def open_trajectory(self):
"""Open xdr trajectory file.
:Returns: pointer to XDRFILE (and sets self.xdrfile)
:Raises: :exc:`IOError` with code EALREADY if file was already opened or
ENOENT if the file cannot be found
"""
if not self.xdrfile is None:
raise IOError(errno.EALREADY, 'XDR file already opened',
self.filename)
if not os.path.exists(self.filename):
# must check; otherwise might segmentation fault
raise IOError(errno.ENOENT, 'XDR file not found', self.filename)
self.xdrfile = libxdrfile2.xdrfile_open(self.filename, 'r')
# reset ts
ts = self.ts
ts.status = libxdrfile2.exdrOK
ts.frame = 0
ts.step = 0
ts.time = 0
# additional data for XTC
ts.prec = 0
# additional data for TRR
ts.lmbda = 0
return self.xdrfile
def open_trajectory(self):
"""Open xdr trajectory file.
:Returns: pointer to XDRFILE (and sets self.xdrfile)
:Raises: :exc:`IOError` with code EALREADY if file was already opened or
ENOENT if the file cannot be found
"""
if not self.xdrfile is None:
raise IOError(errno.EALREADY, 'XDR file already opened', self.filename)
if not os.path.exists(self.filename):
# must check; otherwise might segmentation fault
raise IOError(errno.ENOENT, 'XDR file not found', self.filename)
self.xdrfile = libxdrfile2.xdrfile_open(self.filename, 'r')
# reset ts
ts = self.ts
ts.status = libxdrfile2.exdrOK
ts.frame = 0
ts.step = 0
ts.time = 0
# additional data for XTC
ts.prec = 0
# additional data for TRR
ts.lmbda = 0
return self.xdrfile
def __init__(self, filename, numatoms, start=0, step=1, delta=None, precision=1000.0, remarks=None,
convert_units=None):
""" Create a new TrjWriter
:Arguments:
*filename*
name of output file
*numatoms*
number of atoms in trajectory file
:Keywords:
*start*
starting timestep; only used when *delta* is set.
*step*
skip between subsequent timesteps; only used when *delta* is set.
*delta*
timestep to use. If set will override any time information contained in the
passed :class:`Timestep` objects; otherwise that will be used. If in the
latter case :attr:`~Timestep.time` is unavailable the TrjWriter will default
to setting the trajectory time at 1 MDAnalysis unit (typically 1ps) per step.
*precision*
accuracy for lossy XTC format as a power of 10 (ignored
for TRR) [1000.0]
*convert_units*
``True``: units are converted to the MDAnalysis base format; ``None`` selects
the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
(see :ref:`flags-label`)
.. versionchanged:: 0.8.0
The TRR writer is now able to write TRRs without coordinates/velocities/forces,
depending on the properties available in the :class:`Timestep` objects passed to
:meth:`~TRRWriter.write`.
"""
assert self.format in ('XTC', 'TRR')
if numatoms == 0:
raise ValueError("TrjWriter: no atoms in output trajectory")
self.filename = filename
# Convert filename to ascii because of SWIG bug.
# See: http://sourceforge.net/p/swig/feature-requests/75
# Only needed for Python < 3
if sys.version_info[0] < 3:
if isinstance(filename, unicode):
self.filename = filename.encode("UTF-8")
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units # convert length and time to base units on the fly?
self.numatoms = numatoms
self.frames_written = 0
self.start = start
self.step = step
self.delta = delta
self.remarks = remarks
self.precision = precision # only for XTC
self.xdrfile = libxdrfile2.xdrfile_open(self.filename, 'w')
self.ts = None
# To flag empty properties to be skipped when writing a TRR it suffices to pass an empty 2D array with shape(
# natoms,0)
if self.format == 'TRR':
self._emptyarr = numpy.array([], dtype=numpy.float32).reshape(self.numatoms, 0)
def __init__(self,
filename,
numatoms,
start=0,
step=1,
delta=None,
precision=1000.0,
remarks=None,
convert_units=None):
""" Create a new TrjWriter
:Arguments:
*filename*
name of output file
*numatoms*
number of atoms in trajectory file
:Keywords:
*start*
starting timestep; only used when *delta* is set.
*step*
skip between subsequent timesteps; only used when *delta* is set.
*delta*
timestep to use. If set will override any time information contained in the
passed :class:`Timestep` objects; otherwise that will be used. If in the
latter case :attr:`~Timestep.time` is unavailable the TrjWriter will default
to setting the trajectory time at 1 MDAnalysis unit (typically 1ps) per step.
*precision*
accuracy for lossy XTC format as a power of 10 (ignored
for TRR) [1000.0]
*convert_units*
``True``: units are converted to the MDAnalysis base format; ``None`` selects
the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
(see :ref:`flags-label`)
.. versionchanged:: 0.8.0
The TRR writer is now able to write TRRs without coordinates/velocities/forces,
depending on the properties available in the :class:`Timestep` objects passed to
:meth:`~TRRWriter.write`.
"""
assert self.format in ('XTC', 'TRR')
if numatoms == 0:
raise ValueError("TrjWriter: no atoms in output trajectory")
self.filename = filename
# Convert filename to ascii because of SWIG bug.
# See: http://sourceforge.net/p/swig/feature-requests/75
# Only needed for Python < 3
if sys.version_info[0] < 3:
if isinstance(filename, unicode):
self.filename = filename.encode("UTF-8")
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units # convert length and time to base units on the fly?
self.numatoms = numatoms
self.frames_written = 0
self.start = start
self.step = step
self.delta = delta
self.remarks = remarks
self.precision = precision # only for XTC
self.xdrfile = libxdrfile2.xdrfile_open(self.filename, 'w')
self.ts = None
# To flag empty properties to be skipped when writing a TRR it suffices to pass an empty 2D array with shape(
# natoms,0)
if self.format == 'TRR':
self._emptyarr = numpy.array([], dtype=numpy.float32).reshape(
self.numatoms, 0)