annotate gmxtras_extract_top.py @ 0:9faa4f4b8b76 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b"

#!/usr/bin/env python3
import argparse


def __main__():
    parser = argparse.ArgumentParser(
        description='Adds New topologies to gromacs topology file')
    parser.add_argument(
                        '--top_file', default=None,
                        help="Topologies input")
    parser.add_argument(
                        '--out_bondparam', default=None,
                        help='moleculetype section')
    parser.add_argument(
                        '--out_nonbondparam', default=None,
                        help='atomtypes section')

    args = parser.parse_args()
    # extracts the atom types with nonbonded terms from
    # the new molecules and puts them in a new file
    with open(args.top_file) as inFile:
        with open(args.out_nonbondparam, "w") as outFile:
            buffer = []
            for line in inFile:
                if line.startswith(";name   bond_type"):
                    buffer = ['']
                elif line.startswith("[ moleculetype ]"):
                    outFile.write("".join(buffer))
                    buffer = []
                elif buffer:
                    buffer.append(line)

    # extracts the molecule types (rest of the force field parameters)
    # with bonded terms and puts them in a new file
    with open(args.top_file) as inFile:
        with open(args.out_bondparam, "w") as outFile:
            buffer = []
            for line in inFile:
                if line.startswith("[ moleculetype ]"):
                    buffer = ["\n[ moleculetype ]\n"]
                elif line.startswith("[ system ]"):
                    outFile.write("".join(buffer))
                    buffer = []
                elif buffer:
                    buffer.append(line)


if __name__ == "__main__":
    __main__()