def trajectory_to_mdtraj(trajectory, md_topology=None):
"""
Construct a `mdtraj.Trajectory` object from an :obj:`Trajectory` object
Parameters
----------
trajectory : :obj:`openpathsampling.engines.Trajectory`
Input Trajectory
Returns
-------
:obj:`mdtraj.Trajectory`
the constructed Trajectory instance
"""
if not hasattr(trajectory, 'to_mdtraj'):
try:
_ = len(trajectory)
except TypeError:
trajectory = Trajectory([trajectory])
else:
trajectory = Trajectory(trajectory)
# For now, let's keep all the code in one place, and better for
# engines.openmm.tools to require engines.trajectory than vice versa
return trajectory.to_mdtraj(md_topology)
def trajectory_to_mdtraj(trajectory, md_topology=None):
"""
Construct a `mdtraj.Trajectory` object from an :obj:`Trajectory` object
Parameters
----------
trajectory : :obj:`openpathsampling.engines.Trajectory`
Input Trajectory
Returns
-------
:obj:`mdtraj.Trajectory`
the constructed Trajectory instance
"""
if not hasattr(trajectory, 'to_mdtraj'):
try:
_ = len(trajectory)
except TypeError:
trajectory = Trajectory([trajectory])
else:
trajectory = Trajectory(trajectory)
# TODO: The following would work if we remove trajectory.to_mdtraj()
# For now, let's keep all the code in one place, and better for
# engines.openmm.tools to require engines.trajectory than vice versa
# output = trajectory.xyz
# traj = md.Trajectory(output, md_topology)
# traj.unitcell_vectors = trajectory.box_vectors
return trajectory.to_mdtraj(md_topology)
def trajectory_to_mdtraj(trajectory, md_topology=None):
"""
Construct a `mdtraj.Trajectory` object from an :obj:`Trajectory` object
Parameters
----------
trajectory : :obj:`openpathsampling.engines.Trajectory`
Input Trajectory
Returns
-------
:obj:`mdtraj.Trajectory`
the constructed Trajectory instance
"""
if not hasattr(trajectory, 'to_mdtraj'):
try:
_ = len(trajectory)
except TypeError:
trajectory = Trajectory([trajectory])
else:
trajectory = Trajectory(trajectory)
# TODO: The following would work if we remove trajectory.to_mdtraj()
# For now, let's keep all the code in one place, and better for
# engines.openmm.tools to require engines.trajectory than vice versa
# output = trajectory.xyz
# traj = md.Trajectory(output, md_topology)
# traj.unitcell_vectors = trajectory.box_vectors
return trajectory.to_mdtraj(md_topology)
def trajectory_from_mdtraj(mdtrajectory,
simple_topology=False,
velocities=None):
"""
Construct a Trajectory object from an mdtraj.Trajectory object
Parameters
----------
mdtrajectory : mdtraj.Trajectory
Input mdtraj.Trajectory
simple_topology : bool
if `True` only a simple topology with n_atoms will be created.
This cannot be used with complex CVs but loads and stores very fast
velocities : np.array
velocities in units of nm/ps
Returns
-------
openpathsampling.engines.Trajectory
the constructed Trajectory instance
"""
trajectory = Trajectory()
vel_unit = u.nanometer / u.picosecond
if simple_topology:
topology = Topology(*mdtrajectory.xyz[0].shape)
else:
topology = MDTrajTopology(mdtrajectory.topology)
if velocities is None:
empty_vel = u.Quantity(np.zeros(mdtrajectory.xyz[0].shape), vel_unit)
if mdtrajectory.unitcell_vectors is not None:
box_vects = u.Quantity(mdtrajectory.unitcell_vectors, u.nanometers)
else:
box_vects = [None] * len(mdtrajectory)
engine = TopologyEngine(topology)
for frame_num in range(len(mdtrajectory)):
# mdtraj trajectories only have coordinates and box_vectors
coord = u.Quantity(mdtrajectory.xyz[frame_num], u.nanometers)
if velocities is not None:
vel = u.Quantity(velocities[frame_num], vel_unit)
else:
vel = empty_vel
box_v = box_vects[frame_num]
statics = Snapshot.StaticContainer(coordinates=coord,
box_vectors=box_v)
kinetics = Snapshot.KineticContainer(velocities=vel)
snap = Snapshot(statics=statics, kinetics=kinetics, engine=engine)
trajectory.append(snap)
return trajectory
def trajectory_from_mdtraj(mdtrajectory, simple_topology=False):
"""
Construct a Trajectory object from an mdtraj.Trajectory object
Parameters
----------
mdtrajectory : mdtraj.Trajectory
Input mdtraj.Trajectory
simple_topology : bool
if `True` only a simple topology with n_atoms will be created.
This cannot be used with complex CVs but loads and stores very fast
Returns
-------
openpathsampling.engines.Trajectory
the constructed Trajectory instance
"""
trajectory = Trajectory()
empty_kinetics = Snapshot.KineticContainer(
velocities=u.Quantity(
np.zeros(mdtrajectory.xyz[0].shape), u.nanometer / u.picosecond)
)
if simple_topology:
topology = Topology(*mdtrajectory.xyz[0].shape)
else:
topology = MDTrajTopology(mdtrajectory.topology)
engine = TopologyEngine(topology)
for frame_num in range(len(mdtrajectory)):
# mdtraj trajectories only have coordinates and box_vectors
coord = u.Quantity(mdtrajectory.xyz[frame_num], u.nanometers)
if mdtrajectory.unitcell_vectors is not None:
box_v = u.Quantity(mdtrajectory.unitcell_vectors[frame_num],
u.nanometers)
else:
box_v = None
statics = Snapshot.StaticContainer(
coordinates=coord,
box_vectors=box_v
)
snap = Snapshot(
statics=statics,
kinetics=empty_kinetics,
engine=engine
)
trajectory.append(snap)
return trajectory
def reduce_trajectory_box_vectors(trajectory):
"""Trajectory with reduced box vectors.
OpenMM has strict requirements on the box vectors describing the unit
cell. In some cases, such as trajectories loaded from files that have
rounded the box vectors, these conditions might not be satisfied. This
method forces the box vectors to meet OpenMM's criteria.
Parameters
----------
trajectory : :class:`.Trajectory`
input trajectory
Returns
-------
:class:`.Trajectory`
trajectory with correctly reduced box vectors
"""
return Trajectory([
snap.copy_with_replacement(box_vectors=reduced_box_vectors(snap))
for snap in trajectory
])