def test_match_only_at_rgroups(self):
smiles = ['c1ccccc1']#, 'c1(Cl)ccccc1', 'c1(Cl)cc(Br)ccc1']
mols = [Chem.MolFromSmiles(smi) for smi in smiles]
core1 = Chem.MolFromSmiles("c1([*:5])cc([*:6])ccc1")
params = RGroupDecompositionParameters()
params.onlyMatchAtRGroups=True
rg = RGroupDecomposition(core1, params)
for smi,m in zip(smiles,mols):
self.assertTrue(rg.Add(m)!=-1, smi)
def test_h_options(self):
core = Chem.MolFromSmiles("O=c1oc2ccccc2cc1")
smiles = ("O=c1cc(Cn2ccnc2)c2ccc(Oc3ccccc3)cc2o1",
"O=c1oc2ccccc2c(Cn2ccnc2)c1-c1ccccc1",
"COc1ccc2c(Cn3cncn3)cc(=O)oc2c1")
params = RGroupDecompositionParameters()
rgd = RGroupDecomposition(core,params)
for smi in smiles:
m = Chem.MolFromSmiles(smi)
rgd.Add(m)
rgd.Process()
columns = rgd.GetRGroupsAsColumns()
self.assertEqual(columns['R2'][0].GetNumAtoms(),12)
params.removeHydrogensPostMatch = True
rgd = RGroupDecomposition(core,params)
for smi in smiles:
m = Chem.MolFromSmiles(smi)
rgd.Add(m)
rgd.Process()
columns = rgd.GetRGroupsAsColumns()
self.assertEqual(columns['R2'][0].GetNumAtoms(),7)
def test_timeout(self):
smis = '''CN(C)Cc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
CNc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
Cc1cc2cc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NC4CCN(C)CC4)c([N+](=O)[O-])c3)ccc2[nH]1
Cc1cc2cc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)ccc2[nH]1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccccc1Cl
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(Cl)c1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(Cl)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc([N+](=O)[O-])c1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(CO)c1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2ccccc2Cl)cc1[N+](=O)[O-]
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(Cl)c1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(Cl)cc1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2cccc(Cl)c2)cc1[N+](=O)[O-]
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2ccc(Cl)cc2)cc1[N+](=O)[O-]
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2cccc3c2ccn3C)cc1[N+](=O)[O-]
CC(=O)Nc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
Nc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
Nc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
COc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
CN(C)c1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
N#Cc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
Cc1nc2ccc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCC4CCOCC4)c([N+](=O)[O-])c3)cc2s1
Cc1nc2cc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)ccc2s1
Cc1nc2cc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN(C)C)c([N+](=O)[O-])c3)ccc2s1
CN(C)C(=O)CCc1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)C(=O)Cc1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)CCCc1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)CCc1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)C(=O)c1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)Cc1ccccc1Oc1cc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)ccc1C(=O)NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2cccc(N3CCOCC3)c2)cc1[N+](=O)[O-]
Cc1nc(C)c(-c2cccc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)c2)s1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cc(Cl)cc(Cl)c3)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(Cl)c3)cc2[N+](=O)[O-])CC1
CN(C)CCOc1ccc(-c2ccc(Cl)cc2)c(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NC5CCN(C)CC5)c([N+](=O)[O-])c4)c(Oc4cccc(Cl)c4)c3)CC2)c1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)OC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
CN(C)CCOc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccc(N)c(Cl)c3)cc2[N+](=O)[O-])CC1
CC(C)N1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccccc3Br)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CCCC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
Cc1n[nH]c2cccc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)c12
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(F)c3F)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(Br)c3)cc2[N+](=O)[O-])CC1
CCN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
CN1C(C)(C)CC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1(C)C
CC1(C)CCC(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NC5CCN(C6CCOCC6)CC5)c([N+](=O)[O-])c4)c(Oc4cccc(F)c4F)c3)CC2)=C(c2ccc(Cl)cc2)C1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cc(F)c4[nH]ccc4c3)cc2[N+](=O)[O-])CC1
CC1(C)CCC(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NCCCN5CCOCC5)c([N+](=O)[O-])c4)c(Oc4cccc(F)c4F)c3)CC2)=C(c2ccc(Cl)cc2)C1
CC1(C)CCC(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NCCCN5CCOCC5)c([N+](=O)[O-])c4)c(Oc4ccc(N)c(Cl)c4)c3)CC2)=C(c2ccc(Cl)cc2)C1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3cc(CCN4CCCC4)ccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(Cl)c1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(Cl)c3Cl)cc2[N+](=O)[O-])CC1
Cc1n[nH]c2cccc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NC4CCN(C)CC4)c([N+](=O)[O-])c3)c12
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CCCCC5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(C(F)(F)F)c3)cc2[N+](=O)[O-])CC1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2cccc3c2CCC(=O)N3)cc1[N+](=O)[O-]
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccccc3Cl)cc2S(=O)(=O)C(F)(F)F)CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cc(Cl)ccc3Cl)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3ccc(F)cc3Cl)cc2[N+](=O)[O-])CC1
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)C5)CC4)cc3Oc3ccccc3Cl)cc2[N+](=O)[O-])CC1
Cc1c[nH]c2cccc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)c12
CN1CCC(Nc2ccc(S(=O)(=O)NC(=O)c3ccc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)cc3Oc3cccc(C(F)(F)F)c3Cl)cc2[N+](=O)[O-])CC1
CC1(C)CCC(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NC5CCN(C6CC6)CC5)c([N+](=O)[O-])c4)c(Oc4ccccc4Cl)c3)CC2)=C(c2ccc(Cl)cc2)C1
Cc1c[nH]c2cccc(Oc3cc(N4CCN(CC5=C(c6ccc(Cl)cc6)CC(C)(C)CC5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NC4CCN(C)CC4)c([N+](=O)[O-])c3)c12
CC1(C)CCC(CN2CCN(c3ccc(C(=O)NS(=O)(=O)c4ccc(NCCCN5CCOCC5)c([N+](=O)[O-])c4)c(Oc4cc(Cl)ccc4Cl)c3)CC2)=C(c2ccc(Cl)cc2)C1
Cn1ccc2c(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)cccc21
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(N2CCOCC2)c1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2ccc3[nH]cc(CCC(=O)N4CCOCC4)c3c2)cc1[N+](=O)[O-]
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(OCc2ccccc2)c1
N#Cc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc2[nH]cc(CCC(=O)N3CCOCC3)c2c1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc2[nH]cc(CCCN3CCOCC3)c2c1
CN(C)Cc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(-n2ccnc2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)cc1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc([N+](=O)[O-])c1
CCN(Cc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1)C(=O)OC(C)(C)C
CCN(Cc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1)C(=O)OC(C)(C)C
CCNCc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
CCNCc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
CC(=O)Nc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
CC(C)(C)OC(=O)Nc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccccc1-c1ccccc1
CC(C)(C)OC(=O)Nc1cccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)c1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(-c2ccccc2)c1
CN(C)CCc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(OCc2ccccc2)cc1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(N2CCOCC2)c1
Cc1nc2cc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCC4CCOCC4)c([N+](=O)[O-])c3)ccc2s1
CC(C)(C)OC(=O)N1CCN(c2cccc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCC4CCOCC4)c([N+](=O)[O-])c3)c2)CC1
CN(C)CCCNc1ccc(S(=O)(=O)NC(=O)c2ccc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)cc2Oc2cccc(OCc3ccccc3)c2)cc1[N+](=O)[O-]
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(OCc2ccccc2)c1
O=C(NS(=O)(=O)c1ccc(NCC2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(OCCN2CCOCC2)cc1
O=C1CCc2c(cccc2Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)N1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(OCc2ccccc2)cc1
CC(C)(C)OC(=O)N1CCN(c2ccc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)cc2)CC1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1cccc(-c2ccncc2)c1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(-c2ccncc2)cc1
O=C(NS(=O)(=O)c1ccc(NCCCN2CCOCC2)c([N+](=O)[O-])c1)c1ccc(N2CCN(Cc3ccccc3-c3ccc(Cl)cc3)CC2)cc1Oc1ccc(-c2cccnc2)cc1
CN(C)C(=O)COc1ccc(Oc2cc(N3CCN(Cc4ccccc4-c4ccc(Cl)cc4)CC3)ccc2C(=O)NS(=O)(=O)c2ccc(NCC3CCOCC3)c([N+](=O)[O-])c2)cc1
Cn1cnc2cc(Oc3cc(N4CCN(Cc5ccccc5-c5ccc(Cl)cc5)CC4)ccc3C(=O)NS(=O)(=O)c3ccc(NCCCN4CCOCC4)c([N+](=O)[O-])c3)ccc21'''
mols = [Chem.MolFromSmiles(x) for x in smis.split('\n')]
core = Chem.MolFromSmarts('O=C(NS(=O)(=O)c1ccccc1)c1ccccc1Oc1ccccc1')
ps = RGroupDecompositionParameters()
ps.timeout = 1.0
with self.assertRaises(RuntimeError):
rg = RGroupDecomposition(core, ps)
for m in mols:
rg.Add(m)
with self.assertRaises(RuntimeError):
columns2, unmatched = RGroupDecompose([core],
mols,
asRows=False,
options=ps)
def test_multicore_prelabelled(self):
def multicorergd_test(cores, params, expected_rows, expected_items):
mols = [
Chem.MolFromSmiles(smi)
for smi in ("CNC(=O)C1=CN=CN1CC", "Fc1ccc2ccc(Br)nc2n1")
]
params.removeHydrogensPostMatch = True
params.onlyMatchAtRGroups = True
decomp = RGroupDecomposition(cores, params)
i = 0
for i, m in enumerate(mols):
res = decomp.Add(m)
self.assertEqual(res, i)
self.assertTrue(decomp.Process())
rows = decomp.GetRGroupsAsRows(asSmiles=True)
self.assertEqual(rows, expected_rows)
items = decomp.GetRGroupsAsColumns(asSmiles=True)
self.assertEqual(items, expected_items)
sdcores = """
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
1.1100 -1.3431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.5225 -0.6286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9705 -0.0156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2168 -0.3511 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3029 -1.1716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1419 0.7914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5289 1.3431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9266 1.0463 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-0.4976 0.0613 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 1 0
1 5 2 0
3 6 1 0
6 7 2 0
6 8 1 0
4 9 1 0
M RGP 2 8 1 9 2
V 8 *
V 9 *
M END
$$$$
RDKit 2D
12 13 0 0 0 0 0 0 0 0999 V2000
-6.5623 0.3977 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 0.3977 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4188 -0.8397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1333 -1.2522 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-5.8478 -0.8397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7044 -1.2522 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-3.7044 0.3977 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.9899 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9899 -0.8397 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
-2.2754 0.3978 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
2 3 2 0
2 7 1 0
9 10 2 0
10 11 1 0
8 11 2 0
8 5 1 0
4 9 1 0
10 12 1 0
1 2 1 0
M RGP 2 1 2 12 1
V 1 *
V 12 *
M END
$$$$
"""
sdsup = Chem.SDMolSupplier()
sdsup.SetData(sdcores)
cores = [c for c in sdsup]
expected_rows_autodetect = [{
"Core": "O=C(c1cncn1[*:2])[*:1]",
"R1": "CN[*:1]",
"R2": "CC[*:2]"
}, {
"Core": "*1:*c2c(*c([*:2])c[*:1]2)nc1[*:3]",
"R1": "c(:[*:1]):[*:1]",
"R2": "Br[*:2]"
}]
expected_items_autodetect = {
"Core":
["O=C(c1cncn1[*:2])[*:1]", "*1:*c2c(*c([*:2])c[*:1]2)nc1[*:3]"],
"R1": ["CN[*:1]", "c(:[*:1]):[*:1]"],
"R2": ["CC[*:2]", "Br[*:2]"]
}
expected_rows_no_autodetect = [{
"Core": "O=C(c1cncn1[*:2])[*:1]",
"R1": "CN[*:1]",
"R2": "CC[*:2]"
}, {
"Core": "*1:*c2*cc([*:2])*c2nc1[*:1]",
"R1": "F[*:1]",
"R2": "Br[*:2]"
}]
expected_items_no_autodetect = {
"Core": ["O=C(c1cncn1[*:2])[*:1]", "*1:*c2*cc([*:2])*c2nc1[*:1]"],
"R1": ["CN[*:1]", "F[*:1]"],
"R2": ["CC[*:2]", "Br[*:2]"]
}
expectedLabels = ["Core", "R1", "R2"]
params = RGroupDecompositionParameters()
# test pre-labelled with MDL R-group labels, autodetect
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_autodetect,
expected_items_autodetect)
# test pre-labelled with MDL R-group labels, no autodetect
params.labels = RGroupLabels.MDLRGroupLabels | RGroupLabels.RelabelDuplicateLabels
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
# test pre-labelled with MDL R-group labels, autodetect, no MCS alignment
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.NoAlignment
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
# Reading from a MDL molblock also sets isotopic labels, so no need
# to set them again; we only clear MDL R-group labels
for core in cores:
for a in core.GetAtoms():
if a.HasProp("_MolFileRLabel"):
a.ClearProp("_MolFileRLabel")
# test pre-labelled with isotopic labels, autodetect
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_autodetect,
expected_items_autodetect)
# test pre-labelled with isotopic labels, no autodetect
params.labels = RGroupLabels.IsotopeLabels | RGroupLabels.RelabelDuplicateLabels
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
# test pre-labelled with isotopic labels, autodetect, no MCS alignment
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.NoAlignment
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
for core in cores:
for a in core.GetAtoms():
iso = a.GetIsotope()
if iso:
a.SetAtomMapNum(iso)
a.SetIsotope(0)
# test pre-labelled with atom map labels, autodetect
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_autodetect,
expected_items_autodetect)
# test pre-labelled with atom map labels, no autodetect
params.labels = RGroupLabels.AtomMapLabels | RGroupLabels.RelabelDuplicateLabels
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
# test pre-labelled with atom map labels, autodetect, no MCS alignment
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.NoAlignment
multicorergd_test(cores, params, expected_rows_no_autodetect,
expected_items_no_autodetect)
for core in cores:
for a in core.GetAtoms():
if a.GetAtomMapNum():
a.SetAtomMapNum(0)
# test pre-labelled with dummy atom labels, autodetect
expected_rows_autodetect = [{
"Core": "O=C(c1cncn1[*:2])[*:1]",
"R1": "CN[*:1]",
"R2": "CC[*:2]"
}, {
"Core": "c1c([*:2])[*:3]c2nc([*:6])[*:5]:[*:4]c2[*:1]1",
"R1": "c(:[*:1]):[*:1]",
"R2": "Br[*:2]"
}]
expected_items_autodetect = {
"Core": [
"O=C(c1cncn1[*:2])[*:1]",
"c1c([*:2])[*:3]c2nc([*:6])[*:5]:[*:4]c2[*:1]1"
],
"R1": ["CN[*:1]", "c(:[*:1]):[*:1]"],
"R2": ["CC[*:2]", "Br[*:2]"]
}
params.labels = RGroupLabels.AutoDetect
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_autodetect,
expected_items_autodetect)
# test pre-labelled with dummy atom labels, no autodetect
# in this case there is no difference from autodetect as the RGD code
# cannot tell the difference between query atoms and dummy R-groups
params.labels = RGroupLabels.DummyAtomLabels | RGroupLabels.RelabelDuplicateLabels
params.alignment = RGroupCoreAlignment.MCS
multicorergd_test(cores, params, expected_rows_autodetect,
expected_items_autodetect)
def testRemoveAllHydrogenFlags(self):
core = Chem.MolFromSmiles("[1*]c1ccc([2*])cn1")
mol = Chem.MolFromSmiles("Fc1ccccn1")
params = RGroupDecompositionParameters()
rgd = RGroupDecomposition(core, params)
self.assertEqual(rgd.Add(mol), 0)
self.assertTrue(rgd.Process())
res = rgd.GetRGroupsAsColumns(asSmiles=True)
self.assertEqual(res, {'Core': ['c1ccc([*:1])nc1'], 'R1': ['F[*:1]']})
# no change, as removeAllHydrogenRGroupsAndLabels is True
params = RGroupDecompositionParameters()
params.removeAllHydrogenRGroups = False
rgd = RGroupDecomposition(core, params)
self.assertEqual(rgd.Add(mol), 0)
self.assertTrue(rgd.Process())
res = rgd.GetRGroupsAsColumns(asSmiles=True)
self.assertEqual(res, {'Core': ['c1ccc([*:1])nc1'], 'R1': ['F[*:1]']})
# Unused user-defined labels retained on core
# R groups still retained as removeAllHydrogenRGroups is True
params = RGroupDecompositionParameters()
params.removeAllHydrogenRGroupsAndLabels = False
rgd = RGroupDecomposition(core, params)
self.assertEqual(rgd.Add(mol), 0)
self.assertTrue(rgd.Process())
res = rgd.GetRGroupsAsColumns(asSmiles=True)
self.assertEqual(res, {
'Core': ['c1cc([*:1])ncc1[*:2]'],
'R1': ['F[*:1]']
})
# Unused user-defined labels retained on core and in R groups
params = RGroupDecompositionParameters()
params.removeAllHydrogenRGroups = False
params.removeAllHydrogenRGroupsAndLabels = False
rgd = RGroupDecomposition(core, params)
self.assertEqual(rgd.Add(mol), 0)
self.assertTrue(rgd.Process())
res = rgd.GetRGroupsAsColumns(asSmiles=True)
self.assertEqual(res, {
'Core': ['c1cc([*:1])ncc1[*:2]'],
'R1': ['F[*:1]'],
'R2': ['[H][*:2]']
})
