a quick and dirty python script to modify parts of an ATOM PDB file in a very domain-specific way

pdb-his-change.py

#!/usr/bin/env python3

import re, argparse

#NE2 HIS -> HSE
#standard fields = [ 'record', 'serial', 'name', 'altLoc', 'resName', 'chainID', 'resSeq',
#                    'iCode', 'x', 'y', 'z', 'occupancy', 'tempFactor', 'element', 'charge' ]

parser = argparse.ArgumentParser(description='Changes HIS to HSE in PDB file where "NE2 HIS" found, outputs to sdout')
parser.add_argument("file", type=str)
args = parser.parse_args()

file = args.file

with open(file, 'r', newline='') as pdb_file:
    contents = pdb_file.read()
    matchgroup = re.findall(r'NE2 HIS (\w ?\d+)', contents)
    for line in contents.split("\n"):
        match = re.search(r' HIS (\w ?\d+)', line)
        if match:
            new_line = re.sub('HIS ' + match.group(1), 'HSE ' + match.group(1), line)
            print(new_line)
        else:
            print(line)