diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index 3b9624bcf97133f8f078cbb9104abd7d568ba132..30f201b86c2f344560749e26fdd71ecdbb34f46a 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -73,6 +73,7 @@ const StandardComponents = (function() {
})()
export class ComponentBuilder {
+ private namesMap = new Map<string, string>()
private comps = new Map<string, Component>()
private ids: string[] = []
private names: string[] = []
@@ -129,8 +130,8 @@ export class ComponentBuilder {
} else if (WaterNames.has(compId)) {
this.set({ id: compId, name: 'WATER', type: 'non-polymer' })
} else {
- const atomIds = this.getAtomIds(index)
- this.set({ id: compId, name: compId, type: this.getType(atomIds) })
+ const type = this.getType(this.getAtomIds(index))
+ this.set({ id: compId, name: this.namesMap.get(compId) || compId, type })
}
}
return this.get(compId)!
@@ -145,6 +146,10 @@ export class ComponentBuilder {
return CifCategory.ofFields('chem_comp', chemComp)
}
+ setNames(names: [string, string][]) {
+ names.forEach(n => this.namesMap.set(n[0], n[1]))
+ }
+
constructor(private seqId: Column<number>, private atomId: Column<string>) {
}
diff --git a/src/mol-model-formats/structure/common/entity.ts b/src/mol-model-formats/structure/common/entity.ts
new file mode 100644
index 0000000000000000000000000000000000000000..f416aaeac0cb6659f2a91759b12e6a3d5587201d
--- /dev/null
+++ b/src/mol-model-formats/structure/common/entity.ts
@@ -0,0 +1,80 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { CifCategory, CifField } from '../../../mol-io/reader/cif';
+import { MoleculeType, isPolymer } from '../../../mol-model/structure/model/types';
+import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
+
+export type EntityCompound = { chains: string[], description: string }
+
+export class EntityBuilder {
+ private count = 0
+ private ids: string[] = []
+ private types: string[] = []
+ private descriptions: string[] = []
+
+ private compoundsMap = new Map<string, string>()
+ private namesMap = new Map<string, string>()
+ private heteroMap = new Map<string, string>()
+ private chainMap = new Map<string, string>()
+ private waterId?: string
+
+ private set(type: string, description: string) {
+ this.count += 1
+ this.ids.push(`${this.count}`)
+ this.types.push(type)
+ this.descriptions.push(description)
+ }
+
+ getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
+ if (moleculeType === MoleculeType.water) {
+ if (this.waterId === undefined) {
+ this.set('water', 'Water')
+ this.waterId = `${this.count}`
+ }
+ return this.waterId;
+ } else if (isPolymer(moleculeType)) {
+ if (this.compoundsMap.has(chainId)) {
+ return this.compoundsMap.get(chainId)!
+ } else {
+ if (!this.chainMap.has(chainId)) {
+ this.set('polymer', `Polymer ${this.chainMap.size + 1}`)
+ this.chainMap.set(chainId, `${this.count}`)
+ }
+ return this.chainMap.get(chainId)!
+ }
+ } else {
+ if (!this.heteroMap.has(compId)) {
+ this.set('non-polymer', this.namesMap.get(compId) || compId)
+ this.heteroMap.set(compId, `${this.count}`)
+ }
+ return this.heteroMap.get(compId)!
+ }
+ }
+
+ getEntityCategory() {
+ const entity: CifCategory.SomeFields<mmCIF_Schema['entity']> = {
+ id: CifField.ofStrings(this.ids),
+ type: CifField.ofStrings(this.types),
+ pdbx_description: CifField.ofStrings(this.descriptions),
+ }
+ return CifCategory.ofFields('entity', entity)
+ }
+
+ setCompounds(compounds: EntityCompound[]) {
+ for (let i = 0, il = compounds.length; i < il; ++i) {
+ const { chains, description } = compounds[i]
+ this.set('polymer', description)
+ for (let j = 0, jl = chains.length; j < jl; ++j) {
+ this.compoundsMap.set(chains[j], `${this.count}`)
+ }
+ }
+ }
+
+ setNames(names: [string, string][]) {
+ names.forEach(n => this.namesMap.set(n[0], n[1]))
+ }
+}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/gro.ts b/src/mol-model-formats/structure/gro.ts
index 1b82cc9fca2a0b43589def0ad99d1ca66ec6663f..0ed74bf3399810bfb2a1293e34a01e6bb7f9be04 100644
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -13,61 +13,13 @@ import { CifCategory, CifField } from '../../mol-io/reader/cif';
import { Column } from '../../mol-data/db';
import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
import { guessElementSymbolString } from './util';
-import { MoleculeType, getMoleculeType, isPolymer } from '../../mol-model/structure/model/types';
+import { MoleculeType, getMoleculeType } from '../../mol-model/structure/model/types';
import { ComponentBuilder } from './common/component';
import { getChainId } from './common/util';
+import { EntityBuilder } from './common/entity';
// TODO multi model files
-class EntityBuilder {
- private count = 0
- private ids: string[] = []
- private types: string[] = []
- private descriptions: string[] = []
-
- private heteroMap = new Map<string, string>()
- private chainMap = new Map<string, string>()
- private waterId?: string
-
- private set(type: string, description: string) {
- this.count += 1
- this.ids.push(`${this.count}`)
- this.types.push(type)
- this.descriptions.push(description)
- }
-
- getEntityId(compId: string, moleculeType: MoleculeType, chainId: string): string {
- if (moleculeType === MoleculeType.water) {
- if (this.waterId === undefined) {
- this.set('water', 'Water')
- this.waterId = `${this.count}`
- }
- return this.waterId;
- } else if (isPolymer(moleculeType)) {
- if (!this.chainMap.has(chainId)) {
- this.set('polymer', `Polymer ${this.chainMap.size + 1}`)
- this.chainMap.set(chainId, `${this.count}`)
- }
- return this.chainMap.get(chainId)!
- } else {
- if (!this.heteroMap.has(compId)) {
- this.set('non-polymer', compId)
- this.heteroMap.set(compId, `${this.count}`)
- }
- return this.heteroMap.get(compId)!
- }
- }
-
- getEntityCategory() {
- const entity: CifCategory.SomeFields<mmCIF_Schema['entity']> = {
- id: CifField.ofStrings(this.ids),
- type: CifField.ofStrings(this.types),
- pdbx_description: CifField.ofStrings(this.descriptions),
- }
- return CifCategory.ofFields('entity', entity)
- }
-}
-
function getCategories(atoms: GroAtoms) {
const auth_atom_id = CifField.ofColumn(atoms.atomName)
const auth_comp_id = CifField.ofColumn(atoms.residueName)
diff --git a/src/mol-model-formats/structure/pdb/entity.ts b/src/mol-model-formats/structure/pdb/entity.ts
index 97ecd5d44d6baf8c30b596965b71553504eccef5..3402b32e960930964b157f8f28a955ddcdb53ffa 100644
--- a/src/mol-model-formats/structure/pdb/entity.ts
+++ b/src/mol-model-formats/structure/pdb/entity.ts
@@ -5,8 +5,7 @@
*/
import { Tokens } from '../../../mol-io/reader/common/text/tokenizer';
-import { CifCategory, CifField } from '../../../mol-io/reader/cif';
-import { WaterNames } from '../../../mol-model/structure/model/types';
+import { EntityCompound } from '../common/entity';
const Spec = {
'MOL_ID': '',
@@ -21,14 +20,12 @@ const Spec = {
}
type Spec = keyof typeof Spec
-type Compound = { chains: string[], name: string }
-
export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1])
let currentSpec: Spec | undefined
- let currentCompound: Compound = { chains: [], name: '' }
- const Compounds: Compound[] = []
+ let currentCompound: EntityCompound = { chains: [], description: '' }
+ const Compounds: EntityCompound[] = []
for (let i = lineStart; i < lineEnd; i++) {
let line = getLine(i)
@@ -56,12 +53,12 @@ export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
if (currentSpec === 'MOL_ID') {
currentCompound = {
chains: [],
- name: ''
+ description: ''
}
Compounds.push(currentCompound)
} else if (currentSpec === 'MOLECULE') {
- if (currentCompound.name) currentCompound.name += ' '
- currentCompound.name += value
+ if (currentCompound.description) currentCompound.description += ' '
+ currentCompound.description += value
} else if (currentSpec === 'CHAIN') {
Array.prototype.push.apply(currentCompound.chains, value.split(/\s*,\s*/))
}
@@ -70,66 +67,29 @@ export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
return Compounds
}
-export class EntityBuilder {
- private count = 0
- private ids: string[] = []
- private types: string[] = []
- private descriptions: string[] = []
-
- private compoundsMap = new Map<string, string>()
- private heteroMap = new Map<string, string>()
- private chainMap = new Map<string, string>()
- private waterId?: string
-
- private set(type: string, description: string) {
- this.count += 1
- this.ids.push(`${this.count}`)
- this.types.push(type)
- this.descriptions.push(description)
- }
+export function parseHetnam(lines: Tokens, lineStart: number, lineEnd: number) {
+ const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1])
- getEntityId(residueName: string, chainId: string, isHet: boolean): string {
- if (isHet) {
- if (WaterNames.has(residueName)) {
- if (this.waterId === undefined) {
- this.set('water', 'Water')
- this.waterId = `${this.count}`
- }
- return this.waterId;
- } else {
- if (!this.heteroMap.has(residueName)) {
- this.set('non-polymer', residueName)
- this.heteroMap.set(residueName, `${this.count}`)
- }
- return this.heteroMap.get(residueName)!
- }
- } else if (this.compoundsMap.has(chainId)) {
- return this.compoundsMap.get(chainId)!
- } else {
- if (!this.chainMap.has(chainId)) {
- this.set('polymer', chainId)
- this.chainMap.set(chainId, `${this.count}`)
- }
- return this.chainMap.get(chainId)!
- }
- }
+ const hetnams = new Map<string, string>()
- getEntityCategory() {
- const entity = {
- id: CifField.ofStrings(this.ids),
- type: CifField.ofStrings(this.types),
- pdbx_description: CifField.ofStrings(this.descriptions)
+ for (let i = lineStart; i < lineEnd; i++) {
+ let line = getLine(i)
+ // COLUMNS DATA TYPE FIELD DEFINITION
+ // ----------------------------------------------------------------------------
+ // 1 - 6 Record name "HETNAM"
+ // 9 - 10 Continuation continuation Allows concatenation of multiple records.
+ // 12 - 14 LString(3) hetID Het identifier, right-justified.
+ // 16 - 70 String text Chemical name.
+
+ const het = line.substr(11, 3).trim()
+ const name = line.substr(15).trim()
+
+ if (hetnams.has(het)) {
+ hetnams.set(het, `${hetnams.get(het)!} ${name}`)
+ } else {
+ hetnams.set(het, name)
}
- return CifCategory.ofFields('entity', entity)
}
- setCompounds(compounds: Compound[]) {
- for (let i = 0, il = compounds.length; i < il; ++i) {
- const { chains, name } = compounds[i]
- this.set('polymer', name)
- for (let j = 0, jl = chains.length; j < jl; ++j) {
- this.compoundsMap.set(chains[j], `${this.count}`)
- }
- }
- }
+ return hetnams
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index a7e1aaf826c1508c51685674205e8b4fdd2604f4..573be9a13229ea981d7c296c2194e23733c5a62f 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -13,10 +13,14 @@ import { PdbFile } from '../../../mol-io/reader/pdb/schema';
import { parseCryst1, parseRemark350, parseMtrix } from './assembly';
import { parseHelix, parseSheet } from './secondary-structure';
import { guessElementSymbolTokens } from '../util';
-import { parseCmpnd, EntityBuilder } from './entity';
-
-type AtomSiteTemplate = typeof atom_site_template extends (...args: any) => infer T ? T : never
-function atom_site_template(data: string, count: number) {
+import { parseCmpnd, parseHetnam } from './entity';
+import { ComponentBuilder } from '../common/component';
+import { EntityBuilder } from '../common/entity';
+import { Column } from '../../../mol-data/db';
+import { getMoleculeType } from '../../../mol-model/structure/model/types';
+
+type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
+function getAtomSiteTemplate(data: string, count: number) {
const str = () => [] as string[];
const ts = () => TokenBuilder.create(data, 2 * count);
return {
@@ -41,7 +45,7 @@ function atom_site_template(data: string, count: number) {
};
}
-function _atom_site(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_site']]?: CifField } {
+function getAomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_site']]?: CifField } {
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_atom_id = CifField.ofTokens(sites.auth_atom_id);
const auth_comp_id = CifField.ofTokens(sites.auth_comp_id);
@@ -75,7 +79,7 @@ function _atom_site(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema['atom_s
};
}
-function addAtom(sites: AtomSiteTemplate, entityBuilder: EntityBuilder, model: string, data: Tokenizer, s: number, e: number, isHet: boolean) {
+function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer, s: number, e: number) {
const { data: str } = data;
const length = e - s;
@@ -103,11 +107,9 @@ function addAtom(sites: AtomSiteTemplate, entityBuilder: EntityBuilder, model: s
// 18 - 20 Residue name Residue name.
TokenBuilder.addToken(sites.auth_comp_id, Tokenizer.trim(data, s + 17, s + 20));
- const residueName = str.substring(data.tokenStart, data.tokenEnd);
// 22 Character Chain identifier.
TokenBuilder.add(sites.auth_asym_id, s + 21, s + 22);
- const chainId = str.substring(s + 21, s + 22);
// 23 - 26 Integer Residue sequence number.
// TODO: support HEX
@@ -155,7 +157,6 @@ function addAtom(sites: AtomSiteTemplate, entityBuilder: EntityBuilder, model: s
guessElementSymbolTokens(sites.type_symbol, str, s + 12, s + 16)
}
- sites.label_entity_id[sites.index] = entityBuilder.getEntityId(residueName, chainId, isHet);
sites.pdbx_PDB_model_num[sites.index] = model;
sites.index++;
@@ -180,9 +181,10 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
}
- const atom_site = atom_site_template(data, atomCount);
+ const atomSite = getAtomSiteTemplate(data, atomCount);
const entityBuilder = new EntityBuilder();
const helperCategories: CifCategory[] = [];
+ const heteroNames: [string, string][] = [];
let modelNum = 0, modelStr = '';
@@ -192,7 +194,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
case 'A':
if (!substringStartsWith(data, s, e, 'ATOM ')) continue;
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
- addAtom(atom_site, entityBuilder, modelStr, tokenizer, s, e, false);
+ addAtom(atomSite, modelStr, tokenizer, s, e);
break;
case 'C':
if (substringStartsWith(data, s, e, 'CRYST1')) {
@@ -213,7 +215,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
case 'H':
if (substringStartsWith(data, s, e, 'HETATM')) {
if (!modelNum) { modelNum++; modelStr = '' + modelNum; }
- addAtom(atom_site, entityBuilder, modelStr, tokenizer, s, e, true);
+ addAtom(atomSite, modelStr, tokenizer, s, e);
} else if (substringStartsWith(data, s, e, 'HELIX')) {
let j = i + 1;
while (true) {
@@ -223,8 +225,16 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
helperCategories.push(parseHelix(lines, i, j));
i = j - 1;
+ } else if (substringStartsWith(data, s, e, 'HETNAM')) {
+ let j = i + 1;
+ while (true) {
+ s = indices[2 * j]; e = indices[2 * j + 1];
+ if (!substringStartsWith(data, s, e, 'HETNAM')) break;
+ j++;
+ }
+ heteroNames.push(...Array.from(parseHetnam(lines, i, j).entries()))
+ i = j - 1;
}
- // TODO: HETNAM records => chem_comp (at least partially, needs to be completed with common bases and amino acids)
break;
case 'M':
if (substringStartsWith(data, s, e, 'MODEL ')) {
@@ -274,9 +284,24 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
}
}
+ // build entity and chem_comp categories
+ const seqIds = Column.ofIntTokens(atomSite.auth_seq_id)
+ const atomIds = Column.ofStringTokens(atomSite.auth_atom_id)
+ const compIds = Column.ofStringTokens(atomSite.auth_comp_id)
+ const asymIds = Column.ofStringTokens(atomSite.auth_asym_id)
+ const componentBuilder = new ComponentBuilder(seqIds, atomIds)
+ componentBuilder.setNames(heteroNames)
+ entityBuilder.setNames(heteroNames)
+ for (let i = 0, il = compIds.rowCount; i < il; ++i) {
+ const compId = compIds.value(i)
+ const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId)
+ atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i))
+ }
+
const categories = {
entity: entityBuilder.getEntityCategory(),
- atom_site: CifCategory.ofFields('atom_site', _atom_site(atom_site))
+ chem_comp: componentBuilder.getChemCompCategory(),
+ atom_site: CifCategory.ofFields('atom_site', getAomSite(atomSite))
} as any;
for (const c of helperCategories) {