# -*- coding: utf-8 -*-
"""This module defines functions for fetching and parsing files in the PDB
for the Biologically Interesting Molecule Reference Dictionary (BIRD_).
.. _BIRD: https://www.wwpdb.org/data/bird
The chemical information is stored in Peptide Reference Dictionary (PRD) files,
whereas the biological function is documented in a separate family file."""
import os.path
from prody import LOGGER, getPackagePath
from prody.utilities import isListLike
from prody.proteins import wwPDBServer, WWPDB_FTP_SERVERS, parseSTAR
__all__ = ['fetchBIRDviaFTP', 'parseBIRD']
[docs]def fetchBIRDviaFTP(**kwargs):
"""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 :file:`.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 :file:`.prody/bird-family`.
:arg keys: keys specifying which data to fetch out of ``'prd'``, ``'family'`` or ``'both'``
default is ``'both'``
:type keys: str, tuple, list, :class:`~numpy.ndarray`
The underlying data can be accessed using :func:`parseBIRD`."""
BIRD_PATH = os.path.join(getPackagePath(), 'bird')
keys = kwargs.get('keys', 'both')
if isinstance(keys, str):
if keys == 'both':
keys = ['prd', 'family']
elif keys[:3].lower() == 'prd':
keys = ['prd']
elif keys[:3].lower() == 'fam':
keys = ['family']
else:
raise ValueError("keys should be 'both', 'prd' or 'fam'")
elif isListLike(keys):
keys = list(keys)
else:
raise TypeError("keys should be list-like or string")
ftp_divided = 'pdb/data/bird/'
ftp_pdbext = '.cif.gz'
ftp_prefix = ''
if not os.path.isdir(BIRD_PATH):
os.mkdir(BIRD_PATH)
LOGGER.progress('Downloading BIRD', len(keys),
'_prody_fetchBIRD')
ftp_name, ftp_host, ftp_path = WWPDB_FTP_SERVERS[wwPDBServer() or 'us']
LOGGER.debug('Connecting wwPDB FTP server {0}.'.format(ftp_name))
from ftplib import FTP
try:
ftp = FTP(ftp_host)
except Exception as error:
raise type(error)('FTP connection problem, potential reason: '
'no internet connectivity')
else:
count = 0
success = 0
failure = 0
filenames = []
ftp.login('')
for i, x in enumerate(keys):
data = []
ftp_fn = ftp_prefix + '{0}-all'.format(x) + ftp_pdbext
try:
ftp.cwd(ftp_path)
ftp.cwd(ftp_divided)
ftp.cwd(x)
ftp.retrbinary('RETR ' + ftp_fn, data.append)
except Exception as error:
if ftp_fn in ftp.nlst():
LOGGER.warn('{0} download failed ({1}). It is '
'possible that you do not have rights to '
'download .gz files in the current network.'
.format(x, str(error)))
else:
LOGGER.info('{0} download failed. {1} does not exist '
'on {2}.'.format(ftp_fn, x, ftp_host))
failure += 1
filenames.append(None)
else:
if len(data):
filename = BIRD_PATH + '/{0}-all.cif.gz'.format(x)
with open(filename, 'w+b') as outfile:
write = outfile.write
[write(block) for block in data]
success += 1
else:
failure += 1
count += 1
LOGGER.update(i, label='_prody_fetchBIRD')
LOGGER.finish()
LOGGER.debug('PDB download via FTP completed ({0} downloaded, '
'{1} failed).'.format(success, failure))
[docs]def parseBIRD(*ids, **kwargs):
"""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 :file:`.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 :file:`.prody/bird-family`.
Individual compounds can be selected using **ids**.
If needed, BIRD files are downloaded using :func:`.fetchBIRDviaFTP` function.
You can also provide arguments that you would like passed on to fetchBIRDviaFTP.
:arg ids: one BIRD identifier (starting with PRD or FAM) or a list of them.
If **None** is provided then all of them are returned.
:type ids: str, tuple, list, :class:`~numpy.ndarray`, **None**
:arg key: key specifying which data to fetch out of ``'prd'`` or ``'family'``
default is ``'prd'``
:type key: str
Returns :class:`.StarDataBlock` object or list of them.
"""
key = kwargs.get('key', 'prd')
if not isinstance(key, str):
raise TypeError("key should be a string")
if key[:3].lower() == 'prd':
key = 'prd'
elif key[:3].lower() == 'fam':
key = 'family'
else:
raise ValueError("key should be 'prd' or 'fam'")
n_ids = len(ids)
if n_ids == 1:
if isListLike(ids[0]):
ids = ids[0]
n_ids = len(ids)
if n_ids == 1:
ids = list(ids)
BIRD_PATH = os.path.join(getPackagePath(), 'bird')
filename = BIRD_PATH + '/{0}-all.cif.gz'.format(key)
if not os.path.isfile(filename):
fetchBIRDviaFTP(keys=key, **kwargs)
data = parseSTAR(filename, shlex=True)
ret = []
for id in ids:
try:
ret.append(data[list(data.search(id)._dict.keys())[0]])
except ValueError:
try:
ret.append(data[id])
except ValueError:
LOGGER.warn('id {0} not found in {1} data '
'so appending None'.format(id, key))
ret.append(None)
if n_ids == 1:
return ret[0]
return ret
