def fetchPDB(*pdb, **kwargs):
"""Returns path(s) to PDB file(s) for specified *pdb* identifier(s). Files
will be sought in user specified *folder* or current working director, and
then in local PDB folder and mirror, if they are available. If *copy*
is set **True**, files will be copied into *folder*. If *compressed* is
**False**, all files will be decompressed. See :func:`pathPDBFolder` and
:func:`pathPDBMirror` for managing local resources, :func:`.fetchPDBviaFTP`
and :func:`.fetchPDBviaFTP` for downloading files from PDB servers."""
if len(pdb) == 1 and isinstance(pdb[0], list):
pdb = pdb[0]
if 'format' in kwargs and kwargs.get('format') != 'pdb':
return fetchPDBviaFTP(*pdb, **kwargs)
identifiers = checkIdentifiers(*pdb)
folder = kwargs.get('folder', '.')
compressed = kwargs.get('compressed')
# check *folder* specified by the user, usually pwd ('.')
filedict = findPDBFiles(folder, compressed=compressed)
filenames = []
not_found = []
exists = 0
for i, pdb in enumerate(identifiers):
if pdb is None:
filenames.append(None)
elif pdb in filedict:
filenames.append(filedict[pdb])
exists += 1
else:
filenames.append(None)
not_found.append((i, pdb))
if not not_found:
if len(filenames) == 1:
filenames = filenames[0]
if exists:
LOGGER.debug(
'PDB file is found in working directory ({0}).'.format(
sympath(filenames)))
return filenames
if not isWritable(folder):
raise IOError('permission to write in {0} is denied, please '
'specify another folder'.format(folder))
if compressed is not None and not compressed:
filedict = findPDBFiles(folder, compressed=True)
not_found, decompress = [], not_found
for i, pdb in decompress:
if pdb in filedict:
fn = filedict[pdb]
filenames[i] = gunzip(fn, splitext(fn)[0])
else:
not_found.append((i, pdb))
if not not_found:
return filenames[0] if len(identifiers) == 1 else filenames
local_folder = pathPDBFolder()
copy = kwargs.setdefault('copy', False)
if local_folder:
local_folder, is_divided = local_folder
temp, not_found = not_found, []
for i, pdb in temp:
if is_divided:
fn = join(local_folder, pdb[1:3], 'pdb' + pdb + '.pdb.gz')
else:
fn = join(local_folder, pdb + '.pdb.gz')
if isfile(fn):
if copy or not compressed and compressed is not None:
if compressed:
fn = copyFile(fn, join(folder, pdb + 'pdb.gz'))
else:
fn = gunzip(fn, join(folder, pdb + '.pdb'))
filenames[i] = normpath(fn)
else:
not_found.append((i, pdb))
if not not_found:
if len(identifiers) == 1:
fn = filenames[0]
items = fn.split(pathsep)
if len(items) > 5:
fndisp = pathsep.join(items[:3] + ['...'] + items[-1:])
else:
fndisp = relpath(fn)
LOGGER.debug(
'PDB file is found in the local folder ({0}).'.format(fndisp))
return fn
else:
return filenames
if kwargs['copy'] or (compressed is not None and not compressed):
kwargs['folder'] = folder
downloads = [pdb for i, pdb in not_found]
fns = None
try:
fns = fetchPDBfromMirror(*downloads, **kwargs)
except IOError:
pass
else:
if len(downloads) == 1: fns = [fns]
temp, not_found = not_found, []
for i, fn in enumerate(fns):
if fn is None:
not_found.append(temp[i])
else:
i, _ = temp[i]
filenames[i] = fn
if not not_found:
return filenames[0] if len(identifiers) == 1 else filenames
if fns:
downloads = [pdb for i, pdb in not_found]
fns = None
tp = kwargs.pop('tp', None)
if tp is not None:
tp = tp.lower()
if tp == 'http':
try:
fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
except Exception as err:
LOGGER.warn('Downloading PDB files via HTTP failed '
'({0}).'.format(str(err)))
elif tp == 'ftp':
try:
fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
except Exception as err:
LOGGER.warn('Downloading PDB files via FTP failed '
'({0}).'.format(str(err)))
else:
tryHTTP = False
try:
fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
except Exception as err:
tryHTTP = True
if fns is None or isinstance(fns, list) and None in fns:
tryHTTP = True
elif isinstance(fns, list):
downloads = [
not_found[i][1] for i in range(len(fns)) if fns[i] is None
]
if len(downloads) > 0:
tryHTTP = True
if tryHTTP:
LOGGER.info('Downloading PDB files via FTP failed, '
'trying HTTP.')
try:
fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
except Exception as err:
LOGGER.warn('Downloading PDB files via HTTP also failed '
'({0}).'.format(str(err)))
if len(downloads) == 1: fns = [fns]
if fns:
for i, fn in zip([i for i, pdb in not_found], fns):
filenames[i] = fn
return filenames[0] if len(identifiers) == 1 else filenames
def fetchPDB(*pdb, **kwargs):
"""Returns path(s) to PDB file(s) for specified *pdb* identifier(s). Files
will be sought in user specified *folder* or current working director, and
then in local PDB folder and mirror, if they are available. If *copy*
is set **True**, files will be copied into *folder*. If *compressed* is
**False**, all files will be decompressed. See :func:`pathPDBFolder` and
:func:`pathPDBMirror` for managing local resources, :func:`.fetchPDBviaFTP`
and :func:`.fetchPDBviaFTP` for downloading files from PDB servers."""
if len(pdb) == 1 and isinstance(pdb[0], list):
pdb = pdb[0]
if 'format' in kwargs and kwargs.get('format') != 'pdb':
return fetchPDBviaFTP(*pdb, **kwargs)
identifiers = checkIdentifiers(*pdb)
folder = kwargs.get('folder', '.')
compressed = kwargs.get('compressed')
# check *folder* specified by the user, usually pwd ('.')
filedict = findPDBFiles(folder, compressed=compressed)
filenames = []
not_found = []
exists = 0
for i, pdb in enumerate(identifiers):
if pdb is None:
filenames.append(None)
elif pdb in filedict:
filenames.append(filedict[pdb])
exists += 1
else:
filenames.append(None)
not_found.append((i, pdb))
if not not_found:
if len(filenames) == 1:
filenames = filenames[0]
if exists:
LOGGER.debug('PDB file is found in working directory ({0}).'
.format(sympath(filenames)))
return filenames
if not isWritable(folder):
raise IOError('permission to write in {0} is denied, please '
'specify another folder'.format(folder))
if compressed is not None and not compressed:
filedict = findPDBFiles(folder, compressed=True)
not_found, decompress = [], not_found
for i, pdb in decompress:
if pdb in filedict:
fn = filedict[pdb]
filenames[i] = gunzip(fn, splitext(fn)[0])
else:
not_found.append((i, pdb))
if not not_found:
return filenames[0] if len(identifiers) == 1 else filenames
local_folder = pathPDBFolder()
copy = kwargs.setdefault('copy', False)
if local_folder:
local_folder, is_divided = local_folder
temp, not_found = not_found, []
for i, pdb in temp:
if is_divided:
fn = join(local_folder, pdb[1:3], 'pdb' + pdb + '.pdb.gz')
else:
fn = join(local_folder, pdb + '.pdb.gz')
if isfile(fn):
if copy or not compressed and compressed is not None:
if compressed:
fn = copyFile(fn, join(folder, pdb + 'pdb.gz'))
else:
fn = gunzip(fn, join(folder, pdb + '.pdb'))
filenames[i] = normpath(fn)
else:
not_found.append((i, pdb))
if not not_found:
if len(identifiers) == 1:
fn = filenames[0]
if kwargs.get('report', True):
items = fn.split(pathsep)
if len(items) > 5:
fndisp = pathsep.join(items[:3] + ['...'] + items[-1:])
else:
fndisp = relpath(fn)
LOGGER.debug('PDB file is found in the local folder ({0}).'
.format(fndisp))
return fn
else:
return filenames
if kwargs['copy'] or (compressed is not None and not compressed):
kwargs['folder'] = folder
downloads = [pdb for i, pdb in not_found]
fns = None
try:
fns = fetchPDBfromMirror(*downloads, **kwargs)
except IOError:
pass
else:
if len(downloads) == 1: fns = [fns]
temp, not_found = not_found, []
for i, fn in enumerate(fns):
if fn is None:
not_found.append(temp[i])
else:
i, _ = temp[i]
filenames[i] = fn
if not not_found:
return filenames[0] if len(identifiers) == 1 else filenames
if fns:
downloads = [pdb for i, pdb in not_found]
fns = None
try:
fns = fetchPDBviaFTP(*downloads, check=False, **kwargs)
except Exception as err:
LOGGER.warn('Downloading PDB files via FTP failed ({0}), '
'trying HTTP.'.format(str(err)))
try:
fns = fetchPDBviaHTTP(*downloads, check=False, **kwargs)
except Exception as err:
LOGGER.warn('Downloading PDB files via HTTP also failed '
'({0}).'.format(str(err)))
if len(downloads) == 1: fns = [fns]
if fns:
for i, fn in zip([i for i, pdb in not_found], fns):
filenames[i] = fn
return filenames[0] if len(identifiers) == 1 else filenames
