class GromacsFile(object):
"""
A GROMACS file that recognizes the ";" character as a 'comment' token. It
can be iterated over and generally treated like a file object, but only
spits out strings that have been truncated at its first comment character.
There is currently no way to recognize a ; as a _non_ comment character,
since allowing an escape character does not seem to be common practice and
would likely introduce negative performance implications.
Parameters
----------
fname : str or file-like
Name of the file to parse or file-like object to parse
defines : dict{str : str}, optional
List of defines for the preprocessed file, if any
includes : list of str, optional
List of include files. Default is taken from environment variables
GMXDATA or GMXBIN if they are set. Otherwise, it is looked for in /usr,
/usr/local, /opt, or /opt/local. If it is still not found, it is looked
for relative to whatever ``mdrun`` executable is in your path
notfound_fatal : bool, optional
If True, missing include files are fatal. If False, they are a warning.
Default is True
"""
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0
def __iter__(self):
# Iterate over the file, treating an ending \ as a continuation
parts = []
for line in self._handle:
try:
idx = line.index(';')
if not parts:
yield '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
yield '%s\n' % ''.join(parts)
parts = []
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
yield ''.join(parts)
parts = []
else:
yield line
@property
def included_files(self):
return self._handle.included_files
def readline(self):
parts = []
self.line_number += 1
line = True
while line:
line = self._handle.readline()
try:
idx = line.index(';')
if not parts:
return '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
return '%s\n' % ''.join(parts)
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
return ''.join(parts)
else:
return line
def readlines(self):
return [line for line in self]
def read(self):
return ''.join(self.readlines())
def close(self):
self._handle.close()
self.closed = True
def __del__(self):
try:
self.closed or self._handle.close()
except AttributeError:
# It didn't make it out of the constructor
pass
class GromacsFile(object):
"""
A GROMACS file that recognizes the ";" character as a 'comment' token. It
can be iterated over and generally treated like a file object, but only
spits out strings that have been truncated at its first comment character.
There is currently no way to recognize a ; as a _non_ comment character,
since allowing an escape character does not seem to be common practice and
would likely introduce negative performance implications.
Parameters
----------
fname : str or file-like
Name of the file to parse or file-like object to parse
defines : dict{str : str}, optional
List of defines for the preprocessed file, if any
includes : list of str, optional
List of include files. Default is taken from environment variables
GMXDATA or GMXBIN if they are set. Otherwise, it is looked for in /usr,
/usr/local, /opt, or /opt/local. If it is still not found, it is looked
for relative to whatever ``mdrun`` executable is in your path
notfound_fatal : bool, optional
If True, missing include files are fatal. If False, they are a warning.
Default is True
"""
def __init__(self, fname, **kwargs):
self._handle = CPreProcessor(fname, **kwargs)
self.closed = False
self.line_number = 0
def __iter__(self):
# Iterate over the file, treating an ending \ as a continuation
parts = []
for line in self._handle:
try:
idx = line.index(';')
if not parts:
yield '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
yield '%s\n' % ''.join(parts)
parts = []
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
yield ''.join(parts)
parts = []
else:
yield line
@property
def included_files(self):
return self._handle.included_files
def readline(self):
parts = []
self.line_number += 1
line = True
while line:
line = self._handle.readline()
try:
idx = line.index(';')
if not parts:
return '%s\n' % line[:idx]
else:
parts.append('%s' % line[:idx])
return '%s\n' % ''.join(parts)
except ValueError:
# There is no comment...
if line.rstrip('\r\n').endswith('\\'):
chars = list(reversed(line.rstrip('\r\n')))
del chars[chars.index('\\')]
parts.append('%s ' % ''.join(reversed(chars)))
elif parts:
parts.append(line)
return ''.join(parts)
else:
return line
def readlines(self):
return [line for line in self]
def read(self):
return ''.join(self.readlines())
def close(self):
self._handle.close()
self.closed = True
def __del__(self):
try:
self.closed or self._handle.close()
except AttributeError:
# It didn't make it out of the constructor
pass
