RMSD calculator

#!/usr/bin/python
#RMSD skaiciavimas
#VR
#pagal dockedpse.py is github
#naudojimas: ./dockedpose.py kristalo.pdb docked.pdb

import math
import pybel
import sys

def squared_distance(coordsA, coordsB):
    """Find the squared distance between two 3-tuples"""
    sqrdist = sum( (a-b)**2 for a, b in zip(coordsA, coordsB) )
    return sqrdist

def rmsd(allcoordsA, allcoordsB):
    """Find the RMSD between two lists of 3-tuples"""
    deviation = sum(squared_distance(atomA, atomB) for
                    (atomA, atomB) in zip(allcoordsA, allcoordsB))
    return math.sqrt(deviation / float(len(allcoordsA)))

#if __name__ == "__main__":
crystal = next(pybel.readfile("pdb", sys.argv[1]))
dockedpose = next(pybel.readfile("pdb", sys.argv[2]))
xtalcoords = [atom.coords for atom in crystal if not atom.OBAtom.IsHydrogen()]
#for i, dockedpose in enumerate(pybel.readfile("pdb", sys.argv[1])):
posecoords = [atom.coords for atom in dockedpose if not atom.OBAtom.IsHydrogen()]
mrmsd = rmsd(posecoords, xtalcoords)
print mrmsd