Index A | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W | Z A Acquisition (class in illumination.mechanism) acquisition_value (illumination.base.Molecule attribute) active() (illumination.infrastructure.Controller method) add_fitness_calls() (illumination.infrastructure.Controller method) add_to_archive() (illumination.infrastructure.Archive method) add_to_prior_data() (illumination.functions.surrogate.Fingerprint_Surrogate method) (illumination.functions.surrogate.String_Surrogate method) apply_acquisition() (illuminate.Illuminate method) Arbiter (class in illumination.infrastructure) Archive (class in illumination.infrastructure) C calculate_acquisition_value() (illumination.functions.acquisition.Expected_Improvement method) (illumination.functions.acquisition.Log_Expected_Improvement method) (illumination.functions.acquisition.Posterior_Mean method) (illumination.functions.acquisition.Upper_Confidence_Bound method) calculate_descriptors() (illuminate.Illuminate method) calculate_encodings() (illumination.functions.surrogate.Fingerprint_Surrogate method) (illumination.functions.surrogate.String_Surrogate method) calculate_fitnesses() (illuminate.Illuminate method) calculate_statistics() (illumination.infrastructure.Controller method) calculate_surrogate_metrics() (illumination.infrastructure.Controller method) Controller (class in illumination.infrastructure) coordinate_extractor() (illumination.functions.fitness.Zernike_Fitness method) Crossover (class in illumination.operations) cvt_index() (illumination.infrastructure.Archive method) D Descriptor (class in illumination.mechanism) descriptor (illumination.base.Molecule attribute) E Elite (class in illumination.base) Expected_Improvement (class in illumination.functions.acquisition) F Fingerprint_Fitness (class in illumination.functions.fitness) Fingerprint_Surrogate (class in illumination.functions.surrogate) fitness (illumination.base.Molecule attribute) fragment() (illumination.operations.Crossover method) G Gaucamol_Fitness (class in illumination.functions.fitness) Generator (class in illumination.operations) get_archive_data() (illumination.infrastructure.Controller method) get_ECFP4() (illumination.functions.fitness.Fingerprint_Fitness method) get_ECFP6() (illumination.functions.fitness.Fingerprint_Fitness method) get_FCFP4() (illumination.functions.fitness.Fingerprint_Fitness method) get_FCFP6() (illumination.functions.fitness.Fingerprint_Fitness method) get_fingerprint() (illumination.functions.fitness.Fingerprint_Fitness method) get_zernike() (illumination.functions.fitness.Zernike_Fitness method) H hologenicity() (illumination.infrastructure.Arbiter static method) I illuminate module Illuminate (class in illuminate) initial_population() (illuminate.Illuminate method) invariants() (illumination.functions.fitness.Zernike_Fitness method) L launch() (in module illuminate) load_from_database() (illumination.operations.Generator method) Log_Expected_Improvement (class in illumination.functions.acquisition) M merge() (illumination.operations.Crossover method) module illuminate Molecule (class in illumination.base) molecule_filter() (illumination.infrastructure.Arbiter method) Mutator (class in illumination.operations) N niche_index (illumination.base.Molecule attribute) O OVC_Fitness (class in illumination.functions.fitness) P pedigree (illumination.base.Molecule attribute) Posterior_Mean (class in illumination.functions.acquisition) predicted_fitness (illumination.base.Molecule attribute) predicted_uncertainty (illumination.base.Molecule attribute) process_molecules() (illuminate.Illuminate method) R rescale() (illumination.mechanism.Descriptor static method) ring_infraction() (illumination.infrastructure.Arbiter static method) S sa_score (illumination.base.Molecule attribute) sample() (illumination.infrastructure.Archive method) sample_pairs() (illumination.infrastructure.Archive method) set_archive() (illumination.infrastructure.Controller method) (illumination.operations.Generator method) smiles (illumination.base.Molecule attribute) store_molecules() (illumination.infrastructure.Controller method) store_statistics() (illumination.infrastructure.Controller method) String_Surrogate (class in illumination.functions.surrogate) Surrogate (class in illumination.mechanism) T toxicity() (illumination.infrastructure.Arbiter method) U unique_molecules() (illumination.infrastructure.Arbiter method) unsigned_invariants() (illumination.functions.fitness.Zernike_Fitness method) update() (illumination.base.Elite method) (illumination.infrastructure.Controller method) update_niche_index() (illumination.infrastructure.Archive method) Upper_Confidence_Bound (class in illumination.functions.acquisition) USR_Fitness (class in illumination.functions.fitness) USRCAT_Fitness (class in illumination.functions.fitness) V veber_infraction() (illumination.infrastructure.Arbiter static method) W write_statistics() (illumination.infrastructure.Controller method) Z Zernike_Fitness (class in illumination.functions.fitness)