def cfg_dir(self, pyemma_cfg_dir):
""" Sets PyEMMAs configuration directory.
Also creates it with some default files, if does not exists. """
if not os.path.exists(pyemma_cfg_dir):
try:
mkdir_p(pyemma_cfg_dir)
except EnvironmentError:
raise ConfigDirectoryException(
"could not create configuration directory '%s'" %
pyemma_cfg_dir)
except NotADirectoryError: # on Python 3
raise ConfigDirectoryException(
"pyemma cfg dir (%s) is not a directory" % pyemma_cfg_dir)
if not os.path.isdir(pyemma_cfg_dir):
raise ConfigDirectoryException("%s is no valid directory" %
pyemma_cfg_dir)
if not os.access(pyemma_cfg_dir, os.W_OK):
raise ConfigDirectoryException("%s is not writeable" %
pyemma_cfg_dir)
# give user the default cfg file, if its not there
self.__copy_default_files_to_cfg_dir(pyemma_cfg_dir)
self._cfg_dir = pyemma_cfg_dir
if self.show_config_notification:
stars = '*' * 80
print(
stars,
'\n',
'Changed PyEMMAs config directory to "{dir}".\n'
'To make this change permanent, export the environment variable'
' "PYEMMA_CFG_DIR" \nto point to this location. Eg. edit your .bashrc file!'
.format(dir=pyemma_cfg_dir),
'\n',
stars,
sep='')
def save_dtrajs(self,
trajfiles=None,
prefix='',
output_dir='.',
output_format='ascii',
extension='.dtraj'):
"""saves calculated discrete trajectories. Filenames are taken from
given reader. If data comes from memory dtrajs are written to a default
filename.
Parameters
----------
trajfiles : list of str (optional)
names of input trajectory files, will be used generate output files.
prefix : str
prepend prefix to filenames.
output_dir : str
save files to this directory.
output_format : str
if format is 'ascii' dtrajs will be written as csv files, otherwise
they will be written as NumPy .npy files.
extension : str
file extension to append (eg. '.itraj')
"""
if extension[0] != '.':
extension = '.' + extension
# obtain filenames from input (if possible, reader is a featurereader)
if output_format == 'ascii':
from msmtools.dtraj import write_discrete_trajectory as write_dtraj
else:
from msmtools.dtraj import save_discrete_trajectory as write_dtraj
import os.path as path
output_files = []
if trajfiles is not None: # have filenames available?
for f in trajfiles:
p, n = path.split(f) # path and file
basename, _ = path.splitext(n)
if prefix != '':
name = "%s_%s%s" % (prefix, basename, extension)
else:
name = "%s%s" % (basename, extension)
# name = path.join(p, name)
output_files.append(name)
else:
for i in range(len(self.dtrajs)):
if prefix is not '':
name = "%s_%i%s" % (prefix, i, extension)
else:
name = str(i) + extension
output_files.append(name)
assert len(self.dtrajs) == len(output_files)
if not os.path.exists(output_dir):
mkdir_p(output_dir)
for filename, dtraj in zip(output_files, self.dtrajs):
dest = path.join(output_dir, filename)
self._logger.debug('writing dtraj to "%s"' % dest)
try:
if path.exists(dest) and not self.overwrite_dtrajs:
raise EnvironmentError(
'Attempted to write dtraj "%s" which already existed. To automatically'
' overwrite existing files, set source.overwrite_dtrajs=True.'
% dest)
write_dtraj(dest, dtraj)
except IOError:
self._logger.exception(
'Exception during writing dtraj to "%s"' % dest)