diff --git a/src/mol-model-formats/structure/mmcif/atomic.ts b/src/mol-model-formats/structure/mmcif/atomic.ts
index 7c4fbfbbfba1b8a266302d7bfbb2627186153ead..422d45776d1fdd1f8b89378a0f7f4e902c8de3f5 100644
--- a/src/mol-model-formats/structure/mmcif/atomic.ts
+++ b/src/mol-model-formats/structure/mmcif/atomic.ts
@@ -101,7 +101,7 @@ export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_sit
const index = getAtomicIndex(hierarchyData, entities, hierarchySegments);
const derived = getAtomicDerivedData(hierarchyData, index, formatData.chemicalComponentMap);
- const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, formatData.chemicalComponentMap);
+ const hierarchyRanges = getAtomicRanges(hierarchyData, hierarchySegments, conformation, derived.residue.moleculeType);
const hierarchy: AtomicHierarchy = { ...hierarchyData, ...hierarchySegments, ...hierarchyRanges, index, derived };
return { sameAsPrevious: false, hierarchy, conformation };
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 5d435458b246b19a6efc80e5d43705c89e22a1c6..8a8e4012695ad8af3f777f8ea12e7bd1c6cb6c81 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -23,11 +23,12 @@ import { getSecondaryStructureMmCif } from './secondary-structure';
import { getSequence } from './sequence';
import { sortAtomSite } from './sort';
import { StructConn } from './bonds/struct_conn';
-import { ChemicalComponent, ChemicalComponentMap, CommonChemicalComponentMap } from 'mol-model/structure/model/properties/chemical-component';
+import { ChemicalComponent, ChemicalComponentMap } from 'mol-model/structure/model/properties/chemical-component';
import { ComponentType, getMoleculeType, MoleculeType } from 'mol-model/structure/model/types';
import { ModelFormat } from '../format';
import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from 'mol-model/structure/structure/carbohydrates/constants';
import mmCIF_Format = ModelFormat.mmCIF
+import { memoize1 } from 'mol-util/memoize';
export async function _parse_mmCif(format: mmCIF_Format, ctx: RuntimeContext) {
const formatData = getFormatData(format)
@@ -78,6 +79,7 @@ function getNcsOperators(format: mmCIF_Format) {
}
return opers;
}
+
function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['modifiedResidues'] {
const data = format.data.pdbx_struct_mod_residue;
const parentId = new Map<string, string>();
@@ -95,9 +97,9 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
}
function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
+ const map = new Map<string, ChemicalComponent>();
const { chem_comp } = format.data
if (chem_comp._rowCount > 0) {
- const map = new Map<string, ChemicalComponent>();
const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
for (let i = 0, il = id.rowCount; i < il; ++i) {
const _id = id.value(i)
@@ -113,10 +115,8 @@ function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
}
map.set(_id, cc)
}
- return map
- } else {
- return CommonChemicalComponentMap
}
+ return map
}
function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
@@ -147,12 +147,24 @@ function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap
}
}
} else {
- // TODO check if present in format.data.atom_site.label_comp_id
- SaccharideCompIdMap.forEach((v, k) => map.set(k, v))
+ const uniqueNames = getUniqueComponentNames(format)
+ SaccharideCompIdMap.forEach((v, k) => {
+ if (uniqueNames.has(k)) map.set(k, v)
+ })
}
return map
}
+const getUniqueComponentNames = memoize1((format: mmCIF_Format) => {
+ const uniqueNames = new Set<string>()
+ const data = format.data.atom_site
+ const comp_id = data.label_comp_id.isDefined ? data.label_comp_id : data.auth_comp_id;
+ for (let i = 0, il = comp_id.rowCount; i < il; ++i) {
+ uniqueNames.add(comp_id.value(i))
+ }
+ return uniqueNames
+})
+
export interface FormatData {
modifiedResidues: Model['properties']['modifiedResidues']
chemicalComponentMap: Model['properties']['chemicalComponentMap']
diff --git a/src/mol-model/structure/model/properties/chemical-component.ts b/src/mol-model/structure/model/properties/chemical-component.ts
index 76d23851d5daf220e16c881a0a8c986a995c13b0..35d34e571790872c8e1a110bc125705d7a4b49c4 100644
--- a/src/mol-model/structure/model/properties/chemical-component.ts
+++ b/src/mol-model/structure/model/properties/chemical-component.ts
@@ -16,209 +16,4 @@ export interface ChemicalComponent {
formulaWeight: number
}
-export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
-
-const CommonChemicalComponents: ChemicalComponent[] = [
- {
- id: 'ALA',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'ALANINE',
- synonyms: [],
- formula: 'C3 H7 N O2',
- formulaWeight: 89.093
- },
- {
- id: 'ARG',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'ARGININE',
- synonyms: [],
- formula: 'C6 H15 N4 O2 1',
- formulaWeight: 175.209
- },
- {
- id: 'ASN',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'ASPARAGINE',
- synonyms: [],
- formula: 'C4 H8 N2 O3',
- formulaWeight: 132.118
- },
- {
- id: 'ASP',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'ASPARTIC ACID',
- synonyms: [],
- formula: 'C4 H7 N O4',
- formulaWeight: 133.103
- },
- {
- id: 'CYS',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'CYSTEINE',
- synonyms: [],
- formula: 'C3 H7 N O2 S',
- formulaWeight: 121.158
- },
- {
- id: 'GLN',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'GLUTAMINE',
- synonyms: [],
- formula: 'C5 H10 N2 O3',
- formulaWeight: 146.144
- },
- {
- id: 'GLU',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'GLUTAMIC ACID',
- synonyms: [],
- formula: 'C5 H9 N O4',
- formulaWeight: 147.129
- },
- {
- id: 'GLY',
- type: ComponentType['peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'GLYCINE',
- synonyms: [],
- formula: 'C2 H5 N O2',
- formulaWeight: 75.067
- },
- {
- id: 'HIS',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'HISTIDINE',
- synonyms: [],
- formula: 'C6 H10 N3 O2 1',
- formulaWeight: 156.162
- },
- {
- id: 'ILE',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'ISOLEUCINE',
- synonyms: [],
- formula: 'C6 H13 N O2',
- formulaWeight: 131.173
- },
- {
- id: 'LEU',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'LEUCINE',
- synonyms: [],
- formula: 'C6 H13 N O2',
- formulaWeight: 131.173
- },
- {
- id: 'LYS',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'LYSINE',
- synonyms: [],
- formula: 'C6 H15 N2 O2 1',
- formulaWeight: 147.195
- },
- {
- id: 'MET',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'METHIONINE',
- synonyms: [],
- formula: 'C5 H11 N O2 S',
- formulaWeight: 149.211
- },
- {
- id: 'PHE',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'PHENYLALANINE',
- synonyms: [],
- formula: 'C9 H11 N O2',
- formulaWeight: 165.19
- },
- {
- id: 'PRO',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'PROLINE',
- synonyms: [],
- formula: 'C5 H9 N O2',
- formulaWeight: 115.13
- },
- { // 'O' as per IUPAC definition
- id: 'PYL',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'PYRROLYSINE',
- synonyms: [],
- formula: 'C12 H21 N3 O3',
- formulaWeight: 255.31
- },
- { // 'U' as per IUPAC definition
- id: 'SEC',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'SELENOCYSTEINE',
- synonyms: [],
- formula: 'C3 H7 N O2 Se',
- formulaWeight: 168.05
- },
- {
- id: 'SER',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'SERINE',
- synonyms: [],
- formula: 'C3 H7 N O3',
- formulaWeight: 105.09
- },
- {
- id: 'THR',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'THREONINE',
- synonyms: [],
- formula: 'C4 H9 N O3',
- formulaWeight: 119.12
- },
- {
- id: 'TRP',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'TRYPTOPHAN',
- synonyms: [],
- formula: 'C11 H12 N2 O2',
- formulaWeight: 204.22
- },
- {
- id: 'TYR',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'TYROSINE',
- synonyms: [],
- formula: 'C9 H11 N O3',
- formulaWeight: 181.19
- },
- {
- id: 'VAL',
- type: ComponentType['L-peptide linking'],
- moleculeType: MoleculeType.protein,
- name: 'VALINE',
- synonyms: [],
- formula: 'C5 H11 N O2',
- formulaWeight: 117.15
- }
-]
-export const CommonChemicalComponentMap = new Map()
-for (let i = 0, il = CommonChemicalComponents.length; i < il; ++i) {
- CommonChemicalComponentMap.set(CommonChemicalComponents[i].id, CommonChemicalComponents[i])
-}
\ No newline at end of file
+export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
\ No newline at end of file
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 c998a2513010e4ea9315d3202f148d33b982dfce..5dcb94da5b0f869eee578eca33f241d1846c31af 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-derived.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-derived.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>
*/
@@ -8,22 +8,32 @@ import { AtomicData } from '../atomic';
import { ChemicalComponentMap } from '../chemical-component';
import { AtomicIndex, AtomicDerivedData } from '../atomic/hierarchy';
import { ElementIndex, ResidueIndex } from '../../indexing';
-import { MoleculeType } from '../../types';
+import { MoleculeType, getMoleculeType, getComponentType } from '../../types';
import { getAtomIdForAtomRole } from 'mol-model/structure/util';
export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemicalComponentMap: ChemicalComponentMap): AtomicDerivedData {
-
const { label_comp_id, _rowCount: n } = data.residues
const traceElementIndex = new Uint32Array(n)
const directionElementIndex = new Uint32Array(n)
const moleculeType = new Uint8Array(n)
+ const moleculeTypeMap = new Map<string, MoleculeType>()
+
for (let i = 0; i < n; ++i) {
const compId = label_comp_id.value(i)
const chemCompMap = chemicalComponentMap
const cc = chemCompMap.get(compId)
- const molType = cc ? cc.moleculeType : MoleculeType.unknown
+ let molType: MoleculeType
+ if (cc) {
+ molType = cc.moleculeType
+ } else if (moleculeTypeMap.has(compId)){
+ molType = moleculeTypeMap.get(compId)!
+ } else {
+ molType = getMoleculeType(getComponentType(compId), compId)
+ // TODO if unknown molecule type, use atom names to guess molecule type
+ moleculeTypeMap.set(compId, molType)
+ }
moleculeType[i] = molType
const traceAtomId = getAtomIdForAtomRole(molType, 'trace')
@@ -33,7 +43,6 @@ export function getAtomicDerivedData(data: AtomicData, index: AtomicIndex, chemi
directionElementIndex[i] = index.findAtomOnResidue(i as ResidueIndex, directionAtomId)
}
-
return {
residue: {
traceElementIndex: traceElementIndex as unknown as ArrayLike<ElementIndex>,
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 7853fb37776f4f9abc625c332e08b55883357a20..ed6816364115f26aa64dbf6a981bf35b3a8c751d 100644
--- a/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-ranges.ts
@@ -8,7 +8,6 @@ import { AtomicSegments } from '../atomic';
import { AtomicData, AtomicRanges } from '../atomic/hierarchy';
import { Segmentation, Interval } from 'mol-data/int';
import SortedRanges from 'mol-data/int/sorted-ranges';
-import { ChemicalComponentMap } from '../chemical-component';
import { MoleculeType, isPolymer } from '../../types';
import { ElementIndex, ResidueIndex } from '../../indexing';
import { getAtomIdForAtomRole } from '../../../util';
@@ -17,11 +16,6 @@ import { Vec3 } from 'mol-math/linear-algebra';
// TODO add gaps at the ends of the chains by comparing to the polymer sequence data
-function getMoleculeType(compId: string, chemicalComponentMap: ChemicalComponentMap) {
- const cc = chemicalComponentMap.get(compId)
- return cc ? cc.moleculeType : MoleculeType.unknown
-}
-
function getElementIndexForAtomId(rI: ResidueIndex, atomId: string, data: AtomicData, segments: AtomicSegments): ElementIndex {
const { offsets } = segments.residueAtomSegments
const { label_atom_id } = data.atoms
@@ -31,10 +25,9 @@ function getElementIndexForAtomId(rI: ResidueIndex, atomId: string, data: Atomic
return offsets[rI]
}
-function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap) {
- const { label_comp_id } = data.residues
- const mtStart = getMoleculeType(label_comp_id.value(riStart), chemicalComponentMap)
- const mtEnd = getMoleculeType(label_comp_id.value(riEnd), chemicalComponentMap)
+function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, moleculeType: ArrayLike<MoleculeType>) {
+ const mtStart = moleculeType[riStart]
+ const mtEnd = moleculeType[riEnd]
if (!isPolymer(mtStart) || !isPolymer(mtEnd)) return false
const startId = getAtomIdForAtomRole(mtStart, 'backboneStart')
@@ -49,13 +42,13 @@ function areBackboneConnected(riStart: ResidueIndex, riEnd: ResidueIndex, data:
return Vec3.distance(pStart, pEnd) < 10
}
-export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, chemicalComponentMap: ChemicalComponentMap): AtomicRanges {
+export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conformation: AtomicConformation, moleculeType: ArrayLike<MoleculeType>): AtomicRanges {
const polymerRanges: number[] = []
const gapRanges: number[] = []
const cyclicPolymerMap = new Map<ResidueIndex, ResidueIndex>()
const chainIt = Segmentation.transientSegments(segments.chainAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
const residueIt = Segmentation.transientSegments(segments.residueAtomSegments, Interval.ofBounds(0, data.atoms._rowCount))
- const { label_seq_id, label_comp_id } = data.residues
+ const { label_seq_id } = data.residues
let prevSeqId: number
let prevStart: number
@@ -72,7 +65,7 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
const riStart = segments.residueAtomSegments.index[chainSegment.start]
const riEnd = segments.residueAtomSegments.index[chainSegment.end - 1]
- if (areBackboneConnected(riStart, riEnd, data, segments, conformation, chemicalComponentMap)) {
+ if (areBackboneConnected(riStart, riEnd, data, segments, conformation, moleculeType)) {
cyclicPolymerMap.set(riStart, riEnd)
cyclicPolymerMap.set(riEnd, riStart)
}
@@ -80,9 +73,8 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
while (residueIt.hasNext) {
const residueSegment = residueIt.move();
const residueIndex = residueSegment.index
- const moleculeType = getMoleculeType(label_comp_id.value(residueIndex), chemicalComponentMap)
const seqId = label_seq_id.value(residueIndex)
- if (isPolymer(moleculeType)) {
+ if (isPolymer(moleculeType[residueIndex])) {
if (startIndex !== -1) {
if (seqId !== prevSeqId + 1) {
polymerRanges.push(startIndex, prevEnd - 1)
@@ -93,7 +85,7 @@ export function getAtomicRanges(data: AtomicData, segments: AtomicSegments, conf
} else {
const riStart = segments.residueAtomSegments.index[residueSegment.start]
const riEnd = segments.residueAtomSegments.index[prevEnd - 1]
- if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, chemicalComponentMap)) {
+ if (!areBackboneConnected(riStart, riEnd, data, segments, conformation, moleculeType)) {
polymerRanges.push(startIndex, prevEnd - 1)
startIndex = residueSegment.start
}
diff --git a/src/mol-model/structure/model/types.ts b/src/mol-model/structure/model/types.ts
index 4f2b7d525341c3162d4ae59d58e6a2d1964604e2..20d44428bb70f4bbfcc9d7d7ea7990a172e3a4cd 100644
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -6,6 +6,7 @@
*/
import BitFlags from 'mol-util/bit-flags'
+import { SaccharideCompIdMap } from '../structure/carbohydrates/constants';
const _esCache = (function () {
const cache = Object.create(null);
@@ -158,9 +159,32 @@ export const WaterNames = [
'SOL', 'WAT', 'HOH', 'H2O', 'W', 'DOD', 'D3O', 'TIP3', 'TIP4', 'SPC'
]
-export const ExtraSaccharideNames = [
- 'MLR'
-]
+export const AminoAcidOneLetterCodeMap = {
+ 'HIS': 'H',
+ 'ARG': 'R',
+ 'LYS': 'K',
+ 'ILE': 'I',
+ 'PHE': 'F',
+ 'LEU': 'L',
+ 'TRP': 'W',
+ 'ALA': 'A',
+ 'MET': 'M',
+ 'PRO': 'P',
+ 'CYS': 'C',
+ 'ASN': 'N',
+ 'VAL': 'V',
+ 'GLY': 'G',
+ 'SER': 'S',
+ 'GLN': 'Q',
+ 'TYR': 'Y',
+ 'ASP': 'D',
+ 'GLU': 'E',
+ 'THR': 'T',
+
+ 'SEC': 'U', // as per IUPAC definition
+ 'PYL': 'O', // as per IUPAC definition
+}
+export const AminoAcidNames = Object.keys(AminoAcidOneLetterCodeMap)
export const RnaBaseNames = [ 'A', 'C', 'T', 'G', 'I', 'U' ]
export const DnaBaseNames = [ 'DA', 'DC', 'DT', 'DG', 'DI', 'DU' ]
@@ -184,7 +208,7 @@ export function getMoleculeType(compType: string, compId: string) {
return MoleculeType.RNA
} else if (DNAComponentTypeNames.includes(compType)) {
return MoleculeType.DNA
- } else if (SaccharideComponentTypeNames.includes(compType) || ExtraSaccharideNames.includes(compId)) {
+ } else if (SaccharideComponentTypeNames.includes(compType)) {
return MoleculeType.saccharide
} else if (WaterNames.includes(compId)) {
return MoleculeType.water
@@ -197,6 +221,21 @@ export function getMoleculeType(compType: string, compId: string) {
}
}
+export function getComponentType(compId: string) {
+ compId = compId.toUpperCase()
+ if (AminoAcidNames.includes(compId)) {
+ return 'peptide linking'
+ } else if (RnaBaseNames.includes(compId)) {
+ return 'RNA linking'
+ } else if (DnaBaseNames.includes(compId)) {
+ return 'DNA linking'
+ } else if (SaccharideCompIdMap.has(compId)) {
+ return 'saccharide'
+ } else {
+ return 'other'
+ }
+}
+
export function isPolymer(moleculeType: MoleculeType) {
return moleculeType === MoleculeType.protein || moleculeType === MoleculeType.DNA || moleculeType === MoleculeType.RNA || moleculeType === MoleculeType.PNA
}