adv_config.py

'''
Generates a template config file for use with AutoDock Vina/Vina-Carb
using a grid dimensions file generated with AutoDockTools.

Args:
    -i, --input:    Input grid dimensions file.

Returns:
    File named "config.txt" in the same directory as the input file
'''

from argparse import ArgumentParser
import pathlib

def script_args():
    '''
    Parse command-line arguments and return a Namespace object containing
    pathlib.Path paths to each user-defined input file.

    Returns:
        argparse.Namespace: A Namespace object containing input file paths.
    '''
    parser = ArgumentParser()
    parser.add_argument('-i', '--input', type=pathlib.Path, required=True, nargs='+',
                        help='AutoDockTools gridbox output files')
    return parser.parse_args()

def parse_gridbox(gridbox_file):
    '''
    Converts each user-defined input file into a template AutoDock Vina config file.

    Args:
        gridbox_file:   pathlib.Path path to one of the input files.

    Returns:
        None
    '''

    gridbox_contents = []
    index_npts = None
    index_center = None

    with open(gridbox_file, 'r', encoding='utf-8') as input_file:
        gridbox_contents = [line.split() for line in input_file if line.strip()]

    for index, item in enumerate(gridbox_contents):
        if item[0] == 'npts':
            index_npts = index
        elif item[0] == 'center':
            index_center = index

    variable_mappings = [
        ('center_x', 1),
        ('center_y', 2),
        ('center_z', 3),
        ('size_x', 1),
        ('size_y', 2),
        ('size_z', 3),
    ]

    with open(gridbox_file.with_name('config.txt'), 'w', encoding='utf-8') as file:
        file.writelines('receptor = \nligand = \n\n')

        for variable, index in variable_mappings:
            if variable.startswith('center'):
                data_source = gridbox_contents[index_center]
            elif variable.startswith('size'):
                data_source = gridbox_contents[index_npts]

            file.writelines(f'{variable} = {data_source[index]}\n')

        file.writelines('\nenergy_range = 4\nexhaustiveness = 32\n')
        file.writelines('\nlog = \nout = \n')

def main():
    '''
    Primary execution point of the script.

    Usage:
        To run this script, execute it from the command line as follows:
        $ python3 adv-config.py -i [path/to/file]
    '''

    user_args = script_args()
    for file in user_args.input:
        parse_gridbox(file)

if __name__ == '__main__':
    main()