Run.py

import argparse
import os

import Cycle
from Molecule import HiveMolecule


def main():
    parser = argparse.ArgumentParser(
        description="Optimize a molecule using Hive.", 
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    
    parser.add_argument(
        "input",
        type=str,
        choices=['molfile', 'smiles'],
        help="Type of molecule input (.mol or smiles)",
    )
    parser.add_argument(
        "molecule",
        type=str,
        help="Molecule to be optimized (SMILES or .mol file path)",
    )
    parser.add_argument(
        "--n_confs",
        type=int,
        default=6,
        help="required number of conformations in enseble ",
    )      
    parser.add_argument(
        "--global_iterations",
        type=int,
        default=20,
        help="Number of ABC iterations of global conformation search",
    )
    parser.add_argument(
        "--local_iterations",
        type=int,
        default=20,
        help="Number of ABC iterations of local conformation search",
    )
    parser.add_argument(
        "--global_exists",
        action='store_true',
        help="Provide the local search in respect to user's global conformation",
    )
    
    parser.add_argument(
        "--MP2",
        action='store_true',
        help="flag that enables optimization at the MP2 level of theory",
    )
    parser.add_argument(
    "--basis",
    default='sto-3g',
    help="choose basis available in PySCF package",
    )

    parser.add_argument(
    "--iters",
    default=100,
    help="Number of iterations of final optimization",
    )
    
    args = parser.parse_args()
    print(args)
    print(f"Molecule to be optimized: {args.molecule}")
    mol = HiveMolecule(args.input, args.molecule)
    ensemble = Cycle.full_cycle(mol, args.global_iterations, args.local_iterations, args.global_exists, args.n_confs, args.MP2, args.basis, args.iters)
    return ensemble

if __name__ == "__main__":
    main()