#!/opt/conda/conda-bld/gromacs_py_1619210580721/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/python

""" Create a linear Peptide structure based on a sequence.
Do a minimisation and a vacuum equilibration.
"""

import argparse
from gromacs_py import gmx

__author__ = "Samuel Murail"


def parser_input():

    parser = argparse.ArgumentParser(
        description="Create a linear peptide structure, do a minimisation and"
                    " a vacuum equilibration")
    parser.add_argument('-seq', action="store", dest="seq",
                        help='Peptide sequence', type=str, required=True)
    parser.add_argument('-o', action="store", dest="o",
                        help='Output Directory', type=str, required=True)
    parser.add_argument('-m_steps', action="store", dest="min_steps",
                        help='Minimisation nsteps, default=1000', type=int,
                        default=1000)
    parser.add_argument('-time', action="store", dest="time",
                        help='Vacuum equilibration time(ns), default = 1ns',
                        type=float, default=1)

    return parser


if __name__ == "__main__":

    my_parser = parser_input()
    args = my_parser.parse_args()

    dt = 0.001
    step = 1000 * args.time / dt
    sequence = args.seq
    out_folder = args.o
    em_nsteps = args.min_steps

    peptide = gmx.GmxSys(name='pep_' + sequence)
    peptide.create_peptide(sequence=sequence, out_folder=out_folder,
                           em_nsteps=em_nsteps, equi_nsteps=step)

    print("\n\nPeptide Creation was sucessfull \n\tPeptide directorie :\t"
          + args.o)
    peptide.display()
