add script to generate martini lipid names

README.md

@@ -95,6 +95,10 @@ and navigate to `build/viewer`
     node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
     node ./lib/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
 
+**Lipid names**
+
+    node .\lib\cli\lipid-params -o src\mol-model\structure\model\types\lipids.ts
+
 **GraphQL schemas**
 
     ./node_modules/.bin/graphql-codegen -c ./src/extensions/rcsb/graphql/codegen.yml

src/cli/lipid-params/index.ts

@@ -9,9 +9,9 @@ import * as argparse from 'argparse';
 import * as fs from 'fs';
 import * as path from 'path';
 import fetch from 'node-fetch';
+import { UniqueArray } from '../../mol-data/generic';
 
-const BUILD_DIR = path.resolve(__dirname, '../build/');
-const LIPIDS_DIR = path.resolve(BUILD_DIR, 'lipids/');
+const LIPIDS_DIR = path.resolve(__dirname, '../../../build/lipids/');
 
 const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
 const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
@@ -31,29 +31,58 @@ async function ensureAvailable(path: string, url: string) {
 
 async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
 
-async function run() {
+async function run(out: string) {
     await ensureLipidsAvailable();
     const lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
 
-    const m = lipidsItpStr.match(/\[moleculetype\]\n; molname      nrexcl\n(DGPC)/g);
-    console.log(m);
+    const lipids = UniqueArray.create<string>();
+    const reLipid = /\[moleculetype\]\n; molname      nrexcl\n +([a-zA-Z]{3,5})/g;
+    let m: RegExpExecArray | null;
+
+    while ((m = reLipid.exec(lipidsItpStr)) !== null) {
+        const v = m[0].substr(m[0].lastIndexOf(' ') + 1);
+        UniqueArray.add(lipids, v, v);
+    }
+
+
+    const lipidNames = JSON.stringify(lipids.array);
+
+    if (out) {
+        const output = `/**
+* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+*
+* Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+*
+* @author molstar/lipid-params cli
+*/
+
+export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+        fs.writeFileSync(out, output);
+    } else {
+        console.log(lipidNames);
+    }
 }
 
 const parser = new argparse.ArgumentParser({
     addHelp: true,
     description: 'Create lipid params (from martini lipids itp)'
 });
+parser.addArgument([ '--out', '-o' ], {
+    help: 'Generated lipid params output path, if not given printed to stdout'
+});
 parser.addArgument([ '--forceDownload', '-f' ], {
     action: 'storeTrue',
     help: 'Force download of martini lipids itp'
 });
 interface Args {
+    out: string
     forceDownload: boolean
 }
 const args: Args = parser.parseArgs();
 
 const FORCE_DOWNLOAD = args.forceDownload;
 
-run().catch(e => {
+run(args.out || '').catch(e => {
     console.error(e);
 });

src/mol-model/structure/model/types/lipids.ts

@@ -0,0 +1,9 @@
+/**
+* Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+*
+* Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+*
+* @author molstar/lipid-params cli
+*/
+
+export const LipidNames = new Set(['DAPC', 'DBPC', 'DFPC', 'DGPC', 'DIPC', 'DLPC', 'DNPC', 'DOPC', 'DPPC', 'DRPC', 'DTPC', 'DVPC', 'DXPC', 'DYPC', 'LPPC', 'PAPC', 'PEPC', 'PGPC', 'PIPC', 'POPC', 'PRPC', 'PUPC', 'DAPE', 'DBPE', 'DFPE', 'DGPE', 'DIPE', 'DLPE', 'DNPE', 'DOPE', 'DPPE', 'DRPE', 'DTPE', 'DUPE', 'DVPE', 'DXPE', 'DYPE', 'LPPE', 'PAPE', 'PGPE', 'PIPE', 'POPE', 'PQPE', 'PRPE', 'PUPE', 'DAPS', 'DBPS', 'DFPS', 'DGPS', 'DIPS', 'DLPS', 'DNPS', 'DOPS', 'DPPS', 'DRPS', 'DTPS', 'DUPS', 'DVPS', 'DXPS', 'DYPS', 'LPPS', 'PAPS', 'PGPS', 'PIPS', 'POPS', 'PQPS', 'PRPS', 'PUPS', 'DAPG', 'DBPG', 'DFPG', 'DGPG', 'DIPG', 'DLPG', 'DNPG', 'DOPG', 'DPPG', 'DRPG', 'DTPG', 'DVPG', 'DXPG', 'DYPG', 'LPPG', 'PAPG', 'PGPG', 'PIPG', 'POPG', 'PRPG', 'DAPA', 'DBPA', 'DFPA', 'DGPA', 'DIPA', 'DLPA', 'DNPA', 'DOPA', 'DPPA', 'DRPA', 'DTPA', 'DVPA', 'DXPA', 'DYPA', 'LPPA', 'PAPA', 'PGPA', 'PIPA', 'POPA', 'PRPA', 'PUPA', 'DPP', 'DPPI', 'PAPI', 'PIPI', 'POP', 'POPI', 'PUPI', 'PVP', 'PVPI', 'PADG', 'PIDG', 'PODG', 'PUDG', 'PVDG', 'APC', 'CPC', 'IPC', 'LPC', 'OPC', 'PPC', 'TPC', 'UPC', 'VPC', 'BNSM', 'DBSM', 'DPSM', 'DXSM', 'PGSM', 'PNSM', 'POSM', 'PVSM', 'XNSM', 'DPCE', 'DXCE', 'PNCE', 'XNCE']);