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Commit 5be6c917 authored by McMenemy's avatar McMenemy
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move to separate script

parent f293a024
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src/cli/chem-comp-dict/create-ions.ts 0 → 100644
+ 74
− 0
View file @ 5be6c917
#!/usr/bin/env node
/**
* Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Josh McMenemy <josh.mcmenemy@gmail.com>
*/
import * as argparse from 'argparse';
import * as path from 'path';
import util from 'util';
import fs from 'fs';
require('util.promisify').shim();
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';
function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
const ionNames: string[] = [];
for (const k in ccd) {
const {chem_comp} = ccd[k];
if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
ionNames.push(chem_comp.id.value(0));
}
}
// these are extra ions that don't have ION in their name
ionNames.push('NCO', 'OHX');
return ionNames;
}
function writeIonNamesFile(filePath: string, ionNames: string[]) {
const output = `/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated ion names params file. Names extracted from CCD components.
*
* @author molstar/chem-comp-dict/create-table cli
*/
export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
`;
writeFile(filePath, output);
}
async function run(out: string, forceDownload = false) {
await ensureDataAvailable(forceDownload);
const ccd = await readCCD();
const ionNames = extractIonNames(ccd);
if (!fs.existsSync(path.dirname(out))) {
fs.mkdirSync(path.dirname(out));
}
writeIonNamesFile(out, ionNames);
}
const parser = new argparse.ArgumentParser({
addHelp: true,
description: 'Extract and save IonNames from CCD.'
});
parser.addArgument('out', {
help: 'Generated file output path.'
});
parser.addArgument([ '--forceDownload', '-f' ], {
action: 'storeTrue',
help: 'Force download of CCD and PVCD.'
});
interface Args {
out: string,
forceDownload?: boolean,
}
const args: Args = parser.parseArgs();
run(args.out, args.forceDownload);
src/cli/chem-comp-dict/create-table.ts
+ 8
− 48
View file @ 5be6c917
......@@ -25,8 +25,8 @@ 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) {
if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
export async function ensureAvailable(path: string, url: string, forceDownload = false) {
if (forceDownload || !fs.existsSync(path)) {
console.log(`downloading ${url}...`);
const data = await fetch(url);
if (!fs.existsSync(DATA_DIR)) {
......@@ -41,9 +41,9 @@ export async function ensureAvailable(path: string, url: string) {
}
}
export async function ensureDataAvailable() {
await ensureAvailable(CCD_PATH, CCD_URL);
await ensureAvailable(PVCD_PATH, PVCD_URL);
export async function ensureDataAvailable(forceDownload = false) {
await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
}
export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
......@@ -243,33 +243,8 @@ function createAtoms(ccd: DatabaseCollection<CCD_Schema>) {
);
}
function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
const ionNames: string[] = [];
for (const k in ccd) {
const {chem_comp} = ccd[k];
if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
ionNames.push(chem_comp.id.value(0));
}
}
return ionNames;
}
function writeIonNamesFile(filePath: string, ionNames: string[]) {
const output = `/**
* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated ion names params file. Names extracted from CCD components.
*
* @author molstar/chem-comp-dict/create-table cli
*/
export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
`;
writeFile(filePath, output);
}
async function run(out: string, binary = false, ionNamesOut?: string, ccaOut?: string) {
await ensureDataAvailable();
async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
await ensureDataAvailable(forceDownload);
const ccd = await readCCD();
const pvcd = await readPVCD();
......@@ -288,14 +263,6 @@ async function run(out: string, binary = false, ionNamesOut?: string, ccaOut?: s
}
writeFile(ccaOut, ccaCif);
}
if (!!ionNamesOut) {
const ionNames = extractIonNames(ccd);
if (!fs.existsSync(path.dirname(ionNamesOut))) {
fs.mkdirSync(path.dirname(ionNamesOut));
}
writeIonNamesFile(ionNamesOut, ionNames);
}
}
const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
......@@ -322,10 +289,6 @@ parser.addArgument([ '--binary', '-b' ], {
action: 'storeTrue',
help: 'Output as BinaryCIF.'
});
parser.addArgument([ '--ionNamesOut', '-ino' ], {
help: 'Generated file output path to save extracted ion names.',
required: false
});
parser.addArgument(['--ccaOut', '-a'], {
help: 'Optional generated file output path for chem_comp_atom data.',
required: false
......@@ -334,11 +297,8 @@ interface Args {
out: string,
forceDownload?: boolean,
binary?: boolean,
ionNamesOut?: string,
ccaOut?: string
}
const args: Args = parser.parseArgs();
const FORCE_DOWNLOAD = args.forceDownload;
run(args.out, args.binary, args.ionNamesOut, args.ccaOut);
run(args.out, args.binary, args.forceDownload, args.ccaOut);
src/mol-model/structure/model/types/ions.ts
+ 1
− 1
View file @ 5be6c917
......@@ -6,4 +6,4 @@
* @author molstar/chem-comp-dict/create-table cli
*/
export const IonNames = new Set(['118', '119', '543', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', '3MT', '3NI', '3OF', '3P8', '4MO', '4PU', '4TI', '6MO', 'ACT', 'AG', 'AL', 'ALF', 'AM', 'ATH', 'AU', 'AU3', 'AUC', 'AZI', 'BA', 'BCT', 'BEF', 'BF4', 'BO4', 'BR', 'BS3', 'BSY', 'CA', 'CAC', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CF', 'CHT', 'CL', 'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU', 'CU1', 'CU3', 'CUA', 'CUZ', 'CYN', 'DME', 'DMI', 'DSC', 'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU', 'EU3', 'F', 'FE', 'FE2', 'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'IN', 'IOD', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'KO4', 'LA', 'LCO', 'LCP', 'LI', 'LU', 'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MMC', 'MN', 'MN3', 'MN5', 'MN6', 'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO', 'MOS', 'MOW', 'MW1', 'MW2', 'MW3', 'NA', 'NA2', 'NA5', 'NA6', 'NAO', 'NAW', 'NET', 'NH4', 'NI', 'NI1', 'NI2', 'NI3', 'NO2', 'NO3', 'NRU', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3', 'OC4', 'OC5', 'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2', 'OF3', 'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PDV', 'PER', 'PI', 'PO3', 'PO4', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'SB', 'SCN', 'SE4', 'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SR', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'TH', 'THE', 'TL', 'TMA', 'TRA', 'UNX', 'V', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB', 'YB2', 'YH', 'YT3', 'ZCM', 'ZN', 'ZN2', 'ZN3', 'ZNO', 'ZO3', 'ZR']);
export const IonNames = new Set(['118', '119', '543', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', '3MT', '3NI', '3OF', '3P8', '4MO', '4PU', '4TI', '6MO', 'ACT', 'AG', 'AL', 'ALF', 'AM', 'ATH', 'AU', 'AU3', 'AUC', 'AZI', 'BA', 'BCT', 'BEF', 'BF4', 'BO4', 'BR', 'BS3', 'BSY', 'CA', 'CAC', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CF', 'CHT', 'CL', 'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU', 'CU1', 'CU3', 'CUA', 'CUZ', 'CYN', 'DME', 'DMI', 'DSC', 'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU', 'EU3', 'F', 'FE', 'FE2', 'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'IN', 'IOD', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'KO4', 'LA', 'LCO', 'LCP', 'LI', 'LU', 'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MMC', 'MN', 'MN3', 'MN5', 'MN6', 'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO', 'MOS', 'MOW', 'MW1', 'MW2', 'MW3', 'NA', 'NA2', 'NA5', 'NA6', 'NAO', 'NAW', 'NET', 'NH4', 'NI', 'NI1', 'NI2', 'NI3', 'NO2', 'NO3', 'NRU', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3', 'OC4', 'OC5', 'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2', 'OF3', 'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PDV', 'PER', 'PI', 'PO3', 'PO4', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'SB', 'SCN', 'SE4', 'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SR', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'TH', 'THE', 'TL', 'TMA', 'TRA', 'UNX', 'V', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB', 'YB2', 'YH', 'YT3', 'ZCM', 'ZN', 'ZN2', 'ZN3', 'ZNO', 'ZO3', 'ZR', 'NCO', 'OHX']);
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