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)