test for lprmsd + mdtraj from msmbuilder

testlprmsd.py

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
"""

pdbstring2="""
ATOM     11  CB  ALA     2      10.000   0.000   0.000  1.00  0.00
ATOM     12  H1  ALA     2      20.000   0.000   0.000  1.00  0.00
ATOM     13  H2  ALA     2      30.000   0.000   0.000  1.00  0.00
"""

with open('temp.pdb', 'w') as fh:
    fh.write(pdbstring1)
pdb1 = md.load_pdb('temp.pdb')
pdb1.center_coordinates()

with open('temp.pdb', 'w') as fh:
    fh.write(pdbstring2)
pdb2 = md.load_pdb('temp.pdb')
pdb2.center_coordinates()

def test():
    print pdb1.xyz
    print pdb2.xyz

    dist = md.lprmsd(pdb1, pdb2, superpose=False, atom_indices=[0, 1, 2], permute_groups=[[0], [1], [2]])
    dist2 = md.lprmsd(pdb1, pdb2, superpose=True, atom_indices=[0, 1, 2], permute_groups=[[0], [1], [2]])

    print dist, dist2
    print pdb1.xyz
    print pdb2.xyz

if __name__ == '__main__':
    test()