Python snapshot_from_pdb Examples

Example #1

File: __init__.py Project: marscher/openpathsampling

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()

Example #2

File: __init__.py Project: JM-YE/openpathsampling

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()