mdevaluate/mdevaluate/cli.py

import argparse
from . import logging
from . import open as md_open


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

    md_open("", trajectory=args.xtcfile, topology=args.tpr, nojump=args.nojump)


if __name__ == "__main__":
    run()