def test_rmsd_minimize(mol: molecule.Molecule) -> None:
mol1 = copy.deepcopy(mol)
mol2 = copy.deepcopy(mol)
assert rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0)
assert rmsd.rmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
minimize=True,
) == pytest.approx(0)
for _ in range(10):
mol2.translate(np.random.rand(3))
mol2.rotate(np.random.rand(1), np.random.rand(3))
assert (rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0.0)
assert rmsd.rmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
minimize=True,
) == pytest.approx(0)
def test_rmsd_atol(i: int, j: int, result: float):
"""
Test usage of the :code:`atol` parameter for the QCP method.
This parameter has been exposed to users following Issue 35 from @kjelljorner
(https://github.com/RMeli/spyrmsd/issues/35)
"""
moli = copy.deepcopy(molecules.docking_2viz[i])
molj = copy.deepcopy(molecules.docking_2viz[j])
# Check results are different from 0.0
assert not result == pytest.approx(0.0)
assert (rmsd.rmsd(
moli.coordinates,
molj.coordinates,
moli.atomicnums,
molj.atomicnums,
minimize=True,
) == pytest.approx(result))
assert (rmsd.rmsd(
moli.coordinates,
molj.coordinates,
moli.atomicnums,
molj.atomicnums,
minimize=True,
atol=1e9,
) == pytest.approx(0.0))
def test_symmrmsd_rotated_benzene_stripped(angle: float) -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
mol2.rotate(angle, np.array([0, 0, 1]), units="deg")
mol1.strip()
mol2.strip()
assert (rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0)
assert rmsd.rmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
minimize=True,
) == pytest.approx(0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0, abs=1e-4)
assert rmsd.symmrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
mol1.adjacency_matrix,
mol2.adjacency_matrix,
) == pytest.approx(0, abs=1e-4)
def test_rmsd_qcp_protein(i: int, rmsd_dummy: float, rmsd_min: float):
mol0 = copy.deepcopy(molecules.trp[0])
mol = copy.deepcopy(molecules.trp[i])
assert rmsd.rmsd(mol0.coordinates, mol.coordinates, mol0.atomicnums,
mol.atomicnums) == pytest.approx(rmsd_dummy)
assert rmsd.rmsd(
mol0.coordinates,
mol.coordinates,
mol0.atomicnums,
mol.atomicnums,
minimize=True,
) == pytest.approx(rmsd_min)
def test_rmsd_2viz(i: int, j: int, result: float) -> None:
moli = copy.deepcopy(molecules.docking_2viz[i])
molj = copy.deepcopy(molecules.docking_2viz[j])
assert rmsd.rmsd(moli.coordinates, molj.coordinates, moli.atomicnums,
molj.atomicnums) == pytest.approx(result)
def test_rmsd_centred_benzene() -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
mol2.translate(np.array([0, 0, 1]))
assert rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(1)
assert rmsd.rmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
center=True,
) == pytest.approx(0)
def test_rmsd_hungarian_benzene_rotated(angle: float, tol: float) -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
assert rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0)
# Rotations different than 180 degrees introduce numerical errors (~1e-6)
mol2.rotate(angle, [0, 0, 1], units="deg")
assert (rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) > 0)
assert rmsd.hrmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(0, abs=tol)
def test_rmsd_benzene(t: float, RMSD: float) -> None:
mol1 = copy.deepcopy(molecules.benzene)
mol2 = copy.deepcopy(molecules.benzene)
mol2.translate(np.array([0, 0, t]))
assert rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums) == pytest.approx(RMSD)
def test_rmsd_qcp_2viz_stripped(i: int, j: int, result: float) -> None:
moli = copy.deepcopy(molecules.docking_2viz[i])
molj = copy.deepcopy(molecules.docking_2viz[j])
# Strip hydrogen atoms
moli.strip()
molj.strip()
assert rmsd.rmsd(
moli.coordinates,
molj.coordinates,
moli.atomicnums,
molj.atomicnums,
minimize=True,
) == pytest.approx(result)
def test_symmrmsd_atomicnums_matching_pyridine_stripped() -> None:
mol1 = copy.deepcopy(molecules.pyridine)
mol2 = copy.deepcopy(molecules.pyridine)
mol2.rotate(60, np.array([0, 0, 1]), units="deg")
mol1.strip()
mol2.strip()
# Standard RMSD, correct in this case
RMSD = rmsd.rmsd(mol1.coordinates, mol2.coordinates, mol1.atomicnums,
mol2.atomicnums)
# Isomorphic RMSD with atomic number matching is correct
# Without atomic number matching this would be wrong because of higher symmetry
assert rmsd.symmrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
mol1.adjacency_matrix,
mol2.adjacency_matrix,
) == pytest.approx(RMSD, abs=1e-4)
def rmsdwrapper(
molref,
mols,
symmetry: bool = True,
center: bool = False,
minimize: bool = False,
strip: bool = True,
cache: bool = True,
) -> Any:
"""
Compute RMSD between two molecule.
Parameters
----------
mol1: molecule.Molecule
Molecule 1
mol2: molecule.Molecule
Molecule 2
symmetry: bool, optional
Symmetry-corrected RMSD (using graph isomorphism)
center: bool, optional
Center molecules at origin
minimize: bool, optional
Minimised RMSD (using the quaternion polynomial method)
strip: bool, optional
Strip hydrogen atoms
Returns
-------
List[float]
RMSDs
"""
if strip:
molref.strip()
for mol in mols:
mol.strip()
if minimize:
center = True
cref = coords_from_molecule(molref, center)
cmols = [coords_from_molecule(mol, center) for mol in mols]
RMSDlist = []
if symmetry:
RMSDlist = rmsd.symmrmsd(
cref,
cmols,
molref.atomicnums,
mols[0].atomicnums,
molref.adjacency_matrix,
mols[0].adjacency_matrix,
center=center,
minimize=minimize,
cache=cache,
)
else: # No symmetry
for c in cmols:
RMSDlist.append(
rmsd.rmsd(
cref,
c,
molref.atomicnums,
mols[0].atomicnums,
center=center,
minimize=minimize,
))
return RMSDlist
time = []
rmsds = []
rmsd_nosymm = []
for ts in tqdm.tqdm(traj.trajectory[::step]):
# Align protein backbones
old_rmsd, new_rmsd = align.alignto(traj,
ref,
select="backbone",
strict=True)
assert new_rmsd <= old_rmsd
if symmetry:
r = rmsd.symmrmsd(selection.atoms.positions, ref_positions, atomicmap,
atomicmap, A, A)
else:
r = rmsd.rmsd(selection.atoms.positions, ref_positions, atomicmap,
atomicmap)
time.append(ts.time)
rmsds.append(r)
rmsd_nosymm.append(
rmsd.rmsd(selection.atoms.positions, ref_positions, atomicmap,
atomicmap))
# Check rmsd_nosymm is the same as rms.RMDS
rmsd_mda = rms.RMSD(traj,
ref,
select="backbone",
groupselections=["resname LIG"],
ref_frame=iframe)
R = rmsd_mda.run(verbose=True, step=step)
