added app to create chemCompBond table, removed combine-mmcif app

src/apps/chem-comp-bond/create-table.ts

+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse'
+import * as util from 'util'
+import * as path from 'path'
+import * as fs from 'fs'
+import * as zlib from 'zlib'
+import fetch from 'node-fetch'
+require('util.promisify').shim()
+const readFile = util.promisify(fs.readFile)
+const writeFile = util.promisify(fs.writeFile)
+
+import { Progress } from 'mol-task'
+import { Database, Table, DatabaseCollection, Column } from 'mol-data/db'
+import CIF from 'mol-io/reader/cif'
+import { CifWriter } from 'mol-io/writer/cif'
+import { CCD_Schema } from 'mol-io/reader/cif/schema/ccd'
+import { difference } from 'mol-util/set'
+import { DefaultMap } from 'mol-util/map'
+
+export async function ensureAvailable(path: string, url: string) {
+    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
+        console.log(`downloading ${url}...`)
+        const data = await fetch(url)
+        if (!fs.existsSync(DATA_DIR)) {
+            fs.mkdirSync(DATA_DIR);
+        }
+        if (url.endsWith('.gz')) {
+            await writeFile(path, zlib.gunzipSync(await data.buffer()))
+        } else {
+            await writeFile(path, await data.text())
+        }
+        console.log(`done downloading ${url}`)
+    }
+}
+
+export async function ensureDataAvailable() {
+    await ensureAvailable(CCD_PATH, CCD_URL)
+    await ensureAvailable(PVCD_PATH, PVCD_URL)
+}
+
+export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
+    const parsed = await parseCif(await readFile(path, 'utf8'))
+    return CIF.toDatabaseCollection(schema, parsed.result)
+}
+
+export async function readCCD() {
+    return readFileAsCollection(CCD_PATH, CCD_Schema)
+}
+
+export async function readPVCD() {
+    return readFileAsCollection(PVCD_PATH, CCD_Schema)
+}
+
+async function parseCif(data: string | Uint8Array) {
+    const comp = CIF.parse(data);
+    console.time('parse cif');
+    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
+    console.timeEnd('parse cif');
+    if (parsed.isError) throw parsed;
+    return parsed
+}
+
+export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
+    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
+    CifWriter.Encoder.writeDatabase(encoder, name, database)
+    return encoder.getData();
+}
+
+type CCB = Table<CCD_Schema['chem_comp_bond']>
+type CCA = Table<CCD_Schema['chem_comp_atom']>
+
+const ChemCompBond_Schema = {
+    ...CCD_Schema['chem_comp_bond'],
+    molstar_protonation_variant: Column.Schema.Str()
+}
+
+function ccbKey(compId: string, atomId1: string, atomId2: string) {
+    return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`
+}
+
+function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
+    for (let i = 0, il = ccb._rowCount; i < il; ++i) {
+        set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)))
+    }
+    return set
+}
+
+function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
+    for (let i = 0, il = cca._rowCount; i < il; ++i) {
+        set.add(cca.atom_id.value(i))
+    }
+    return set
+}
+
+function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccbSetByParent = DefaultMap<string, Set<string>>(() => new Set())
+
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_bond } = pvcd[k]
+        if (chem_comp_bond._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            if (parentIds.length === 0) {
+                const set = ccbSetByParent.getDefault(chem_comp.id.value(0))
+                addChemCompBondToSet(set, chem_comp_bond)
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    const parentId = parentIds[i]
+                    const set = ccbSetByParent.getDefault(parentId)
+                    addChemCompBondToSet(set, chem_comp_bond)
+                }
+            }
+        }
+    }
+
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_atom, chem_comp_bond } = pvcd[k]
+        if (chem_comp_bond._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            if (parentIds.length > 0) {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    const entryBonds = addChemCompBondToSet(new Set<string>(), chem_comp_bond)
+                    const entryAtoms = addChemCompAtomToSet(new Set<string>(), chem_comp_atom)
+                    const extraBonds = difference(ccbSetByParent.get(parentIds[i])!, entryBonds)
+                    extraBonds.forEach(bk => {
+                        const [a1, a2] = bk.split('|')
+                        if (entryAtoms.has(a1) && entryAtoms.has(a2)) {
+                            console.error(`Adding all PVCD bonds would wrongly add bond ${bk} for ${k}`)
+                        }
+                    })
+                }
+            }
+        }
+    }
+}
+
+async function createBonds() {
+    await ensureDataAvailable()
+    const ccd = await readCCD()
+    const pvcd = await readPVCD()
+
+    const ccbSet = new Set<string>()
+
+    const comp_id: string[] = []
+    const atom_id_1: string[] = []
+    const atom_id_2: string[] = []
+    const value_order: string[] = []
+    const pdbx_aromatic_flag: string[] = []
+    const pdbx_stereo_config: string[] = []
+    const molstar_protonation_variant: string[] = []
+
+    function addBonds(compId: string, ccb: CCB, protonationVariant: boolean) {
+        for (let i = 0, il = ccb._rowCount; i < il; ++i) {
+            const atomId1 = ccb.atom_id_1.value(i)
+            const atomId2 = ccb.atom_id_2.value(i)
+            const k = ccbKey(compId, atomId1, atomId2)
+            if (!ccbSet.has(k)) {
+                atom_id_1.push(atomId1)
+                atom_id_2.push(atomId2)
+                comp_id.push(compId)
+                value_order.push(ccb.value_order.value(i))
+                pdbx_aromatic_flag.push(ccb.pdbx_aromatic_flag.value(i))
+                pdbx_stereo_config.push(ccb.pdbx_stereo_config.value(i))
+                molstar_protonation_variant.push(protonationVariant ? 'Y' : 'N')
+                ccbSet.add(k)
+            }
+        }
+    }
+
+    // check adding bonds from PVCD
+    checkAddingBondsFromPVCD(pvcd)
+
+    // add bonds from PVCD
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_bond } = pvcd[k]
+        if (chem_comp_bond._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0)
+            if (parentIds.length === 0) {
+                addBonds(chem_comp.id.value(0), chem_comp_bond, false)
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    addBonds(parentIds[i], chem_comp_bond, true)
+                }
+            }
+        }
+    }
+
+    // add bonds from CCD
+    for (const k in ccd) {
+        const { chem_comp, chem_comp_bond } = ccd[k]
+        if (chem_comp_bond._rowCount) {
+            addBonds(chem_comp.id.value(0), chem_comp_bond, false)
+        }
+    }
+
+    const bondTable = Table.ofArrays(ChemCompBond_Schema, {
+        comp_id, atom_id_1, atom_id_2, value_order,
+        pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
+    })
+
+    const bondDatabase =  Database.ofTables(
+        TABLE_NAME,
+        { chem_comp_bond: ChemCompBond_Schema },
+        { chem_comp_bond: bondTable }
+    )
+
+    return bondDatabase
+}
+
+async function run(out: string, binary = false) {
+    const bonds = await createBonds()
+
+    const cif = getEncodedCif(TABLE_NAME, bonds, binary)
+    writeFile(out, cif)
+}
+
+const TABLE_NAME = 'CHEM_COMP_BONDS'
+
+const DATA_DIR = path.join(__dirname, '..', '..', '..', 'data')
+const CCD_PATH = path.join(DATA_DIR, 'components.cif')
+const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.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 parser = new argparse.ArgumentParser({
+  addHelp: true,
+  description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
+});
+parser.addArgument('out', {
+    help: 'Generated file output path.'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of CCD and PVCD.'
+});
+parser.addArgument([ '--binary', '-b' ], {
+    action: 'storeTrue',
+    help: 'Output as BinaryCIF.'
+});
+interface Args {
+    out: string
+    forceDownload?: boolean
+    binary?: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DOWNLOAD = args.forceDownload
+
+run(args.out, args.binary)

src/apps/combine-mmcif/index.ts

-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-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 readFile = util.promisify(fs.readFile);
-const writeFile = util.promisify(fs.writeFile);
-
-import { Progress } from 'mol-task'
-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 { CifWriter } from 'mol-io/writer/cif'
-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'
-// import to_mmCIF from 'mol-model/structure/export/mmcif'
-
-export async function ensureAvailable(path: string, url: string) {
-    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
-        console.log(`downloading ${url}...`)
-        const data = await fetch(url)
-        if (!fs.existsSync(DATA_DIR)) {
-            fs.mkdirSync(DATA_DIR);
-        }
-        if (url.endsWith('.gz')) {
-            await writeFile(path, zlib.gunzipSync(await data.buffer()))
-        } else {
-            await writeFile(path, await data.text())
-        }
-        console.log(`done downloading ${url}`)
-    }
-}
-
-export async function ensureDataAvailable() {
-    await ensureAvailable(CCD_PATH, CCD_URL)
-    await ensureAvailable(PVCD_PATH, PVCD_URL)
-    await ensureAvailable(BIRD_PATH, BIRD_URL)
-}
-
-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 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() {
-    await ensureDataAvailable()
-    return readPVCD()
-}
-
-export async function getBIRD() {
-    await ensureDataAvailable()
-    return readBIRD()
-}
-
-async function parseCif(data: string|Uint8Array) {
-    const comp = CIF.parse(data);
-    console.time('parse cif');
-    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
-    console.timeEnd('parse cif');
-    if (parsed.isError) throw parsed;
-    return parsed
-}
-
-export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
-    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
-    CifWriter.Encoder.writeDatabase(encoder, name, database)
-    return encoder.getData();
-}
-
-export async function getPdb(pdb: string) {
-    console.log(`downloading ${pdb}...`)
-    const data = await fetch(`https://files.rcsb.org/download/${pdb}.cif`)
-    console.log(`done downloading ${pdb}`)
-
-    const parsed = await parseCif(await data.text())
-    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()
-    const bird = await getBIRD()
-
-    const mmcif = await getPdb(pdb)
-    // console.log(mmcif.chem_comp.id.toArray())
-
-    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 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))
-            }
-        }
-
-        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))
-            }
-        }
-    }
-
-    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))
-
-    // 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,
-  description: 'Create a mmcif file that includes relevant CCD and BIRD entries'
-});
-parser.addArgument([ '--pdb', '-p' ], {
-    help: 'Pdb entry id'
-});
-parser.addArgument([ '--out', '-o' ], {
-    help: 'Generated file output path, if not given printed to stdout'
-});
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
-    help: 'Force download of CCD and BIRD'
-});
-interface Args {
-    pdb: string
-    out: string
-    forceDownload: boolean
-}
-const args: Args = parser.parseArgs();
-
-const FORCE_DOWNLOAD = args.forceDownload
-
-run(args.pdb, args.out)