Chemistry

// Node 18 or later, from the Gold package: check a batch of submissions and register the new ones.
import { readFileSync, writeFileSync } from 'node:fs';
import { readSdf, writeSdf, writeSmiles, perceiveStereo, molecularFormula, molecularWeight, valenceProblems } from './dist/node/bmx-chem-editor.mjs';

const known = new Set(readFileSync('registry/canonical.smi', 'utf8').split('\n').filter(Boolean));
let next = Number(readFileSync('registry/next-id.txt', 'utf8'));
const registered = [];
for (const { mol, data, problems } of readSdf(readFileSync('submissions/batch-17.sdf', 'utf8'))) {
  const issues = [...problems, ...valenceProblems(mol)];
  if (issues.length) { console.log(`${mol.name}: held back - ${issues.map(p => p.message).join(' ')}`); continue; }
  const smiles = writeSmiles(perceiveStereo(mol), { canonical: true });
  if (known.has(smiles)) { console.log(`${mol.name}: already registered`); continue; }
  known.add(smiles);
  const id = `KX-${String(next++).padStart(6, '0')}`;
  registered.push({ ...mol, properties: { ...data, REG_ID: id, FORMULA: molecularFormula(mol).text, MW: molecularWeight(mol).toFixed(2), SMILES: smiles } });
}
writeFileSync('out/registered.sdf', writeSdf(registered));
writeFileSync('registry/next-id.txt', String(next));