diff --git a/src/mol-model-formats/structure/common/entity.ts b/src/mol-model-formats/structure/common/entity.ts
index f416aaeac0cb6659f2a91759b12e6a3d5587201d..d44fefb2f7f9e7d5117333b80731f81d7181c604 100644
--- a/src/mol-model-formats/structure/common/entity.ts
+++ b/src/mol-model-formats/structure/common/entity.ts
@@ -30,7 +30,7 @@ export class EntityBuilder {
}
getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
- if (moleculeType === MoleculeType.water) {
+ if (moleculeType === MoleculeType.Water) {
if (this.waterId === undefined) {
this.set('water', 'Water')
this.waterId = `${this.count}`
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index 0ed74bf3399810bfb2a1293e34a01e6bb7f9be04..905e171de0d80688a27871d82c627031dfbbe94d 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -36,7 +36,7 @@ function getCategories(atoms: GroAtoms) {
let currentAsymIndex = 0
let currentAsymId = ''
let currentSeqId = 0
- let prevMoleculeType = MoleculeType.unknown
+ let prevMoleculeType = MoleculeType.Unknown
let prevResidueNumber = -1
for (let i = 0, il = atoms.count; i < il; ++i) {
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index ff143a1ffb4f1750026f703bfec8fd816cf19613..47f8648f228b2c4e7a3db70c82459835671b8b4f 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -180,7 +180,7 @@ function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap
const _type = type.value(i)
if (SaccharideCompIdMap.has(_id)) {
map.set(_id, SaccharideCompIdMap.get(_id)!)
- } else if (getMoleculeType(_type, _id) === MoleculeType.saccharide) {
+ } else if (getMoleculeType(_type, _id) === MoleculeType.Saccharide) {
map.set(_id, UnknownSaccharideComponent)
}
}
diff --git a/src/mol-model/structure/model/properties/atomic/hierarchy.ts b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
index ae7337b34afe2b8bba8985620b833eb2e356fff6..26c26dbab5e12e6796c33b07ed8f63aefbcb9140 100644
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -8,7 +8,7 @@
import { Column, Table } from '../../../../../mol-data/db'
import { Segmentation } from '../../../../../mol-data/int'
import { mmCIF_Schema as mmCIF } from '../../../../../mol-io/reader/cif/schema/mmcif'
-import { ElementSymbol, MoleculeType } from '../../types'
+import { ElementSymbol, MoleculeType, PolymerType } from '../../types'
import { ChainIndex, EntityIndex, ResidueIndex, ElementIndex } from '../../indexing';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
@@ -116,6 +116,7 @@ export interface AtomicDerivedData {
readonly directionFromElementIndex: ArrayLike<ElementIndex | -1>
readonly directionToElementIndex: ArrayLike<ElementIndex | -1>
readonly moleculeType: ArrayLike<MoleculeType>
+ readonly polymerType: ArrayLike<PolymerType>
}
}
diff --git a/src/mol-model/structure/model/properties/utils/atomic-derived.ts b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
index 8c1a1bb429545a4bf29672b96a49615f286c2e30..c0cf4cc84f61da049cea848aad3cca0a793d11d3 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.ts
@@ -7,9 +7,10 @@
import { AtomicData } from '../atomic';
import { AtomicIndex, AtomicDerivedData } from '../atomic/hierarchy';
import { ElementIndex, ResidueIndex } from '../../indexing';
-import { MoleculeType, getMoleculeType, getComponentType } from '../../types';
+import { MoleculeType, getMoleculeType, getComponentType, PolymerType, getPolymerType } from '../../types';
import { getAtomIdForAtomRole } from '../../../../../mol-model/structure/util';
import { ChemicalComponentMap } from '../common';
+import { isProductionMode } from '../../../../../mol-util/debug';
export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemicalComponentMap: ChemicalComponentMap): AtomicDerivedData {
const { label_comp_id, _rowCount: n } = data.residues
@@ -18,38 +19,49 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
const directionFromElementIndex = new Int32Array(n)
const directionToElementIndex = new Int32Array(n)
const moleculeType = new Uint8Array(n)
+ const polymerType = new Uint8Array(n)
const moleculeTypeMap = new Map<string, MoleculeType>()
+ const polymerTypeMap = new Map<string, PolymerType>()
for (let i = 0 as ResidueIndex; i < n; ++i) {
const compId = label_comp_id.value(i)
const chemCompMap = chemicalComponentMap
+
let molType: MoleculeType
+ let polyType: PolymerType
if (moleculeTypeMap.has(compId)) {
molType = moleculeTypeMap.get(compId)!
- } else if (chemCompMap.has(compId)) {
- molType = getMoleculeType(chemCompMap.get(compId)!.type, compId)
- moleculeTypeMap.set(compId, molType)
+ polyType = polymerTypeMap.get(compId)!
} else {
- console.log('chemComp not found', compId)
- molType = getMoleculeType(getComponentType(compId), compId)
+ let type: string
+ if (chemCompMap.has(compId)) {
+ type = chemCompMap.get(compId)!.type
+ } else {
+ if (!isProductionMode) console.info('chemComp not found', compId)
+ type = getComponentType(compId)
+ }
+ molType = getMoleculeType(type, compId)
// TODO if unknown molecule type, use atom names to guess molecule type
+ polyType = getPolymerType(type, molType)
moleculeTypeMap.set(compId, molType)
+ polymerTypeMap.set(compId, polyType)
}
moleculeType[i] = molType
+ polymerType[i] = polyType
- const traceAtomId = getAtomIdForAtomRole(molType, 'trace')
+ const traceAtomId = getAtomIdForAtomRole(polyType, 'trace')
let traceIndex = index.findAtomsOnResidue(i, traceAtomId)
if (traceIndex === -1) {
- const coarseAtomId = getAtomIdForAtomRole(molType, 'coarseBackbone')
+ const coarseAtomId = getAtomIdForAtomRole(polyType, 'coarseBackbone')
traceIndex = index.findAtomsOnResidue(i, coarseAtomId)
}
traceElementIndex[i] = traceIndex
- const directionFromAtomId = getAtomIdForAtomRole(molType, 'directionFrom')
+ const directionFromAtomId = getAtomIdForAtomRole(polyType, 'directionFrom')
directionFromElementIndex[i] = index.findAtomsOnResidue(i, directionFromAtomId)
- const directionToAtomId = getAtomIdForAtomRole(molType, 'directionTo')
+ const directionToAtomId = getAtomIdForAtomRole(polyType, 'directionTo')
directionToElementIndex[i] = index.findAtomsOnResidue(i, directionToAtomId)
}
@@ -59,6 +71,7 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
directionFromElementIndex: directionFromElementIndex as unknown as ArrayLike<ElementIndex | -1>,
directionToElementIndex: directionToElementIndex as unknown as ArrayLike<ElementIndex | -1>,
moleculeType: moleculeType as unknown as ArrayLike<MoleculeType>,
+ polymerType: polymerType as unknown as ArrayLike<PolymerType>,
}
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
index 9c9d48d2653b5197909dfcef1e01ef31e1db2698..52d414c221d65ec25704d700c989580cd53707a9 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -7,7 +7,7 @@
import { AtomicRanges, AtomicIndex, AtomicHierarchy, AtomicDerivedData } from '../atomic/hierarchy';
import { Segmentation, Interval } from '../../../../../mol-data/int';
import SortedRanges from '../../../../../mol-data/int/sorted-ranges';
-import { isPolymer } from '../../types';
+import { isPolymer, PolymerType } from '../../types';
import { ElementIndex, ResidueIndex } from '../../indexing';
import { getAtomIdForAtomRole } from '../../../util';
import { AtomicConformation } from '../atomic/conformation';
@@ -16,18 +16,18 @@ import { Entities } from '../common';
import StructureSequence from '../sequence';
function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, conformation: AtomicConformation, index: AtomicIndex, derived: AtomicDerivedData) {
- const { moleculeType, traceElementIndex, directionFromElementIndex, directionToElementIndex } = derived.residue
- const mtStart = moleculeType[riStart]
- const mtEnd = moleculeType[riEnd]
- if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
+ const { polymerType, traceElementIndex, directionFromElementIndex, directionToElementIndex } = derived.residue
+ const ptStart = polymerType[riStart]
+ const ptEnd = polymerType[riEnd]
+ if (ptStart === PolymerType.NA || ptEnd === PolymerType.NA) return false
if (traceElementIndex[riStart] === -1 || traceElementIndex[riEnd] === -1) return false
- let eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'backboneStart'))
- let eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'backboneEnd'))
+ let eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(ptStart, 'backboneStart'))
+ let eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(ptEnd, 'backboneEnd'))
if (eiStart === -1 || eiEnd === -1) {
- eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(mtStart, 'coarseBackbone'))
- eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(mtEnd, 'coarseBackbone'))
+ eiStart = index.findAtomsOnResidue(riStart, getAtomIdForAtomRole(ptStart, 'coarseBackbone'))
+ eiEnd = index.findAtomsOnResidue(riEnd, getAtomIdForAtomRole(ptEnd, 'coarseBackbone'))
}
const { x, y, z } = conformation
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 1302c2fe162aab2725f6c6d8de932312db602389..db24b3aa672630dad7dfcbf3d7ef3eae5469599c 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -40,30 +40,49 @@ export const enum EntityType {
}
export const enum MoleculeType {
- /** the molecule type is not known */
- unknown,
- /** a known, but here not listed molecule type */
- other,
- /** water molecule */
- water,
- /** small ionic molecule */
- ion,
- /** protein, e.g. component type included in `ProteinComponentTypeNames` */
- protein,
+ /** The molecule type is not known */
+ Unknown,
+ /** A known, but here not listed molecule type */
+ Other,
+ /** Water molecule */
+ Water,
+ /** Small ionic molecule */
+ Ion,
+ /** Protein, e.g. component type included in `ProteinComponentTypeNames` */
+ Protein,
/** RNA, e.g. component type included in `RNAComponentTypeNames` */
RNA,
/** DNA, e.g. component type included in `DNAComponentTypeNames` */
DNA,
/** PNA, peptide nucleic acid, comp id included in `PeptideBaseNames` */
PNA,
- /** sacharide, e.g. component type included in `SaccharideComponentTypeNames` */
- saccharide
+ /** Saccharide, e.g. component type included in `SaccharideComponentTypeNames` */
+ Saccharide
+}
+
+export const enum PolymerType {
+ /** not applicable */
+ NA,
+ Protein,
+ GammaProtein,
+ BetaProtein,
+ RNA,
+ DNA,
+ PNA,
}
export type AtomRole = 'trace' | 'directionFrom' | 'directionTo' | 'backboneStart' | 'backboneEnd' | 'coarseBackbone'
-export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<string> } } = {
- [MoleculeType.protein]: {
+export const PolymerTypeAtomRoleId: { [k in PolymerType]: { [k in AtomRole]: Set<string> } } = {
+ [PolymerType.NA]: {
+ trace: new Set(),
+ directionFrom: new Set(),
+ directionTo: new Set(),
+ backboneStart: new Set(),
+ backboneEnd: new Set(),
+ coarseBackbone: new Set()
+ },
+ [PolymerType.Protein]: {
trace: new Set(['CA']),
directionFrom: new Set(['C']),
directionTo: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT']),
@@ -73,7 +92,23 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
// BB is often used for coarse grained models
coarseBackbone: new Set(['CA', 'BB', 'CA1'])
},
- [MoleculeType.RNA]: {
+ [PolymerType.GammaProtein]: {
+ trace: new Set(['CA']),
+ directionFrom: new Set(['C']),
+ directionTo: new Set(['O']),
+ backboneStart: new Set(['N']),
+ backboneEnd: new Set(['CD']),
+ coarseBackbone: new Set(['CA'])
+ },
+ [PolymerType.BetaProtein]: {
+ trace: new Set(['CA']),
+ directionFrom: new Set(['C']),
+ directionTo: new Set(['O']),
+ backboneStart: new Set(['N']),
+ backboneEnd: new Set(['CG']),
+ coarseBackbone: new Set(['CA'])
+ },
+ [PolymerType.RNA]: {
trace: new Set(['C4\'', 'C4*']),
directionFrom: new Set(['C4\'', 'C4*']),
directionTo: new Set(['C3\'', 'C3*']),
@@ -81,7 +116,7 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
backboneEnd: new Set(['O3\'', 'O3*']),
coarseBackbone: new Set(['P'])
},
- [MoleculeType.DNA]: {
+ [PolymerType.DNA]: {
trace: new Set(['C3\'', 'C3*']),
directionFrom: new Set(['C3\'', 'C3*']),
directionTo: new Set(['C1\'', 'C1*']),
@@ -89,7 +124,7 @@ export const MoleculeTypeAtomRoleId: { [k: number]: { [k in AtomRole]: Set<strin
backboneEnd: new Set(['O3\'', 'O3*']),
coarseBackbone: new Set(['P'])
},
- [MoleculeType.PNA]: {
+ [PolymerType.PNA]: {
trace: new Set(['N4\'', 'N4*']),
directionFrom: new Set(['N4\'', 'N4*']),
directionTo: new Set(['C7\'', 'C7*']),
@@ -127,6 +162,16 @@ export const LProteinComponentTypeNames = new Set([
'L-BETA-PEPTIDE, C-GAMMA LINKING'
])
+/** Chemical component type names for gamma protein, overlaps with D/L-linked */
+export const GammaProteinComponentTypeNames = new Set([
+ 'D-GAMMA-PEPTIDE, C-DELTA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING'
+])
+
+/** Chemical component type names for beta protein, overlaps with D/L-linked */
+export const BetaProteinComponentTypeNames = new Set([
+ 'D-BETA-PEPTIDE, C-GAMMA LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING'
+])
+
/** Chemical component type names for pepdite-like protein */
export const OtherProteinComponentTypeNames = new Set([
'PEPTIDE LINKING', 'PEPTIDE-LIKE',
@@ -206,32 +251,53 @@ export const isPyrimidineBase = (compId: string) => PyrimidineBaseNames.has(comp
export const PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames)
/** get the molecule type from component type and id */
-export function getMoleculeType(compType: string, compId: string) {
+export function getMoleculeType(compType: string, compId: string): MoleculeType {
compType = compType.toUpperCase()
compId = compId.toUpperCase()
if (PeptideBaseNames.has(compId)) {
return MoleculeType.PNA
} else if (ProteinComponentTypeNames.has(compType)) {
- return MoleculeType.protein
+ return MoleculeType.Protein
} else if (RNAComponentTypeNames.has(compType)) {
return MoleculeType.RNA
} else if (DNAComponentTypeNames.has(compType)) {
return MoleculeType.DNA
} else if (SaccharideComponentTypeNames.has(compType)) {
- return MoleculeType.saccharide
+ return MoleculeType.Saccharide
} else if (WaterNames.has(compId)) {
- return MoleculeType.water
+ return MoleculeType.Water
} else if (IonNames.has(compId)) {
- return MoleculeType.ion
+ return MoleculeType.Ion
} else if (OtherComponentTypeNames.has(compType)) {
if (SaccharideCompIdMap.has(compId)) {
// trust our saccharide table more than given 'non-polymer' or 'other' component type
- return MoleculeType.saccharide
+ return MoleculeType.Saccharide
+ } else {
+ return MoleculeType.Other
+ }
+ } else {
+ return MoleculeType.Unknown
+ }
+}
+
+export function getPolymerType(compType: string, molType: MoleculeType): PolymerType {
+ compType = compType.toUpperCase()
+ if (molType === MoleculeType.Protein) {
+ if (GammaProteinComponentTypeNames.has(compType)) {
+ return PolymerType.GammaProtein
+ } else if (BetaProteinComponentTypeNames.has(compType)) {
+ return PolymerType.BetaProtein
} else {
- return MoleculeType.other
+ return PolymerType.Protein
}
+ } else if (molType === MoleculeType.RNA) {
+ return PolymerType.RNA
+ } else if (molType === MoleculeType.DNA) {
+ return PolymerType.DNA
+ } else if (molType === MoleculeType.PNA) {
+ return PolymerType.PNA
} else {
- return MoleculeType.unknown
+ return PolymerType.NA
}
}
@@ -316,7 +382,7 @@ export function isNucleic(moleculeType: MoleculeType) {
}
export function isProtein(moleculeType: MoleculeType) {
- return moleculeType === MoleculeType.protein
+ return moleculeType === MoleculeType.Protein
}
/**
diff --git a/src/mol-model/structure/structure/accessible-surface-area.ts b/src/mol-model/structure/structure/accessible-surface-area.ts
index 4f9dc1aae44425795dbc308e6392fcd553b0cc1c..bead67b128e0f5f32e693b897397889ebb74d8e3 100644
--- a/src/mol-model/structure/structure/accessible-surface-area.ts
+++ b/src/mol-model/structure/structure/accessible-surface-area.ts
@@ -192,7 +192,7 @@ namespace AccessibleSurfaceArea {
if (isNucleic(residueType)) {
ctx.atomRadius[aI] = determineRadiusNucl(atomId, element, compId);
- } else if (residueType === MoleculeType.protein) {
+ } else if (residueType === MoleculeType.Protein) {
ctx.atomRadius[aI] = determineRadiusAmino(atomId, element, compId);
} else {
ctx.atomRadius[aI] = handleNonStandardCase(element);
diff --git a/src/mol-model/structure/util.ts b/src/mol-model/structure/util.ts
index f1622f24ade5d773f3141deaba08afd3f3450e07..aed81f1015eace998d15a188e50a01687677c9cb 100644
--- a/src/mol-model/structure/util.ts
+++ b/src/mol-model/structure/util.ts
@@ -5,7 +5,7 @@
*/
import { Model, ResidueIndex, ElementIndex } from './model';
-import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId, getMoleculeType } from './model/types';
+import { MoleculeType, AtomRole, PolymerTypeAtomRoleId, getMoleculeType, PolymerType } from './model/types';
import { Vec3 } from '../../mol-math/linear-algebra';
import { Unit } from './structure';
import Matrix from '../../mol-math/linear-algebra/matrix/matrix';
@@ -28,7 +28,7 @@ export function getElementMoleculeType(unit: Unit, element: ElementIndex): Molec
const cc = unit.model.properties.chemicalComponentMap.get(compId)
if (cc) return getMoleculeType(cc.type, compId)
}
- return MoleculeType.unknown
+ return MoleculeType.Unknown
}
export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeType {
@@ -36,10 +36,10 @@ export function getAtomicMoleculeType(model: Model, rI: ResidueIndex): MoleculeT
}
const EmptyAtomIds = new Set<string>()
-export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
- const m = MoleculeTypeAtomRoleId[moleculeType]
- if (m !== undefined) {
- const a = m[atomRole]
+export function getAtomIdForAtomRole(polymerType: PolymerType, atomRole: AtomRole) {
+ const p = PolymerTypeAtomRoleId[polymerType]
+ if (p !== undefined) {
+ const a = p[atomRole]
if (a !== undefined) return a
}
return EmptyAtomIds
diff --git a/src/mol-plugin/behavior/dynamic/labels.ts b/src/mol-plugin/behavior/dynamic/labels.ts
index e559d04cf7a19443d4a99a99820619d863fba560..52d1af8daf9fcecf1f4dfae85c5a792c2e31f439 100644
--- a/src/mol-plugin/behavior/dynamic/labels.ts
+++ b/src/mol-plugin/behavior/dynamic/labels.ts
@@ -159,7 +159,7 @@ export const SceneLabels = PluginBehavior.create<SceneLabelsProps>({
if (p.levels.includes('ligand') && !u.polymerElements.length) {
const moleculeType = getElementMoleculeType(u, u.elements[0])
- if (moleculeType === MoleculeType.other || moleculeType === MoleculeType.saccharide) {
+ if (moleculeType === MoleculeType.Other || moleculeType === MoleculeType.Saccharide) {
label = `${StructureProperties.entity.pdbx_description(l).join(', ')} (${getAsymId(u)(l)})`
}
}
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index d8964ad78ab6b28e2e627b9ebdb39d522c45a61f..b9d63dcec58562581c9d35e0ffbfefb1351ab8bf 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -56,7 +56,7 @@ function createPolymerTraceElement (unit: Unit): PolymerTraceElement {
initial: false, final: false,
secStrucFirst: false, secStrucLast: false,
secStrucType: SecStrucTypeNA,
- moleculeType: MoleculeType.unknown,
+ moleculeType: MoleculeType.Unknown,
coarseBackboneFirst: false, coarseBackboneLast: false,
isCoarseBackbone: false,
p0: Vec3(), p1: Vec3(), p2: Vec3(), p3: Vec3(), p4: Vec3(),
diff --git a/src/mol-theme/color/molecule-type.ts b/src/mol-theme/color/molecule-type.ts
index a1c808c3b488201d970540f4dc6153b1908ee928..65ae157ca242e0010d46b211a9785f1eb76b3e29 100644
--- a/src/mol-theme/color/molecule-type.ts
+++ b/src/mol-theme/color/molecule-type.ts
@@ -41,13 +41,13 @@ export function getMoleculeTypeColorThemeParams(ctx: ThemeDataContext) {
export function moleculeTypeColor(colorMap: MoleculeTypeColors, unit: Unit, element: ElementIndex): Color {
const moleculeType = getElementMoleculeType(unit, element)
switch (moleculeType) {
- case MoleculeType.water: return colorMap.water
- case MoleculeType.ion: return colorMap.ion
- case MoleculeType.protein: return colorMap.protein
+ case MoleculeType.Water: return colorMap.water
+ case MoleculeType.Ion: return colorMap.ion
+ case MoleculeType.Protein: return colorMap.protein
case MoleculeType.RNA: return colorMap.RNA
case MoleculeType.DNA: return colorMap.DNA
case MoleculeType.PNA: return colorMap.PNA
- case MoleculeType.saccharide: return colorMap.saccharide
+ case MoleculeType.Saccharide: return colorMap.saccharide
}
return DefaultMoleculeTypeColor
}
diff --git a/src/mol-theme/color/secondary-structure.ts b/src/mol-theme/color/secondary-structure.ts
index 006a3dbaab484afa41cabae8874626019029f6b0..dbdf62b48e1fb95b0a8b0499c23f1f7195373690 100644
--- a/src/mol-theme/color/secondary-structure.ts
+++ b/src/mol-theme/color/secondary-structure.ts
@@ -75,9 +75,9 @@ export function secondaryStructureColor(colorMap: SecondaryStructureColors, unit
return colorMap.dna
} else if (moleculeType === MoleculeType.RNA) {
return colorMap.rna
- } else if (moleculeType === MoleculeType.saccharide) {
+ } else if (moleculeType === MoleculeType.Saccharide) {
return colorMap.carbohydrate
- } else if (moleculeType === MoleculeType.protein) {
+ } else if (moleculeType === MoleculeType.Protein) {
return colorMap.coil
}
}