def pathPDBMirror(path=None, format=None):
"""Returns or specify PDB mirror path to be used by :func:`.fetchPDB`.
To release the current mirror, pass an invalid path, e.g. ``path=''``.
If you are keeping a partial mirror, such as PDB files in
:file:`/data/structures/divided/pdb/` folder, specify *format*, which is
``'pdb'`` in this case."""
if path is None:
path = SETTINGS.get('pdb_mirror_path')
format = SETTINGS.get('pdb_mirror_format', None)
if path:
if isdir(path):
if format is None:
return path
else:
return path, format
else:
LOGGER.warning('PDB mirror path {0} is not a accessible.'
.format(repr(path)))
else:
if isdir(path):
path = abspath(path)
LOGGER.info('Local PDB mirror path is set: {0}'
.format(repr(path)))
SETTINGS['pdb_mirror_path'] = path
SETTINGS['pdb_mirror_format'] = format
SETTINGS.save()
else:
current = SETTINGS.pop('pdb_mirror_path')
if current:
LOGGER.info('PDB mirror {0} is released.'
.format(repr(current)))
SETTINGS.save()
else:
raise IOError('{0} is not a valid path.'.format(repr(path)))
def pathEVmutationFolder(folder=None):
"""Returns or sets path of local folder where EVmutation data are stored.
To release the current folder, pass an invalid path, e.g.
``folder=''``.
"""
if folder is None:
folder = SETTINGS.get('EVmutation_local_folder')
if folder:
if isdir(folder):
return folder
else:
LOGGER.warn('Local folder {} is not accessible.'.format(
repr(folder)))
else:
if isdir(folder):
folder = abspath(folder)
LOGGER.info('Local EVmutation folder is set: {}'.format(
repr(folder)))
SETTINGS['EVmutation_local_folder'] = folder
SETTINGS.save()
else:
current = SETTINGS.pop('EVmutation_local_folder')
if current:
LOGGER.info('EVmutation folder {0} is released.'.format(
repr(current)))
SETTINGS.save()
else:
raise IOError('{} is not a valid path.'.format(repr(folder)))
def wwPDBServer(*key):
"""Set/get `wwPDB`_ FTP/HTTP server location used for downloading PDB
structures. Use one of the following keywords for setting a server:
+---------------------------+-----------------------------+
| wwPDB FTP server | *Key* (case insensitive) |
+===========================+=============================+
| RCSB PDB (USA) (default) | RCSB, USA, US |
+---------------------------+-----------------------------+
| PDBe (Europe) | PDBe, Europe, Euro, EU |
+---------------------------+-----------------------------+
| PDBj (Japan) | PDBj, Japan, Jp |
+---------------------------+-----------------------------+
.. _wwPDB: http://www.wwpdb.org/"""
if not key:
return SETTINGS.get('wwpdb', None)
elif len(key) == 1:
try:
key = key[0].lower()
except AttributeError:
raise TypeError('key must be a string')
if key in WWPDB_FTP_SERVERS:
SETTINGS['wwpdb'] = key
SETTINGS.save()
LOGGER.info('wwPDB server is set to {}.'
.format(WWPDB_FTP_SERVERS[key][0]))
else:
raise ValueError('{0} is not a valid wwPDB server identifier'
.format(repr(key)))
else:
raise TypeError('one wwPDB server identifier is expected, {0} given'
.format(len(key)))
def pathVMD(*path):
"""Returns VMD path, or set it to be a user specified *path*."""
if not path:
path = SETTINGS.get('vmd', None)
if isExecutable(path):
return path
else:
LOGGER.warning('VMD path is not set by user, looking for it.')
vmdbin = None
vmddir = None
if PLATFORM == 'Windows':
if PY3K:
import winreg
else:
import _winreg as winreg # PY3K: OK
for vmdversion in ('1.8.7', '1.9', '1.9.1'):
try:
key = winreg.OpenKey(
winreg.HKEY_LOCAL_MACHINE,
'Software\\University of Illinois\\VMD\\' +
vmdversion)
vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
vmdbin = join(vmddir, 'vmd.exe')
except:
pass
try:
key = winreg.OpenKey(
winreg.HKEY_LOCAL_MACHINE,
'Software\\WOW6432node\\University of Illinois\\VMD\\'
+ vmdversion)
vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
vmdbin = join(vmddir, 'vmd.exe')
except:
pass
else:
vmdbin = which('vmd')
if False:
pipe = os.popen('which vmd')
vmdbin = pipe.next().strip()
vmdfile = open(vmdbin)
for line in vmdfile:
if line.startswith('defaultvmddir='):
vmddir = line.split('=')[1].replace('"', '')
break
vmdfile.close()
if isExecutable(vmdbin):
setVMDpath(vmdbin)
return vmdbin
elif len(path) == 1:
path = path[0]
if isExecutable(path):
SETTINGS['vmd'] = path
SETTINGS.save()
LOGGER.info("VMD path is set to '{0}'.".format(path))
else:
raise OSError('{0} is not executable.'.format(str(path)))
else:
raise ValueError('specify a single path string')
def pathRhapsodyFolder(folder=None):
"""Returns or sets path of local folder where files and pickles necessary
to run Rhapsody will be stored. To release the current folder, pass an
invalid path, e.g. ``folder=''``.
"""
if folder is None:
folder = SETTINGS.get('rhapsody_local_folder')
if folder:
if isdir(folder):
return folder
else:
LOGGER.warn('Local folder {} is not accessible.'.format(
repr(folder)))
else:
if isdir(folder):
folder = abspath(folder)
LOGGER.info('Local Rhapsody folder is set: {}'.format(
repr(folder)))
SETTINGS['rhapsody_local_folder'] = folder
SETTINGS.save()
else:
current = SETTINGS.pop('rhapsody_local_folder')
if current:
LOGGER.info('Rhapsody folder {0} is released.'.format(
repr(current)))
SETTINGS.save()
else:
raise IOError('{} is not a valid path.'.format(repr(folder)))
def pathPDBMirror(path=None, format=None):
"""Returns or specify PDB mirror path to be used by :func:`.fetchPDB`.
To release the current mirror, pass an invalid path, e.g. ``path=''``.
If you are keeping a partial mirror, such as PDB files in
:file:`/data/structures/divided/pdb/` folder, specify *format*, which is
``'pdb'`` in this case."""
if path is None:
path = SETTINGS.get('pdb_mirror_path')
format = SETTINGS.get('pdb_mirror_format', None)
if path:
if isdir(path):
if format is None:
return path
else:
return path, format
else:
LOGGER.warning(
'PDB mirror path {0} is not a accessible.'.format(
repr(path)))
else:
if isdir(path):
path = abspath(path)
LOGGER.info('Local PDB mirror path is set: {0}'.format(repr(path)))
SETTINGS['pdb_mirror_path'] = path
SETTINGS['pdb_mirror_format'] = format
SETTINGS.save()
else:
current = SETTINGS.pop('pdb_mirror_path')
if current:
LOGGER.info('PDB mirror {0} is released.'.format(
repr(current)))
SETTINGS.save()
else:
raise IOError('{0} is not a valid path.'.format(repr(path)))
def changeDefinitions(**kwargs):
defs = SETTINGS.get(DEFINITIONS_KEY, {})
defs.update(kwargs)
SETTINGS[DEFINITIONS_KEY] = defs
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
def changeDefinitions(**kwargs):
defs = SETTINGS.get(DEFINITIONS_KEY, {})
defs.update(kwargs)
SETTINGS[DEFINITIONS_KEY] = defs
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
def pathVMD(*path):
"""Return VMD path, or set it to be a user specified *path*."""
if not path:
path = SETTINGS.get('vmd', None)
if isExecutable(path):
return path
else:
LOGGER.warning('VMD path is not set by user, looking for it.')
vmdbin = None
vmddir = None
if PLATFORM == 'Windows':
if PY3K:
import winreg
else:
import _winreg as winreg # PY3K: OK
for vmdversion in ('1.8.7', '1.9', '1.9.1'):
try:
key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
'Software\\University of Illinois\\VMD\\' +
vmdversion)
vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
vmdbin = join(vmddir, 'vmd.exe')
except:
pass
try:
key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE,
'Software\\WOW6432node\\University of Illinois\\VMD\\' +
vmdversion)
vmddir = winreg.QueryValueEx(key, 'VMDDIR')[0]
vmdbin = join(vmddir, 'vmd.exe')
except:
pass
else:
vmdbin = which('vmd')
if False:
pipe = os.popen('which vmd')
vmdbin = pipe.next().strip()
vmdfile = open(vmdbin)
for line in vmdfile:
if line.startswith('defaultvmddir='):
vmddir = line.split('=')[1].replace('"', '')
break
vmdfile.close()
if isExecutable(vmdbin):
setVMDpath(vmdbin)
return vmdbin
elif len(path) == 1:
path = path[0]
if isExecutable(path):
SETTINGS['vmd'] = path
SETTINGS.save()
LOGGER.info("VMD path is set to '{0}'.".format(path))
else:
raise OSError('{0} is not executable.'.format(str(path)))
else:
raise ValueError('specify a single path string')
def setVMDpath(path):
"""Set path to a VMD executable."""
if isExecutable(path):
SETTINGS["vmd"] = path
SETTINGS.save()
LOGGER.info("VMD path is set to '{0:s}'.".format(path))
else:
raise OSError("{0:s} is not executable.".format(str(path)))
def setPDBMirrorPath(path):
"""Set the path to a local PDB mirror."""
if not isinstance(path, str):
raise TypeError('path must be a string')
if isdir(path):
path = abspath(path)
LOGGER.info('Local PDB mirror path is set: {0:s}'.format(repr(path)))
SETTINGS['pdb_mirror_path'] = path
SETTINGS.save()
else:
raise IOError('No such directory: {0:s}'.format(repr(path)))
def pathPDBFolder(folder=None, divided=False):
"""Returns or specify local PDB folder for storing PDB files downloaded from
`wwPDB <http://www.wwpdb.org/>`_ servers. Files stored in this folder can
be accessed via :func:`.fetchPDB` from any working directory. To release
the current folder, pass an invalid path, e.g. ``folder=''``.
If *divided* is **True**, the divided folder structure of wwPDB servers
will be assumed when reading from and writing to the local folder. For
example, a structure with identifier **1XYZ** will be present as
:file:`pdblocalfolder/yz/pdb1xyz.pdb.gz`.
If *divided* is **False**, a plain folder structure will be expected and
adopted when saving files. For example, the same structure will be
present as :file:`pdblocalfolder/1xyz.pdb.gz`.
Finally, in either case, lower case letters will be used and compressed
files will be stored."""
if folder is None:
folder = SETTINGS.get('pdb_local_folder')
if folder:
if isdir(folder):
return folder, SETTINGS.get('pdb_local_divided', True)
else:
LOGGER.warn('PDB local folder {0} is not a accessible.'
.format(repr(folder)))
else:
if isdir(folder):
folder = abspath(folder)
LOGGER.info('Local PDB folder is set: {0}'.format(repr(folder)))
if divided:
LOGGER.info('wwPDB divided folder structure will be assumed.')
else:
LOGGER.info('A plain folder structure will be assumed.')
SETTINGS['pdb_local_folder'] = folder
SETTINGS['pdb_local_divided'] = bool(divided)
SETTINGS.save()
else:
current = SETTINGS.pop('pdb_local_folder')
if current:
LOGGER.info('PDB folder {0} is released.'
.format(repr(current)))
SETTINGS.pop('pdb_local_divided')
SETTINGS.save()
else:
raise IOError('{0} is not a valid path.'.format(repr(folder)))
def pathPDBFolder(folder=None, divided=False):
"""Returns or specify local PDB folder for storing PDB files downloaded from
`wwPDB <http://www.wwpdb.org/>`_ servers. Files stored in this folder can
be accessed via :func:`.fetchPDB` from any working directory. To release
the current folder, pass an invalid path, e.g. ``folder=''``.
If *divided* is **True**, the divided folder structure of wwPDB servers
will be assumed when reading from and writing to the local folder. For
example, a structure with identifier **1XYZ** will be present as
:file:`pdblocalfolder/yz/pdb1xyz.pdb.gz`.
If *divided* is **False**, a plain folder structure will be expected and
adopted when saving files. For example, the same structure will be
present as :file:`pdblocalfolder/1xyz.pdb.gz`.
Finally, in either case, lower case letters will be used and compressed
files will be stored."""
if folder is None:
folder = SETTINGS.get('pdb_local_folder')
if folder:
if isdir(folder):
return folder, SETTINGS.get('pdb_local_divided', True)
else:
LOGGER.warn('PDB local folder {0} is not a accessible.'.format(
repr(folder)))
else:
if isdir(folder):
folder = abspath(folder)
LOGGER.info('Local PDB folder is set: {0}'.format(repr(folder)))
if divided:
LOGGER.info('wwPDB divided folder structure will be assumed.')
else:
LOGGER.info('A plain folder structure will be assumed.')
SETTINGS['pdb_local_folder'] = folder
SETTINGS['pdb_local_divided'] = bool(divided)
SETTINGS.save()
else:
current = SETTINGS.pop('pdb_local_folder')
if current:
LOGGER.info('PDB folder {0} is released.'.format(
repr(current)))
SETTINGS.pop('pdb_local_divided')
SETTINGS.save()
else:
raise IOError('{0} is not a valid path.'.format(repr(folder)))
def setWWPDBFTPServer(key):
"""Set the `wwPDB <http://www.wwpdb.org/>`_ FTP server used for downloading
PDB structures when needed. Use one of the following keywords for setting
a different server.
+---------------------------+-----------------------------+
| wwPDB FTP server | *Key* (case insensitive) |
+===========================+=============================+
| RCSB PDB (USA) (default) | RCSB, USA, US |
+---------------------------+-----------------------------+
| PDBe (Europe) | PDBe, Europe, Euro, EU |
+---------------------------+-----------------------------+
| PDBj (Japan) | PDBj, Japan, Jp |
+---------------------------+-----------------------------+
"""
server = WWPDB_FTP_SERVERS.get(key.lower())
if server is not None:
SETTINGS['wwpdb_ftp'] = server
SETTINGS.save()
else:
LOGGER.warning('{0:s} is not a valid key.'.format(key))
def setPDBLocalFolder(folder, divided=False):
"""Set a local PDB folder. Setting a local PDB folder will make
:func:`fetchPDB` function to seek that folder for presence of requested
PDB files. Also, files downloaded from `wwPDB <http://www.wwpdb.org/>`_
FTP servers will be saved in this folder. This may help users to store
PDB files in a single place and have access to them in different working
directories.
If *divided* is **True**, the divided folder structure of wwPDB servers
will be assumed when reading from and writing to the local folder. For
example, a structure with identifier **1XYZ** will be present as
:file:`pdblocalfolder/yz/pdb1xyz.pdb.gz`.
If *divided* is **False**, a plain folder structure will be expected and
adopted when saving files. For example, the same structure will be
present as :file:`pdblocalfolder/1xyz.pdb.gz`.
Finally, in either case, lower case letters will be used and compressed
files will be stored."""
if not isinstance(folder, str):
raise TypeError('folder must be a string')
assert isinstance(divided, bool), 'divided must be a boolean'
if isdir(folder):
folder = abspath(folder)
LOGGER.info('Local PDB folder is set: {0:s}'.format(repr(folder)))
if divided:
LOGGER.info('When using local PDB folder, wwPDB divided '
'folder structure will be assumed.')
else:
LOGGER.info('When using local PDB folder, a plain folder structure '
'will be assumed.')
SETTINGS['pdb_local_folder'] = folder
SETTINGS['pdb_local_divided'] = divided
SETTINGS.save()
else:
raise IOError('No such directory: {0:s}'.format(repr(folder)))
def resetDefinitions(flag):
if flag == 'all':
SETTINGS.pop(DEFINITIONS_KEY, None)
SETTINGS.pop(NONSTANDARD_KEY, None)
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
elif flag == 'nonstdaa':
SETTINGS.pop(NONSTANDARD_KEY, None)
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
else:
try:
SETTINGS.pop(DEFINITIONS_KEY, {}).pop(flag)
except KeyError:
pass
else:
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
def resetDefinitions(flag):
if flag == 'all':
SETTINGS.pop(DEFINITIONS_KEY, None)
SETTINGS.pop(NONSTANDARD_KEY, None)
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
elif flag == 'nonstdaa':
SETTINGS.pop(NONSTANDARD_KEY, None)
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
else:
try:
SETTINGS.pop(DEFINITIONS_KEY, {}).pop(flag)
except KeyError:
pass
else:
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
def updateNonstandard(nonstd):
SETTINGS[NONSTANDARD_KEY] = nonstd
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
def updateNonstandard(nonstd):
SETTINGS[NONSTANDARD_KEY] = nonstd
SETTINGS[TIMESTAMP_KEY] = int(time())
SETTINGS.save()
updateDefinitions()
