run.py

import argparse
import os
import nanome
from plugin.Docking import Autodock4Docking, SminaDocking

default_algorithm = os.environ.get('ALGORITHM', 'smina').lower()

default_algorithm = os.environ.get('ALGORITHM', 'smina').lower()


def main():
    parser = argparse.ArgumentParser(description='Parse Arguments to determine flavor of Docking to instantiate')
    parser.add_argument(
        '--algorithm',
        choices=['smina', 'autodock4'],
        default=default_algorithm,
        help='Docking algorithm to use')

    args, _ = parser.parse_known_args()
    plugin_class = None
    name = ''
    algo = args.algorithm
    if algo == "smina":
        name = "Smina"
        plugin_class = SminaDocking
    elif algo == "autodock4":
        name = "Autodock4"
        plugin_class = Autodock4Docking

    # Create the plugin, register Docking as the class to instantiate, and start listening
    plugin_name = f'{name} Docking'
    description = f'Run docking using {plugin_name}. Lets user choose the ligands, receptor, and docking site.'
    category = "Docking"
    advanced_settings = True
    plugin = nanome.Plugin(plugin_name, description, category, advanced_settings)
    plugin.set_plugin_class(plugin_class)
    plugin.run()


if __name__ == "__main__":
    main()