drugforge.alchemy.cli.utils.get_cdd_molecules

drugforge.alchemy.cli.utils.get_cdd_molecules(protocol_name: str, defined_stereo_only: bool = True, remove_covalent: bool = True) → list[Ligand]

Search the CDD protocol for molecules with experimental values and return a list of drugforge ligands.

Notes:

The ligands will contain a tag which can be used to identify them as experimental compounds later.

Args:

protocol_name: The name of the experimental protocol in CDD we should extract molecules from. defined_stereo_only: Only return ligands which have fully defined stereochemistry remove_covalent: If True remove potential covalent ligands from the protocol based on the presence of warheads

found via smarts matches.

Returns:

A list of molecules with experimental data.