poli.objective_repository

poli.objective_repository#

All objective factories and black boxes inside poli.

Functions

get_problems()

Modules

`poli.objective_repository.albuterol_similarity`
`poli.objective_repository.aloha`	The ALOHA objective factory and function.
`poli.objective_repository.amlodipine_mpo`
`poli.objective_repository.celecoxib_rediscovery`
`poli.objective_repository.deco_hop`
`poli.objective_repository.dockstring`	Dockstring objective factory and function.
`poli.objective_repository.drd2_docking`
`poli.objective_repository.drd3_docking`	A wrapper around TDC's DRD3 docking objective function.
`poli.objective_repository.ehrlich`
`poli.objective_repository.ehrlich_holo`	A closed-form black box simulating epistatic effects [1].
`poli.objective_repository.fexofenadine_mpo`
`poli.objective_repository.foldx_rfp_lambo`	A wrapper around the RFP task of LamBO [1].
`poli.objective_repository.foldx_sasa`	A black box function for solvent accessible surface area (SASA) prediction.
`poli.objective_repository.foldx_stability`	Black box objective factory and function for FoldX stability.
`poli.objective_repository.foldx_stability_and_sasa`	A black box for computing stability and solvent accessible surface area (SASA) using FoldX.
`poli.objective_repository.gfp_cbas`
`poli.objective_repository.gfp_select`
`poli.objective_repository.gsk3_beta`
`poli.objective_repository.isomer_c7h8n2o2`
`poli.objective_repository.isomer_c9h10n2o2pf2cl`
`poli.objective_repository.jnk3`
`poli.objective_repository.median_1`
`poli.objective_repository.median_2`
`poli.objective_repository.mestranol_similarity`
`poli.objective_repository.osimetrinib_mpo`
`poli.objective_repository.penalized_logp_lambo`	The exact same computation of LogP used by LamBO.
`poli.objective_repository.perindopril_mpo`
`poli.objective_repository.ranolazine_mpo`
`poli.objective_repository.rasp`
`poli.objective_repository.rdkit_logp`	Log-solubility (LogP) computed using RDKit.
`poli.objective_repository.rdkit_qed`	Quantitative Estimate of Druglikeness (QED) using RDKit.
`poli.objective_repository.rfp_foldx_stability`
`poli.objective_repository.rfp_foldx_stability_and_sasa`	A black box for computing stability and solvent accessible surface area (SASA) using FoldX on a particular RFP problem with a defined Pareto front.
`poli.objective_repository.rfp_rasp`
`poli.objective_repository.rmf_landscape`	Rough Mount Fuji (RMF) fitness landscapes w/ tunable ruggedness using Numpy. See J Neidhart, IG Szendro, J Krug Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model. Genetics 2014 . DOI: https://doi.org/10.1534/genetics.114.167668 See Aita et al. Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin. Biopolymers 2000 . DOI: https://doi.org/10.1002/(SICI)1097-0282(200007)54:1<64::AID-BIP70>3.0.CO;2-R.
`poli.objective_repository.rosetta_energy`
`poli.objective_repository.sa_tdc`	A wrapper around the synthetic accessiblity (SA) oracle of TDC.
`poli.objective_repository.scaffold_hop`
`poli.objective_repository.sitagliptin_mpo`
`poli.objective_repository.super_mario_bros`	A toy problem avout creating Super Mario Bros levels.
`poli.objective_repository.thiothixene_rediscovery`
`poli.objective_repository.toy_continuous_problem`	A collection of toy continuous functions for optimization.
`poli.objective_repository.troglitazone_rediscovery`
`poli.objective_repository.valsartan_smarts`
`poli.objective_repository.white_noise`	A toy problem that returns white noise.
`poli.objective_repository.zaleplon_mpo`