#!python
# -*- coding: utf-8 -*-
"""
Created on Fri May 28 09:33:45 2021

@author: bs15ansj
"""

from amberpy.experiments import ProteinExperiment
import argparse
import os

def main():
    # Get the username of the persom using the script from ~
    username = os.path.basename(os.path.expanduser("~"))
    
    parser = argparse.ArgumentParser()
    
    parser.add_argument('pdb_file', metavar='pdb_file', help='Pdb file to simulate.')
    
    # Add arc argument
    parser.add_argument('-a', '--arc', default=3, help=('The Arc version you want'
                        'to run simulations on. Can be 3 or 4. Default is 3'), 
                        type=int)

    
    args = parser.parse_args()

    
    protein_simulation = ProteinExperiment(args.pdb_file)
    protein_simulation.make_system()
    protein_simulation.add_minimisation_step()
    protein_simulation.add_equilibration_step()
    protein_simulation.add_production_step()
    protein_simulation.run(arc=args.arc)

if __name__ == "__main__":

    main()
