def get_prots(docked_prot_file):
    """
    gets list of all protein, target ligands, and starting ligands in the index file
    :param docked_prot_file: (string) file listing proteins to process
    :return: process (list) list of all protein, target ligands, and starting ligands to process
    """
    process = []
    with open(docked_prot_file) as fp:
        for line in fp:
            if line[0] == '#': continue
            protein, target, start = line.strip().split()
            process.append((protein, target, start))

    return process