fix create-ion, add chem-comp-dict util

src/cli/chem-comp-dict/create-ions.ts

 #!/usr/bin/env node
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
  */
@@ -14,8 +14,7 @@ const writeFile = util.promisify(fs.writeFile);
 
 import { DatabaseCollection } from '../../mol-data/db';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
-import { ensureDataAvailable, readCCD } from './create-table';
-
+import { ensureDataAvailable, readCCD } from './util';
 
 function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
     const ionNames: string[] = [];

src/cli/chem-comp-dict/create-table.ts

 #!/usr/bin/env node
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,70 +9,16 @@ 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 } 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 { SetUtils } from '../../mol-util/set';
 import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
 import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
-
-export async function ensureAvailable(path: string, url: string, forceDownload = false) {
-    if (forceDownload || !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(forceDownload = false) {
-    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
-    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
-}
-
-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();
-}
+import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 
 type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
@@ -268,12 +214,6 @@ async function run(out: string, binary = false, forceDownload = false, ccaOut?:
 const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
 const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
 
-const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/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.'

src/cli/chem-comp-dict/util.ts

+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+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 } 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';
+
+export async function ensureAvailable(path: string, url: string, forceDownload = false) {
+    if (forceDownload || !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(forceDownload = false) {
+    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
+    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
+}
+
+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();
+}
+
+const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/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';