wip, common chem comps

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 {

src/mol-model/structure/model/properties/chemical-component.ts

@@ -16,4 +16,209 @@ export interface ChemicalComponent {
     formulaWeight: number
 }
 
-export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
+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])
+}