def load_arc(filename, top=None, stride=None, atom_indices=None):
"""Load a TINKER .arc file.
Parameters
----------
filename : str
String filename of TINKER .arc file.
top : {str, Trajectory, Topology}
The .arc 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.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.ArcTrajectoryFile : Low level interface to TINKER .arc files
"""
from mdtraj.trajectory import _parse_topology, Trajectory
# we make it not required in the signature, but required here. 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_arc')
if not isinstance(filename, str):
raise TypeError('filename must be of type string for load_arc. '
'you supplied %s' % type(filename))
topology = _parse_topology(top)
atom_indices = _cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with ArcTrajectoryFile(filename) as f:
xyz = f.read(stride=stride, atom_indices=atom_indices)
_convert(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
time = np.arange(len(xyz))
if stride is not None:
# if we loaded with a stride, the Trajectories's time field should
# respect that
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
return t
def load_arc(filename, top=None, stride=None, atom_indices=None):
"""Load a TINKER .arc file.
Parameters
----------
filename : str
String filename of TINKER .arc file.
top : {str, Trajectory, Topology}
The .arc 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.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
See Also
--------
mdtraj.ArcTrajectoryFile : Low level interface to TINKER .arc files
"""
from mdtraj.trajectory import _parse_topology, Trajectory
# we make it not required in the signature, but required here. 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_arc')
if not isinstance(filename, string_types):
raise TypeError('filename must be of type string for load_arc. '
'you supplied %s' % type(filename))
topology = _parse_topology(top)
atom_indices = _cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with ArcTrajectoryFile(filename) as f:
xyz = 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 stride is not None:
# if we loaded with a stride, the Trajectories's time field should
# respect that
time *= stride
t = Trajectory(xyz=xyz, topology=topology, time=time)
return t
def load_netcdf(filename, top=None, stride=None, atom_indices=None, frame=None):
"""Load an AMBER NetCDF file. Since the NetCDF format doesn't contain
information to specify the topology, you need to supply a topology
Parameters
----------
filename : str
filename of AMBER NetCDF file.
top : {str, Trajectory, Topology}
The NetCDF 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. This may be slightly slower than the standard read because it
requires an extra copy, but will save memory.
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.NetCDFTrajectoryFile : Low level interface to NetCDF files
"""
from mdtraj.trajectory import _parse_topology, Trajectory
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with NetCDFTrajectoryFile(filename) as f:
if frame is not None:
f.seek(frame)
xyz, time, cell_lengths, cell_angles = f.read(n_frames=1, atom_indices=atom_indices)
else:
xyz, time, cell_lengths, cell_angles = f.read(stride=stride, atom_indices=atom_indices)
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(cell_lengths, f.distance_unit, Trajectory._distance_unit, inplace=True)
trajectory = Trajectory(xyz=xyz, topology=topology, time=time,
unitcell_lengths=cell_lengths,
unitcell_angles=cell_angles)
return trajectory
def load_xml(filename, top=None):
"""Load a single conformation from an XML file, such as those
produced by OpenMM
Note: The OpenMM serialized state XML format contains information that
is not read by this method, including forces, energies, and velocities.
Here, we just read the positions and the box vectors.
Parameters
----------
filename : string
The path on disk to the XML file
top : {str, Trajectory, Topology}
The XML format does not contain topology information. Pass in either the
path to a pdb file, a trajectory, or a topology to supply this information.
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object.
"""
import xml.etree.cElementTree as etree
from mdtraj.trajectory import _parse_topology, Trajectory
topology = _parse_topology(top)
tree = etree.parse(filename)
# get all of the positions from the XML into a list of tuples
# then convert to a numpy array
positions = []
for position in tree.getroot().find('Positions'):
positions.append((float(position.attrib['x']),
float(position.attrib['y']),
float(position.attrib['z'])))
box = []
vectors = tree.getroot().find('PeriodicBoxVectors')
for name in ['A', 'B', 'C']:
box.append((float(vectors.find(name).attrib['x']),
float(vectors.find(name).attrib['y']),
float(vectors.find(name).attrib['z'])))
traj = Trajectory(xyz=np.array(positions), topology=topology)
traj.unitcell_vectors = np.array(box).reshape(1,3,3)
return traj
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.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)
if atom_indices is not None:
topology = topology.subset(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)
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_netcdf(filename,
top=None,
stride=None,
atom_indices=None,
frame=None):
"""Load an AMBER NetCDF file. Since the NetCDF format doesn't contain
information to specify the topology, you need to supply a topology
Parameters
----------
filename : str
filename of AMBER NetCDF file.
top : {str, Trajectory, Topology}
The NetCDF 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. This may be slightly slower than the standard read because it
requires an extra copy, but will save memory.
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.NetCDFTrajectoryFile : Low level interface to NetCDF files
"""
from mdtraj.trajectory import _parse_topology, Trajectory
topology = _parse_topology(top)
atom_indices = cast_indices(atom_indices)
if atom_indices is not None:
topology = topology.subset(atom_indices)
with NetCDFTrajectoryFile(filename) as f:
if frame is not None:
f.seek(frame)
xyz, time, cell_lengths, cell_angles = f.read(
n_frames=1, atom_indices=atom_indices)
else:
xyz, time, cell_lengths, cell_angles = f.read(
stride=stride, atom_indices=atom_indices)
in_units_of(xyz,
f.distance_unit,
Trajectory._distance_unit,
inplace=True)
in_units_of(cell_lengths,
f.distance_unit,
Trajectory._distance_unit,
inplace=True)
trajectory = Trajectory(xyz=xyz,
topology=topology,
time=time,
unitcell_lengths=cell_lengths,
unitcell_angles=cell_angles)
return trajectory
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.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)
if atom_indices is not None:
topology = topology.subset(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)
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