Utils

Utility functions for structure module.

check_ligand(pdb, reference)

Compare the ligand in the PDB file with the ligand in the reference file.

PARAMETER	DESCRIPTION
pdb	str or file-like Path to the PDB file or file-like object.
reference	str or file-like Path to the csv file or file-like object.

RETURNS	DESCRIPTION
bool	True if the ligand is the same in the two PDB files, False otherwise.

chery_pick_ligand(pdb, ligand, remove_water=True, water_selection=None)

Cherry pick a ligand from a PDB file.

PARAMETER	DESCRIPTION
pdb	str or file-like Path to the PDB file or file-like object.
ligand	str The ligand to cherry pick.
remove_water	bool Remove crystallographic waters from the protein structures. Default is True.
water_selection	str The selection of water molecules to keep. Default is "none".

RETURNS	DESCRIPTION
Literal['Protein', 'Ligand']	Universe object containing the protein.
Literal['Protein', 'Ligand']	Universe object containing the ligand.

find_resolution(pdb_id, rcsb_data=None)

Find the resolution of a PDB file using the RCSB API.

PARAMETER	DESCRIPTION
pdb_id	str The PDB ID to find the resolution for.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
float	The resolution of the PDB file.

get_entity_ids(pdb_id, rcsb_data=None)

Get the entity IDs for a given PDB ID using the RCSB API.

PARAMETER	DESCRIPTION
pdb_id	str The PDB ID to retrieve the entity IDs for.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
dict[str, list[str]]	The entity IDs for the given PDB ID as a dictionary. The keys are the entity type and the values are the entity numbers.
dict[str, list[str]]	The data for the PDB ID from the RCSB API. If None, the data will be fetched.

get_ligand_names(pdb)

Get the names of the ligands in a PDB file.

PARAMETER	DESCRIPTION
pdb	str or file-like Path to the PDB file or file-like object.

RETURNS	DESCRIPTION
list	The names of the ligands in the PDB file.

get_nonpolymer_names(pdb_id, rcsb_data=None)

Get the names of the non-polymer entities in a PDB file.

PARAMETER	DESCRIPTION
pdb_id	str The PDB ID to retrieve the non-polymer entity names for.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
list	The names of the non-polymer entities in the PDB file.

get_rcsb_data(pdb_id)

Get entry data for a given PDB ID using the RCSB API.

PARAMETER	DESCRIPTION
pdb_id	The PDB ID to retrieve the entry data for. TYPE: str

RETURNS	DESCRIPTION
	The entry data for the given PDB ID.

get_smiles(ligand_resname)

Get the SMILES string of a ligand from a PDB file.

PARAMETER	DESCRIPTION
ligand_resname	str or file-like The residue name of the ligand.

RETURNS	DESCRIPTION
dict[str, str]	The SMILES string of the ligand.

has_covalent_bonds(pdb, rcsb_data=None)

Check if the PDB file has covalent bonds or not.

PARAMETER	DESCRIPTION
pdb	str the PDB id needed to be checked.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
bool	True if the PDB file has covalent bonds, False otherwise.

has_ligands(pdb, rcsb_data=None)

Check if the PDB file has ligands or not.

PARAMETER	DESCRIPTION
pdb	str the PDB id needed to be checked.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
bool	True if the PDB file has ligands which can be ions/additatives, False otherwise.

is_xray_structure(pdb)

Check if the PDB file was generated from X-ray diffraction data.

Arg

pdb : Path to the PDB file. or file-like object. or just pdb id

RETURNS	DESCRIPTION
bool	True if the PDB was generated from X-ray data, False otherwise.

map_genid_to_pdb(gene_ids)

Map a list of gene IDs to PDB IDs using the UniProt ID Mapping API.

PARAMETER	DESCRIPTION
gene_ids	list of str The list of gene IDs to map.

RETURNS	DESCRIPTION
list[dict]	The mapping of each gene ID to the PDB ID and other attributes.

pdb_has_mutation(pdb_id, rcsb_data=None)

Check if a PDB file has mutations or not

PARAMETER	DESCRIPTION
pdb	str Path to the PDB file.
rcsb_data	dict or None The data for the PDB ID from the RCSB API. If None, the data will be fetched.

RETURNS	DESCRIPTION
bool	True if the PDB file has mutations, False otherwise.

separate_protein_ligand(pdb, remove_water=True, keep_het_chain=None, water_selection=None, hetatm='valid_ligand', context=ProteinContext.default())

Separate protein and ligand from a PDB file.

PARAMETER	DESCRIPTION
pdb	str or file-like Path to the PDB file or file-like object.
remove_water	bool Remove crystallographic waters from the protein structures. Default is True.
keep_het_chain	str or list Chain(s) to keep their HETATM in the protein structure. Default is None. If None, all HETATM will be kept.
water_selection	str The selection of water molecules to keep if remove_water is False. Default is "none"
hetatm	str The selection of hetatoms to keep in the protein structure. Default is "valid_ligand".
context	ProteinContext or None or str or dict ProteinContext object or path to ProteinContext YAML file. Default is ProteinContext.

Returns: a tuple of: - mda Universe object containing the protein. - mda Universe object containing the ligand.

validate_ligands(pdb, impurities=ProteinContext.default().impurities)

Validate the ligands from pdb id using the impurities list.

PARAMETER	DESCRIPTION
pdb	str The PDB ID to validate.
impurities	list or None or ProteinContext List of impurities to check against. Default is impurities from the ProteinContext.

RETURNS	DESCRIPTION
bool	True if the ligands are valid, False otherwise.

validate_pdb(pdb_id)

Validate a PDB file using the RCSB API.

PARAMETER	DESCRIPTION
pdb_id	str The PDB ID to validate.

RETURNS	DESCRIPTION
bool	True if the PDB file is valid (i.e has ligand, no covalent bond and no mutation), False otherwise.