├── .DS_Store ├── .github ├── .DS_Store └── workflows │ ├── .DS_Store │ └── test.yml ├── .vscode └── settings.json ├── LICENSE ├── MANIFEST.in ├── README.md ├── data ├── .DS_Store ├── Anderson_MPH_CaPTM.csv ├── Anderson_MPH_CdPTM.csv ├── Anderson_MPH_CoPTM.csv ├── Anderson_MPH_CuPTM.csv ├── Anderson_MPH_MgPTM.csv ├── Anderson_MPH_MnPTM.csv ├── Bakerlee2022_hap_37C.csv ├── Bakerlee2022_hap_4NQO.csv ├── Bakerlee2022_hap_YPDA.csv ├── Bakerlee2022_hap_gu.csv ├── Bakerlee2022_hap_salt.csv ├── Bakerlee2022_hap_suloc.csv ├── Bakerlee2022_hom_37C.csv ├── Bakerlee2022_hom_4NQO.csv ├── Bakerlee2022_hom_YPDA.csv ├── Bakerlee2022_hom_gu.csv ├── Bakerlee2022_hom_salt.csv ├── Bakerlee2022_hom_suloc.csv ├── Bank2016a.csv ├── Bank2016b.csv ├── Bendixsen2019_hdv.csv ├── Bendixsen2019_ligase.csv ├── Bridgham2009.csv ├── Centurion2019.csv ├── Chou2011.csv ├── Diaz-Colunga_colorants.csv ├── Diaz-Colunga_pseudo.csv ├── Domingo2018.csv ├── Frohlich21_OXA-48_ic50_CAZtraj1.csv ├── Frohlich21_OXA-48_ic50_CAZtraj2.csv ├── Frohlich21_OXA-48_ic50_CAZtraj3.csv ├── Frohlich21_OXA-48_ic50_PIPtraj1.csv ├── Frohlich21_OXA-48_ic50_PIPtraj2.csv ├── Frohlich21_OXA-48_ic50_PIPtraj3.csv ├── Guerrero2019_C_muridarum_GroEL.csv ├── Guerrero2019_C_muridarum_LON.csv ├── Guerrero2019_C_muridarum_WT.csv ├── Guerrero2019_E_coli_GroEL.csv ├── Guerrero2019_E_coli_LON.csv ├── Guerrero2019_E_coli_WT.csv ├── Guerrero2019_L_grayi_GroEL.csv ├── Guerrero2019_L_grayi_LON.csv ├── Guerrero2019_L_grayi_WT.csv ├── Hall2010_diploid.csv ├── Hall2010_haploid.csv ├── Hall2019_Acetate.csv ├── Hall2019_Beef.csv ├── Hall2019_Casamino.csv ├── Hall2019_Glucose.csv ├── Hall2019_Milk.csv ├── Hall2019_NAG.csv ├── Hall2019_Rhamnose.csv ├── Hall2019_Trypsin.csv ├── Hall2020_NfsA_ec50_2039.csv ├── Hall2020_NfsA_ec50_3637.csv ├── Jalal2020_NBS.csv ├── Jalal2020_parS.csv ├── Johnston2024_TrpB3A.csv ├── Johnston2024_TrpB3B.csv ├── Johnston2024_TrpB3C.csv ├── Johnston2024_TrpB3D.csv ├── Johnston2024_TrpB3E.csv ├── Johnston2024_TrpB3F.csv ├── Johnston2024_TrpB3G.csv ├── Johnston2024_TrpB3H.csv ├── Johnston2024_TrpB3I.csv ├── Johnston2024_TrpB4.csv ├── Khan2011Flynn2013_DM25.csv ├── Khan2011Flynn2013_DM25_EGTA.csv ├── Khan2011Flynn2013_DM25_guanazole.csv ├── Kuo2020.csv ├── Lite2020_ParD2.csv ├── Lite2020_ParD3.csv ├── Lozovsky2009Jiang2013_Jiang2013.csv ├── Lozovsky2009Jiang2013_Lozovsky2009.csv ├── Lozovsky_DHFR_ic50_c57.csv ├── Lozovsky_DHFR_ic50_c58.csv ├── Lozovsky_DHFR_ic50_c59.csv ├── Lozovsky_DHFR_ic50_c60.csv ├── Lozovsky_DHFR_ic50_c61.csv ├── Lunzer2005_fitness.csv ├── Lunzer2005_nad.csv ├── Lunzer2005_nadp.csv ├── Malcolm1990.csv ├── Meini2015.csv ├── Michael2024_LamB.csv ├── Michael2024_Lspec.csv ├── Michael2024_OmpF.csv ├── Michael2024_Ospec.csv ├── Michael2024_base.csv ├── Mira2015_TEM_AM.csv ├── Mira2015_TEM_AMC.csv ├── Mira2015_TEM_AMP.csv ├── Mira2015_TEM_CAZ.csv ├── Mira2015_TEM_CEC.csv ├── Mira2015_TEM_CPD.csv ├── Mira2015_TEM_CPR.csv ├── Mira2015_TEM_CRO.csv ├── Mira2015_TEM_CTT.csv ├── Mira2015_TEM_CTX.csv ├── Mira2015_TEM_CXM.csv ├── Mira2015_TEM_FEP.csv ├── Mira2015_TEM_SAM.csv ├── Mira2015_TEM_TZP.csv ├── Mira2015_TEM_ZOX.csv ├── Moulana2022_ACE2.csv ├── Moulana2023_CB6.csv ├── Moulana2023_CoV555.csv ├── Moulana2023_REGN10987.csv ├── Moulana2023_S309.csv ├── NEW_Chen2023_CreiLOV.csv ├── NEW_Rotrattanadumrong2022_F1*U(m)_Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.csv ├── Ogbunugafor22_cyc.csv ├── Ogbunugafor22_pyr.csv ├── Palmer2015.csv ├── Palmer_DHFR_ic75.csv ├── Papkou2023_DHFR.csv ├── Phillips2021_CR6261_h1.csv ├── Phillips2021_CR6261_h9.csv ├── Phillips2021_CR9114_fluB.csv ├── Phillips2021_CR9114_h1.csv ├── Phillips2021_CR9114_h3.csv ├── Phillips2023_G189E.csv ├── Phillips2023_MA90.csv ├── Phillips2023_SI06.csv ├── Podgornaia2015_PhoQ.csv ├── Poelwijk2019.csv ├── Schulz2025.csv ├── Skwara2023_Butyrate.csv ├── Skwara2023_GE_biomass.csv ├── Skwara2023_Kehe_data.csv ├── Skwara2023_Langenheder.csv ├── Skwara2023_pyoverdine.csv ├── Skwara2023_starch_data.csv ├── Soo2021_30C.csv ├── Soo2021_37C.csv ├── Sunden_AP.csv ├── Tamer_DHFR_kcat_trajg.csv ├── Tamer_DHFR_kcat_trajr.csv ├── Tamer_DHFR_ki_trajg.csv ├── Tamer_DHFR_ki_trajr.csv ├── Tu2022_T7.csv ├── Tu2022_TEV.csv ├── Weinreich2006Tan2011_Tan2011.csv ├── Weinreich2006Tan2011_Weinreich2006.csv ├── Westmann2024.csv ├── Whitlock2000.csv ├── Wong2018_brca2.csv ├── Wong2018_ikbkap.csv ├── Wong2018_smn1.csv ├── Wu2016_GB1.csv ├── Wu2020_Bei89.csv ├── Wu2020_Bk79.csv ├── Wu2020_Bris07L194.csv ├── Wu2020_Bris07P194.csv ├── Wu2020_HK68.csv ├── Wu2020_Mos99.csv ├── Wu2020_NDako16.csv ├── [unpublished] A complete map of specificity encoding for a partially fuzzy protein interaction │ └── datacard.rtf ├── daSilva2010_CCR5.csv ├── daSilva2010_CXCR5.csv ├── deVisser2009.csv ├── new_PTE_catact_2NH.csv └── new_PTE_catact_butyrate.csv ├── dist ├── graphfla-0.1.0-py3-none-any.whl └── graphfla-0.1.0.tar.gz ├── graphfla.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── graphfla ├── .DS_Store ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-38.pyc │ ├── __init__.cpython-39.pyc │ ├── _base.cpython-310.pyc │ ├── _base.cpython-39.pyc │ ├── _neighbors.cpython-310.pyc │ ├── _neighbors.cpython-38.pyc │ ├── _neighbors.cpython-39.pyc │ ├── _processor.cpython-310.pyc │ ├── _processor.cpython-38.pyc │ ├── _processor.cpython-39.pyc │ ├── algorithms.cpython-310.pyc │ ├── algorithms.cpython-39.pyc │ ├── base.cpython-310.pyc │ ├── base2.cpython-310.pyc │ ├── distances.cpython-310.pyc │ ├── distances.cpython-38.pyc │ ├── distances.cpython-39.pyc │ ├── filters.cpython-310.pyc │ ├── filters.cpython-38.pyc │ ├── filters.cpython-39.pyc │ ├── landscape.cpython-310.pyc │ ├── landscape.cpython-38.pyc │ ├── landscape.cpython-39.pyc │ ├── landscape_copy.cpython-310.pyc │ ├── lon.cpython-310.pyc │ ├── lon.cpython-38.pyc │ ├── lon.cpython-39.pyc │ ├── metrics.cpython-310.pyc │ ├── metrics.cpython-39.pyc │ ├── neighbors.cpython-310.pyc │ ├── problems.cpython-310.pyc │ ├── problems.cpython-39.pyc │ ├── sampling.cpython-310.pyc │ ├── utils.cpython-310.pyc │ ├── utils.cpython-38.pyc │ ├── utils.cpython-39.pyc │ ├── visualization.cpython-310.pyc │ └── visualization.cpython-39.pyc ├── _neighbors.py ├── _processor.py ├── algorithms │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── adaptive_walk.cpython-310.pyc │ │ ├── adaptive_walk.cpython-38.pyc │ │ ├── adaptive_walk.cpython-39.pyc │ │ ├── random_walk.cpython-310.pyc │ │ ├── random_walk.cpython-38.pyc │ │ └── random_walk.cpython-39.pyc │ ├── adaptive_walk.py │ └── random_walk.py ├── analysis │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── correlation.cpython-310.pyc │ │ ├── correlation.cpython-38.pyc │ │ ├── correlation.cpython-39.pyc │ │ ├── epistasis.cpython-310.pyc │ │ ├── epistasis.cpython-38.pyc │ │ ├── epistasis.cpython-39.pyc │ │ ├── fitness.cpython-310.pyc │ │ ├── fitness.cpython-38.pyc │ │ ├── fitness.cpython-39.pyc │ │ ├── navigability.cpython-310.pyc │ │ ├── navigability.cpython-38.pyc │ │ ├── navigability.cpython-39.pyc │ │ ├── robustness.cpython-310.pyc │ │ ├── robustness.cpython-38.pyc │ │ ├── robustness.cpython-39.pyc │ │ ├── ruggedness.cpython-310.pyc │ │ ├── ruggedness.cpython-38.pyc │ │ └── ruggedness.cpython-39.pyc │ ├── correlation.py │ ├── epistasis.py │ ├── fitness.py │ ├── navigability.py │ ├── robustness.py │ └── ruggedness.py ├── distances.py ├── filters.py ├── landscape │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── boolean.cpython-310.pyc │ │ ├── dna.cpython-310.pyc │ │ ├── landscape.cpython-310.pyc │ │ ├── protein.cpython-310.pyc │ │ ├── rna.cpython-310.pyc │ │ └── sequence.cpython-310.pyc │ ├── boolean.py │ ├── dna.py │ ├── landscape.py │ ├── protein.py │ ├── rna.py │ └── sequence.py ├── lon.py ├── plotting │ ├── __init__.py │ └── plotting.py ├── problems │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── base.cpython-310.pyc │ │ ├── base_problem.cpython-310.pyc │ │ ├── base_problem.cpython-38.pyc │ │ ├── base_problem.cpython-39.pyc │ │ ├── biological.cpython-310.pyc │ │ ├── biological.cpython-38.pyc │ │ ├── biological.cpython-39.pyc │ │ ├── combinatorial.cpython-310.pyc │ │ ├── combinatorial.cpython-38.pyc │ │ └── combinatorial.cpython-39.pyc │ ├── base_problem.py │ ├── biological.py │ └── combinatorial.py ├── sampling.py └── utils.py ├── images └── landscape.jpg ├── pyproject.toml ├── requirements.txt ├── setup.py ├── tests ├── __pycache__ │ ├── test.cpython-310-pytest-8.3.5.pyc │ ├── test.cpython-38-pytest-8.3.5.pyc │ ├── test.cpython-39-pytest-8.3.5.pyc │ └── 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