orthonym.decomposition.fragment_capping#

Note

Internal API. Names and behaviour may change between releases.

Fragment capping for decomposition engine.

After bond cleavage, replaces dummy atoms with H or OH to produce valid molecule fragments for recursive naming.

IUPAC: Principal characteristic group determines which side of a cleavage retains the parent suffix. Acid-side fragments are capped with OH to reconstruct the parent acid; alkyl/amine-side fragments are capped with H.

orthonym.decomposition.fragment_capping.cleave_and_cap(mol, bond_infos, acid_side_oh=True)#

Cleave molecule at specified bonds and return H/OH-capped fragments.

Uses RDKit FragmentOnBonds to cleave, then replaces dummy atoms: - Acid-side fragments: cap with OH (produces carboxylic acid) if acid_side_oh=True

per IUPAC principal characteristic group preservation

  • Alkyl/amine-side fragments: cap with H

Fragment side labeling uses dummyLabels to track which dummy came from which side of the bond: label 1 = acid side, label 2 = alkyl/amine side.

Parameters:

  • mol – RDKit Mol object

  • bond_infos (List[Dict]) – List of bond info dicts from find_cleavable_bonds

  • acid_side_oh (bool) – If True, cap acid-side fragments with OH

Returns:

List of dicts with keys – smiles, side, original_atoms

Return type:

List[Dict]