writing in particular positions

[Gribouillis]

I like generators (tested code here)

import itertools as itt
import os
import sys

def gen_names():
    for cnt in itt.count(1):
        yield 'MOLECULE{}'.format(cnt)

def augmented_lines(line_seq, name_seq):
    name_seq = iter(name_seq)
    for line in line_seq:
        yield line
        if line.startswith('@<TRIPOS>MOLECULE'):
            yield next(name_seq) + '\n'

if __name__ == '__main__':
    src_fn = os.path.join(os.path.dirname(__file__), 'five-molecules.txt')
    with open(src_fn) as infile:
        sys.stdout.writelines(augmented_lines(infile, gen_names()))