def __init__(self, outfilename, **kwargs):
self.filename = outfilename
# the filename has been parsed to be either b(g)zipped or not
self.outfile = util.anyopen(self.filename, 'r')
# note that, like for xtc and trr files, _numatoms and _numframes are used quasi-private variables
# to prevent the properties being recalculated
# this is because there is no indexing so the way it measures the number of frames is to read the whole file!
self._numatoms = None
self._numframes = None
self._runtyp = None
self.ts = Timestep(0) # need for properties initial calculations
self.fixed = 0
self.skip = 1
self.periodic = False
self.delta = kwargs.pop("delta", 1.0) # there is no time, so let delta be 1
# update runtyp property
self.runtyp
if not self.runtyp in ['optimize', 'surface']:
raise AttributeError('Wrong RUNTYP= '+self.runtyp)
self.skip_timestep = 1
self.ts = Timestep(self.numatoms)
# update numframes property
self.numframes
# Read in the first timestep
self._read_next_timestep()
def __init__(self, filename, numatoms=None, start=0, step=1,
convert_units=None, multiframe=None):
"""Create a new PDBWriter
:Arguments:
*filename*
name of output file
*start*
starting timestep
*step*
skip between subsequent timesteps
*convert_units*
units are converted to the MDAnalysis base format; ``None`` selects
the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
"""
self.filename = filename
if convert_units is None:
convert_units = core.flags['convert_lengths']
self.convert_units = convert_units # convert length and time to base units
self.frames_written = 0
if start < 0:
raise ValueError("'Start' must be a positive value")
self.start = start
self.step = step
self.file = util.anyopen(self.filename, 'w') # open file on init
def __init__(self, *args, **kwargs):
"""Initialize the XYZ trajectory writer
:Arguments:
*filename*
file name of trajectory file. If it ends with "gz" then the file
will be gzip-compressed; if it ends with "bz2" it will be bzip2
compressed.
:Keywords:
*atoms*
Provide atom names: This can be a list of names or an :class:`AtomGroup`.
If none is provided, atoms will be called 'X' in the output. These atom
names will be used when a trajectory is written from raw :class:`Timestep`
objects which do not contain atom information.
If you write a :class:`AtomGroup` with :meth:`XYZWriter.write` then atom
information is taken at each step and *atoms* is ignored.
*remark*
single line of text ("molecule name")
"""
# numatoms is ignored ...
self.filename = args[0]
# convert length and time to base units on the fly?
convert_units = kwargs.pop('convert_units', None)
self.convert_units = convert_units if convert_units is not None else MDAnalysis.core.flags[
'convert_lengths']
self.atomnames = self._get_atomnames(kwargs.pop('atoms', "X"))
self.remark = kwargs.pop(
'remark',
"Written by {0} (release {1})".format(self.__class__.__name__,
MDAnalysis.__version__))
self.xyz = util.anyopen(self.filename, 'w') # can also be gz, bz2
def __init__(self, *args, **kwargs):
"""Initialize the XYZ trajectory writer
:Arguments:
*filename*
file name of trajectory file. If it ends with "gz" then the file
will be gzip-compressed; if it ends with "bz2" it will be bzip2
compressed.
:Keywords:
*atoms*
Provide atom names: This can be a list of names or an :class:`AtomGroup`.
If none is provided, atoms will be called 'X' in the output. These atom
names will be used when a trajectory is written from raw :class:`Timestep`
objects which do not contain atom information.
If you write a :class:`AtomGroup` with :meth:`XYZWriter.write` then atom
information is taken at each step and *atoms* is ignored.
*remark*
single line of text ("molecule name")
"""
# numatoms is ignored ...
self.filename = args[0]
# convert length and time to base units on the fly?
convert_units = kwargs.pop('convert_units', None)
self.convert_units = convert_units if convert_units is not None else MDAnalysis.core.flags['convert_lengths']
self.atomnames = self._get_atomnames(kwargs.pop('atoms', "X"))
self.remark = kwargs.pop('remark',
"Written by {0} (release {1})".format(self.__class__.__name__, MDAnalysis.__version__))
self.xyz = util.anyopen(self.filename, 'w') # can also be gz, bz2
def __init__(self, filename, **kwargs):
self.filename = filename
# the filename has been parsed to be either be foo.xyz or foo.xyz.bz2 by coordinates::core.py
# so the last file extension will tell us if it is bzipped or not
root, ext = os.path.splitext(self.filename)
self.xyzfile = util.anyopen(self.filename, "r")
self.compression = ext[1:] if ext[1:] != "xyz" else None
# note that, like for xtc and trr files, __numatoms and __numframes are used quasi-private variables
# to prevent the properties being recalculated
# this is because there is no indexing so the way it measures the number of frames is to read the whole file!
self.__numatoms = None
self.__numframes = None
self.fixed = 0
self.skip = 1
self.periodic = False
self.delta = kwargs.pop(
"delta", 1.0
) # can set delta manually, default is 1ps (taken from TRJReader)
self.skip_timestep = 1
self.ts = self._Timestep(
self.numatoms
) # numatoms has sideeffects: read trajectory... (FRAGILE)
# Read in the first timestep (FRAGILE);
# FIXME: Positions on frame 0 (whatever that means) instead of 1 (as all other readers do).
# Haven't quite figured out where to start with all the self._reopen() etc.
# (Also cannot just use seek() or reset() because that would break with urllib2.urlopen() streams)
self._read_next_timestep()
def __init__(self, outfilename, **kwargs):
self.filename = outfilename
# the filename has been parsed to be either b(g)zipped or not
self.outfile = util.anyopen(self.filename, 'r')
# note that, like for xtc and trr files, _numatoms and _numframes are used quasi-private variables
# to prevent the properties being recalculated
# this is because there is no indexing so the way it measures the number of frames is to read the whole file!
self._numatoms = None
self._numframes = None
self._runtyp = None
self.ts = Timestep(0) # need for properties initial calculations
self.fixed = 0
self.skip = 1
self.periodic = False
self.delta = kwargs.pop("delta",
1.0) # there is no time, so let delta be 1
# update runtyp property
self.runtyp
if not self.runtyp in ['optimize', 'surface']:
raise AttributeError('Wrong RUNTYP= ' + self.runtyp)
self.skip_timestep = 1
self.ts = Timestep(self.numatoms)
# update numframes property
self.numframes
# Read in the first timestep
self._read_next_timestep()
def __init__(self, filename, **kwargs):
self.filename = filename
# the filename has been parsed to be either be foo.xyz or foo.xyz.bz2 by coordinates::core.py
# so the last file extension will tell us if it is bzipped or not
root, ext = os.path.splitext(self.filename)
self.xyzfile = util.anyopen(self.filename, "r")
self.compression = ext[1:] if ext[1:] != "xyz" else None
# note that, like for xtc and trr files, __numatoms and __numframes are used quasi-private variables
# to prevent the properties being recalculated
# this is because there is no indexing so the way it measures the number of frames is to read the whole file!
self.__numatoms = None
self.__numframes = None
self.fixed = 0
self.skip = 1
self.periodic = False
self.delta = kwargs.pop("delta", 1.0) # can set delta manually, default is 1ps (taken from TRJReader)
self.skip_timestep = 1
self.ts = self._Timestep(self.numatoms) # numatoms has sideeffects: read trajectory... (FRAGILE)
# Read in the first timestep (FRAGILE);
# FIXME: Positions on frame 0 (whatever that means) instead of 1 (as all other readers do).
# Haven't quite figured out where to start with all the self._reopen() etc.
# (Also cannot just use seek() or reset() because that would break with urllib2.urlopen() streams)
self._read_next_timestep()
def __init__(self,
trzfilename,
numatoms=None,
convert_units=None,
**kwargs):
"""Creates a TRZ Reader
:Arguments:
*trzfilename*
name of input file
*numatoms*
number of atoms in trajectory, must taken from topology file!
*convert_units*
converts units to MDAnalysis defaults
"""
if numatoms is None:
raise ValueError('TRZReader requires the numatoms keyword')
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.filename = trzfilename
self.trzfile = util.anyopen(self.filename, 'rb')
self.__numatoms = numatoms
self.fixed = False
self.periodic = True
self.skip = 1
self.__numframes = None
self.__delta = None
self.__dt = None
self.__skip_timestep = None
self._read_trz_header()
self.ts = Timestep(self.numatoms, has_force=self.has_force)
# structured dtype of a single trajectory frame
readarg = str(numatoms) + 'f4'
frame_contents = [('p1', 'i4'), ('nframe', 'i4'), ('ntrj', 'i4'),
('natoms', 'i4'), ('treal', 'f8'), ('p2', '2i4'),
('box', '9f8'), ('p3', '2i4'), ('pressure', 'f8'),
('ptensor', '6f8'), ('p4', '3i4'), ('etot', 'f8'),
('ptot', 'f8'), ('ek', 'f8'), ('T', 'f8'),
('p5', '6i4'), ('rx', readarg), ('pad2', '2i4'),
('ry', readarg), ('pad3', '2i4'), ('rz', readarg),
('pad4', '2i4'), ('vx', readarg), ('pad5', '2i4'),
('vy', readarg), ('pad6', '2i4'), ('vz', readarg)]
if not self.has_force:
frame_contents += [('pad7', 'i4')]
else:
frame_contents += [
('pad7', '2i4'), ('fx', readarg), ('pad8', '2i4'),
('fy', readarg), ('pad9', '2i4'), ('fz', readarg),
('pad10', 'i4')
]
self._dtype = numpy.dtype(frame_contents)
self._read_next_timestep()
def __init__(self, filename, numatoms, title='TRZ', convert_units=None):
"""Create a TRZWriter
:Arguments:
*filename*
name of output file
*numatoms*
number of atoms in trajectory
:Keywords:
*title*
title of the trajectory
*convert_units*
units are converted to the MDAnalysis base format; ``None`` selects
the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
(see :ref:`flags-label`)
"""
self.filename = filename
if numatoms is None:
raise ValueError("TRZWriter requires the numatoms keyword")
if numatoms == 0:
raise ValueError("TRZWriter: no atoms in output trajectory")
self.numatoms = numatoms
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.trzfile = util.anyopen(self.filename, 'wb')
self._writeheader(title)
floatsize = str(numatoms) + 'f4'
self.frameDtype = numpy.dtype([('p1a', 'i4'), ('nframe', 'i4'),
('ntrj', 'i4'), ('natoms', 'i4'),
('treal', 'f8'), ('p1b', 'i4'),
('p2a', 'i4'), ('box', '9f8'),
('p2b', 'i4'), ('p3a', 'i4'),
('pressure', 'f8'), ('ptensor', '6f8'),
('p3b', 'i4'), ('p4a', 'i4'),
('six', 'i4'), ('etot', 'f8'),
('ptot', 'f8'), ('ek', 'f8'),
('T', 'f8'), ('blanks', '2f8'),
('p4b', 'i4'), ('p5a', 'i4'),
('rx', floatsize), ('p5b', 'i4'),
('p6a', 'i4'), ('ry', floatsize),
('p6b', 'i4'), ('p7a', 'i4'),
('rz', floatsize), ('p7b', 'i4'),
('p8a', 'i4'), ('vx', floatsize),
('p8b', 'i4'), ('p9a', 'i4'),
('vy', floatsize), ('p9b', 'i4'),
('p10a', 'i4'), ('vz', floatsize),
('p10b', 'i4')])
def open_trajectory(self):
if self.xyzfile is not None:
raise IOError(errno.EALREADY, 'XYZ file already opened', self.filename)
self.xyzfile = util.anyopen(self.filename, "r")
# reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.xyzfile
def open_trajectory(self):
if self.xyzfile is not None:
raise IOError(errno.EALREADY, 'XYZ file already opened',
self.filename)
self.xyzfile = util.anyopen(self.filename, "r")
# reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.xyzfile
def open_trajectory(self):
"""Open the trajectory for reading and load first frame."""
self.trjfile = util.anyopen(self.filename, 'r')
self.header = self.trjfile.readline() # ignore first line
if len(self.header.rstrip()) > 80:
# Chimera uses this check
raise OSError("Header of AMBER formatted trajectory has more than 80 chars. "
"This is probably not a AMBER trajectory.")
# reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.trjfile
def open_trajectory(self):
"""Open the trajectory file"""
if not self.trzfile is None:
raise IOError(errno.EALREADY, 'TRZ file already opened', self.filename)
if not os.path.exists(self.filename):
raise IOError(errno.ENOENT, 'TRZ file not found', self.filename)
self.trzfile = util.anyopen(self.filename, 'rb')
#Reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.trzfile
def open_trajectory(self):
if not self.outfile is None:
raise IOError(errno.EALREADY, 'GMS file already opened', self.filename)
if not os.path.exists(self.filename):
# must check; otherwise might segmentation fault
raise IOError(errno.ENOENT, 'GMS file not found', self.filename)
self.outfile = util.anyopen(self.filename, 'r')
# reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.outfile
def open_trajectory(self):
if not self.outfile is None:
raise IOError(errno.EALREADY, 'GMS file already opened',
self.filename)
if not os.path.exists(self.filename):
# must check; otherwise might segmentation fault
raise IOError(errno.ENOENT, 'GMS file not found', self.filename)
self.outfile = util.anyopen(self.filename, 'r')
# reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.outfile
def open_trajectory(self):
"""Open the trajectory file"""
if not self.trzfile is None:
raise IOError(errno.EALREADY, 'TRZ file already opened',
self.filename)
if not os.path.exists(self.filename):
raise IOError(errno.ENOENT, 'TRZ file not found', self.filename)
self.trzfile = util.anyopen(self.filename, 'rb')
#Reset ts
ts = self.ts
ts.status = 1
ts.frame = 0
ts.step = 0
ts.time = 0
return self.trzfile
def __init__(self, filename, numatoms, title='TRZ', convert_units=None):
"""Create a TRZWriter
:Arguments:
*filename*
name of output file
*numatoms*
number of atoms in trajectory
:Keywords:
*title*
title of the trajectory
*convert_units*
units are converted to the MDAnalysis base format; ``None`` selects
the value of :data:`MDAnalysis.core.flags` ['convert_lengths'].
(see :ref:`flags-label`)
"""
self.filename = filename
if numatoms is None:
raise ValueError("TRZWriter requires the numatoms keyword")
if numatoms == 0:
raise ValueError("TRZWriter: no atoms in output trajectory")
self.numatoms = numatoms
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.trzfile = util.anyopen(self.filename, 'wb')
self._writeheader(title)
floatsize = str(numatoms) + 'f4'
self.frameDtype = numpy.dtype([
('p1a', 'i4'),
('nframe', 'i4'),
('ntrj', 'i4'),
('natoms', 'i4'),
('treal', 'f8'),
('p1b', 'i4'),
('p2a', 'i4'),
('box', '9f8'),
('p2b', 'i4'),
('p3a', 'i4'),
('pressure', 'f8'),
('ptensor', '6f8'),
('p3b', 'i4'),
('p4a', 'i4'),
('six', 'i4'),
('etot', 'f8'),
('ptot', 'f8'),
('ek', 'f8'),
('T', 'f8'),
('blanks', '2f8'),
('p4b', 'i4'),
('p5a', 'i4'),
('rx', floatsize),
('p5b', 'i4'),
('p6a', 'i4'),
('ry', floatsize),
('p6b', 'i4'),
('p7a', 'i4'),
('rz', floatsize),
('p7b', 'i4'),
('p8a', 'i4'),
('vx', floatsize),
('p8b', 'i4'),
('p9a', 'i4'),
('vy', floatsize),
('p9b', 'i4'),
('p10a', 'i4'),
('vz', floatsize),
('p10b', 'i4')])
def __init__(self, trzfilename, numatoms=None, convert_units=None, **kwargs):
"""Creates a TRZ Reader
:Arguments:
*trzfilename*
name of input file
*numatoms*
number of atoms in trajectory, must taken from topology file!
*convert_units*
converts units to MDAnalysis defaults
"""
if numatoms is None:
raise ValueError('TRZReader requires the numatoms keyword')
if convert_units is None:
convert_units = MDAnalysis.core.flags['convert_lengths']
self.convert_units = convert_units
self.filename = trzfilename
self.trzfile = util.anyopen(self.filename, 'rb')
self.__numatoms = numatoms
self.fixed = False
self.periodic = True
self.skip = 1
self.__numframes = None
self.__delta = None
self.__dt = None
self.__skip_timestep = None
self._read_trz_header()
self.ts = Timestep(self.numatoms, has_force=self.has_force)
# structured dtype of a single trajectory frame
readarg = str(numatoms) + 'f4'
frame_contents = [
('p1', 'i4'),
('nframe', 'i4'),
('ntrj', 'i4'),
('natoms', 'i4'),
('treal', 'f8'),
('p2', '2i4'),
('box', '9f8'),
('p3', '2i4'),
('pressure', 'f8'),
('ptensor', '6f8'),
('p4', '3i4'),
('etot', 'f8'),
('ptot', 'f8'),
('ek', 'f8'),
('T', 'f8'),
('p5', '6i4'),
('rx', readarg),
('pad2', '2i4'),
('ry', readarg),
('pad3', '2i4'),
('rz', readarg),
('pad4', '2i4'),
('vx', readarg),
('pad5', '2i4'),
('vy', readarg),
('pad6', '2i4'),
('vz', readarg)]
if not self.has_force:
frame_contents += [('pad7', 'i4')]
else:
frame_contents += [
('pad7', '2i4'),
('fx', readarg),
('pad8', '2i4'),
('fy', readarg),
('pad9', '2i4'),
('fz', readarg),
('pad10', 'i4')]
self._dtype = numpy.dtype(frame_contents)
self._read_next_timestep()
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='pdbqt')
self.pdb = util.anyopen(self.filename, 'w')
