def orientational_rmsd(ref_A, ref_B, coords_A, coords_B):
'''
Calculates an RMSD meassure to assess the quality of the alignment of the reference structure.
Two RMSD values are calculated, A_rmsd for the alignment of reference A to sample A and B_rmsd for the alignment of reference B to sample B.
Parameters:
-----
Requires:
ref_A; a numpy array of shape (n_atoms, 3), containing the coordinates of reference domain A
ref_B; a numpy array of shape (n_atoms, 3), containing the coordinates of reference domain B
coords_A; a numpy array of shape (n_atoms, 3), containing the coordinates of sample domain A
coords_B; a numpy array of shape (n_atoms, 3), containing the coordinates of sample domain B
Returns:
A_rmsd; a float describing the RMSD value for the alignment of reference domain A to sample domain A
B_rmsd; a float describing the RMSD value for the alignment of reference domain B to sample domain B
'''
A_rmsd = al.rmsd_kabsch(ref_A, coords_A)
B_rmsd = al.rmsd_kabsch(ref_B, coords_B)
return A_rmsd, B_rmsd
def test_rmsd_nonzero():
rmsd_kabsch = alignment.rmsd_kabsch(xyz1, xyz3)
rmsd_qcp = alignment.rmsd_qcp(xyz1, xyz3)
eq(rmsd_kabsch, rmsd_qcp, decimal=5)
def test_rmsd_nonzero():
rmsd_kabsch = alignment.rmsd_kabsch(xyz1, xyz3)
rmsd_qcp = alignment.rmsd_qcp(xyz1, xyz3)
eq(rmsd_kabsch, rmsd_qcp, decimal=5)
def test_rmsd_zero():
rmsd_kabsch = alignment.rmsd_kabsch(xyz1, xyz2)
rmsd_qcp = alignment.rmsd_qcp(xyz1, xyz2)
eq(float(rmsd_kabsch), 0.0, decimal=5)
eq(float(rmsd_qcp), 0.0, decimal=5)
def test_rmsd_zero():
rmsd_kabsch = alignment.rmsd_kabsch(xyz1, xyz2)
rmsd_qcp = alignment.rmsd_qcp(xyz1, xyz2)
eq(float(rmsd_kabsch), 0.0, decimal=5)
eq(float(rmsd_qcp), 0.0, decimal=5)
