def setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = paths.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
# once we have a template configuration (coordinates to not really matter)
# we can create a storage. We might move this logic out of the dynamics engine
# and keep sotrage and engine generation completely separate!
storage = Storage(filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w')
mytraj = paths.tools.trajectory_from_mdtraj(mdtrajectory)
storage.trajectories.save(mytraj)
storage.close()
def setup_package():
# this should generate the trajectory.nc file which we'll use for
# everything else
mdtrajectory = md.load(data_filename("ala_small_traj.pdb"))
snapshot = paths.snapshot_from_pdb(data_filename("ala_small_traj.pdb"))
# once we have a template configuration (coordinates to not really matter)
# we can create a storage. We might move this logic out of the dynamics engine
# and keep sotrage and engine generation completely separate!
storage = Storage(
filename=data_filename("ala_small_traj.nc"),
template=snapshot,
mode='w'
)
mytraj = paths.Trajectory.from_mdtraj(mdtrajectory)
storage.trajectories.save(mytraj)
storage.close()
