pypath.utils.pdb.ResidueMapper

class pypath.utils.pdb.ResidueMapper

Bases: Logger

This class stores and serves the PDB –> UniProt residue level mapping. Attempts to download the mapping, and stores it for further use. Converts PDB residue numbers to the corresponding UniProt ones.

__init__()

Make this instance a logger.

Parameters:

• name – The label of this instance that will be prepended to all messages it sends to the logger.

• module – Send the messages by the logger of this module.

Methods

__init__()	Make this instance a logger.
clean()	Removes cached mappings, freeing up memory.
get_residue(pdb, resnum[, chain])	For a residue in a PDB structure returns the UniProt ID and the position of the residue in the UniProt sequence.
load_mapping(pdbs)	Loads PDB-UniProt sequence mapping for one or more PDB IDs.

clean()

Removes cached mappings, freeing up memory.

get_residue(pdb, resnum, chain=None)

For a residue in a PDB structure returns the UniProt ID and the position of the residue in the UniProt sequence.

Args

pdb (str): A PDB structure ID. resnum (int): The position of the residue. chain (str): The chain ID, optional.

Returns

Tuple of residue number, offset, UniProt ID and chain ID. Returns None if the residue can not be found.

load_mapping(pdbs)

Loads PDB-UniProt sequence mapping for one or more PDB IDs.

Args

pdb (str,list): One or more PDB IDs.