def test_symmrmsd_atol(i: bool, reference: float) -> None:
moli = copy.deepcopy(molecules.docking_1cbr[0])
molj = copy.deepcopy(molecules.docking_1cbr[i])
moli.strip()
molj.strip()
# Check results are different from 0.0
assert not reference == pytest.approx(0.0)
assert (rmsd.symmrmsd(
moli.coordinates,
molj.coordinates,
moli.atomicnums,
molj.atomicnums,
moli.adjacency_matrix,
molj.adjacency_matrix,
minimize=True,
) == pytest.approx(reference, abs=1e-5))
assert (rmsd.symmrmsd(
moli.coordinates,
molj.coordinates,
moli.atomicnums,
molj.atomicnums,
moli.adjacency_matrix,
molj.adjacency_matrix,
minimize=True,
atol=1e9,
) == pytest.approx(0.0))
def test_symmrmsd_centred(mol: molecule.Molecule) -> None:
mol1 = copy.deepcopy(mol)
mol2 = copy.deepcopy(mol)
mol2.translate(np.random.rand(3))
assert (rmsd.symmrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
mol1.adjacency_matrix,
mol2.adjacency_matrix,
) > 0)
assert rmsd.symmrmsd(
mol1.coordinates,
mol2.coordinates,
mol1.atomicnums,
mol2.atomicnums,
mol1.adjacency_matrix,
mol2.adjacency_matrix,
center=True,
) == pytest.approx(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_symmrmsd_disconnected_node() -> None:
c = np.array([[0.0, 1.0, 2.0], [1.0, 2.0, 3.0], [2.0, 3.0, 4.0]])
a = np.array([0, 1, 4])
# Adjacency matrix with disconnected node
A = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 0]])
with pytest.warns(UserWarning, match="Disconnected graph detected."):
assert rmsd.symmrmsd(c, c, a, a, A, A) == pytest.approx(0.0, abs=1e-5)
def test_issue_35_2():
"""
GitHub Issue #35 from @kjelljorner
https://github.com/RMeli/spyrmsd/issues/35
"""
elements = np.array([6, 6, 1, 1, 1, 1, 1, 1])
connectivity_matrix = np.array([
[0, 1, 1, 1, 1, 0, 0, 0],
[1, 0, 0, 0, 0, 1, 1, 1],
[1, 0, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0],
[1, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0],
])
coordinates_1 = np.array([
[-0.7513646148641476, 0.0212153090068301, 0.0811236469164399],
[0.7513646329421021, -0.0212139873589844, -0.0811234544788992],
[-1.1912097695762844, -0.9520810297276773, -0.1560519813078418],
[-1.0197601491429782, 0.2790338755490671, 1.1099648032811764],
[-1.1891251185534542, 0.769045487934088, -0.5868099187409093],
[1.1891224079259752, -0.7690462686978631, 0.5868095572711365],
[1.0197615786233758, -0.2790344505405097, -1.1099636171164908],
[1.191211032645396, 0.9520810638350493, 0.1560509641753798],
])
coordinates_2 = np.array([
[0.752989230839992, 0.0675001892809206, -0.0055472904918074],
[-0.7529892426611152, -0.0675008847728476, 0.0055489067798057],
[1.0506759954349485, 1.0138756198991818, -0.4668239152871582],
[1.2080371182091196, -0.7501873566674166, -0.5724157781772267],
[1.148732484392816, 0.0417675099494674, 1.0141322717252037],
[-1.050678518706957, -1.0138763219763327, 0.4668256362472835],
[-1.148731454954795, -0.0417698443724041, -1.0141315673229787],
[-1.208035612554004, 0.7501910886594293, 0.5724117365268774],
], )
mask = elements != 1
r = rmsd.symmrmsd(
coordinates_1[mask],
coordinates_2[mask],
elements[mask],
elements[mask],
connectivity_matrix[mask, :][:, mask],
connectivity_matrix[mask, :][:, mask],
center=True,
minimize=True,
)
assert r == pytest.approx(0.0)
def test_symmrmsd_atol_multi() -> None:
references = [0.476858, 1.68089, 1.50267]
molc = copy.deepcopy(molecules.docking_1cbr[0])
mols = [copy.deepcopy(mol) for mol in molecules.docking_1cbr[1:4]]
molc.strip()
for mol in mols:
mol.strip()
# Check results are different from 0.0
assert not np.allclose(references, 0.0)
RMSDs = rmsd.symmrmsd(
molc.coordinates,
[mol.coordinates for mol in mols],
molc.atomicnums,
mols[0].atomicnums,
molc.adjacency_matrix,
mols[0].adjacency_matrix,
minimize=True,
)
for r, ref in zip(RMSDs, references):
assert r == pytest.approx(ref, abs=1e-5)
RMSDs = rmsd.symmrmsd(
molc.coordinates,
[mol.coordinates for mol in mols],
molc.atomicnums,
mols[0].atomicnums,
molc.adjacency_matrix,
mols[0].adjacency_matrix,
minimize=True,
atol=1e9,
)
for r in RMSDs:
assert r == pytest.approx(0.0)
def test_rmsd_symmrmsd(index: int, RMSD: float, minimize: bool) -> None:
molc = copy.deepcopy(molecules.docking_1cbr[0])
mol = copy.deepcopy(molecules.docking_1cbr[index])
molc.strip()
mol.strip()
assert rmsd.symmrmsd(
molc.coordinates,
mol.coordinates,
molc.atomicnums,
mol.atomicnums,
molc.adjacency_matrix,
mol.adjacency_matrix,
minimize=minimize,
) == pytest.approx(RMSD, abs=1e-5)
def test_issue_35_1():
"""
GitHub Issue #35 from @kjelljorner
https://github.com/RMeli/spyrmsd/issues/35
"""
elements = np.array([6, 1, 1, 1, 1])
connectivity_matrix = np.array([
[0, 1, 1, 1, 1],
[1, 0, 0, 0, 0],
[1, 0, 0, 0, 0],
[1, 0, 0, 0, 0],
[1, 0, 0, 0, 0],
])
coordinates_1 = np.array([
[2.416690358222e-09, -2.979634307864e-08, -9.782357562900e-09],
[-6.669665490935e-01, -6.162099127861e-01, -6.069106091317e-01],
[-4.258088724928e-01, 9.999808728518e-01, 1.078170393201e-01],
[1.178459756093e-01, -4.538168967035e-01, 9.864390766805e-01],
[9.749294435604e-01, 7.004596643409e-02, -4.873454970866e-01],
])
coordinates_2 = np.array([
[-2.118450971480e-07, 2.238951108509e-07, 1.839989120690e-07],
[-5.297519571039e-01, -4.011375110922e-01, 8.668054003529e-01],
[-5.107749001064e-01, 8.975573096842e-01, -3.555275589573e-01],
[1.644944812511e-02, -7.486078704316e-01, -7.951194721576e-01],
[1.024077620930e00, 2.521878479445e-01, 2.838414467631e-01],
])
r = rmsd.symmrmsd(
coordinates_1,
coordinates_2,
elements,
elements,
connectivity_matrix,
connectivity_matrix,
center=True,
minimize=True,
)
assert r == pytest.approx(0.0)
def test_multi_spyrmsd(minimize: bool, referenceRMSDs: List[float]) -> None:
molc = copy.deepcopy(molecules.docking_1cbr[0])
mols = [copy.deepcopy(mol) for mol in molecules.docking_1cbr[1:]]
molc.strip()
for mol in mols:
mol.strip()
RMSDs = rmsd.symmrmsd(
molc.coordinates,
[mol.coordinates for mol in mols],
molc.atomicnums,
mols[0].atomicnums,
molc.adjacency_matrix,
mols[0].adjacency_matrix,
minimize=minimize,
)
for RMSD, referenceRMSD in zip(RMSDs, referenceRMSDs):
assert RMSD == pytest.approx(referenceRMSD, abs=1e-5)
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
if verbose:
print(f"Atomic mapping: '{select}'\n{atomicmap}")
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",