├── ActiveSiteDesign.py ├── Analysis.py ├── BaseClases.py ├── Constants.py ├── Constants.pyc ├── Docking.py ├── Energy.pyx ├── Gradient.pyx ├── IO.py ├── LICENSE ├── LoopDesign.py ├── MDSimulations.py ├── MiscellaneousUtilityFunctions.py ├── MoversRosetta.py ├── PlotDifference.py ├── PlotSimulation.py ├── README.md ├── Setup.py ├── Templatized_control_file ├── DesignCatalyticSite.yaml ├── Input_file.pdb ├── Insilico_directedevolution.yaml ├── LIG.fa.params ├── TOC.png ├── Templatized_control_file.tar ├── molfile_to_params.py └── parm.sh ├── __init__.py ├── asitedesign.yaml └── example ├── chymotripsin ├── 1afq-Mut.pdb ├── 1afq.pdb ├── AS.pdb ├── AS.png ├── ZZZ.cen.params ├── ZZZ.fa.params ├── ZZZ.mol2 ├── ZZZ_0001.cen.pdb ├── ZZZ_0001.fa.pdb ├── catalytic.yaml ├── getParm.sh └── tripsin_final_pose │ ├── tripsin_I_N0_-854.9.pdb │ ├── tripsin_I_N1_-850.8.pdb │ └── tripsin_I_N2_-848.2.pdb └── esterase ├── 1VA4-wt-min.pdb ├── Figure_1.png ├── PEF.out ├── VS1.cen.params ├── VS1.fa.params ├── VS1.mol2 ├── VS1_0001.cen.pdb ├── VS1_0001.fa.pdb ├── VS1_SCCoupling-005_final_pose ├── VS1_SCCoupling-005_I_N0_-3152.1.pdb ├── VS1_SCCoupling-005_I_N10_-3138.2.pdb ├── VS1_SCCoupling-005_I_N11_-3138.1.pdb ├── VS1_SCCoupling-005_I_N12_-3137.9.pdb ├── VS1_SCCoupling-005_I_N13_-3137.8.pdb ├── VS1_SCCoupling-005_I_N14_-3134.9.pdb ├── VS1_SCCoupling-005_I_N15_-3133.2.pdb ├── VS1_SCCoupling-005_I_N16_-3132.0.pdb ├── VS1_SCCoupling-005_I_N17_-3130.4.pdb ├── VS1_SCCoupling-005_I_N18_-3129.9.pdb ├── VS1_SCCoupling-005_I_N19_-3129.4.pdb ├── VS1_SCCoupling-005_I_N1_-3149.4.pdb ├── VS1_SCCoupling-005_I_N20_-3128.8.pdb ├── VS1_SCCoupling-005_I_N2_-3147.4.pdb ├── VS1_SCCoupling-005_I_N3_-3146.9.pdb ├── VS1_SCCoupling-005_I_N4_-3146.0.pdb ├── VS1_SCCoupling-005_I_N5_-3144.2.pdb ├── VS1_SCCoupling-005_I_N6_-3144.1.pdb ├── VS1_SCCoupling-005_I_N7_-3139.8.pdb ├── VS1_SCCoupling-005_I_N8_-3138.6.pdb └── VS1_SCCoupling-005_I_N9_-3138.5.pdb ├── clusters_AS1.0_LIG2.0_Final_PEF.out ├── input.yaml ├── 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