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import argparse
from . import logging
from . import open as md_open
def run(*args, **kwargs):
parser = argparse.ArgumentParser()
parser.add_argument(
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"xtcfile",
help="The xtc file to index.",
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)
parser.add_argument(
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"--tpr", help="The tprfile of the trajectory.", dest="tpr", default=None
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)
parser.add_argument(
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"--nojump",
help="Generate Nojump Matrices, requires a tpr file.",
dest="nojump",
action="store_true",
default=False,
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)
parser.add_argument(
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"--debug",
help="Set logging level to debug.",
dest="debug",
action="store_true",
default=False,
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)
args = parser.parse_args()
if args.debug:
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logging.setlevel("DEBUG")
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md_open("", trajectory=args.xtcfile, topology=args.tpr, nojump=args.nojump)
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if __name__ == "__main__":
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run()