
if (!residueIt.hasNext) {
this.state = AtomicPolymerTraceIteratorState.nextPolymer
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index d983593c0036ca5c3107a784781e6406c984e366..68dae32ba3bca65faaac36855f150d215c5f513d 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -13,7 +13,7 @@ import PrincipalAxes from 'mol-math/linear-algebra/matrix/principal-axes';
import { fillSerial } from 'mol-util/array';
import { ResidueIndex } from '../../model';
import { ElementSymbol, MoleculeType } from '../../model/types';
-import { getMoleculeType, getPositionMatrix } from '../../util';
+import { getAtomicMoleculeType, getPositionMatrix } from '../../util';
import StructureElement from '../element';
import Structure from '../structure';
import Unit from '../unit';
@@ -164,7 +164,7 @@ export function computeCarbohydrates(structure: Structure): Carbohydrates {
const saccharideComp = SaccharideNameMap.get(label_comp_id.value(residueIndex)) || UnknownSaccharideComponent
if (saccharideComp === UnknownSaccharideComponent) {
- if (getMoleculeType(unit.model, residueIndex) !== MoleculeType.saccharide) continue
+ if (getAtomicMoleculeType(unit.model, residueIndex) !== MoleculeType.saccharide) continue
}
if (!sugarResidueMap) {
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index ba416db932b2ef93f2ae7a66884dcbc214773c16..d09d0c6378ba524a2e05a2e0f24bb3b645dd9fdc 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -10,7 +10,30 @@ import { Vec3 } from 'mol-math/linear-algebra';
import { Unit } from './structure';
import Matrix from 'mol-math/linear-algebra/matrix/matrix';
-export function getMoleculeType(model: Model, rI: ResidueIndex) {
+export function getCoarseBegCompId(unit: Unit.Spheres | Unit.Gaussians, element: ElementIndex) {
+ const entityKey = unit.coarseElements.entityKey[element]
+ const seq = unit.model.sequence.byEntityKey[entityKey]
+ const seq_id_begin = unit.coarseElements.seq_id_begin.value(element)
+ return seq.compId.value(seq_id_begin - 1) // 1-indexed
+}
+
+export function getElementMoleculeType(unit: Unit, element: ElementIndex) {
+ let compId = ''
+ switch (unit.kind) {
+ case Unit.Kind.Atomic:
+ compId = unit.model.atomicHierarchy.residues.label_comp_id.value(unit.residueIndex[element])
+ break
+ case Unit.Kind.Spheres:
+ case Unit.Kind.Gaussians:
+ compId = getCoarseBegCompId(unit, element)
+ break
+ }
+ const chemCompMap = unit.model.properties.chemicalComponentMap
+ const cc = chemCompMap.get(compId)
+ return cc ? cc.moleculeType : MoleculeType.unknown
+}
+
+export function getAtomicMoleculeType(model: Model, rI: ResidueIndex) {
const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
const chemCompMap = model.properties.chemicalComponentMap
const cc = chemCompMap.get(compId)
@@ -36,7 +59,7 @@ export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId:
}
export function getElementIndexForAtomRole(model: Model, rI: ResidueIndex, atomRole: AtomRole) {
- const atomId = getAtomIdForAtomRole(getMoleculeType(model, rI), atomRole)
+ const atomId = getAtomIdForAtomRole(getAtomicMoleculeType(model, rI), atomRole)
return getElementIndexForAtomId(model, rI, atomId)
}
diff --git a/src/mol-util/color/tables.ts b/src/mol-util/color/tables.ts
index eff1da231b8a5e3f26ff1b21c158a1206d84b542..6ee4aa931104f3307f87d2717ec01a9f36d391c4 100644
--- a/src/mol-util/color/tables.ts
+++ b/src/mol-util/color/tables.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { ColorMap, ColorTable, Color } from './color';
+import { ColorMap, ColorTable } from './color';
/**
* Brewer Color Lists
diff --git a/src/mol-view/label.ts b/src/mol-view/label.ts
index 39fad6853ccecbd87d3a706083bc9708eba2d550..840ca3f4bed5f2a2776612b7966d8e3253197983 100644
--- a/src/mol-view/label.ts
+++ b/src/mol-view/label.ts
@@ -53,24 +53,24 @@ export function linkLabel(link: Link.Location) {
return `${elementLabel(elementLocA)} - ${elementLabel(elementLocB)}`
}
-export function elementLabel(element: StructureElement) {
- const model = element.unit.model.label
- const instance = element.unit.conformation.operator.name
+export function elementLabel(location: StructureElement) {
+ const model = location.unit.model.label
+ const instance = location.unit.conformation.operator.name
let label = ''
- if (Unit.isAtomic(element.unit)) {
- const asym_id = Props.chain.auth_asym_id(element)
- const seq_id = Props.residue.auth_seq_id(element)
- const comp_id = Props.residue.auth_comp_id(element)
- const atom_id = Props.atom.auth_atom_id(element)
+ if (Unit.isAtomic(location.unit)) {
+ const asym_id = Props.chain.auth_asym_id(location)
+ const seq_id = Props.residue.auth_seq_id(location)
+ const comp_id = Props.residue.auth_comp_id(location)
+ const atom_id = Props.atom.auth_atom_id(location)
label = `[${comp_id}]${seq_id}:${asym_id}.${atom_id}`
- } else if (Unit.isCoarse(element.unit)) {
- const asym_id = Props.coarse.asym_id(element)
- const seq_id_begin = Props.coarse.seq_id_begin(element)
- const seq_id_end = Props.coarse.seq_id_end(element)
+ } else if (Unit.isCoarse(location.unit)) {
+ const asym_id = Props.coarse.asym_id(location)
+ const seq_id_begin = Props.coarse.seq_id_begin(location)
+ const seq_id_end = Props.coarse.seq_id_end(location)
if (seq_id_begin === seq_id_end) {
- const entityKey = Props.coarse.entityKey(element)
- const seq = element.unit.model.sequence.byEntityKey[entityKey]
+ const entityIndex = Props.coarse.entityKey(location)
+ const seq = location.unit.model.sequence.byEntityKey[entityIndex]
const comp_id = seq.compId.value(seq_id_begin - 1) // 1-indexed
label = `[${comp_id}]${seq_id_begin}:${asym_id}`
} else {
diff --git a/src/mol-view/theme/color.ts b/src/mol-view/theme/color.ts
index 4f6ff16bd608337a7e4b11d37275836ce53c59e1..6f0cecf67eb5bc476adf0a83157f05702a53073c 100644
--- a/src/mol-view/theme/color.ts
+++ b/src/mol-view/theme/color.ts
@@ -19,6 +19,8 @@ import { CrossLinkColorTheme } from './color/cross-link';
import { ShapeGroupColorTheme } from './color/shape-group';
import { CustomColorTheme } from './color/custom';
import { ResidueNameColorTheme } from './color/residue-name';
+import { SequenceIdColorTheme } from './color/sequence-id';
+import { SecondaryStructureColorTheme } from './color/secondary-structure';
export type LocationColor = (location: Location, isSecondary: boolean) => Color
@@ -49,16 +51,18 @@ export interface ColorTheme {
export function ColorTheme(props: ColorThemeProps): ColorTheme {
switch (props.name) {
- case 'element-index': return ElementIndexColorTheme(props)
case 'carbohydrate-symbol': return CarbohydrateSymbolColorTheme(props)
- case 'cross-link': return CrossLinkColorTheme(props)
case 'chain-id': return ChainIdColorTheme(props)
+ case 'cross-link': return CrossLinkColorTheme(props)
+ case 'custom': return CustomColorTheme(props)
+ case 'element-index': return ElementIndexColorTheme(props)
case 'element-symbol': return ElementSymbolColorTheme(props)
case 'residue-name': return ResidueNameColorTheme(props)
+ case 'secondary-structure': return SecondaryStructureColorTheme(props)
+ case 'sequence-id': return SequenceIdColorTheme(props)
+ case 'shape-group': return ShapeGroupColorTheme(props)
case 'unit-index': return UnitIndexColorTheme(props)
case 'uniform': return UniformColorTheme(props)
- case 'shape-group': return ShapeGroupColorTheme(props)
- case 'custom': return CustomColorTheme(props)
}
}
@@ -74,16 +78,18 @@ export interface ColorThemeProps {
}
export const ColorThemeInfo = {
- 'element-index': {},
'carbohydrate-symbol': {},
- 'cross-link': {},
'chain-id': {},
+ 'cross-link': {},
+ 'custom': {},
+ 'element-index': {},
'element-symbol': {},
'residue-name': {},
+ 'secondary-structure': {},
+ 'sequence-id': {},
+ 'shape-group': {},
'unit-index': {},
'uniform': {},
- 'shape-group': {},
- 'custom': {}
}
export type ColorThemeName = keyof typeof ColorThemeInfo
export const ColorThemeNames = Object.keys(ColorThemeInfo)
\ No newline at end of file
diff --git a/src/mol-view/theme/color/secondary-structure.ts b/src/mol-view/theme/color/secondary-structure.ts
new file mode 100644
index 0000000000000000000000000000000000000000..55e76a3da44858ad6703322fc7956abfc38f3434
--- /dev/null
+++ b/src/mol-view/theme/color/secondary-structure.ts
@@ -0,0 +1,82 @@
+/**
+ * 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';
+import { SecondaryStructureType, MoleculeType } from 'mol-model/structure/model/types';
+import { getElementMoleculeType } from 'mol-model/structure/util';
+
+// from Jmol http://jmol.sourceforge.net/jscolors/ (shapely)
+const SecondaryStructureColors = ColorMap({
+ 'alphaHelix': 0xFF0080,
+ 'threeTenHelix': 0xA00080,
+ 'piHelix': 0x600080,
+ 'betaTurn': 0x6080FF,
+ 'betaStrand': 0xFFC800,
+ 'coil': 0xFFFFFF,
+
+ 'dna': 0xAE00FE,
+ 'rna': 0xFD0162,
+
+ 'carbohydrate': 0xA6A6FA
+})
+
+const DefaultSecondaryStructureColor = Color(0x808080)
+const Description = 'Assigns a color based on the type of secondary structure and basic molecule type.'
+
+export function secondaryStructureColor(unit: Unit, element: ElementIndex): Color {
+ let secStrucType = SecondaryStructureType.create(SecondaryStructureType.Flag.None)
+ if (Unit.isAtomic(unit)) {
+ secStrucType = unit.model.properties.secondaryStructure.type[unit.residueIndex[element]]
+ }
+
+ if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Helix)) {
+ if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Helix3Ten)) {
+ return SecondaryStructureColors.threeTenHelix
+ } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.HelixPi)) {
+ return SecondaryStructureColors.piHelix
+ }
+ return SecondaryStructureColors.alphaHelix
+ } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Beta)) {
+ return SecondaryStructureColors.betaStrand
+ } else if (SecondaryStructureType.is(secStrucType, SecondaryStructureType.Flag.Turn)) {
+ return SecondaryStructureColors.coil
+ } else {
+ const moleculeType = getElementMoleculeType(unit, element)
+ if (moleculeType === MoleculeType.DNA) {
+ return SecondaryStructureColors.dna
+ } else if (moleculeType === MoleculeType.RNA) {
+ return SecondaryStructureColors.rna
+ } else if (moleculeType === MoleculeType.saccharide) {
+ return SecondaryStructureColors.carbohydrate
+ } else if (moleculeType === MoleculeType.protein) {
+ return SecondaryStructureColors.coil
+ }
+ }
+ return DefaultSecondaryStructureColor
+}
+
+export function SecondaryStructureColorTheme(props: ColorThemeProps): ColorTheme {
+ function color(location: Location): Color {
+ if (StructureElement.isLocation(location)) {
+ return secondaryStructureColor(location.unit, location.element)
+ } else if (Link.isLocation(location)) {
+ return secondaryStructureColor(location.aUnit, location.aUnit.elements[location.aIndex])
+ }
+ return DefaultSecondaryStructureColor
+ }
+
+ return {
+ granularity: 'group',
+ color,
+ description: Description,
+ legend: TableLegend(Object.keys(SecondaryStructureColors).map(name => {
+ return [name, (SecondaryStructureColors as any)[name] as Color] as [string, Color]
+ }).concat([[ 'Other', DefaultSecondaryStructureColor ]]))
+ }
+}
\ No newline at end of file
diff --git a/src/mol-view/theme/color/sequence-id.ts b/src/mol-view/theme/color/sequence-id.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7f68bf57e787716054a599e67c789c1214e5814e
--- /dev/null
+++ b/src/mol-view/theme/color/sequence-id.ts
@@ -0,0 +1,92 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Unit, StructureElement, Link, ElementIndex } from 'mol-model/structure';
+
+import { ColorScale, Color } from 'mol-util/color';
+import { Location } from 'mol-model/location';
+import { ColorThemeProps, ColorTheme } from '../color';
+import { ColorOther } from 'mol-util/color/tables';
+
+const DefaultColor = Color(0xCCCCCC)
+const Description = 'Gives every polymer residue a color based on its `seq_id` value.'
+
+function getSeqId(unit: Unit, element: ElementIndex): number {
+ const { model } = unit
+ switch (unit.kind) {
+ case Unit.Kind.Atomic:
+ const residueIndex = model.atomicHierarchy.residueAtomSegments.index[element]
+ return model.atomicHierarchy.residues.label_seq_id.value(residueIndex)
+ case Unit.Kind.Spheres:
+ return Math.round(
+ (model.coarseHierarchy.spheres.seq_id_begin.value(element) +
+ model.coarseHierarchy.spheres.seq_id_end.value(element)) / 2
+ )
+ case Unit.Kind.Gaussians:
+ return Math.round(
+ (model.coarseHierarchy.gaussians.seq_id_begin.value(element) +
+ model.coarseHierarchy.gaussians.seq_id_end.value(element)) / 2
+ )
+ }
+}
+
+function getSequenceLength(unit: Unit, element: ElementIndex) {
+ const { model } = unit
+ let entityId = ''
+ switch (unit.kind) {
+ case Unit.Kind.Atomic:
+ const chainIndex = model.atomicHierarchy.chainAtomSegments.index[element]
+ entityId = model.atomicHierarchy.chains.label_entity_id.value(chainIndex)
+ break
+ case Unit.Kind.Spheres:
+ entityId = model.coarseHierarchy.spheres.entity_id.value(element)
+ break
+ case Unit.Kind.Gaussians:
+ entityId = model.coarseHierarchy.gaussians.entity_id.value(element)
+ break
+ }
+ if (entityId === '') return 0
+ const entityIndex = model.entities.getEntityIndex(entityId)
+ if (entityIndex === -1) return 0
+ return model.sequence.byEntityKey[entityIndex].sequence.sequence.length
+}
+
+export function SequenceIdColorTheme(props: ColorThemeProps): ColorTheme {
+ const p = {
+ ...props,
+ colors: ColorOther.rainbow,
+ minLabel: 'Start',
+ maxLabel: 'End',
+ }
+
+ const scale = ColorScale.create(p)
+ const color = (location: Location): Color => {
+ if (StructureElement.isLocation(location)) {
+ const { unit, element } = location
+ const seq_id = getSeqId(unit, element)
+ if (seq_id > 0) {
+ scale.setDomain(0, getSequenceLength(unit, element) - 1)
+ return scale.color(seq_id)
+ }
+ } else if (Link.isLocation(location)) {
+ const { aUnit, aIndex } = location
+ const seq_id = getSeqId(aUnit, aUnit.elements[aIndex])
+ if (seq_id > 0) {
+ scale.setDomain(0, getSequenceLength(aUnit, aUnit.elements[aIndex]) - 1)
+ return scale.color(seq_id)
+ }
+ }
+ return DefaultColor
+ }
+
+ return {
+ granularity: 'group',
+ color,
+ description: Description,
+ // legend: scale ? TableLegend(table) : undefined
+ legend: scale ? scale.legend : undefined
+ }
+}
\ No newline at end of file