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)