def rms(config, inp: Tuple[str, str], out: click.File):
"""Calculate the root mean squared deviation between two structures using quaternions.
Based on a Fortran implementation by Chaok Seok, Evangelos
Coutsias, and Ken Dill."""
from kallisto.rmsd import rmsd
mol1 = ksr.constructMolecule(geometry=inp[0], out=out)
nat1 = mol1.get_number_of_atoms()
mol2 = ksr.constructMolecule(geometry=inp[1], out=out)
nat2 = mol2.get_number_of_atoms()
# for RMSD comparison both coordinates need the same atom count
if nat1 != nat2:
errorbye(
"Error: number of atoms do not match in {} and in {}".format(
inp[0], inp[1]), )
coord1 = mol1.get_positions()
coord2 = mol2.get_positions()
# get RMSD error and rotation matrix u
error, u = rmsd(nat1, coord1, coord2)
silentPrinter(config.silent, "RMSD {} Angstrom".format(error), out)
silentPrinter(config.silent, "Rotation Matrix", out)
click.echo(u, file=out) # type: ignore
return error, u
def test_rms():
mol1 = propanolLowest()
nat1 = mol1.get_number_of_atoms()
coord1 = mol1.get_positions()
mol2 = propanolIntermediate()
coord2 = mol2.get_positions()
_, u = rmsd(nat1, coord1, coord2)
assert np.isclose(u[0, 0], 0.98139458)
assert np.isclose(u[0, 1], -0.04965545)
assert np.isclose(u[0, 2], -0.18546973)
assert np.isclose(u[1, 0], 0.06170977)
assert np.isclose(u[1, 1], 0.9963015)
assert np.isclose(u[1, 2], 0.05979323)
assert np.isclose(u[2, 0], 0.18181471)
assert np.isclose(u[2, 1], -0.07012604)
assert np.isclose(u[2, 2], 0.98082911)
def test_rms():
mol1 = propanolLowest()
nat1 = mol1.get_number_of_atoms()
coord1 = mol1.get_positions()
mol2 = propanolIntermediate()
coord2 = mol2.get_positions()
error, u = rmsd(nat1, coord1, coord2)
assert (error - 1.12070194) < epsilon
assert (u[0, 0] - 0.98139458) < epsilon
assert (u[0, 1] - -0.04965545) < epsilon
assert (u[0, 2] - -0.18546973) < epsilon
assert (u[1, 0] - 0.06170977) < epsilon
assert (u[1, 1] - 0.9963015) < epsilon
assert (u[1, 2] - 0.05979323) < epsilon
assert (u[2, 0] - 0.18181471) < epsilon
assert (u[2, 1] - -0.07012604) < epsilon
assert (u[2, 2] - 0.98082911) < epsilon