BIRD Classes and Functions

This module defines functions for fetching and parsing files in the PDB for the Biologically Interesting Molecule Reference Dictionary (BIRD).

The chemical information is stored in Peptide Reference Dictionary (PRD) files, whereas the biological function is documented in a separate family file.

fetchBIRDviaFTP(**kwargs)[source]

Retrieve the whole Biologically Interesting Molecule Reference Dictionary (BIRD) resource, which is updated every week. This includes 2 kinds of keys, which can be selected with the keys keyword argument.

The chemical information is found in a zipped (tar.gz) directory at https://files.rcsb.org/pub/pdb/data/bird/prd/prd-all.cif.gz, which contains individual CIF files within it. This data will be downloaded and extracted to .prody/bird-prd.

Biological function information is also found in a zipped (tar.gz) directory at https://files.rcsb.org/pub/pdb/data/bird/family/family-all.cif.gz, which contains individual CIF files within it. This data will be downloaded and extracted to .prody/bird-family.

Parameters:keys (str, tuple, list, ndarray) – keys specifying which data to fetch out of 'prd', 'family' or 'both' default is 'both'

The underlying data can be accessed using parseBIRD().

parseBIRD(*ids, **kwargs)[source]

Parse data from the Biologically Interesting Molecule Reference Dictionary (BIRD) resource, which is updated every week. This includes 2 kinds of keys, which can be selected with the keys keyword argument.

The chemical information is found in a single CIF file at https://files.rcsb.org/pub/pdb/data/bird/prd/prd-all.cif.gz. This data will be downloaded and extracted to .prody/bird-prd.

Biological function information is also found in a single CIF file at https://files.rcsb.org/pub/pdb/data/bird/family/family-all.cif.gz. This data will be downloaded and extracted to .prody/bird-family.

Individual compounds can be selected using ids. If needed, BIRD files are downloaded using fetchBIRDviaFTP() function.

You can also provide arguments that you would like passed on to fetchBIRDviaFTP.

Parameters:
  • ids (str, tuple, list, ndarray, None) – one BIRD identifier (starting with PRD or FAM) or a list of them. If None is provided then all of them are returned.
  • key (str) – key specifying which data to fetch out of 'prd' or 'family' default is 'prd'

Returns StarDataBlock object or list of them.