Function parseSdf

parseSdf(text: string): undefined | Molecule

Parses an MDL SDF / molfile V2000 record into atoms and bonds.

Only the counts line, atom block and bond block are read — charge, isotope and property lines after M END are ignored, as none of them affect a ball-and-stick rendering. Malformed or empty records return undefined rather than throwing, so a caller can fall straight through to its next option.

Parameters

text: string
The raw SDF text as returned by PubChem's PUG-REST SDF operation

Returns undefined | Molecule

The parsed molecule, or undefined if the record has no usable atoms

Example

const molecule = parseSdf(await getStructureSdf(962));
// { atoms: [{ symbol: 'O', x: 0, y: 0, z: 0 }, …], bonds: [{ from: 0, to: 1, order: 1 }, …],
//   isPlanar: false }
parseSdf('not a molfile'); // undefined

Source

export function parseSdf(text: string): Molecule | undefined {
  const lines = text.split(/\r?\n/);
  const countsLine = lines[COUNTS_LINE_INDEX];
  if (countsLine === undefined) return undefined;

  const atomCount = readIntField(countsLine, 0, 3);
  const bondCount = readIntField(countsLine, 3, 6);
  if (atomCount === undefined || atomCount <= 0) return undefined;

  const atoms = parseAtomBlock(lines, atomCount);
  if (atoms.length === 0) return undefined;

  const bonds = parseBondBlock(lines, atomCount, bondCount ?? 0);

  const firstZ = atoms[0].z;
  const isPlanar = atoms.every((atom) => Math.abs(atom.z - firstZ) < PLANAR_EPSILON);

  return { atoms, bonds, isPlanar };
}