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)
# 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)
