def setup(self):
self.p = ArgumentParser()
logger.info("Generated: %s, Trajectories/", projectfn)
return
if __name__ == "__main__":
parser = ArgumentParser(description="""
Merges individual XTC files into continuous lossy HDF5 (.lh5) trajectories.
Can read data from a FAH project (PROJECT/RUN*/CLONE*/frame*.xtc) or from
a directory containing one directory for each trajectory, with all the
relevant XTCs inside that directory (PROJECT/TRAJ*/frame*.xtc).
Output:
-- 'Trajectories' directory containing all the merged lh5 files
-- 'ProjectInfo' file containing information MSMBuilder uses in subsequent
calculations.
NOTE: There has been a change from previous versions of MSMBuilder with
regards to the way snapshots are discarded. In the 'FAH' style reader,
there is an automatic check to see if any two snapshots are the same at
the beginning/end of consecutive xtc/dcd files. If they are the same, one
gets discarded. Further, the FahProject object retains a little more discard
functionality.
""")
parser.add_argument('project',
type=str,
help='''The ProjectInfo (.h5) file
that contains a mapping of the previous work done. If you specify a file that
exists on disk, conversion will pick up where it left off and simply add data
