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
