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Commit dda4eb27 authored by Alexander Rose's avatar Alexander Rose
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wip, common chem comps

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src/mol-model/structure/model/formats/mmcif.ts
+ 21
− 16
View file @ dda4eb27
...@@ -24,7 +24,7 @@ import { getSecondaryStructureMmCif } from './mmcif/secondary-structure'; ...@@ -24,7 +24,7 @@ import { getSecondaryStructureMmCif } from './mmcif/secondary-structure';
import { getSequence } from './mmcif/sequence'; import { getSequence } from './mmcif/sequence';
import { sortAtomSite } from './mmcif/sort'; import { sortAtomSite } from './mmcif/sort';
import { StructConn } from './mmcif/bonds/struct_conn'; 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 { ComponentType, getMoleculeType, MoleculeType } from '../types';
import mmCIF_Format = Format.mmCIF import mmCIF_Format = Format.mmCIF
...@@ -90,23 +90,28 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m ...@@ -90,23 +90,28 @@ function getModifiedResidueNameMap(format: mmCIF_Format): Model['properties']['m
} }
function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap { function getChemicalComponentMap(format: mmCIF_Format): ChemicalComponentMap {
const map = new Map<string, ChemicalComponent>(); const { chem_comp } = format.data
const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp if (chem_comp._rowCount > 0) {
for (let i = 0, il = id.rowCount; i < il; ++i) { const map = new Map<string, ChemicalComponent>();
const _id = id.value(i) const { id, type, name, pdbx_synonyms, formula, formula_weight } = format.data.chem_comp
const _type = type.value(i) for (let i = 0, il = id.rowCount; i < il; ++i) {
const cc: ChemicalComponent = { const _id = id.value(i)
id: _id, const _type = type.value(i)
type: ComponentType[_type], const cc: ChemicalComponent = {
moleculeType: getMoleculeType(_type, _id), id: _id,
name: name.value(i), type: ComponentType[_type],
synonyms: pdbx_synonyms.value(i), moleculeType: getMoleculeType(_type, _id),
formula: formula.value(i), name: name.value(i),
formulaWeight: formula_weight.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 { function getSaccharideComponentMap(format: mmCIF_Format): SaccharideComponentMap {
......
src/mol-model/structure/model/properties/chemical-component.ts
+ 206
− 1
View file @ dda4eb27
...@@ -16,4 +16,209 @@ export interface ChemicalComponent { ...@@ -16,4 +16,209 @@ export interface ChemicalComponent {
formulaWeight: number formulaWeight: number
} }
export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent> export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
\ No newline at end of file
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
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