schwancr

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):

schwancr

from msmbuilder.metrics import LPRMSD
import mdtraj as md
import numpy as np
import IPython

pdbstring1="""
ATOM     11  CB  ALA     2       0.000   0.000   0.000  1.00  0.00
ATOM     12  H1  ALA     2       0.000  10.000   0.000  1.00  0.00
ATOM     13  H2  ALA     2       0.000  20.000   0.000  1.00  0.00
"""