`kinoml.databases.pdb`¶

Module Contents¶

kinoml.databases.pdb.logger¶

kinoml.databases.pdb.smiles_from_pdb(ligand_ids: Iterable[str]) → dict¶

Retrieve SMILES of molecules defined by their PDB chemical identifier.

Parameters: ligand_ids (iterable of str) – PDB chemical identifier.
Returns: ligands – Dictionary with PDB chemical identifier as keys and SMILES as values.
Return type: dict

kinoml.databases.pdb.download_pdb_structure(pdb_id: str, directory: Union[str, pathlib.Path] = user_cache_dir()) → Union[pathlib.Path, bool]¶

Download a PDB structure. If the structure is not available in PDB format, it will be download in CIF format.

Parameters

pdb_id (str) – The PDB ID of interest.
directory (str or Path, default=user_cache_dir) – The directory for saving the downloaded structure.

Returns

The path to the the downloaded file if successful, else False.

Return type

Path or False

kinoml.databases.pdb.download_pdb_ligand(pdb_id: str, chain_id: str, expo_id: str, smiles: str = '', directory: Union[str, pathlib.Path] = user_cache_dir()) → Union[pathlib.Path, bool]¶

Download a ligand co-crystallized to a PDB structure and save in SDF format. If a SMILES is provided, the connectivity and protonation will be adjusted accordingly.