haddock.libs.libligand module

Ligand topology utilities.

haddock.libs.libligand.identify_unknown_hetatms(pdb_file: str | Path) → list[str]

Return residue names in a PDB that are not in the supported residues.

Parameters:

pdb_file (FilePath) – Path to the PDB file to inspect.

Returns:

list[str] – Unique residue names not found in the supported residues set, in order of first appearance.

haddock.libs.libligand.run_prodrg(pdb_file: str | Path, output_dir: str | Path) → tuple[Path, Path]

Run prodrg on a ligand PDB and write CNS topology and parameter files.

prodrg writes its output to fixed filenames in the current working directory, so the process is executed inside a managed temporary directory that is cleaned up automatically. The resulting files are written to output_dir named after the input PDB stem.

Parameters:

• pdb_file (FilePath) – Path to the ligand PDB file.

• output_dir (FilePath) – Directory where the named .top and .param files are written.

Returns:

tuple[Path, Path] – Paths to the written <stem>_prodrg.top and <stem>_prodg.param files.

Raises:

RuntimeError – If prodrg exits with a non-zero return code or the expected output files are not created.