예제 #1
0
def goal_directed_suite_v1() -> List[GoalDirectedBenchmark]:
    max_logP = 6.35584
    return [
        isomers_c11h24(mean_function='arithmetic'),
        isomers_c7h8n2o2(mean_function='arithmetic'),
        isomers_c9h10n2o2pf2cl(mean_function='arithmetic', n_samples=100),
        hard_cobimetinib(max_logP=max_logP),
        hard_osimertinib(ArithmeticMeanScoringFunction),
        hard_fexofenadine(ArithmeticMeanScoringFunction),
        weird_physchem(),

        # start pop benchmark
        # e.g.
        start_pop_ranolazine(),

        # similarity Benchmarks

        # explicit rediscovery
        similarity(
            smiles='CC1=CC=C(C=C1)C1=CC(=NN1C1=CC=C(C=C1)S(N)(=O)=O)C(F)(F)F',
            name='Celecoxib',
            fp_type='ECFP4',
            threshold=1.0,
            rediscovery=True),
        similarity(
            smiles='Cc1c(C)c2OC(C)(COc3ccc(CC4SC(=O)NC4=O)cc3)CCc2c(C)c1O',
            name='Troglitazone',
            fp_type='ECFP4',
            threshold=1.0,
            rediscovery=True),
        similarity(
            smiles='CN(C)S(=O)(=O)c1ccc2Sc3ccccc3C(=CCCN4CCN(C)CC4)c2c1',
            name='Thiothixene',
            fp_type='ECFP4',
            threshold=1.0,
            rediscovery=True),

        # generate similar stuff
        similarity(smiles='Clc4cccc(N3CCN(CCCCOc2ccc1c(NC(=O)CC1)c2)CC3)c4Cl',
                   name='Aripiprazole',
                   fp_type='FCFP4',
                   threshold=0.75),
        similarity(smiles='CC(C)(C)NCC(O)c1ccc(O)c(CO)c1',
                   name='Albuterol',
                   fp_type='FCFP4',
                   threshold=0.75),
        similarity(
            smiles=
            'COc1ccc2[C@H]3CC[C@@]4(C)[C@@H](CC[C@@]4(O)C#C)[C@@H]3CCc2c1',
            name='Mestranol',
            fp_type='AP',
            threshold=0.75),
        logP_benchmark(target=-1.0),
        logP_benchmark(target=8.0),
        tpsa_benchmark(target=150.0),
        cns_mpo(max_logP=max_logP),
        qed_benchmark(),
        median_camphor_menthol(ArithmeticMeanScoringFunction)
    ]
예제 #2
0
def goal_directed_suite_trivial() -> List[GoalDirectedBenchmark]:
    """
    Trivial goal-directed benchmarks from the paper.
    """
    return [
        logP_benchmark(target=-1.0),
        logP_benchmark(target=8.0),
        tpsa_benchmark(target=150.0),
        cns_mpo(),
        qed_benchmark(),
        isomers_c7h8n2o2(),
        pioglitazone_mpo(),
    ]