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Commit f1a4053c authored by Alexander Rose's avatar Alexander Rose
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wip, combine-mmcif script

parent 75c68689
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src/apps/combine-mmcif/index.ts
+ 162
− 48
View file @ f1a4053c
......@@ -7,17 +7,20 @@
import * as argparse from 'argparse'
import * as util from 'util'
import * as fs from 'fs'
import * as zlib from 'zlib'
import fetch from 'node-fetch'
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
const readFile = util.promisify(fs.readFile);
const writeFile = util.promisify(fs.writeFile);
import { DatabaseCollection, Database, Table } from 'mol-data/db'
import { Database, Table, DatabaseCollection } from 'mol-data/db'
import CIF from 'mol-io/reader/cif'
// import { CCD_Schema } from 'mol-io/reader/cif/schema/ccd'
import * as Encoder from 'mol-io/writer/cif'
import Computation from 'mol-util/computation'
import { mmCIF_Schema } from 'mol-io/reader/cif/schema/mmcif';
import { mmCIF_Schema, mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
import { CCD_Schema } from 'mol-io/reader/cif/schema/ccd';
import { BIRD_Schema } from 'mol-io/reader/cif/schema/bird';
// import { Table } from 'mol-io/reader/csv/data-model';
// import { Model, Structure } from 'mol-model/structure'
......@@ -30,7 +33,11 @@ export async function ensureAvailable(path: string, url: string) {
if (!fs.existsSync(DATA_DIR)) {
fs.mkdirSync(DATA_DIR);
}
fs.writeFileSync(path, await data.text())
if (url.endsWith('.gz')) {
await writeFile(path, zlib.gunzipSync(await data.buffer()))
} else {
await writeFile(path, await data.text())
}
console.log(`done downloading ${url}`)
}
}
......@@ -38,30 +45,28 @@ export async function ensureAvailable(path: string, url: string) {
export async function ensureDataAvailable() {
await ensureAvailable(CCD_PATH, CCD_URL)
await ensureAvailable(PVCD_PATH, PVCD_URL)
await ensureAvailable(BIRD_PATH, BIRD_URL)
}
function showProgress(tag: string, p: Computation.Progress) {
console.log(`[${tag}] ${p.message} ${p.isIndeterminate ? '' : (p.current / p.max * 100).toFixed(2) + '% '}(${p.elapsedMs | 0}ms)`)
}
export async function readCCD(bcif = false) {
const parsed = await parseCif(await readFileAsync(CCD_PATH, 'utf8'))
const ccd: DatabaseCollection<CCD_Schema> = {}
for (const data of parsed.result.blocks) {
// console.log(data.header)
ccd[data.header] = CIF.schema.CCD(data)
}
return ccd;
export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
const parsed = await parseCif(await readFile(path, 'utf8'))
return CIF.toDatabaseCollection(schema, parsed.result)
}
export async function readPVCD(bcif = false) {
const parsed = await parseCif(await readFileAsync(PVCD_PATH, 'utf8'))
const ccd: DatabaseCollection<CCD_Schema> = {}
for (const data of parsed.result.blocks) {
// console.log(data.header)
ccd[data.header] = CIF.schema.CCD(data)
}
return ccd;
export async function readCCD() {
return readFileAsCollection(CCD_PATH, CCD_Schema)
}
export async function readPVCD() {
return readFileAsCollection(PVCD_PATH, CCD_Schema)
}
export async function readBIRD() {
return readFileAsCollection(BIRD_PATH, BIRD_Schema)
}
export async function getCCD() {
......@@ -69,6 +74,11 @@ export async function getCCD() {
return readPVCD()
}
export async function getBIRD() {
await ensureDataAvailable()
return readBIRD()
}
async function parseCif(data: string|Uint8Array) {
const comp = CIF.parse(data)
const ctx = Computation.observable({
......@@ -97,53 +107,157 @@ export async function getPdb(pdb: string) {
return CIF.schema.mmCIF(parsed.result.blocks[0])
}
type extraTables = {
chem_comp_bond: Table<mmCIF_Schema['chem_comp_bond']>,
pdbx_reference_entity_list: Table<mmCIF_Schema['pdbx_reference_entity_list']>,
pdbx_reference_entity_link: Table<mmCIF_Schema['pdbx_reference_entity_link']>,
pdbx_reference_entity_poly_link: Table<mmCIF_Schema['pdbx_reference_entity_poly_link']>,
}
type extraTablesLists = {
[k in keyof extraTables]: extraTables[k][]
}
export function getExtraTables(mmcif: mmCIF_Database, ccd: DatabaseCollection<CCD_Schema>, bird: DatabaseCollection<BIRD_Schema>) {
const extraTablesLists: extraTablesLists = {
chem_comp_bond: [],
pdbx_reference_entity_list: [],
pdbx_reference_entity_link: [],
pdbx_reference_entity_poly_link: []
}
for (let i = 0, n = mmcif.chem_comp._rowCount; i < n; ++i) {
const ccdId = mmcif.chem_comp.id.value(i);
if (ccdId in ccd) {
extraTablesLists.chem_comp_bond.push(ccd[ccdId].chem_comp_bond)
} else {
console.error(`ccdId ${ccdId} not found`)
}
}
for (let i = 0, n = mmcif.pdbx_molecule_features._rowCount; i < n; ++i) {
const birdId = mmcif.pdbx_molecule_features.prd_id.value(i);
if (birdId in bird) {
const e = bird[birdId]
extraTablesLists.pdbx_reference_entity_list.push(e.pdbx_reference_entity_list)
extraTablesLists.pdbx_reference_entity_link.push(e.pdbx_reference_entity_link)
extraTablesLists.pdbx_reference_entity_poly_link.push(e.pdbx_reference_entity_poly_link)
} else {
console.error(`birdId ${birdId} not found`)
}
}
const extraTables: extraTables = Object.assign({}, ...Object.keys(extraTablesLists).map(k => {
// TODO how to avoid type casting?
return { [k]: Table.concat((extraTablesLists as any)[k], (mmCIF_Schema as any)[k]) }
}))
return extraTables
}
type PartialStructConnRow = Partial<Table.Row<mmCIF_Schema['struct_conn']>>
export function getStructConnValueOrder(value: any): mmCIF_Schema['struct_conn']['pdbx_value_order']['T'] {
return mmCIF_Schema.struct_conn.pdbx_value_order['T'].includes(value) ? value : 'sing'
}
export function getBirdBonds(mmcif: mmCIF_Database) {
const bonds: PartialStructConnRow[] = []
const mol = mmcif.pdbx_molecule
const molFeat = mmcif.pdbx_molecule_features
for (let i = 0, n = molFeat._rowCount; i < n; ++i) {
// console.log(Table.getRow(molFeat, i))
const instancesAsymIdList: { [k: number]: string[] } = {}
for (let j = 0, m = mol._rowCount; j < m; ++j) {
if (mol.prd_id.value(j) === molFeat.prd_id.value(i)) {
// console.log(Table.getRow(mol, j))
const instanceId = mol.instance_id.value(j)
if (instancesAsymIdList[instanceId] === undefined) {
instancesAsymIdList[instanceId] = []
}
instancesAsymIdList[instanceId].push(mol.asym_id.value(j))
}
}
// console.log(instancesAsymIdList)
const entityLink = mmcif.pdbx_reference_entity_link
for (const instanceId of Object.keys(instancesAsymIdList)) {
const asymIdList = instancesAsymIdList[instanceId as any]
for (let j = 0, m = entityLink._rowCount; j < m; ++j) {
if (entityLink.prd_id.value(j) === molFeat.prd_id.value(i)) {
// console.log(Table.getRow(entityLink, j))
const link: PartialStructConnRow = {
ptnr1_label_asym_id: asymIdList[ entityLink.component_1.value(j) - 1 ],
ptnr1_label_atom_id: entityLink.atom_id_1.value(j),
ptnr1_label_comp_id: entityLink.comp_id_1.value(j),
ptnr1_label_seq_id: entityLink.entity_seq_num_1.value(j),
ptnr2_label_asym_id: asymIdList[ entityLink.component_2.value(j) - 1 ],
ptnr2_label_atom_id: entityLink.atom_id_2.value(j),
ptnr2_label_comp_id: entityLink.comp_id_2.value(j),
ptnr2_label_seq_id: entityLink.entity_seq_num_2.value(j),
pdbx_value_order: getStructConnValueOrder(entityLink.value_order.value(j)),
}
// console.log(link)
bonds.push(link)
}
}
}
}
return bonds
}
export function getCcdBonds(mmcif: mmCIF_Database) {
const bonds: PartialStructConnRow[] = []
}
async function run(pdb: string, out?: string) {
const ccd = await getCCD()
// console.log(Object.keys(ccd).length)
const bird = await getBIRD()
const mmcif = await getPdb(pdb)
// console.log(mmcif.chem_comp.id.toArray())
// const chemCompBond_Schema = { chem_comp_bond: mmCIF_Schema.chem_comp_bond }
// type chemCompBond_Schema = typeof chemCompBond_Schema;
// type chemCompBond_Database = Database<chemCompBond_Schema>;
// interface chemCompBond_Database extends Database<chemCompBond_Schema> {}
for (const k of Object.keys(bird)) {
const entity = bird[k].pdbx_reference_entity_list
for (let i = 0, n = entity._rowCount; i < n; ++i) {
if (entity.ref_entity_id.value(i) !== entity.component_id.value(i).toString()) {
console.log(Table.getRow(entity, i))
}
}
const chemCompBondTables: Table<mmCIF_Schema['chem_comp_bond']>[] = []
const link = bird[k].pdbx_reference_entity_link
for (let i = 0, n = link._rowCount; i < n; ++i) {
if (link.value_order.value(i) !== 'sing') {
console.log(Table.getRow(link, i))
}
}
for (let i = 0, n = mmcif.chem_comp._rowCount; i < n; ++i) {
const ccdId = mmcif.chem_comp.id.value(i);
// console.log(ccdId)
if (ccdId in ccd) {
// console.log(`ccdId ${ccdId} has ${ccd[ccdId].chem_comp_atom._rowCount} atoms`)
// console.log(ccd[ccdId].chem_comp_bond.atom_id_1.toArray())
chemCompBondTables.push(ccd[ccdId].chem_comp_bond)
} else {
console.error(`ccdId ${ccdId} not found`)
const polyLink = bird[k].pdbx_reference_entity_poly_link
for (let i = 0, n = link._rowCount; i < n; ++i) {
if (polyLink.value_order.value(i) !== 'sing') {
console.log(Table.getRow(polyLink, i))
}
}
}
// for (const k of Object.keys(ccd)) {
// console.log(k)
// }
const extraTables = getExtraTables(mmcif, ccd, bird)
const combinedMmcif = Database.ofTables('mmcif_combined', mmCIF_Schema, Object.assign({}, mmcif, extraTables))
// console.log(getEncodedCif(pdb, combinedMmcif))
// console.log(Database.getTablesAsRows(combinedMmcif))
// const combinedChemCompBonds = Database.ofTables('chemCompBond', chemCompBond_Schema, {
// chem_comp_bond: Table.concat(chemCompBondTables, mmCIF_Schema.chem_comp_bond)
// })
// console.log('concat done')
// console.log(getEncodedCif('chemCompBond', combinedChemCompBonds))
const combinedMmcif = Database.ofTables('chemCompBond', mmCIF_Schema, Object.assign({},
mmcif,
{ chem_comp_bond: Table.concat(chemCompBondTables, mmCIF_Schema.chem_comp_bond) }
))
console.log(getEncodedCif(pdb, combinedMmcif))
// console.log(getBirdBonds(combinedMmcif))
console.log(getCcdBonds(combinedMmcif))
}
const DATA_DIR = './build/data'
const CCD_PATH = `${DATA_DIR}/components.cif`
const PVCD_PATH = `${DATA_DIR}/aa-variants-v1.cif`
const BIRD_PATH = `${DATA_DIR}/prd-all.cif`
const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif'
const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif'
const BIRD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/bird/prd/prd-all.cif.gz'
const parser = new argparse.ArgumentParser({
addHelp: true,
......
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