def read_as_traj(self, topology, n_frames=None, stride=None, atom_indices=None):
"""Read a trajectory from a lammpstrj file
Parameters
----------
topology : Topology
The system topology
n_frames : int, optional
If positive, then read only the next `n_frames` frames. Otherwise read all
of the frames in the file.
stride : np.ndarray, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file. This may be slightly slower than the standard read because it required
an extra copy, but will save memory.
Returns
-------
trajectory : Trajectory
A trajectory object containing the loaded portion of the file.
See Also
--------
read : Returns the raw data from the file
Notes
-----
If coordinates are specified in more than one style, the first complete
trio of x/y/z coordinates will be read in according to the following
order:
1) x,y,z (unscaled coordinates)
2) xs,ys,zs (scaled atom coordinates)
3) xu,yu,zu (unwrapped atom coordinates)
4) xsu,ysu,zsu (scaled unwrapped atom coordinates)
E.g., if the file contains x, y, z, xs, ys, zs then x, y, z will be used.
if the file contains x, y, xs, ys, zs then xs, ys, zs will be used.
"""
from mdtraj.core.trajectory import Trajectory
if atom_indices is not None:
topology = topology.subset(atom_indices)
initial = int(self._frame_index)
xyz, cell_lengths, cell_angles = self.read(n_frames=n_frames, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)
in_units_of(xyz, self.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(cell_lengths, self.distance_unit, Trajectory._distance_unit, inplace=True)
if stride is None:
stride = 1
time = (stride*np.arange(len(xyz))) + initial
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def read_as_traj(self, topology, n_frames=None, stride=None, atom_indices=None):
"""Read a trajectory from a mdcrd file
Parameters
----------
topology : Topology
The system topology
n_frames : int, optional
If positive, then read only the next `n_frames` frames. Otherwise read all
of the frames in the file.
stride : np.ndarray, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file. This may be slightly slower than the standard read because it required
an extra copy, but will save memory.
Returns
-------
trajectory : Trajectory
A trajectory object containing the loaded portion of the file.
"""
from mdtraj.core.trajectory import Trajectory
if atom_indices is not None:
topology = topology.subset(atom_indices)
initial = int(self._frame_index)
xyz, cell_lengths = self.read(n_frames=n_frames, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)
in_units_of(xyz, self.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(cell_lengths, self.distance_unit, Trajectory._distance_unit, inplace=True)
if cell_lengths is None:
cell_angles = None
else:
# Assume that its a rectilinear box
cell_angles = 90.0 * np.ones_like(cell_lengths)
if stride is None:
stride = 1
time = (stride*np.arange(len(xyz))) + initial
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def read_as_traj(self, topology, n_frames=None, stride=None, atom_indices=None):
"""Read a trajectory from a mdcrd file
Parameters
----------
topology : Topology
The system topology
n_frames : int, optional
If positive, then read only the next `n_frames` frames. Otherwise read all
of the frames in the file.
stride : np.ndarray, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file. This may be slightly slower than the standard read because it required
an extra copy, but will save memory.
Returns
-------
trajectory : Trajectory
A trajectory object containing the loaded portion of the file.
"""
from mdtraj.core.trajectory import Trajectory
if atom_indices is not None:
topology = topology.subset(atom_indices)
initial = int(self._frame_index)
xyz, cell_lengths = self.read(n_frames=n_frames, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)
in_units_of(xyz, self.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(cell_lengths, self.distance_unit, Trajectory._distance_unit, inplace=True)
if cell_lengths is None:
cell_angles = None
else:
# Assume that its a rectilinear box
cell_angles = 90.0 * np.ones_like(cell_lengths)
if stride is None:
stride = 1
time = (stride*np.arange(len(xyz))) + initial
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def load_lammpstrj(filename,
top=None,
stride=None,
atom_indices=None,
frame=None,
unit_set='real'):
"""Load a LAMMPS trajectory file.
Parameters
----------
filename : str
String filename of LAMMPS trajectory file.
top : {str, Trajectory, Topology}
The lammpstrj format does not contain topology information. Pass in
either the path to a pdb file, a trajectory, or a topology to supply
this information.
stride : int, default=None
Only read every stride-th frame
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file.
frame : int, optional
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, ``stride`` will be ignored.
unit_set : str, optional
The LAMMPS unit set that the simulation was performed in. See
http://lammps.sandia.gov/doc/units.html for options. Currently supported
unit sets: 'real'.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.LAMMPSTrajectoryFile : Low level interface to lammpstrj files
"""
from mdtraj.core.trajectory import _parse_topology, Trajectory
# We make `top` required. Although this is a little weird, its good because
# this function is usually called by a dispatch from load(), where top comes
# from **kwargs. So if its not supplied, we want to give the user an
# informative error message.
if top is None:
raise ValueError('"top" argument is required for load_lammpstrj')
if not isinstance(filename, string_types):
raise TypeError('filename must be of type string for load_lammpstrj. '
'you supplied %s'.format(type(filename)))
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with LAMMPSTrajectoryFile(filename) as f:
# TODO: Support other unit sets.
if unit_set == 'real':
f.distance_unit == 'angstroms'
else:
raise ValueError(
'Unsupported unit set specified: {0}.'.format(unit_set))
if frame is not None:
f.seek(frame)
xyz, cell_lengths, cell_angles = f.read(n_frames=1,
atom_indices=atom_indices)
else:
xyz, cell_lengths, cell_angles = f.read(stride=stride,
atom_indices=atom_indices)
in_units_of(xyz,
f.distance_unit,
Trajectory._distance_unit,
inplace=True)
time = np.arange(len(xyz))
if frame is not None:
time += frame
elif stride is not None:
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def read_as_traj(self,
topology,
n_frames=None,
stride=None,
atom_indices=None):
"""Read a trajectory from a lammpstrj file
Parameters
----------
topology : Topology
The system topology
n_frames : int, optional
If positive, then read only the next `n_frames` frames. Otherwise read all
of the frames in the file.
stride : np.ndarray, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file. This may be slightly slower than the standard read because it required
an extra copy, but will save memory.
Returns
-------
trajectory : Trajectory
A trajectory object containing the loaded portion of the file.
See Also
--------
read : Returns the raw data from the file
Notes
-----
If coordinates are specified in more than one style, the first complete
trio of x/y/z coordinates will be read in according to the following
order:
1) x,y,z (unscaled coordinates)
2) xs,ys,zs (scaled atom coordinates)
3) xu,yu,zu (unwrapped atom coordinates)
4) xsu,ysu,zsu (scaled unwrapped atom coordinates)
E.g., if the file contains x, y, z, xs, ys, zs then x, y, z will be used.
if the file contains x, y, xs, ys, zs then xs, ys, zs will be used.
"""
from mdtraj.core.trajectory import Trajectory
if atom_indices is not None:
topology = topology.subset(atom_indices)
initial = int(self._frame_index)
xyz, cell_lengths, cell_angles = self.read(n_frames=n_frames,
stride=stride,
atom_indices=atom_indices)
if len(xyz) == 0:
return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)),
topology=topology)
in_units_of(xyz,
self.distance_unit,
Trajectory._distance_unit,
inplace=True)
in_units_of(cell_lengths,
self.distance_unit,
Trajectory._distance_unit,
inplace=True)
if stride is None:
stride = 1
time = (stride * np.arange(len(xyz))) + initial
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def load_mdcrd(filename, top=None, stride=None, atom_indices=None, frame=None):
"""Load an AMBER mdcrd file.
Parameters
----------
filename : str
String filename of AMBER mdcrd file.
top : {str, Trajectory, Topology}
The BINPOS format does not contain topology information. Pass in either
the path to a pdb file, a trajectory, or a topology to supply this
information.
stride : int, default=None
Only read every stride-th frame
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file.
frame : int, optional
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, ``stride`` will be ignored.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.MDCRDTrajectoryFile : Low level interface to MDCRD files
"""
from mdtraj.core.trajectory import _parse_topology, Trajectory
# we make it not required in the signature, but required here. although this
# is a little wierd, its good because this function is usually called by a
# dispatch from load(), where top comes from **kwargs. So if its not supplied
# we want to give the user an informative error message
if top is None:
raise ValueError('"top" argument is required for load_mdcrd')
if not isinstance(filename, string_types):
raise TypeError('filename must be of type string for load_mdcrd. '
'you supplied %s' % type(filename))
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
with MDCRDTrajectoryFile(filename, n_atoms=topology._numAtoms) as f:
if frame is not None:
f.seek(frame)
xyz, cell_lengths = f.read(n_frames=1, atom_indices=atom_indices)
else:
xyz, cell_lengths = f.read(stride=stride, atom_indices=atom_indices)
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
if cell_lengths is not None:
in_units_of(cell_lengths, f.distance_unit, Trajectory._distance_unit, inplace=True)
# Assume that its a rectilinear box
cell_angles = 90.0 * np.ones_like(cell_lengths)
if atom_indices is not None:
topology = topology.subset(atom_indices)
time = np.arange(len(xyz))
if frame is not None:
time += frame
elif stride is not None:
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
if cell_lengths is not None:
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def load_mdcrd(filename, top=None, stride=None, atom_indices=None, frame=None):
"""Load an AMBER mdcrd file.
Parameters
----------
filename : str
String filename of AMBER mdcrd file.
top : {str, Trajectory, Topology}
The BINPOS format does not contain topology information. Pass in either
the path to a pdb file, a trajectory, or a topology to supply this
information.
stride : int, default=None
Only read every stride-th frame
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file.
frame : int, optional
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, ``stride`` will be ignored.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.MDCRDTrajectoryFile : Low level interface to MDCRD files
"""
from mdtraj.core.trajectory import _parse_topology, Trajectory
# we make it not required in the signature, but required here. although this
# is a little wierd, its good because this function is usually called by a
# dispatch from load(), where top comes from **kwargs. So if its not supplied
# we want to give the user an informative error message
if top is None:
raise ValueError('"top" argument is required for load_mdcrd')
if not isinstance(filename, string_types):
raise TypeError('filename must be of type string for load_mdcrd. '
'you supplied %s' % type(filename))
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
with MDCRDTrajectoryFile(filename, n_atoms=topology._numAtoms) as f:
if frame is not None:
f.seek(frame)
xyz, cell_lengths = f.read(n_frames=1, atom_indices=atom_indices)
else:
xyz, cell_lengths = f.read(stride=stride,
atom_indices=atom_indices)
in_units_of(xyz,
f.distance_unit,
Trajectory._distance_unit,
inplace=True)
if cell_lengths is not None:
in_units_of(cell_lengths,
f.distance_unit,
Trajectory._distance_unit,
inplace=True)
# Assume that its a rectilinear box
cell_angles = 90.0 * np.ones_like(cell_lengths)
if atom_indices is not None:
topology = topology.subset(atom_indices)
time = np.arange(len(xyz))
if frame is not None:
time += frame
elif stride is not None:
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
if cell_lengths is not None:
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
def load_lammpstrj(filename, top=None, stride=None, atom_indices=None,
frame=None, unit_set='real'):
"""Load a LAMMPS trajectory file.
Parameters
----------
filename : str
String filename of LAMMPS trajectory file.
top : {str, Trajectory, Topology}
The lammpstrj format does not contain topology information. Pass in
either the path to a pdb file, a trajectory, or a topology to supply
this information.
stride : int, default=None
Only read every stride-th frame
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file.
frame : int, optional
Use this option to load only a single frame from a trajectory on disk.
If frame is None, the default, the entire trajectory will be loaded.
If supplied, ``stride`` will be ignored.
unit_set : str, optional
The LAMMPS unit set that the simulation was performed in. See
http://lammps.sandia.gov/doc/units.html for options. Currently supported
unit sets: 'real'.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.LAMMPSTrajectoryFile : Low level interface to lammpstrj files
"""
from mdtraj.core.trajectory import _parse_topology, Trajectory
# We make `top` required. Although this is a little weird, its good because
# this function is usually called by a dispatch from load(), where top comes
# from **kwargs. So if its not supplied, we want to give the user an
# informative error message.
if top is None:
raise ValueError('"top" argument is required for load_lammpstrj')
if not isinstance(filename, string_types):
raise TypeError('filename must be of type string for load_lammpstrj. '
'you supplied %s'.format(type(filename)))
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with LAMMPSTrajectoryFile(filename) as f:
# TODO: Support other unit sets.
if unit_set == 'real':
f.distance_unit == 'angstroms'
else:
raise ValueError('Unsupported unit set specified: {0}.'.format(unit_set))
if frame is not None:
f.seek(frame)
xyz, cell_lengths, cell_angles = f.read(n_frames=1, atom_indices=atom_indices)
else:
xyz, cell_lengths, cell_angles = f.read(stride=stride, atom_indices=atom_indices)
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
time = np.arange(len(xyz))
if frame is not None:
time += frame
elif stride is not None:
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
t.unitcell_lengths = cell_lengths
t.unitcell_angles = cell_angles
return t
