diff --git a/molscore/configs/MolOpt/Albuterol_similarity.json b/molscore/configs/MolOpt/Albuterol_similarity.json index 96f39fd809..ce26d50cd9 100644 --- a/molscore/configs/MolOpt/Albuterol_similarity.json +++ b/molscore/configs/MolOpt/Albuterol_similarity.json @@ -17,7 +17,7 @@ "CC(C)(C)NCC(O)c1ccc(O)c(CO)c1" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": true, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Amlodipine_MPO.json b/molscore/configs/MolOpt/Amlodipine_MPO.json index 36158e8b82..76936245b7 100644 --- a/molscore/configs/MolOpt/Amlodipine_MPO.json +++ b/molscore/configs/MolOpt/Amlodipine_MPO.json @@ -17,7 +17,7 @@ "CCOC(=O)C1=C(COCCN)NC(C)=C(C(=O)OC)C1c1ccccc1Cl" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Celecoxxib_rediscovery.json b/molscore/configs/MolOpt/Celecoxxib_rediscovery.json index 8691b8d929..144a902479 100644 --- a/molscore/configs/MolOpt/Celecoxxib_rediscovery.json +++ b/molscore/configs/MolOpt/Celecoxxib_rediscovery.json @@ -17,7 +17,7 @@ "Cc1ccc(-c2cc(C(F)(F)F)nn2-c2ccc(S(N)(=O)=O)cc2)cc1" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Deco_hop.json b/molscore/configs/MolOpt/Deco_hop.json index e0d80527a7..caa56895dc 100644 --- a/molscore/configs/MolOpt/Deco_hop.json +++ b/molscore/configs/MolOpt/Deco_hop.json @@ -53,7 +53,7 @@ "CCCOc1cc2ncnc(Nc3ccc4ncsc4c3)c2cc1S(=O)(=O)C(C)(C)C" ], "fp": "PHCO", - "bits": 1024, + "bits": 16384, "similarity_measure": "Tanimoto", "method": "mean", "n_jobs": 1 @@ -87,9 +87,9 @@ "modifier": "lin_thresh", "parameters": { "objective": "maximize", - "upper": 0.75, + "upper": 0.85, "lower": 0.0, - "buffer": 0.75 + "buffer": 0.85 } } ] diff --git a/molscore/configs/MolOpt/Fexofenadine_MPO.json b/molscore/configs/MolOpt/Fexofenadine_MPO.json index 5b96a5f695..ddb46126a8 100644 --- a/molscore/configs/MolOpt/Fexofenadine_MPO.json +++ b/molscore/configs/MolOpt/Fexofenadine_MPO.json @@ -17,7 +17,7 @@ "CC(C)(C1=CC=C(C=C1)C(CCCN2CCC(CC2)C(C3=CC=CC=C3)(C4=CC=CC=C4)O)O)C(=O)O" ], "fp": "AP", - "bits": 1024, + "bits": 16384, "similarity_measure": "Tanimoto", "method": "mean", "n_jobs": 1 @@ -53,7 +53,7 @@ "parameters": { "objective": "maximize", "mu": 90.0, - "sigma": 2.0 + "sigma": 10.0 } }, { @@ -63,7 +63,7 @@ "parameters": { "objective": "minimize", "mu": 4.0, - "sigma": 2.0 + "sigma": 1.0 } } ] diff --git a/molscore/configs/MolOpt/Median_molecules_1.json b/molscore/configs/MolOpt/Median_molecules_1.json index f2a97e4236..7d2ba99381 100644 --- a/molscore/configs/MolOpt/Median_molecules_1.json +++ b/molscore/configs/MolOpt/Median_molecules_1.json @@ -17,7 +17,7 @@ "CC1(C)[C@H]2CC[C@]1(C)C(=O)C2" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Median_molecules_2.json b/molscore/configs/MolOpt/Median_molecules_2.json index 2b35b6d8bf..e0aa976a40 100644 --- a/molscore/configs/MolOpt/Median_molecules_2.json +++ b/molscore/configs/MolOpt/Median_molecules_2.json @@ -17,7 +17,7 @@ "CN1CC(=O)N2[C@H](Cc3c([nH]c4ccccc34)[C@H]2c2ccc3c(c2)OCO3)C1=O" ], "radius": 3, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", @@ -33,7 +33,7 @@ "CCCc1nn(C)c2c(=O)[nH]c(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)nc12" ], "radius": 3, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Mestranol_similarity.json b/molscore/configs/MolOpt/Mestranol_similarity.json index 73c5282fd9..2007b6cdba 100644 --- a/molscore/configs/MolOpt/Mestranol_similarity.json +++ b/molscore/configs/MolOpt/Mestranol_similarity.json @@ -17,7 +17,7 @@ "CC12CCC3C(C1CCC2(C#C)O)CCC4=C3C=CC(=C4)OC" ], "fp": "AP", - "bits": 1024, + "bits": 16384, "similarity_measure": "Tanimoto", "method": "mean", "n_jobs": 1 diff --git a/molscore/configs/MolOpt/Osimertinib_MPO.json b/molscore/configs/MolOpt/Osimertinib_MPO.json index 405b838d11..ff57ce3286 100644 --- a/molscore/configs/MolOpt/Osimertinib_MPO.json +++ b/molscore/configs/MolOpt/Osimertinib_MPO.json @@ -17,7 +17,7 @@ "C=CC(=O)Nc1cc(Nc2nccc(-c3cn(C)c4ccccc34)n2)c(OC)cc1N(C)CCN(C)C" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": true, "counts": true, "method": "max", @@ -33,7 +33,7 @@ "C=CC(=O)Nc1cc(Nc2nccc(-c3cn(C)c4ccccc34)n2)c(OC)cc1N(C)CCN(C)C" ], "radius": 3, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", @@ -70,7 +70,7 @@ "parameters": { "objective": "minimize", "mu": 0.85, - "sigma": 2.0 + "sigma": 0.1 } }, { @@ -80,7 +80,7 @@ "parameters": { "objective": "maximize", "mu": 100.0, - "sigma": 2.0 + "sigma": 10.0 } }, { @@ -90,7 +90,7 @@ "parameters": { "objective": "minimize", "mu": 1.0, - "sigma": 2.0 + "sigma": 1.0 } } ] diff --git a/molscore/configs/MolOpt/Perindopril_MPO.json b/molscore/configs/MolOpt/Perindopril_MPO.json index 666e0c0197..2684748445 100644 --- a/molscore/configs/MolOpt/Perindopril_MPO.json +++ b/molscore/configs/MolOpt/Perindopril_MPO.json @@ -17,7 +17,7 @@ "CCCC(C(=O)OCC)NC(C)C(=O)N1C2CCCCC2CC1C(=O)O" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Ranolazine_MPO.json b/molscore/configs/MolOpt/Ranolazine_MPO.json index 26d941191f..6831f68db0 100644 --- a/molscore/configs/MolOpt/Ranolazine_MPO.json +++ b/molscore/configs/MolOpt/Ranolazine_MPO.json @@ -17,7 +17,7 @@ "CC1=C(C(=CC=C1)C)NC(=O)CN2CCN(CC2)CC(COC3=CC=CC=C3OC)O" ], "fp": "AP", - "bits": 1024, + "bits": 16384, "similarity_measure": "Tanimoto", "method": "mean", "n_jobs": 1 diff --git a/molscore/configs/MolOpt/Scaffold_hop.json b/molscore/configs/MolOpt/Scaffold_hop.json index f80b612b70..7c5852fa56 100644 --- a/molscore/configs/MolOpt/Scaffold_hop.json +++ b/molscore/configs/MolOpt/Scaffold_hop.json @@ -26,7 +26,7 @@ "parameters": { "prefix": "S6", "smarts": [ - "[#6]-[#6]-[#6]-[#8]-[#6]\u223c[#6]\u223c[#6]\u223c[#6]\u223c[#6]-[#7]-c1ccc2ncsc2c1" + "[#6]-[#6]-[#6]-[#8]-[#6]~[#6]~[#6]~[#6]~[#6]-[#7]-c1ccc2ncsc2c1" ], "n_jobs": 1, "method": "any" @@ -41,7 +41,7 @@ "CCCOc1cc2ncnc(Nc3ccc4ncsc4c3)c2cc1S(=O)(=O)C(C)(C)C" ], "fp": "PHCO", - "bits": 1024, + "bits": 16384, "similarity_measure": "Tanimoto", "method": "mean", "n_jobs": 1 diff --git a/molscore/configs/MolOpt/Sitagliptin_MPO.json b/molscore/configs/MolOpt/Sitagliptin_MPO.json index 55ba6a377d..dfba80b421 100644 --- a/molscore/configs/MolOpt/Sitagliptin_MPO.json +++ b/molscore/configs/MolOpt/Sitagliptin_MPO.json @@ -17,7 +17,7 @@ "C1CN2C(=NN=C2C(F)(F)F)CN1C(=O)CC(CC3=CC(=C(C=C3F)F)F)N" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Thiothixene_rediscovery.json b/molscore/configs/MolOpt/Thiothixene_rediscovery.json index a0b5b27df5..23d5626cac 100644 --- a/molscore/configs/MolOpt/Thiothixene_rediscovery.json +++ b/molscore/configs/MolOpt/Thiothixene_rediscovery.json @@ -17,7 +17,7 @@ "CN1CCN(CC/C=C2/c3ccccc3Sc3ccc(S(=O)(=O)N(C)C)cc32)CC1" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Troglitazone_rediscovery.json b/molscore/configs/MolOpt/Troglitazone_rediscovery.json index 9135dca36f..739d6b1993 100644 --- a/molscore/configs/MolOpt/Troglitazone_rediscovery.json +++ b/molscore/configs/MolOpt/Troglitazone_rediscovery.json @@ -17,7 +17,7 @@ "Cc1c(C)c2OC(C)(CCc2c(C)c1O)COc1ccc(CC2SC(=O)NC2=O)cc1" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/configs/MolOpt/Zaleplon_MPO.json b/molscore/configs/MolOpt/Zaleplon_MPO.json index 1c5bb6f86e..926a1874cb 100644 --- a/molscore/configs/MolOpt/Zaleplon_MPO.json +++ b/molscore/configs/MolOpt/Zaleplon_MPO.json @@ -17,7 +17,7 @@ "CCN(C(C)=O)c1cccc(-c2ccnc3c(C#N)cnn23)c1" ], "radius": 2, - "bits": 1024, + "bits": 16384, "features": false, "counts": true, "method": "max", diff --git a/molscore/manager.py b/molscore/manager.py index de78eeaede..810bf1647f 100644 --- a/molscore/manager.py +++ b/molscore/manager.py @@ -956,7 +956,6 @@ class MolScoreBenchmark: "GuacaMol_Scaffold": resources.files("molscore.configs.GuacaMol_Scaffold"), "MolOpt": resources.files("molscore.configs.MolOpt"), "MolOpt-CF": resources.files("molscore.configs.MolOpt-CF"), - "MolOpt-DF": resources.files("molscore.configs.MolOpt-DF"), "5HT2A_PhysChem": resources.files("molscore.configs.5HT2A.PhysChem"), "5HT2A_Selectivity": resources.files( "molscore.configs.5HT2A.PIDGIN_Selectivity" diff --git a/molscore/scoring_functions/isomer.py b/molscore/scoring_functions/isomer.py index 48ccf952f8..235364b8a8 100644 --- a/molscore/scoring_functions/isomer.py +++ b/molscore/scoring_functions/isomer.py @@ -51,7 +51,6 @@ def calculate_isomer_score(self, smi): query_formula = Descriptors.rdMolDescriptors.CalcMolFormula(mol) query_elements = self.formula2elements(query_formula) elements = set(self.ref_elements) - elements.update(query_elements) scores = [] # Add per element scores for e in elements: diff --git a/molscore/scoring_functions/legacy_qsar.py b/molscore/scoring_functions/legacy_qsar.py index 9964ac0963..b767eb5c1b 100644 --- a/molscore/scoring_functions/legacy_qsar.py +++ b/molscore/scoring_functions/legacy_qsar.py @@ -48,7 +48,7 @@ class LegacyQSAR(BaseServerSF): resources.files("molscore.data.models.molopt"), "gsk3b.pkl", "legacy_qsar_server.py", - "ECFP6", + "ECFP4", 2048, ), "molopt_GSK3B_current": ( @@ -56,7 +56,7 @@ class LegacyQSAR(BaseServerSF): resources.files("molscore.data.models.molopt"), "gsk3b_current.pkl", "legacy_qsar_server.py", - "ECFP6", + "ECFP4", 2048, ), "molopt_JNK3": ( @@ -64,7 +64,7 @@ class LegacyQSAR(BaseServerSF): resources.files("molscore.data.models.molopt"), "jnk3.pkl", "legacy_qsar_server.py", - "ECFP6", + "ECFP4", 2048, ), "molopt_JNK3_current": ( @@ -72,7 +72,7 @@ class LegacyQSAR(BaseServerSF): resources.files("molscore.data.models.molopt"), "jnk3_current.pkl", "legacy_qsar_server.py", - "ECFP6", + "ECFP4", 2048, ), }