diff --git a/src/mol-model/structure/model/formats/mmcif.ts b/src/mol-model/structure/model/formats/mmcif.ts
index 971eebd0ab62dd2edd7799954dddffc5fa759bd7..aa0e73a544466f23c428e0b749884b445454788c 100644
--- a/src/mol-model/structure/model/formats/mmcif.ts
+++ b/src/mol-model/structure/model/formats/mmcif.ts
@@ -24,7 +24,7 @@ import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
import { getSequence } from './mmcif/sequence';
import { sortAtomSite } from './mmcif/sort';
import { StructConn } from './mmcif/bonds/struct_conn';
-import { ChemicalComponent, ChemicalComponentMap } from '../properties/chemical-component';
+import { ChemicalComponent, ChemicalComponentMap, CommonChemicalComponentMap } from '../properties/chemical-component';
import { ComponentType, getMoleculeType, MoleculeType } from '../types';
import mmCIF_Format = Format.mmCIF
@@ -90,23 +90,28 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
}
function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
- 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)
- const _type = type.value(i)
- const cc: ChemicalComponent = {
- id: _id,
- type: ComponentType[_type],
- moleculeType: getMoleculeType(_type, _id),
- name: name.value(i),
- synonyms: pdbx_synonyms.value(i),
- formula: formula.value(i),
- formulaWeight: formula_weight.value(i),
+ 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)
+ const _type = type.value(i)
+ const cc: ChemicalComponent = {
+ id: _id,
+ type: ComponentType[_type],
+ moleculeType: getMoleculeType(_type, _id),
+ name: name.value(i),
+ synonyms: pdbx_synonyms.value(i),
+ formula: formula.value(i),
+ formulaWeight: formula_weight.value(i),
+ }
+ map.set(_id, cc)
}
- map.set(_id, cc)
+ return map
+ } else {
+ return CommonChemicalComponentMap
}
- return map
}
function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
diff --git a/src/mol-model/structure/model/properties/chemical-component.ts b/src/mol-model/structure/model/properties/chemical-component.ts
index 35d34e571790872c8e1a110bc125705d7a4b49c4..76d23851d5daf220e16c881a0a8c986a995c13b0 100644
--- a/src/mol-model/structure/model/properties/chemical-component.ts
+++ b/src/mol-model/structure/model/properties/chemical-component.ts
@@ -16,4 +16,209 @@ export interface ChemicalComponent {
formulaWeight: number
}
-export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
\ No newline at end of file
+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