translation for theobald rmsd code from original syntax/indexing to mdtraj's

trans.py

import re

with open('toadd.txt') as fh:
    lines = fh.readlines()

def trans(m):
    s = m.group(0)
    return 'k%d%d%s' % tuple([int(s[i]) - 1 for i in [1, 2]] + [s[-1]])

def trans2(m):
    s = m.group(0)
    return 'k%d%d%d%d_%d%d%d%d%s' % tuple([int(s[i]) - 1 for i in [1, 2, 3, 4] + [6, 7, 8, 9]] + [s[-1]])

def transq(m):
    s = m.group(0)
    return 'q%d%s' % (int(s[1]) - 1, s[-1])

for line in lines:
    line = re.sub('q\d\D', transq, line)
    line = re.sub('a\d\d\D', trans, line)
    line = re.sub('a\d\d\d\d_\d\d\d\d\D', trans2, line)

    print line,