def __init__(self, filename, mode="wa", numterms=None, preamble=None, **kwargs):
"""Set up for writing to *filename*.
:Arguments:
*filename*
output file
*mode*
overwrite ("w") for every write, append ("a") to existing
file, or overwrite an existing file and then append ("wa") ["wa"]
*numterms*
number of individual index numbers per line for output
formats that write multiple entries in one line. If set
to 0 or ``False`` then no special formatting is done [8]
*preamble*
string that is written as a comment at the top of the file []
*kwargs*
use as defaults for :meth:`write`
"""
self.filename = util.filename(filename, ext=self.ext)
if not mode in ('a', 'w', 'wa'):
raise ValueError("mode must be one of 'w', 'a', 'wa', not %r" % mode)
self.mode = mode
self._current_mode = mode[0]
if numterms is None or numterms < 0:
self.numterms = self.default_numterms
elif numterms is False:
self.numterms = 0
else:
self.numterms = numterms
self.preamble = preamble
self.otherargs = kwargs # hack
self.number = 0
self.write_preamble()
def testNamedStream(self):
ns = util.NamedStream(cStringIO.StringIO(), self.filename)
fn = util.filename(ns, ext=self.ext)
# assert_equal replace by this if loop to avoid segfault on some systems
if fn != ns:
raise AssertionError("fn and ns are different")
assert_equal(str(fn), self.filename2)
assert_equal(ns.name, self.filename2)
def __init__(self, filename, convert_units=None, **kwargs):
"""Set up a GROWriter with a precision of 3 decimal places.
:Arguments:
*filename*
output filename
"""
self.filename = util.filename(filename, ext='gro')
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units # convert length and time to base units
def __init__(self, filename, convert_units=None, **kwargs):
"""Set up a GROWriter with a precision of 3 decimal places.
:Arguments:
*filename*
output filename
"""
self.filename = util.filename(filename, ext="gro")
if convert_units is None:
convert_units = MDAnalysis.core.flags["convert_lengths"]
self.convert_units = convert_units # convert length and time to base units
def __init__(self, filename, convert_units=None, **kwargs):
"""Set up a PQRWriter with full whitespace separation.
:Arguments:
*filename*
output filename
*remarks*
remark lines (list of strings) or single string to be added to the
top of the PQR file
"""
self.filename = util.filename(filename, ext='pqr')
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units # convert length and time to base units
self.remarks = kwargs.pop('remarks', "PQR file written by MDAnalysis")
def __init__(self,
filename,
mode="wa",
numterms=None,
preamble=None,
**kwargs):
"""Set up for writing to *filename*.
:Arguments:
*filename*
output file
*mode*
overwrite ("w") for every write, append ("a") to existing
file, or overwrite an existing file and then append ("wa") ["wa"]
*numterms*
number of individual index numbers per line for output
formats that write multiple entries in one line. If set
to 0 or ``False`` then no special formatting is done [8]
*preamble*
string that is written as a comment at the top of the file []
*kwargs*
use as defaults for :meth:`write`
"""
self.filename = util.filename(filename, ext=self.ext)
if not mode in ('a', 'w', 'wa'):
raise ValueError("mode must be one of 'w', 'a', 'wa', not %r" %
mode)
self.mode = mode
self._current_mode = mode[0]
if numterms is None or numterms < 0:
self.numterms = self.default_numterms
elif numterms is False:
self.numterms = 0
else:
self.numterms = numterms
self.preamble = preamble
self.otherargs = kwargs # hack
self.number = 0
self.write_preamble()
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext='crd')
self.crd = None
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext='pdbqt')
self.pdb = util.anyopen(self.filename, 'w')
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext='crd')
self.crd = None
def __init__(self, filename, **kwargs):
self.filename = util.filename(filename, ext='pdbqt')
self.pdb = util.anyopen(self.filename, 'w')
def testStringRootExtKeep(self):
fn = util.filename(self.root, ext=self.ext, keep=True)
assert_equal(fn, self.filename2)
def testStringRootExt(self):
fn = util.filename(self.root, ext=self.ext)
assert_equal(fn, self.filename2)
def testStringKeep(self):
fn = util.filename(self.filename, ext=self.ext, keep=True)
assert_equal(fn, self.filename)
def testStringNoExt(self):
fn = util.filename(self.filename)
assert_equal(fn, self.filename)