to_iupac.py

# to_iupac.py
from util import *
import sys
from paths import *

if len(sys.argv) < 2:
    print("python3 to_iupac.py <pdb_id>")
    raise

pdb_id = sys.argv[1].lower()

es_dir1 = PDB_FILES + pdb_id.upper() 
es_dir2 = PDB_FILES + pdb_id.upper() + '_alt'

# get files
files = []
if isdir(es_dir1):
    for f in listdir(es_dir1):
        files.append(es_dir1 + '/' + f )

if isdir(es_dir2):
    for f in listdir(es_dir2):
        files.append(es_dir2 + '/' + f)


if exists(f'{experimental_structures}exp_'+pdb_id+'.pdb'):
    files.append(f'{experimental_structures}exp_'+pdb_id+'.pdb')

if isdir(f'{experimental_structures}'+pdb_id):
    for f in listdir(f'{experimental_structures}'+pdb_id):
        files.append(f'{experimental_structures}'+pdb_id + '/' + f)

if exists(f'{computational_structures}comp_'+pdb_id+'.pdb'):
    files.append(f'{computational_structures}comp_'+pdb_id+'.pdb')

for inf in tqdm(files):
    string = ""
    string += 'load coo pdb ' + inf + '\n'
    string += 'to iupac\n'
    string += 'write coo pdb ' + inf +"\n"
    with open('cmd.txt', 'w') as outf:
        outf.write(string)
    os.system('pdbstat -s < cmd.txt')