Index

_

__call__() (poli.core.abstract_black_box.AbstractBlackBox method) __del__() (poli.core.abstract_black_box.AbstractBlackBox method) __enter__() (poli.core.abstract_black_box.AbstractBlackBox method) __exit__() (poli.core.abstract_black_box.AbstractBlackBox method) __getattr__() (poli.core.util.external_observer.ExternalObserver method) __init__() (poli.core.abstract_black_box.AbstractBlackBox method) (poli.core.abstract_black_box.NegativeBlackBox method) (poli.core.abstract_problem_factory.AbstractProblemFactory method) (poli.core.abstract_problem_factory.MetaProblemFactory method) (poli.core.chemistry.tdc_black_box.TDCBlackBox method) (poli.core.multi_objective_black_box.MultiObjectiveBlackBox method) (poli.core.proteins.foldx_black_box.FoldxBlackBox method) (poli.core.util.abstract_observer.AbstractObserver method) (poli.core.util.external_observer.ExternalObserver method) (poli.core.util.inter_process_communication.process_wrapper.ProcessWrapper method) (poli.core.util.proteins.foldx.FoldxInterface method) (poli.objective_repository.aloha.register.AlohaBlackBox method) (poli.objective_repository.aloha.register.AlohaProblemFactory method) (poli.objective_repository.dockstring.register.DockstringBlackBox method) (poli.objective_repository.dockstring.register.DockstringProblemFactory method) (poli.objective_repository.drd3_docking.register.DRD3BlackBox method), [1] (poli.objective_repository.drd3_docking.register.DRD3ProblemFactory method) (poli.objective_repository.foldx_sasa.register.FoldXSASABlackBox method) (poli.objective_repository.foldx_sasa.register.FoldXSASAProblemFactory method) (poli.objective_repository.foldx_stability.register.FoldXStabilityBlackBox method) (poli.objective_repository.foldx_stability.register.FoldXStabilityProblemFactory method) (poli.objective_repository.foldx_stability_and_sasa.register.FoldXStabilityAndSASABlackBox method) (poli.objective_repository.foldx_stability_and_sasa.register.FoldXStabilityAndSASAProblemFactory method) (poli.objective_repository.gfp_cbas.abstract_vae_wrapper.AbstractVAEWrapper method) (poli.objective_repository.gfp_cbas.cbas_wrapper.CBASVAEWrapper method) (poli.objective_repository.gfp_cbas.cbas_wrapper.ConvertedTorchVaeDecoder method) (poli.objective_repository.gfp_cbas.cbas_wrapper.ConvertedTorchVaeEncoder method) (poli.objective_repository.gfp_cbas.make_vae.BaseVAE method) (poli.objective_repository.gfp_cbas.make_vae.SimpleVAE method) (poli.objective_repository.gfp_cbas.register.GFPCBasBlackBox method) (poli.objective_repository.gfp_cbas.register.GFPCBasProblemFactory method) (poli.objective_repository.gfp_select.register.GFPSelectionProblemFactory method) (poli.objective_repository.penalized_logp_lambo.register.PenalizedLogPLamboBlackBox method) (poli.objective_repository.penalized_logp_lambo.register.PenalizedLogPLamboProblemFactory method) (poli.objective_repository.rdkit_logp.register.LogPBlackBox method) (poli.objective_repository.rdkit_logp.register.LogPProblemFactory method) (poli.objective_repository.rdkit_qed.register.QEDBlackBox method) (poli.objective_repository.rdkit_qed.register.QEDProblemFactory method) (poli.objective_repository.sa_tdc.register.SABlackBox method) (poli.objective_repository.sa_tdc.register.SAProblemFactory method) (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox method) (poli.objective_repository.toy_continuous_problem.register.ToyContinuousProblemFactory method) (poli.objective_repository.toy_continuous_problem.toy_continuous_problem.ToyContinuousProblem method) (poli.objective_repository.white_noise.register.WhiteNoiseBlackBox method) (poli.objective_repository.white_noise.register.WhiteNoiseProblemFactory method)

__neg__() (poli.core.abstract_black_box.AbstractBlackBox method) _black_box() (poli.core.abstract_black_box.AbstractBlackBox method) (poli.core.multi_objective_black_box.MultiObjectiveBlackBox method) (poli.objective_repository.aloha.register.AlohaBlackBox method) (poli.objective_repository.dockstring.register.DockstringBlackBox method) (poli.objective_repository.foldx_stability.register.FoldXStabilityBlackBox method) (poli.objective_repository.rdkit_logp.register.LogPBlackBox method) (poli.objective_repository.rdkit_qed.register.QEDBlackBox method) (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox method) (poli.objective_repository.white_noise.register.WhiteNoiseBlackBox method) _compute_sasa() (poli.core.util.proteins.foldx.FoldxInterface method) _read_energy() (poli.core.util.proteins.foldx.FoldxInterface method) _repair_if_necessary_and_provide_path() (poli.core.util.proteins.foldx.FoldxInterface method) _simulate_mutations() (poli.core.util.proteins.foldx.FoldxInterface method)

A

AbstractBlackBox (class in poli.core.abstract_black_box) AbstractObserver (class in poli.core.util.abstract_observer) AbstractProblemFactory (class in poli.core.abstract_problem_factory) AbstractVAEWrapper (class in poli.objective_repository.gfp_cbas.abstract_vae_wrapper) ackley_function_01() (in module poli.objective_repository.toy_continuous_problem.definitions) add_padding_to_level() (in module poli.objective_repository.super_mario_bros.level_utils)

AlohaBlackBox (class in poli.objective_repository.aloha.register) AlohaProblemFactory (class in poli.objective_repository.aloha.register) alphabet (poli.objective_repository.aloha.register.AlohaBlackBox attribute) (poli.objective_repository.dockstring.register.DockstringBlackBox attribute) alpine_01() (in module poli.objective_repository.toy_continuous_problem.definitions) alpine_02() (in module poli.objective_repository.toy_continuous_problem.definitions)

B

BaseVAE (class in poli.objective_repository.gfp_cbas.make_vae) batch_size (poli.core.abstract_black_box.AbstractBlackBox attribute) batched() (in module poli.core.util.batch.batch_input) bent_cigar() (in module poli.objective_repository.toy_continuous_problem.definitions)

bounds (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox attribute) brown() (in module poli.objective_repository.toy_continuous_problem.definitions) BudgetExhaustedException build_vae() (in module poli.objective_repository.gfp_cbas.make_vae)

C

camelback_2d() (in module poli.objective_repository.toy_continuous_problem.definitions) cavity_model (in module poli.core.util.proteins.rasp.inner_rasp) CBASVAEWrapper (class in poli.objective_repository.gfp_cbas.cbas_wrapper) chung_reynolds() (in module poli.objective_repository.toy_continuous_problem.definitions) clean_level() (in module poli.objective_repository.super_mario_bros.level_utils) compute_md5_from_filepath() (in module poli.core.util.files.integrity) compute_sasa() (poli.core.util.proteins.foldx.FoldxInterface method) compute_stability() (poli.core.util.proteins.foldx.FoldxInterface method) compute_stability_and_sasa() (poli.core.util.proteins.foldx.FoldxInterface method) construct_optimal_solution() (poli.objective_repository.ehrlich.register.EhrlichBlackBox method) construct_random_motifs() (poli.objective_repository.ehrlich.register.EhrlichBlackBox method) construct_random_offsets() (poli.objective_repository.ehrlich.register.EhrlichBlackBox method) convert_aas_to_idx_array() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing)

convert_idx_array_to_aas() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) convert_mutations_to_sequence() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) ConvertedTorchVaeDecoder (class in poli.objective_repository.gfp_cbas.cbas_wrapper) ConvertedTorchVaeEncoder (class in poli.objective_repository.gfp_cbas.cbas_wrapper) copy_foldx_files() (poli.core.util.proteins.foldx.FoldxInterface method) cosine_mixture() (in module poli.objective_repository.toy_continuous_problem.definitions) create() (in module poli.objective_factory) (poli.objective_repository.aloha.register.AlohaProblemFactory method) (poli.objective_repository.dockstring.register.DockstringProblemFactory method) (poli.objective_repository.ehrlich.register.EhrlichProblemFactory method) (poli.objective_repository.rdkit_qed.register.QEDProblemFactory method) (poli.objective_repository.sa_tdc.register.SAProblemFactory method) create_working_directory() (poli.core.proteins.foldx_black_box.FoldxBlackBox method) cross_in_tray() (in module poli.objective_repository.toy_continuous_problem.definitions)

D

deb_01() (in module poli.objective_repository.toy_continuous_problem.definitions) deb_02() (in module poli.objective_repository.toy_continuous_problem.definitions) deflected_corrugated_spring() (in module poli.objective_repository.toy_continuous_problem.definitions) DockstringBlackBox (class in poli.objective_repository.dockstring.register)

DockstringProblemFactory (class in poli.objective_repository.dockstring.register) download_file_from_github_repository() (in module poli.core.util.files.download_files_from_github) DRD3BlackBox (class in poli.objective_repository.drd3_docking.register) DRD3ProblemFactory (class in poli.objective_repository.drd3_docking.register)

E

easom() (in module poli.objective_repository.toy_continuous_problem.definitions) edits_between_strings() (in module poli.core.util.proteins.mutations) egg_holder() (in module poli.objective_repository.toy_continuous_problem.definitions) EhrlichBlackBox (class in poli.objective_repository.ehrlich.register)

EhrlichProblemFactory (class in poli.objective_repository.ehrlich.register) embed_in (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox attribute) experiment_id (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute) ExternalObserver (class in poli.core.util.external_observer)

F

find_closest_wildtype_pdb_file_to_mutant() (in module poli.core.util.proteins.mutations) finish() (poli.core.util.abstract_observer.AbstractObserver method) (poli.core.util.external_observer.ExternalObserver method) FoldxBlackBox (class in poli.core.proteins.foldx_black_box) FoldxInterface (class in poli.core.util.proteins.foldx) FoldXSASABlackBox (class in poli.objective_repository.foldx_sasa.register) FoldXSASAProblemFactory (class in poli.objective_repository.foldx_sasa.register) FoldXStabilityAndSASABlackBox (class in poli.objective_repository.foldx_stability_and_sasa.register)

FoldXStabilityAndSASAProblemFactory (class in poli.objective_repository.foldx_stability_and_sasa.register) FoldXStabilityBlackBox (class in poli.objective_repository.foldx_stability.register) FoldXStabilityProblemFactory (class in poli.objective_repository.foldx_stability.register) from_selfies (poli.objective_repository.rdkit_logp.register.LogPBlackBox attribute) (poli.objective_repository.rdkit_qed.register.QEDBlackBox attribute) from_smiles (poli.objective_repository.rdkit_logp.register.LogPBlackBox attribute) (poli.objective_repository.rdkit_qed.register.QEDBlackBox attribute) function (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox attribute) function_name (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox attribute)

G

get_argmax() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) get_balaji_predictions() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) get_connection() (in module poli.core.util.inter_process_communication.process_wrapper) get_experimental_X_y() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) get_gfp_base_seq() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing)

get_gfp_X_y_aa() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) get_samples() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) get_sha_for_tag() (in module poli.core.util.files.download_files_from_github) GFPCBasBlackBox (class in poli.objective_repository.gfp_cbas.register) GFPCBasProblemFactory (class in poli.objective_repository.gfp_cbas.register) GFPSelectionProblemFactory (class in poli.objective_repository.gfp_select.register)

I

identity_loss() (in module poli.objective_repository.gfp_cbas.make_vae)

initialize_observer() (poli.core.util.abstract_observer.AbstractObserver method) (poli.core.util.external_observer.ExternalObserver method)

L

level_to_array() (in module poli.objective_repository.super_mario_bros.level_utils) level_to_list() (in module poli.objective_repository.super_mario_bros.level_utils) levels_to_onehot() (in module poli.objective_repository.super_mario_bros.level_utils)

load_config() (in module poli.objective_factory) load_models (in module poli.core.util.proteins.rasp) LogPBlackBox (class in poli.objective_repository.rdkit_logp.register) LogPProblemFactory (class in poli.objective_repository.rdkit_logp.register)

M

make_observer_script() (in module poli.core.util.objective_management.make_run_script) MetaProblemFactory (class in poli.core.abstract_problem_factory) module poli poli.core poli.core.abstract_benchmark poli.core.abstract_black_box poli.core.abstract_isolated_function poli.core.abstract_problem_factory poli.core.benchmark_information poli.core.black_box_information poli.core.chemistry poli.core.chemistry.data_packages poli.core.chemistry.data_packages.random_molecules_data_package poli.core.chemistry.tdc_black_box poli.core.chemistry.tdc_isolated_function poli.core.chemistry.tdc_problem poli.core.data_package poli.core.exceptions poli.core.lambda_black_box poli.core.multi_objective_black_box poli.core.problem poli.core.proteins poli.core.proteins.data_packages poli.core.proteins.data_packages.foldx_supervised_data_packages poli.core.proteins.data_packages.rasp_supervised_data_packages poli.core.proteins.foldx_black_box poli.core.proteins.foldx_isolated_function poli.core.registry poli.core.util poli.core.util.abstract_observer poli.core.util.algorithm_observer_wrapper poli.core.util.alignment poli.core.util.alignment.is_aligned poli.core.util.batch poli.core.util.batch.batch_input poli.core.util.chemistry poli.core.util.chemistry.string_to_molecule poli.core.util.default_observer poli.core.util.external_observer poli.core.util.files poli.core.util.files.download_files_from_github poli.core.util.files.integrity poli.core.util.inter_process_communication poli.core.util.inter_process_communication.process_wrapper poli.core.util.isolation poli.core.util.isolation.external_function poli.core.util.isolation.instancing poli.core.util.isolation.isolated_black_box poli.core.util.objective_management poli.core.util.objective_management.make_run_script poli.core.util.observer_wrapper poli.core.util.proteins poli.core.util.proteins.defaults poli.core.util.proteins.foldx poli.core.util.proteins.mutations poli.core.util.proteins.pdb_parsing poli.core.util.proteins.rasp poli.core.util.proteins.rasp.inner_rasp poli.core.util.seeding poli.core.util.seeding.seeding poli.objective_factory poli.objective_repository poli.objective_repository.albuterol_similarity poli.objective_repository.albuterol_similarity.register poli.objective_repository.aloha poli.objective_repository.aloha.register poli.objective_repository.amlodipine_mpo poli.objective_repository.amlodipine_mpo.register poli.objective_repository.celecoxib_rediscovery poli.objective_repository.celecoxib_rediscovery.register poli.objective_repository.deco_hop poli.objective_repository.deco_hop.register poli.objective_repository.dockstring poli.objective_repository.dockstring.isolated_function poli.objective_repository.dockstring.register poli.objective_repository.drd2_docking poli.objective_repository.drd2_docking.register poli.objective_repository.drd3_docking poli.objective_repository.drd3_docking.register poli.objective_repository.ehrlich poli.objective_repository.ehrlich.register poli.objective_repository.ehrlich_holo poli.objective_repository.ehrlich_holo.isolated_function poli.objective_repository.ehrlich_holo.register poli.objective_repository.fexofenadine_mpo poli.objective_repository.fexofenadine_mpo.register poli.objective_repository.foldx_rfp_lambo poli.objective_repository.foldx_rfp_lambo.information poli.objective_repository.foldx_rfp_lambo.isolated_function poli.objective_repository.foldx_rfp_lambo.register poli.objective_repository.foldx_sasa poli.objective_repository.foldx_sasa.isolated_function poli.objective_repository.foldx_sasa.register poli.objective_repository.foldx_stability poli.objective_repository.foldx_stability.isolated_function poli.objective_repository.foldx_stability.register poli.objective_repository.foldx_stability_and_sasa poli.objective_repository.foldx_stability_and_sasa.isolated_function poli.objective_repository.foldx_stability_and_sasa.register poli.objective_repository.gfp_cbas poli.objective_repository.gfp_cbas.abstract_vae_wrapper poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing poli.objective_repository.gfp_cbas.cbas_wrapper poli.objective_repository.gfp_cbas.gfp_gp poli.objective_repository.gfp_cbas.information poli.objective_repository.gfp_cbas.isolated_function poli.objective_repository.gfp_cbas.make_vae poli.objective_repository.gfp_cbas.register poli.objective_repository.gfp_select poli.objective_repository.gfp_select.information poli.objective_repository.gfp_select.isolated_function poli.objective_repository.gfp_select.register poli.objective_repository.gsk3_beta poli.objective_repository.gsk3_beta.register poli.objective_repository.isomer_c7h8n2o2 poli.objective_repository.isomer_c7h8n2o2.register poli.objective_repository.isomer_c9h10n2o2pf2cl poli.objective_repository.isomer_c9h10n2o2pf2cl.register poli.objective_repository.jnk3 poli.objective_repository.jnk3.register poli.objective_repository.median_1 poli.objective_repository.median_1.register poli.objective_repository.median_2 poli.objective_repository.median_2.register poli.objective_repository.mestranol_similarity poli.objective_repository.mestranol_similarity.register poli.objective_repository.osimetrinib_mpo poli.objective_repository.osimetrinib_mpo.register poli.objective_repository.penalized_logp_lambo poli.objective_repository.penalized_logp_lambo.isolated_function poli.objective_repository.penalized_logp_lambo.register poli.objective_repository.perindopril_mpo poli.objective_repository.perindopril_mpo.register poli.objective_repository.ranolazine_mpo poli.objective_repository.ranolazine_mpo.register poli.objective_repository.rasp poli.objective_repository.rasp.isolated_function poli.objective_repository.rasp.register poli.objective_repository.rdkit_logp poli.objective_repository.rdkit_logp.register poli.objective_repository.rdkit_qed poli.objective_repository.rdkit_qed.register poli.objective_repository.rfp_foldx_stability poli.objective_repository.rfp_foldx_stability.assets poli.objective_repository.rfp_foldx_stability.register poli.objective_repository.rfp_foldx_stability_and_sasa poli.objective_repository.rfp_foldx_stability_and_sasa.register poli.objective_repository.rfp_rasp poli.objective_repository.rfp_rasp.assets poli.objective_repository.rfp_rasp.register poli.objective_repository.rmf_landscape poli.objective_repository.rmf_landscape.isolated_function poli.objective_repository.rmf_landscape.register poli.objective_repository.rosetta_energy poli.objective_repository.rosetta_energy.information poli.objective_repository.rosetta_energy.isolated_function poli.objective_repository.rosetta_energy.register poli.objective_repository.sa_tdc poli.objective_repository.sa_tdc.information poli.objective_repository.sa_tdc.isolated_function poli.objective_repository.sa_tdc.register poli.objective_repository.scaffold_hop poli.objective_repository.scaffold_hop.information poli.objective_repository.scaffold_hop.register poli.objective_repository.sitagliptin_mpo poli.objective_repository.sitagliptin_mpo.information poli.objective_repository.sitagliptin_mpo.register poli.objective_repository.super_mario_bros poli.objective_repository.super_mario_bros.information poli.objective_repository.super_mario_bros.level_utils poli.objective_repository.super_mario_bros.register poli.objective_repository.thiothixene_rediscovery poli.objective_repository.thiothixene_rediscovery.register poli.objective_repository.toy_continuous_problem poli.objective_repository.toy_continuous_problem.definitions poli.objective_repository.toy_continuous_problem.register poli.objective_repository.toy_continuous_problem.toy_continuous_problem poli.objective_repository.troglitazone_rediscovery poli.objective_repository.troglitazone_rediscovery.register poli.objective_repository.valsartan_smarts poli.objective_repository.valsartan_smarts.register poli.objective_repository.white_noise poli.objective_repository.white_noise.register poli.objective_repository.zaleplon_mpo poli.objective_repository.zaleplon_mpo.register poli.tests poli.tests.benchmarks poli.tests.benchmarks.test_benchmark_creation poli.tests.conftest poli.tests.information poli.tests.information.test_dynamic_information poli.tests.observers poli.tests.observers.test_observers poli.tests.registry poli.tests.registry.basic_objectives poli.tests.registry.basic_objectives.test_basic_objectives poli.tests.registry.basic_objectives.test_budget_exhaustion poli.tests.registry.chemistry poli.tests.registry.chemistry.test_chemistry_objectives poli.tests.registry.proteins poli.tests.registry.proteins.test_foldx poli.tests.registry.proteins.test_foldx_rfp_lambo poli.tests.registry.proteins.test_rasp poli.tests.registry.proteins.test_rmf poli.tests.registry.proteins.test_rosetta poli.tests.registry.test_basic_loop_without_create poli.tests.registry.test_force_isolation poli.tests.registry.test_multi_objective_and_negative poli.tests.registry.test_passing_array_of_strings poli.tests.registry.toy_continuous_problems poli.tests.registry.toy_continuous_problems.test_embedding_problems_into_higher_dims poli.tests.registry.toy_continuous_problems.test_instancing_of_toy_continuous_problems poli.tests.registry.toy_discrete_problems poli.tests.registry.toy_discrete_problems.test_ehrlich poli.tests.registry.toy_discrete_problems.test_ehrlich_holo poli.tests.test_core_promises poli.tests.test_data_packages poli.tests.test_lambda_black_box poli.tests.test_seeding poli.tests.util poli.tests.util.test_foldx_interface poli.tests.util.test_protein_utilities

MultiObjectiveBlackBox (class in poli.core.multi_objective_black_box) mutations_from_wildtype_residues_and_mutant() (in module poli.core.util.proteins.mutations)

N

n_dimensions (poli.objective_repository.toy_continuous_problem.register.ToyContinuousBlackBox attribute)

NegativeBlackBox (class in poli.core.abstract_black_box) num_workers (poli.core.abstract_black_box.AbstractBlackBox attribute)

O

objective_functions (poli.core.multi_objective_black_box.MultiObjectiveBlackBox attribute) observe() (poli.core.util.abstract_observer.AbstractObserver method) (poli.core.util.external_observer.ExternalObserver method) observer (poli.core.abstract_black_box.AbstractBlackBox attribute) observer_info (poli.core.abstract_black_box.AbstractBlackBox attribute)

one_hot_encode_aa() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) one_hot_encode_aa_array() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) one_hot_encode_dna() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) onehot_to_levels() (in module poli.objective_repository.super_mario_bros.level_utils) oracle_name (poli.core.chemistry.tdc_black_box.TDCBlackBox attribute) (poli.objective_repository.drd3_docking.register.DRD3BlackBox attribute)

P

parallelize (poli.core.abstract_black_box.AbstractBlackBox attribute) parse_pdb_as_residue_strings() (in module poli.core.util.proteins.pdb_parsing) parse_pdb_as_residues() (in module poli.core.util.proteins.pdb_parsing) parse_pdb_as_structure() (in module poli.core.util.proteins.pdb_parsing) partition_data() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing) PenalizedLogPLamboBlackBox (class in poli.objective_repository.penalized_logp_lambo.register) PenalizedLogPLamboProblemFactory (class in poli.objective_repository.penalized_logp_lambo.register) poli module poli.core module poli.core.abstract_benchmark module poli.core.abstract_black_box module poli.core.abstract_isolated_function module poli.core.abstract_problem_factory module poli.core.benchmark_information module poli.core.black_box_information module poli.core.chemistry module poli.core.chemistry.data_packages module poli.core.chemistry.data_packages.random_molecules_data_package module poli.core.chemistry.tdc_black_box module poli.core.chemistry.tdc_isolated_function module poli.core.chemistry.tdc_problem module poli.core.data_package module poli.core.exceptions module poli.core.lambda_black_box module poli.core.multi_objective_black_box module poli.core.problem module poli.core.proteins module poli.core.proteins.data_packages module poli.core.proteins.data_packages.foldx_supervised_data_packages module poli.core.proteins.data_packages.rasp_supervised_data_packages module poli.core.proteins.foldx_black_box module poli.core.proteins.foldx_isolated_function module poli.core.registry module poli.core.util module poli.core.util.abstract_observer module poli.core.util.algorithm_observer_wrapper module poli.core.util.alignment module poli.core.util.alignment.is_aligned module poli.core.util.batch module poli.core.util.batch.batch_input module poli.core.util.chemistry module poli.core.util.chemistry.string_to_molecule module poli.core.util.default_observer module poli.core.util.external_observer module poli.core.util.files module poli.core.util.files.download_files_from_github module poli.core.util.files.integrity module poli.core.util.inter_process_communication module poli.core.util.inter_process_communication.process_wrapper module poli.core.util.isolation module poli.core.util.isolation.external_function module poli.core.util.isolation.instancing module poli.core.util.isolation.isolated_black_box module poli.core.util.objective_management module poli.core.util.objective_management.make_run_script module poli.core.util.observer_wrapper module poli.core.util.proteins module poli.core.util.proteins.defaults module poli.core.util.proteins.foldx module poli.core.util.proteins.mutations module poli.core.util.proteins.pdb_parsing module poli.core.util.proteins.rasp module poli.core.util.proteins.rasp.inner_rasp module poli.core.util.seeding module poli.core.util.seeding.seeding module poli.objective_factory module poli.objective_repository module poli.objective_repository.albuterol_similarity module poli.objective_repository.albuterol_similarity.register module poli.objective_repository.aloha module poli.objective_repository.aloha.register module poli.objective_repository.amlodipine_mpo module poli.objective_repository.amlodipine_mpo.register module poli.objective_repository.celecoxib_rediscovery module poli.objective_repository.celecoxib_rediscovery.register module poli.objective_repository.deco_hop module poli.objective_repository.deco_hop.register module poli.objective_repository.dockstring module poli.objective_repository.dockstring.isolated_function module poli.objective_repository.dockstring.register module poli.objective_repository.drd2_docking module poli.objective_repository.drd2_docking.register module poli.objective_repository.drd3_docking module poli.objective_repository.drd3_docking.register module poli.objective_repository.ehrlich module poli.objective_repository.ehrlich.register module poli.objective_repository.ehrlich_holo module poli.objective_repository.ehrlich_holo.isolated_function module poli.objective_repository.ehrlich_holo.register module poli.objective_repository.fexofenadine_mpo module poli.objective_repository.fexofenadine_mpo.register module poli.objective_repository.foldx_rfp_lambo module poli.objective_repository.foldx_rfp_lambo.information module poli.objective_repository.foldx_rfp_lambo.isolated_function module poli.objective_repository.foldx_rfp_lambo.register module poli.objective_repository.foldx_sasa module poli.objective_repository.foldx_sasa.isolated_function module poli.objective_repository.foldx_sasa.register module poli.objective_repository.foldx_stability module poli.objective_repository.foldx_stability.isolated_function module poli.objective_repository.foldx_stability.register module poli.objective_repository.foldx_stability_and_sasa module poli.objective_repository.foldx_stability_and_sasa.isolated_function module poli.objective_repository.foldx_stability_and_sasa.register module poli.objective_repository.gfp_cbas module poli.objective_repository.gfp_cbas.abstract_vae_wrapper module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing module poli.objective_repository.gfp_cbas.cbas_wrapper module poli.objective_repository.gfp_cbas.gfp_gp module poli.objective_repository.gfp_cbas.information module poli.objective_repository.gfp_cbas.isolated_function module poli.objective_repository.gfp_cbas.make_vae module poli.objective_repository.gfp_cbas.register module poli.objective_repository.gfp_select module poli.objective_repository.gfp_select.information module poli.objective_repository.gfp_select.isolated_function module

poli.objective_repository.gfp_select.register module poli.objective_repository.gsk3_beta module poli.objective_repository.gsk3_beta.register module poli.objective_repository.isomer_c7h8n2o2 module poli.objective_repository.isomer_c7h8n2o2.register module poli.objective_repository.isomer_c9h10n2o2pf2cl module poli.objective_repository.isomer_c9h10n2o2pf2cl.register module poli.objective_repository.jnk3 module poli.objective_repository.jnk3.register module poli.objective_repository.median_1 module poli.objective_repository.median_1.register module poli.objective_repository.median_2 module poli.objective_repository.median_2.register module poli.objective_repository.mestranol_similarity module poli.objective_repository.mestranol_similarity.register module poli.objective_repository.osimetrinib_mpo module poli.objective_repository.osimetrinib_mpo.register module poli.objective_repository.penalized_logp_lambo module poli.objective_repository.penalized_logp_lambo.isolated_function module poli.objective_repository.penalized_logp_lambo.register module poli.objective_repository.perindopril_mpo module poli.objective_repository.perindopril_mpo.register module poli.objective_repository.ranolazine_mpo module poli.objective_repository.ranolazine_mpo.register module poli.objective_repository.rasp module poli.objective_repository.rasp.isolated_function module poli.objective_repository.rasp.register module poli.objective_repository.rdkit_logp module poli.objective_repository.rdkit_logp.register module poli.objective_repository.rdkit_qed module poli.objective_repository.rdkit_qed.register module poli.objective_repository.rfp_foldx_stability module poli.objective_repository.rfp_foldx_stability.assets module poli.objective_repository.rfp_foldx_stability.register module poli.objective_repository.rfp_foldx_stability_and_sasa module poli.objective_repository.rfp_foldx_stability_and_sasa.register module poli.objective_repository.rfp_rasp module poli.objective_repository.rfp_rasp.assets module poli.objective_repository.rfp_rasp.register module poli.objective_repository.rmf_landscape module poli.objective_repository.rmf_landscape.isolated_function module poli.objective_repository.rmf_landscape.register module poli.objective_repository.rosetta_energy module poli.objective_repository.rosetta_energy.information module poli.objective_repository.rosetta_energy.isolated_function module poli.objective_repository.rosetta_energy.register module poli.objective_repository.sa_tdc module poli.objective_repository.sa_tdc.information module poli.objective_repository.sa_tdc.isolated_function module poli.objective_repository.sa_tdc.register module poli.objective_repository.scaffold_hop module poli.objective_repository.scaffold_hop.information module poli.objective_repository.scaffold_hop.register module poli.objective_repository.sitagliptin_mpo module poli.objective_repository.sitagliptin_mpo.information module poli.objective_repository.sitagliptin_mpo.register module poli.objective_repository.super_mario_bros module poli.objective_repository.super_mario_bros.information module poli.objective_repository.super_mario_bros.level_utils module poli.objective_repository.super_mario_bros.register module poli.objective_repository.thiothixene_rediscovery module poli.objective_repository.thiothixene_rediscovery.register module poli.objective_repository.toy_continuous_problem module poli.objective_repository.toy_continuous_problem.definitions module poli.objective_repository.toy_continuous_problem.register module poli.objective_repository.toy_continuous_problem.toy_continuous_problem module poli.objective_repository.troglitazone_rediscovery module poli.objective_repository.troglitazone_rediscovery.register module poli.objective_repository.valsartan_smarts module poli.objective_repository.valsartan_smarts.register module poli.objective_repository.white_noise module poli.objective_repository.white_noise.register module poli.objective_repository.zaleplon_mpo module poli.objective_repository.zaleplon_mpo.register module poli.tests module poli.tests.benchmarks module poli.tests.benchmarks.test_benchmark_creation module poli.tests.conftest module poli.tests.information module poli.tests.information.test_dynamic_information module poli.tests.observers module poli.tests.observers.test_observers module poli.tests.registry module poli.tests.registry.basic_objectives module poli.tests.registry.basic_objectives.test_basic_objectives module poli.tests.registry.basic_objectives.test_budget_exhaustion module poli.tests.registry.chemistry module poli.tests.registry.chemistry.test_chemistry_objectives module poli.tests.registry.proteins module poli.tests.registry.proteins.test_foldx module poli.tests.registry.proteins.test_foldx_rfp_lambo module poli.tests.registry.proteins.test_rasp module poli.tests.registry.proteins.test_rmf module poli.tests.registry.proteins.test_rosetta module poli.tests.registry.test_basic_loop_without_create module poli.tests.registry.test_force_isolation module poli.tests.registry.test_multi_objective_and_negative module poli.tests.registry.test_passing_array_of_strings module poli.tests.registry.toy_continuous_problems module poli.tests.registry.toy_continuous_problems.test_embedding_problems_into_higher_dims module poli.tests.registry.toy_continuous_problems.test_instancing_of_toy_continuous_problems module poli.tests.registry.toy_discrete_problems module poli.tests.registry.toy_discrete_problems.test_ehrlich module poli.tests.registry.toy_discrete_problems.test_ehrlich_holo module poli.tests.test_core_promises module poli.tests.test_data_packages module poli.tests.test_lambda_black_box module poli.tests.test_seeding module poli.tests.util module poli.tests.util.test_foldx_interface module poli.tests.util.test_protein_utilities module PoliException PrismData (in module poli.core.util.proteins.rasp.inner_rasp) ProcessWrapper (class in poli.core.util.inter_process_communication.process_wrapper)

Q

QEDBlackBox (class in poli.objective_repository.rdkit_qed.register)

QEDProblemFactory (class in poli.objective_repository.rdkit_qed.register)

R

rasp_interface (in module poli.core.util.proteins.rasp) read_gfp_data() (in module poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing)

repair() (poli.core.util.proteins.foldx.FoldxInterface method) reset_evaluation_budget() (poli.core.abstract_black_box.AbstractBlackBox method)

S

SABlackBox (class in poli.objective_repository.sa_tdc.register) SAProblemFactory (class in poli.objective_repository.sa_tdc.register) seed_numpy() (in module poli.core.util.seeding.seeding) seed_python() (in module poli.core.util.seeding.seeding) selfies_to_molecules() (in module poli.core.util.chemistry.string_to_molecule) set_observer() (poli.core.abstract_black_box.AbstractBlackBox method) shifted_sphere() (in module poli.objective_repository.toy_continuous_problem.definitions)

SimpleVAE (class in poli.objective_repository.gfp_cbas.make_vae) smiles_to_molecules() (in module poli.core.util.chemistry.string_to_molecule) start() (in module poli.objective_factory) start_observer_process() (in module poli.core.util.observer_wrapper) strings_to_molecules() (in module poli.core.util.chemistry.string_to_molecule) styblinski_tang() (in module poli.objective_repository.toy_continuous_problem.definitions) summed_categorical_crossentropy() (in module poli.objective_repository.gfp_cbas.make_vae)

T

TDCBlackBox (class in poli.core.chemistry.tdc_black_box) terminate() (poli.core.abstract_black_box.AbstractBlackBox method) test_embed_camelback_into_high_dimensions() (in module poli.tests.registry.toy_continuous_problems.test_embedding_problems_into_higher_dims) test_registering_aloha() (in module poli.tests.registry.basic_objectives.test_basic_objectives) test_registering_white_noise() (in module poli.tests.registry.basic_objectives.test_basic_objectives)

tmp_folder (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute) ToyContinuousBlackBox (class in poli.objective_repository.toy_continuous_problem.register) ToyContinuousProblem (class in poli.objective_repository.toy_continuous_problem.toy_continuous_problem) ToyContinuousProblemFactory (class in poli.objective_repository.toy_continuous_problem.register) translate_selfies_to_smiles() (in module poli.core.util.chemistry.string_to_molecule) translate_smiles_to_selfies() (in module poli.core.util.chemistry.string_to_molecule)

V

vectorized() (in module poli.objective_repository.super_mario_bros.level_utils)

verbose (poli.core.util.proteins.foldx.FoldxInterface attribute)

W

WhiteNoiseBlackBox (class in poli.objective_repository.white_noise.register) WhiteNoiseProblemFactory (class in poli.objective_repository.white_noise.register) wildtype_amino_acids (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute) wildtype_pdb_paths (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute)

wildtype_residue_strings (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute) wildtype_residues (poli.core.proteins.foldx_black_box.FoldxBlackBox attribute) working_dir (poli.core.util.proteins.foldx.FoldxInterface attribute) write_mutations_to_file() (poli.core.util.proteins.foldx.FoldxInterface method)