def test8MatchParams(self):
smis = ("CCC1NC1", "CCC1N(C)C1", "CCC1OC1")
ms = [Chem.MolFromSmiles(x) for x in smis]
mcs = rdFMCS.FindMCS(ms)
self.assertEqual(mcs.numAtoms, 4)
ps = rdFMCS.MCSParameters()
ps.BondCompareParameters.CompleteRingsOnly = True
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 3)
ps = rdFMCS.MCSParameters()
ps.BondCompareParameters.MatchFusedRings = True
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 3)
ps = rdFMCS.MCSParameters()
ps.BondCompareParameters.MatchFusedRingsStrict = True
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 3)
ps = rdFMCS.MCSParameters()
ps.SetAtomTyper(rdFMCS.AtomCompare.CompareAny)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 5)
def test18GitHub3693(self):
mols = [Chem.MolFromSmiles(smi) for smi in [
"Nc1ccc(O)cc1c1ccc2ccccc2c1", "Oc1cnc(NC2CCC2)c(c1)c1ccc2ccccc2c1"]]
params = rdFMCS.MCSParameters()
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 17)
self.assertEqual(res.numBonds, 18)
self.assertEqual(res.smartsString, "[#7]-,:[#6]:[#6](:[#6]:[#6](:[#6])-[#8])-[#6]1:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2")
params = rdFMCS.MCSParameters()
params.BondCompareParameters.CompleteRingsOnly = True
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 11)
self.assertEqual(res.numBonds, 12)
self.assertEqual(res.smartsString, "[#6]-&!@[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2")
params = rdFMCS.MCSParameters()
params.AtomCompareParameters.CompleteRingsOnly = True
params.BondCompareParameters.CompleteRingsOnly = True
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 10)
self.assertEqual(res.numBonds, 11)
self.assertEqual(res.smartsString, "[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2")
params = rdFMCS.MCSParameters()
params.AtomCompareParameters.CompleteRingsOnly = True
# this will automatically be set to True
params.BondCompareParameters.CompleteRingsOnly = False
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 10)
self.assertEqual(res.numBonds, 11)
self.assertEqual(res.smartsString, "[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2")
def draw_mols(x_list: list, y_list: list, names: list):
error_names = []
error = []
for x, y, name in zip(x_list, y_list, names):
e = abs(float(x) - float(y))
if e > 10:
error_names.append(name)
error.append(e)
ps = rdFMCS.MCSParameters()
ps.AtomCompareParameters.RingMatchesRingOnly = True
ps.SetAtomTyper(rdFMCS.AtomCompare.CompareAny)
for name in error_names:
mol1, mol2 = (
Chem.MolFromSmiles(exp_results[name]["t1-smiles"]),
Chem.MolFromSmiles(exp_results[name]["t2-smiles"]),
)
mcs = Chem.MolFromSmarts(
rdFMCS.FindMCS(
[mol1, mol2],
bondCompare=Chem.rdFMCS.BondCompare.CompareOrder.CompareAny,
).smartsString)
AllChem.Compute2DCoords(mol1)
match1 = mol1.GetSubstructMatch(mcs)
match2 = mol2.GetSubstructMatch(mcs)
coords = [mol1.GetConformer().GetAtomPosition(x) for x in match1]
coords2D = [Geometry.Point2D(pt.x, pt.y) for pt in coords]
coordDict = {}
for i, coord in enumerate(coords2D):
coordDict[match2[i]] = coord
AllChem.Compute2DCoords(mol2, coordMap=coordDict)
Draw.MolsToGridImage([mol1, mol2], subImgSize=(250, 250), molsPerRow=2)
def getParams(**kwargs):
params = rdFMCS.MCSParameters()
for kw in ("AtomTyper", "BondTyper"):
v = kwargs.get(kw, None)
if v is not None:
v_instance = v()
setattr(params, kw, v_instance)
return params
def test16MCSProgressCallbackExceptions(self):
ps = rdFMCS.MCSParameters()
smis = ['CCCC(C)CC(CC)CC', 'OC(N)CC(C)CC(CC)CC']
ms = [Chem.MolFromSmiles(x) for x in smis]
self.assertRaises(TypeError, lambda ps: setattr(ps, "ProgressCallback",
ProgressCallbackCallbackIsInt()))
self.assertRaises(TypeError, lambda ps: setattr(ps, "ProgressCallback",
ProgressCallbackNoCallback()))
def test14MCSBondCompareExceptions(self):
ps = rdFMCS.MCSParameters()
smis = ['CCCCC', 'CCC1CCCCC1']
ms = [Chem.MolFromSmiles(x) for x in smis]
self.assertRaises(TypeError, lambda ps: setattr(ps, "BondTyper",
BondCompareCompareIsInt()))
self.assertRaises(TypeError, lambda ps: setattr(ps, "BondTyper",
BondCompareNoCompare()))
def test20AtomCompareCompleteRingsOnly(self):
mols = [Chem.MolFromSmiles(smi) for smi in ["C1CCCC1C", "C1CCCC1C1CCCCC1"]]
params = rdFMCS.MCSParameters()
params.AtomCompareParameters.CompleteRingsOnly = True
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 5)
self.assertEqual(res.numBonds, 5)
self.assertEqual(res.smartsString, "[#6&R]1-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@1")
params = rdFMCS.MCSParameters()
params.AtomCompareParameters.CompleteRingsOnly = True
# this will automatically be set to True
params.BondCompareParameters.CompleteRingsOnly = False
res = rdFMCS.FindMCS(mols, params)
self.assertEqual(res.numAtoms, 5)
self.assertEqual(res.numBonds, 5)
self.assertEqual(res.smartsString, "[#6&R]1-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@1")
def test12MCSAtomCompareExceptions(self):
ps = rdFMCS.MCSParameters()
smis = ['CCCCC', 'CCC1CCCCC1']
ms = [Chem.MolFromSmiles(x) for x in smis]
self.assertRaises(TypeError, lambda ps: setattr(ps, "AtomTyper",
AtomCompareCompareIsInt()))
ps.AtomTyper = AtomCompareNoCompare()
self.assertRaises(TypeError, lambda ms, ps: rdFMCS.FindMCS(ms, ps))
def test17MCSProgressCallbackCancel(self):
ps = rdFMCS.MCSParameters()
smis = ['CCCC(C)CC(CC)CC', 'OC(N)CC(C)CC(CC)CC']
ms = [Chem.MolFromSmiles(x) for x in smis]
ps.AtomTyper = CompareElements()
ps.ProgressCallback = ProgressCallback(self)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertTrue(mcs.canceled)
self.assertEqual(ps.ProgressCallback.callCount, 3)
def test13MCSAtomCompareUserData(self):
smis = ['CCOCCOC', 'CCNCCCC']
ms = [Chem.MolFromSmiles(x) for x in smis]
ps = rdFMCS.MCSParameters()
ps.AtomTyper = AtomCompareUserData()
ps.AtomTyper.setMatchAnyHet(False)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 2)
ps.AtomTyper.setMatchAnyHet(True)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 5)
def test9MatchCharge(self):
smis = ("CCNC", "CCN(C)C", "CC[N+](C)C")
ms = [Chem.MolFromSmiles(x) for x in smis]
mcs = rdFMCS.FindMCS(ms)
self.assertEqual(mcs.numAtoms, 4)
ps = rdFMCS.MCSParameters()
ps.AtomCompareParameters.MatchFormalCharge = True
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 2)
def mcs_map(a, b, threshold: float = 0.5, timeout: int = 5, smarts: Optional[str] = None):
"""Find the MCS map of going from A to B"""
params = rdFMCS.MCSParameters()
params.BondCompareParameters.CompleteRingsOnly = 1
params.BondCompareParameters.RingMatchesRingOnly = 1
params.AtomCompareParameters.matchValences = 1
params.AtomTyper = CompareDist(threshold=threshold)
params.Timeout = timeout
if smarts is not None:
params.InitialSeed = smarts
return rdFMCS.FindMCS([a, b], params)
def test15MCSBondCompareUserData(self):
smis = ['C1CC=CCC1', 'c1ccccc1']
ms = [Chem.MolFromSmiles(x) for x in smis]
ps = rdFMCS.MCSParameters()
ps.BondTyper = BondCompareUserData()
ps.BondCompareParameters.CompleteRingsOnly = True
ps.BondTyper.setIgnoreAromatization(False)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 0)
ps.BondTyper.setIgnoreAromatization(True)
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 6)
def getParams(**kwargs):
have_kw = False
params = rdFMCS.MCSParameters()
for kw in ("AtomTyper", "BondTyper"):
try:
v = kwargs[kw]
except KeyError:
pass
else:
have_kw = True
setattr(params, kw, v())
return params
def test11Github2034(self):
smis = ("C1CC1N2CC2", "C1CC1N")
ms = [Chem.MolFromSmiles(x) for x in smis]
mcs = rdFMCS.FindMCS(ms)
self.assertEqual(mcs.numAtoms, 4)
self.assertEqual(mcs.numBonds, 4)
mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True)
self.assertEqual(mcs.numAtoms, 3)
self.assertEqual(mcs.numBonds, 3)
ps = rdFMCS.MCSParameters()
ps.AtomCompareParameters.RingMatchesRingOnly = True
mcs = rdFMCS.FindMCS(ms, ps)
self.assertEqual(mcs.numAtoms, 3)
self.assertEqual(mcs.numBonds, 3)
def test_setting_up_restraints_using_smarts():
seed = 814
mcs_params = rdFMCS.MCSParameters()
mcs_params.AtomTyper = CompareDistNonterminal()
mcs_params.BondTyper = rdFMCS.BondCompare.CompareAny
smi_a = "CCCONNN"
smi_b = "CCCNNN"
mol_a = Chem.MolFromSmiles(smi_a)
mol_a = Chem.AddHs(mol_a)
mol_b = Chem.MolFromSmiles(smi_b)
mol_b = Chem.AddHs(mol_b)
for mol in [mol_a, mol_b]:
AllChem.EmbedMolecule(mol, randomSeed=seed)
result = rdFMCS.FindMCS([mol_a, mol_b], mcs_params)
core = setup_relative_restraints_using_smarts(mol_a, mol_b,
result.smartsString)
assert core.shape == (2, 2)
