"""ProDy is a package for Protein Dynamics, Sequence, and Structure Analysis"""
__version__ = '2.4.1'
__release__ = __version__ # + '-dev' # comment out '-dev' before a release
import sys
import warnings
if sys.version_info[:2] < (2, 7):
sys.stderr.write('Python 2.6 and older is not supported\n')
sys.exit()
if sys.version_info[0] == 3:
if sys.version_info[1] < 6:
sys.stderr.write('Python 3.5 and older is not supported\n')
sys.exit()
try:
import numpy as np
except ImportError:
raise ImportError('Numpy is a required package for ProDy')
else:
if tuple(map(int, np.__version__.split('.')[:2])) < (1, 10):
raise ImportError('Numpy v1.10 or later is required for ProDy')
try:
import scipy
except ImportError:
raise ImportError('Scipy is a required package for ProDy')
DEPRECATION_WARNINGS = False
def deprecate(dep, alt, ver=None, sl=3):
"""Issue a deprecation warning for *dep* and recommend using *alt*."""
if ver is None:
ver = list(__version__.split('.')[:2])
ver[1] = str(int(ver[1]) + 1)
ver = '.'.join(ver)
warnings.warn('`{0:s}` is deprecated for removal in v{1:s}, use `{2:s}`.'
.format(dep, ver, alt), DeprecationWarning, stacklevel=sl)
def turnonDeprecationWarnings(action='always'):
"""Turn on deprecation warnings for the current session. By default
(``action='always'``), deprecation warnings will be printed every time
a function is called to help identification of multiple occurrence
of deprecated function and method names. When ``action='default'``
is passed, warning will be issued at the first call of a function.
The latter behavior will automatically kick in when v0.9 is released.
Until v0.9 is released, restarting the session will turn of warnings.
This function must be called as ``prody.turnonDeprecationWarnings``."""
global DEPRECATION_WARNINGS
DEPRECATION_WARNINGS = True
warnings.filterwarnings(action, category=DeprecationWarning)
_PY3K = PY3K = sys.version_info[0] > 2
PY2K = not PY3K
__all__ = ['checkUpdates', 'confProDy', 'startLogfile', 'closeLogfile', 'plog']
from . import utilities
from .utilities import *
from .utilities import LOGGER, PackageSettings
from .utilities import getPackagePath, joinRepr, tabulate
__all__.extend(utilities.__all__)
__all__.append('utilities')
SETTINGS = PackageSettings('prody', logger=LOGGER)
SETTINGS.load()
from . import kdtree
from .kdtree import *
__all__.extend(kdtree.__all__)
__all__.append('kdtree')
from . import atomic
from .atomic import *
__all__.extend(atomic.__all__)
__all__.append('atomic')
from .atomic import SELECT
from . import proteins
from .proteins import *
__all__.extend(proteins.__all__)
__all__.append('proteins')
from . import compounds
from .compounds import *
__all__.extend(compounds.__all__)
__all__.append('compounds')
from . import measure
from .measure import *
__all__.extend(measure.__all__)
__all__.append('measure')
from . import database
from .database import *
__all__.extend(database.__all__)
__all__.append('database')
from . import sequence
from .sequence import *
__all__.extend(sequence.__all__)
__all__.append('sequence')
from . import dynamics
from .dynamics import *
__all__.extend(dynamics.__all__)
__all__.append('dynamics')
from . import ensemble
from .ensemble import *
__all__.extend(ensemble.__all__)
__all__.append('ensemble')
from . import trajectory
from .trajectory import *
__all__.extend(trajectory.__all__)
__all__.append('trajectory')
from . import chromatin
from .chromatin import *
__all__.extend(chromatin.__all__)
__all__.append('chromatin')
from . import domain_decomposition
from .domain_decomposition import *
__all__.extend(domain_decomposition.__all__)
__all__.append('domain_decomposition')
#from . import comd
#from .comd import *
#__all__.extend(comd.__all__)
#__all__.append('comd')
import prody
__all__.append('prody')
# default, acceptable values, setter
CONFIGURATION = {
'backup': (False, None, None),
'backup_ext': ('.BAK', None, None),
'auto_show': (False, None, None),
'ligand_xml_save': (False, None, None),
'typo_warnings': (True, None, None),
'check_updates': (0, None, None),
'auto_secondary': (False, None, None),
'auto_bonds': (False, None, None),
'selection_warning': (True, None, None),
'verbosity': ('debug', list(utilities.LOGGING_LEVELS),
LOGGER._setverbosity),
'pdb_mirror_path': ('', None, proteins.pathPDBMirror),
'local_pdb_folder': ('', None, proteins.pathPDBFolder),
}
[docs]def confProDy(*args, **kwargs):
"""Configure ProDy."""
if args:
values = []
for option in args:
try:
values.append(SETTINGS[option])
except KeyError:
raise KeyError('{0:s} is not a valid configuration option'
.format(repr(option)))
if len(values) == 1:
return values[0]
else:
return values
for option, value in kwargs.items():
try:
default, acceptable, setter = CONFIGURATION[option]
except KeyError:
raise KeyError('{0:s} is not a valid configuration option'
.format(repr(option)))
else:
try:
value = type(default)(value)
except ValueError:
raise TypeError('{0:s} must be a {1:s}'
.format(option, type(default).__name__))
if acceptable is not None and value not in acceptable:
raise ValueError('{0:s} must be one of {1:s}'.format(option,
joinRepr(acceptable, sort=True,
last=', or ')))
SETTINGS[option] = value
LOGGER.info('ProDy is configured: {0:s}={1:s}'
.format(option, repr(value)))
SETTINGS.save()
if setter is not None:
setter(value)
_keys = list(CONFIGURATION)
_keys.sort()
_vals = []
for _key in _keys:
default, acceptable, setter = CONFIGURATION[_key]
try:
if not setter.func_name.startswith('_'):
seealso = ' See also :func:`.' + setter.func_name + '`.'
except AttributeError:
seealso = ''
if acceptable is None:
_vals.append(repr(default) + seealso)
else:
_vals.append(repr(default) + ' (' +
joinRepr(acceptable, sort=True, last=', or ') + ')' +
seealso)
if _key not in SETTINGS:
SETTINGS[_key] = default
LOGGER._setverbosity(confProDy('verbosity'))
confProDy.__doc__ += '\n\n' + tabulate(['Option'] + _keys,
['Default (acceptable values)'] + _vals
) + """
Usage example::
confProDy('backup')
confProDy('backup', 'backup_ext')
confProDy(backup=True, backup_ext='.bak')
confProDy(backup_ext='.BAK')"""
[docs]def plog(*text):
"""Log *text* using ProDy logger at log level info. Multiple arguments
are accepted. Each argument will be converted to string and joined using
a white space as delimiter."""
LOGGER.info(' '.join([str(s) for s in text]))
[docs]def startLogfile(filename, **kwargs):
LOGGER.start(filename, **kwargs)
startLogfile.__doc__ = LOGGER.start.__doc__
[docs]def closeLogfile(filename):
"""Close logfile with *filename*."""
LOGGER.close(filename)
[docs]def checkUpdates():
"""Check PyPI to see if there is a newer ProDy version available. Setting
ProDy configuration parameter *check_updates* to a positive integer will
make ProDy automatically check updates, e.g.::
confProDy(check_updates=7) # check at most once a week
confProDy(check_updates=0) # do not auto check updates
confProDy(check_updates=-1) # check at the start of every session"""
pypi_url = 'https://pypi.python.org/pypi'
if PY3K:
import xmlrpc.client
pypi = xmlrpc.client.Server(pypi_url)
else:
import xmlrpclib
pypi = xmlrpclib.Server(pypi_url)
releases = pypi.package_releases('ProDy')
if releases[0] == __version__:
LOGGER.info('You are using the latest ProDy release (v{0:s}).'
.format(__version__))
else:
LOGGER.info('ProDy v{0:s} is available, you are using {1:s}.'
.format(releases[0], __version__))
if SETTINGS['check_updates']:
import time
SETTINGS['last_check'] = time.time()
SETTINGS.save()
if SETTINGS['check_updates']:
if SETTINGS.get('last_check') is None:
SETTINGS['last_check'] = 0
import time
if ((time.time() - SETTINGS.get('last_check')) / 3600 / 24 >
SETTINGS['check_updates']):
LOGGER.info('Checking PyPI for ProDy updates:')
checkUpdates()
