Importing a trajectory in DCD format — MMTK User Guide 2.7.7 documentation

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# Importing a trajectory in DCD format

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    # Conversion of a DCD trajectory (CHARMM/XPlor) to MMTK's trajectory format.
    #
    # Note: In order to create the files "rotation.dcd" and "rotation.pdb" which
    #       are read by this example, you must run the example dcd_export.py.
    #

    from MMTK import *
    from MMTK.Proteins import Protein
    from MMTK.PDB import PDBConfiguration
    from MMTK.Trajectory import Trajectory, TrajectoryOutput
    from MMTK.DCD import DCDReader

    # Create the universe.
    universe = InfiniteUniverse()

    # Create all objects from the PDB file. The PDB file *must* match the
    # the DCD file (same atom order), and you *must* create all objects
    # defined in the PDB file, otherwise interpretation of the DCD file
    # is not possible.
    conf = PDBConfiguration('rotation.pdb')
    chain = conf.peptide_chains[0].createPeptideChain(c_terminus=1)
    universe.addObject(Protein([chain]))

    # Create the trajectory object for output.
    t = Trajectory(universe, "rotation_from_dcd.nc", "w", "Converted from DCD")

    # Create a DCD reader that reads all configurations.
    dcd_reader = DCDReader(universe, dcd_file = 'rotation.dcd',
                           actions = [TrajectoryOutput(t, "all", 0, None, 1)])
    # Run the reader...
    dcd_reader()
    # ... and close the output trajectory.
    t.close()

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