prepare_amber.py

def run_command(cmd):
    """Runs command, writes to stdout, raises exception on error"""
    print(cmd)
    #!{cmd}
    exit_code = os.system(cmd)
    assert exit_code == 0, 'Error running command'
        
def prepare_system(input_pdb, out_base, suffix='00_raw', skip_existing=True):
    assert os.path.exists(input_pdb), f'{input_pdb} does not exists!'
    final_name = f'{out_base}__{suffix}.top'
    if skip_existing and os.path.exists(final_name):
        print(f'File {final_name} exists. Skipping preparation.')
        return final_name
    #with Timer(f'Preparing system {input_pdb}...') as t:
    pdb4amber_cmd = f'pdb4amber -i {input_pdb} -o {out_base}__{suffix}_00_clean.pdb --nohyd --reduce --dry '+\
                     '--strip @/H --add-missing-atoms --logfile stdout'
    run_command(pdb4amber_cmd)

    leap_in = f"""
        source leaprc.protein.ff14SBonlysc 
        set default PBRadii mbondi3
        x = loadPDB {out_base}__{suffix}_00_clean.pdb
        saveAmberParm x {out_base}__{suffix}.top {out_base}__{suffix}.rst
        quit
        """
    with open(f'{out_base}__{suffix}_00_leap.in', 'wt') as fin:
        print(leap_in, file=fin)
    run_command(f'tleap -f {out_base}__{suffix}_00_leap.in')
        #TODO clean up all the temp files

    return final_name

os.makedirs('out', exist_ok=True)
prepare_system('../../models/1wa3_BA-05_modl.pdb', 'out/1BH_69_modl', suffix='00_raw', skip_existing=False)