writing in particular positions

[ichabod801]

You would want something like this:

with open('old_file.txt') as in_file:
    with open('new_file.txt, 'w') as out_file:
        for line in old_file:
            new_file.write(line)
            if new_file.startswith('@<TRIPOS>MOLECULE'):
                new_file.write('MOLECULE NAME')