├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── README.md ├── RGA.py ├── RunAutogrow.py ├── accessory_scripts ├── README.md ├── __init__.py ├── convert_directory_ligands_pdb_to_smi.py ├── convert_single_ligand_pdbqt_to_pdb.py ├── convert_vina_docked_pdbqt_to_pdbs.py ├── file_concatenate_and_compression.py ├── fragmenter_of_smi_mol.py ├── make_lineage_figures.py ├── plot_autogrow_run.py ├── remove_duplicates_from_smi.sh ├── support_scripts │ ├── Multiprocess.py │ ├── __init__.py │ └── mol_object_handling.py └── test_complementary_mol_library.py ├── autogrow ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ └── model.cpython-37.pyc ├── autogrow_main_execute.py ├── docking │ ├── __init__.py │ ├── concatenate_files.py │ ├── delete_failed_mol.py │ ├── docking_class │ │ ├── __init__.py │ │ ├── docking_class_children │ │ │ ├── __init__.py │ │ │ ├── quick_vina_2_docking.py │ │ │ └── vina_docking.py │ │ ├── docking_file_conversion │ │ │ ├── __init__.py │ │ │ ├── convert_with_mgltools.py │ │ │ └── convert_with_obabel.py │ │ ├── get_child_class.py │ │ ├── parent_dock_class.py │ │ └── parent_pdbqt_converter.py │ ├── docking_executables │ │ ├── README │ │ ├── q_vina_2 │ │ │ ├── LICENSE │ │ │ ├── LICENSE Qvina │ │ │ ├── README.md │ │ │ ├── q_vina_2_1_linux │ │ │ │ ├── LICENSE │ │ │ │ ├── LICENSE Qvina │ │ │ │ ├── README.md │ │ │ │ ├── qvina-w │ │ │ │ ├── qvina02 │ │ │ │ ├── qvina2.1 │ │ │ │ ├── qvina_split02 │ │ │ │ ├── vina │ │ │ │ └── vina_split │ │ │ └── q_vina_2_1_mac │ │ │ │ ├── LICENSE │ │ │ │ ├── LICENSE Qvina │ │ │ │ ├── qvina2.1 │ │ │ │ └── qvina2.1_split │ │ └── vina │ │ │ ├── README │ │ │ ├── autodock_vina_1_1_2_linux_x86 │ │ │ ├── README │ │ │ └── bin │ │ │ │ ├── LICENSE │ │ │ │ ├── vina │ │ │ │ └── vina_split │ │ │ ├── autodock_vina_1_1_2_mac │ │ │ ├── LICENSE │ │ │ └── bin │ │ │ │ ├── vina │ │ │ │ └── vina_split │ │ │ └── autodock_vina_1_1_2_win32.msi │ ├── execute_docking.py │ ├── ranking │ │ ├── __init__.py │ │ ├── ranking_mol.py │ │ └── selecting │ │ │ ├── __init__.py │ │ │ ├── rank_selection.py │ │ │ ├── roulette_selection.py │ │ │ └── tournament_selection.py │ └── scoring │ │ ├── __init__.py │ │ ├── execute_scoring_mol.py │ │ ├── nn_score_exe │ │ ├── __init__.py │ │ ├── nnscore1 │ │ │ ├── CHANGELOG.md │ │ │ ├── CONTRIBUTORS.md │ │ │ ├── NNScore.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── examples │ │ │ │ ├── myligand.pdbqt │ │ │ │ ├── myreceptor.pdbqt │ │ │ │ └── run.sh │ │ │ ├── gpl-3.0.txt │ │ │ └── networks │ │ │ │ ├── top_24_networks │ │ │ │ ├── 1.net │ │ │ │ ├── 10.net │ │ │ │ ├── 11.net │ │ │ │ ├── 12.net │ │ │ │ ├── 13.net │ │ │ │ ├── 14.net │ │ │ │ ├── 15.net │ │ │ │ ├── 16.net │ │ │ │ ├── 17.net │ │ │ │ ├── 18.net │ │ │ │ ├── 19.net │ │ │ │ ├── 2.net │ │ │ │ ├── 20.net │ │ │ │ ├── 21.net │ │ │ │ ├── 22.net │ │ │ │ ├── 23.net │ │ │ │ ├── 24.net │ │ │ │ ├── 3.net │ │ │ │ ├── 4.net │ │ │ │ ├── 5.net │ │ │ │ ├── 6.net │ │ │ │ ├── 7.net │ │ │ │ ├── 8.net │ │ │ │ └── 9.net │ │ │ │ └── top_3_networks │ │ │ │ ├── 12.net │ │ │ │ ├── 16.net │ │ │ │ └── 20.net │ │ ├── nnscore2 │ │ │ ├── CHANGELOG.md │ │ │ ├── CONTRIBUTORS.md │ │ │ ├── NNScore2.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── examples │ │ │ │ ├── myligand.pdbqt │ │ │ │ ├── myreceptor.pdbqt │ │ │ │ └── run.sh │ │ │ └── gpl-3.0.txt │ │ └── update_nn_score_from_git.sh │ │ └── scoring_classes │ │ ├── __init__.py │ │ ├── parent_scoring_class.py │ │ └── scoring_functions │ │ ├── __init__.py │ │ ├── lig_efficiency.py │ │ ├── nn1.py │ │ ├── nn2.py │ │ └── vina.py ├── model.py ├── operators │ ├── __init__.py │ ├── convert_files │ │ ├── __init__.py │ │ ├── conversion_to_3d.py │ │ ├── gypsum_dl │ │ │ ├── CHANGELOG.md │ │ │ ├── CONTRIBUTORS.md │ │ │ ├── LICENSE.txt │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── examples │ │ │ │ ├── Pitt_CRC │ │ │ │ │ ├── README.md │ │ │ │ │ ├── mpi_gypsum_dl.sh │ │ │ │ │ ├── mpi_sample_molecules.json │ │ │ │ │ ├── smp_gypsum_dl.sh │ │ │ │ │ ├── smp_sample_molecules.json │ │ │ │ │ └── tmp │ │ │ │ │ │ ├── sample_molecules.json │ │ │ │ │ │ └── sample_molecules_multi.json │ │ │ │ ├── run_gypsum_dl_test.sh │ │ │ │ ├── sample_molecules.json │ │ │ │ └── sample_molecules.smi │ │ │ ├── gypsum_dl │ │ │ │ ├── ChemUtils.py │ │ │ │ ├── MolContainer.py │ │ │ │ ├── MolObjectHandling.py │ │ │ │ ├── MyMol.py │ │ │ │ ├── Parallelizer.py │ │ │ │ ├── Start.py │ │ │ │ ├── Steps │ │ │ │ │ ├── IO │ │ │ │ │ │ ├── LoadFiles.py │ │ │ │ │ │ ├── ProcessOutput.py │ │ │ │ │ │ ├── SaveToPDB.py │ │ │ │ │ │ ├── SaveToSDF.py │ │ │ │ │ │ ├── Web2DOutput.py │ │ │ │ │ │ └── __init__.py │ │ │ │ │ ├── SMILES │ │ │ │ │ │ ├── AddHydrogens.py │ │ │ │ │ │ ├── DeSaltOrigSmiles.py │ │ │ │ │ │ ├── DurrantLabFilter.py │ │ │ │ │ │ ├── EnumerateChiralMols.py │ │ │ │ │ │ ├── EnumerateDoubleBonds.py │ │ │ │ │ │ ├── MakeTautomers.py │ │ │ │ │ │ ├── PrepareSmiles.py │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ ├── dimorphite_dl │ │ │ │ │ │ │ ├── CHANGES.md │ │ │ │ │ │ │ ├── CONTRIBUTORS.md │ │ │ │ │ │ │ ├── LICENSE.txt │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ ├── __init__.py │ │ │ │ │ │ │ ├── dimorphite_dl.py │ │ │ │ │ │ │ ├── sample_molecules.smi │ │ │ │ │ │ │ ├── site_substructures.smarts │ │ │ │ │ │ │ └── training_data │ │ │ │ │ │ │ │ ├── README.md │ │ │ │ │ │ │ │ └── training_data.json │ │ │ │ │ │ └── site_structures.smarts │ │ │ │ │ ├── ThreeD │ │ │ │ │ │ ├── Convert2DTo3D.py │ │ │ │ │ │ ├── GenerateAlternate3DNonaromaticRingConfs.py │ │ │ │ │ │ ├── Minimize3D.py │ │ │ │ │ │ ├── PrepareThreeD.py │ │ │ │ │ │ └── __init__.py │ │ │ │ │ └── __init__.py │ │ │ │ ├── Test │ │ │ │ │ ├── Tester.py │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── sample_molecules.json │ │ │ │ │ └── sample_molecules.smi │ │ │ │ ├── Utils.py │ │ │ │ ├── __init__.py │ │ │ │ └── molvs │ │ │ │ │ ├── CHANGELOG.md │ │ │ │ │ ├── CONTRIBUTING.rst │ │ │ │ │ ├── LICENSE │ │ │ │ │ ├── README.rst │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── charge.py │ │ │ │ │ ├── cli.py │ │ │ │ │ ├── errors.py │ │ │ │ │ ├── fragment.py │ │ │ │ │ ├── metal.py │ │ │ │ │ ├── normalize.py │ │ │ │ │ ├── resonance.py │ │ │ │ │ ├── standardize.py │ │ │ │ │ ├── tautomer.py │ │ │ │ │ ├── utils.py │ │ │ │ │ ├── validate.py │ │ │ │ │ └── validations.py │ │ │ └── run_gypsum_dl.py │ │ ├── run_single_gypsum_gtimeout.sh │ │ ├── run_single_gypsum_timeout.sh │ │ └── update_gypsum.sh │ ├── crossover │ │ ├── __init__.py │ │ ├── execute_crossover.py │ │ └── smiles_merge │ │ │ ├── __init__.py │ │ │ ├── merge_functions │ │ │ ├── __init__.py │ │ │ ├── alignment_and_breaks.py │ │ │ ├── dict_and_r_groups.py │ │ │ ├── mapping_class.py │ │ │ └── merge_w_core.py │ │ │ └── smiles_merge.py │ ├── filter │ │ ├── __init__.py │ │ ├── execute_filters.py │ │ └── filter_classes │ │ │ ├── __init__.py │ │ │ ├── filter_children_classes │ │ │ ├── __init__.py │ │ │ ├── brenk_filter.py │ │ │ ├── ghose_filter.py │ │ │ ├── ghose_modified_filter.py │ │ │ ├── lipinski_lenient_filter.py │ │ │ ├── lipinski_strict_filter.py │ │ │ ├── mozziconacci_filter.py │ │ │ ├── nih_filter.py │ │ │ ├── pains_filter.py │ │ │ └── vande_waterbeemd_filter.py │ │ │ ├── get_child_filter_class.py │ │ │ └── parent_filter_class.py │ ├── mutation │ │ ├── __init__.py │ │ ├── execute_mutations.py │ │ └── smiles_click_chem │ │ │ ├── __init__.py │ │ │ ├── reaction_libraries │ │ │ ├── all_rxns │ │ │ │ ├── All_Rxns_functional_groups.json │ │ │ │ ├── All_Rxns_rxn_library.json │ │ │ │ ├── Notes_on_reactions │ │ │ │ ├── complementary_mol_dir │ │ │ │ │ ├── 1_4_dione_robust.smi │ │ │ │ │ ├── 2_acetylphenol_robust.smi │ │ │ │ │ ├── 4_piperidone_robust.smi │ │ │ │ │ ├── 5_mem_aryl_w_NH_max2N_robust.smi │ │ │ │ │ ├── Acid_Anhydride_Noncyclic_clickchem.smi │ │ │ │ │ ├── Alcohol_clickchem.smi │ │ │ │ │ ├── Alkene_clickchem.smi │ │ │ │ │ ├── Alkyne_clickchem.smi │ │ │ │ │ ├── Amine_2R_clickchem.smi │ │ │ │ │ ├── Azide_1R_clickchem.smi │ │ │ │ │ ├── Carbonochloridate_clickchem.smi │ │ │ │ │ ├── Carboxylate_clickchem.smi │ │ │ │ │ ├── Epoxide_clickchem.smi │ │ │ │ │ ├── Ester_clickchem.smi │ │ │ │ │ ├── Halide_clickchem.smi │ │ │ │ │ ├── Isocyanate_clickchem.smi │ │ │ │ │ ├── Isothiocyanate_clickchem.smi │ │ │ │ │ ├── Primary_Amine_1R_clickchem.smi │ │ │ │ │ ├── Sulfonyl_Azide_clickchem.smi │ │ │ │ │ ├── Thio_Acid_clickchem.smi │ │ │ │ │ ├── Thiol_1R_clickchem.smi │ │ │ │ │ ├── acetohydrazide_robust.smi │ │ │ │ │ ├── alcohol_robust.smi │ │ │ │ │ ├── aldehyde_or_ketone_flexible_robust.smi │ │ │ │ │ ├── aldehyde_or_ketone_restricted_robust.smi │ │ │ │ │ ├── aldehyde_or_ketone_robust.smi │ │ │ │ │ ├── aldehyde_robust.smi │ │ │ │ │ ├── aliphatic_alkyne_robust.smi │ │ │ │ │ ├── aliphatic_alkyne_w_aro_alkyl_group_robust.smi │ │ │ │ │ ├── alkene_robust.smi │ │ │ │ │ ├── alkyl_halide_robust.smi │ │ │ │ │ ├── alkyl_halogen_or_alcohol_robust.smi │ │ │ │ │ ├── alkyl_halogen_robust.smi │ │ │ │ │ ├── alkyne_robust.smi │ │ │ │ │ ├── alpha_halo_ketone_robust.smi │ │ │ │ │ ├── amide_robust.smi │ │ │ │ │ ├── amidine_robust.smi │ │ │ │ │ ├── aminobenzenethiol_robust.smi │ │ │ │ │ ├── anthranilic_acid_robust.smi │ │ │ │ │ ├── aryl_aldehyde_robust.smi │ │ │ │ │ ├── aryl_boronic_acid_robust.smi │ │ │ │ │ ├── aryl_carboxylic_acid_robust.smi │ │ │ │ │ ├── aryl_halide_flexible_robust.smi │ │ │ │ │ ├── aryl_halide_nitrogen_optional_robust.smi │ │ │ │ │ ├── aryl_halide_type_1_robust.smi │ │ │ │ │ ├── aryl_halide_type_2_robust.smi │ │ │ │ │ ├── aryl_or_vinyl_halide_robust.smi │ │ │ │ │ ├── benzil_or_benzoin_robust.smi │ │ │ │ │ ├── beta_arylethylamine_robust.smi │ │ │ │ │ ├── beta_dicarbonyl_robust.smi │ │ │ │ │ ├── boronic_acid_robust.smi │ │ │ │ │ ├── carboxylic_acid_or_ester_robust.smi │ │ │ │ │ ├── carboxylic_acid_or_extended_esters_robust.smi │ │ │ │ │ ├── carboxylic_acid_robust.smi │ │ │ │ │ ├── cyclohexanone_robust.smi │ │ │ │ │ ├── halide_type_1_robust.smi │ │ │ │ │ ├── halide_type_2_robust.smi │ │ │ │ │ ├── halide_type_3_robust.smi │ │ │ │ │ ├── haloketone_robust.smi │ │ │ │ │ ├── hydrazine_robust.smi │ │ │ │ │ ├── imide_robust.smi │ │ │ │ │ ├── indole_robust.smi │ │ │ │ │ ├── isocyanate_robust.smi │ │ │ │ │ ├── isothiocyanate_robust.smi │ │ │ │ │ ├── ketone_robust.smi │ │ │ │ │ ├── nitrile_type_1_robust.smi │ │ │ │ │ ├── nitrile_type_2_robust.smi │ │ │ │ │ ├── ortho_1amine_2alcohol_arylcyclic_robust.smi │ │ │ │ │ ├── ortho_aminobenzaldehyde_robust.smi │ │ │ │ │ ├── ortho_aminophenol_robust.smi │ │ │ │ │ ├── ortho_aminothiophenol_robust.smi │ │ │ │ │ ├── ortho_halo_nitrobenzene_robust.smi │ │ │ │ │ ├── ortho_halo_phenol_robust.smi │ │ │ │ │ ├── ortho_halo_thioanizole_robust.smi │ │ │ │ │ ├── ortho_phenylenediamine_robust.smi │ │ │ │ │ ├── para_halo_nitrobenzene_robust.smi │ │ │ │ │ ├── phenole_robust.smi │ │ │ │ │ ├── phenylhydrazine_robust.smi │ │ │ │ │ ├── phthalazinone_precursor_robust.smi │ │ │ │ │ ├── primary_amine_robust.smi │ │ │ │ │ ├── primary_or_secondary_alcohol_robust.smi │ │ │ │ │ ├── primary_or_secondary_amine_C_aryl_alkyl_robust.smi │ │ │ │ │ ├── primary_or_secondary_amine_aro_optional_robust.smi │ │ │ │ │ ├── primary_or_secondary_amine_type_1_robust.smi │ │ │ │ │ ├── primary_or_secondary_amine_type_2_robust.smi │ │ │ │ │ ├── primary_or_secondary_halide_robust.smi │ │ │ │ │ ├── pyridine_pyrimidine_triazine_robust.smi │ │ │ │ │ ├── restricted_hydrazine_robust.smi │ │ │ │ │ ├── sulfonamide_robust.smi │ │ │ │ │ ├── sulfonic_acid_robust.smi │ │ │ │ │ ├── terminal_alkene_robust.smi │ │ │ │ │ ├── terminal_alkyne_robust.smi │ │ │ │ │ ├── tetrazole_1_robust.smi │ │ │ │ │ ├── tetrazole_2_robust.smi │ │ │ │ │ └── thioamide_robust.smi │ │ │ │ ├── complementary_mol_preperation_notes.txt │ │ │ │ └── fix.py │ │ │ ├── click_chem_rxns │ │ │ │ ├── ClickChem_functional_groups.json │ │ │ │ ├── ClickChem_rxn_library.json │ │ │ │ ├── Reaction_notes.txt │ │ │ │ ├── complementary_mol_dir │ │ │ │ │ ├── Acid_Anhydride_Noncyclic_clickchem.smi │ │ │ │ │ ├── Alcohol_clickchem.smi │ │ │ │ │ ├── Alkene_clickchem.smi │ │ │ │ │ ├── Alkyne_clickchem.smi │ │ │ │ │ ├── Amine_2R_clickchem.smi │ │ │ │ │ ├── Azide_1R_clickchem.smi │ │ │ │ │ ├── Carbonochloridate_clickchem.smi │ │ │ │ │ ├── Carboxylate_clickchem.smi │ │ │ │ │ ├── Epoxide_clickchem.smi │ │ │ │ │ ├── Ester_clickchem.smi │ │ │ │ │ ├── Halide_clickchem.smi │ │ │ │ │ ├── Isocyanate_clickchem.smi │ │ │ │ │ ├── Isothiocyanate_clickchem.smi │ │ │ │ │ ├── Primary_Amine_1R_clickchem.smi │ │ │ │ │ ├── Sulfonyl_Azide_clickchem.smi │ │ │ │ │ ├── Thio_Acid_clickchem.smi │ │ │ │ │ └── Thiol_1R_clickchem.smi │ │ │ │ └── complementary_mol_preperation_notes.txt │ │ │ ├── complementary_mol_preperation.txt │ │ │ └── robust_rxns │ │ │ │ ├── Notes_on_reactions │ │ │ │ ├── Robust_Rxns_functional_groups.json │ │ │ │ ├── Robust_Rxns_rxn_library.json │ │ │ │ ├── complementary_mol_dir │ │ │ │ ├── 1_4_dione_robust.smi │ │ │ │ ├── 2_acetylphenol_robust.smi │ │ │ │ ├── 4_piperidone_robust.smi │ │ │ │ ├── 5_mem_aryl_w_NH_max2N_robust.smi │ │ │ │ ├── acetohydrazide_robust.smi │ │ │ │ ├── alcohol_robust.smi │ │ │ │ ├── aldehyde_or_ketone_flexible_robust.smi │ │ │ │ ├── aldehyde_or_ketone_restricted_robust.smi │ │ │ │ ├── aldehyde_or_ketone_robust.smi │ │ │ │ ├── aldehyde_robust.smi │ │ │ │ ├── aliphatic_alkyne_robust.smi │ │ │ │ ├── aliphatic_alkyne_w_aro_alkyl_group_robust.smi │ │ │ │ ├── alkene_robust.smi │ │ │ │ ├── alkyl_halide_robust.smi │ │ │ │ ├── alkyl_halogen_or_alcohol_robust.smi │ │ │ │ ├── alkyl_halogen_robust.smi │ │ │ │ ├── alkyne_robust.smi │ │ │ │ ├── alpha_halo_ketone_robust.smi │ │ │ │ ├── amide_robust.smi │ │ │ │ ├── amidine_robust.smi │ │ │ │ ├── aminobenzenethiol_robust.smi │ │ │ │ ├── anthranilic_acid_robust.smi │ │ │ │ ├── aryl_aldehyde_robust.smi │ │ │ │ ├── aryl_boronic_acid_robust.smi │ │ │ │ ├── aryl_carboxylic_acid_robust.smi │ │ │ │ ├── aryl_halide_flexible_robust.smi │ │ │ │ ├── aryl_halide_nitrogen_optional_robust.smi │ │ │ │ ├── aryl_halide_type_1_robust.smi │ │ │ │ ├── aryl_halide_type_2_robust.smi │ │ │ │ ├── aryl_or_vinyl_halide_robust.smi │ │ │ │ ├── benzil_or_benzoin_robust.smi │ │ │ │ ├── beta_arylethylamine_robust.smi │ │ │ │ ├── beta_dicarbonyl_robust.smi │ │ │ │ ├── boronic_acid_robust.smi │ │ │ │ ├── carboxylic_acid_or_ester_robust.smi │ │ │ │ ├── carboxylic_acid_or_extended_esters_robust.smi │ │ │ │ ├── carboxylic_acid_robust.smi │ │ │ │ ├── cyclohexanone_robust.smi │ │ │ │ ├── halide_type_1_robust.smi │ │ │ │ ├── halide_type_2_robust.smi │ │ │ │ ├── halide_type_3_robust.smi │ │ │ │ ├── haloketone_robust.smi │ │ │ │ ├── hydrazine_robust.smi │ │ │ │ ├── imide_robust.smi │ │ │ │ ├── indole_robust.smi │ │ │ │ ├── isocyanate_robust.smi │ │ │ │ ├── isothiocyanate_robust.smi │ │ │ │ ├── ketone_robust.smi │ │ │ │ ├── nitrile_type_1_robust.smi │ │ │ │ ├── nitrile_type_2_robust.smi │ │ │ │ ├── ortho_1amine_2alcohol_arylcyclic_robust.smi │ │ │ │ ├── ortho_aminobenzaldehyde_robust.smi │ │ │ │ ├── ortho_aminophenol_robust.smi │ │ │ │ ├── ortho_aminothiophenol_robust.smi │ │ │ │ ├── ortho_halo_nitrobenzene_robust.smi │ │ │ │ ├── ortho_halo_phenol_robust.smi │ │ │ │ ├── ortho_halo_thioanizole_robust.smi │ │ │ │ ├── ortho_phenylenediamine_robust.smi │ │ │ │ ├── para_halo_nitrobenzene_robust.smi │ │ │ │ ├── phenole_robust.smi │ │ │ │ ├── phenylhydrazine_robust.smi │ │ │ │ ├── phthalazinone_precursor_robust.smi │ │ │ │ ├── primary_amine_robust.smi │ │ │ │ ├── primary_or_secondary_alcohol_robust.smi │ │ │ │ ├── primary_or_secondary_amine_C_aryl_alkyl_robust.smi │ │ │ │ ├── primary_or_secondary_amine_aro_optional_robust.smi │ │ │ │ ├── primary_or_secondary_amine_type_1_robust.smi │ │ │ │ ├── primary_or_secondary_amine_type_2_robust.smi │ │ │ │ ├── primary_or_secondary_halide_robust.smi │ │ │ │ ├── pyridine_pyrimidine_triazine_robust.smi │ │ │ │ ├── restricted_hydrazine_robust.smi │ │ │ │ ├── sulfonamide_robust.smi │ │ │ │ ├── sulfonic_acid_robust.smi │ │ │ │ ├── terminal_alkene_robust.smi │ │ │ │ ├── terminal_alkyne_robust.smi │ │ │ │ ├── tetrazole_1_robust.smi │ │ │ │ ├── tetrazole_2_robust.smi │ │ │ │ └── thioamide_robust.smi │ │ │ │ └── complementary_mol_preperation_notes.txt │ │ │ └── smiles_click_chem.py │ ├── operations.py │ └── operations1.py ├── plotting │ ├── __init__.py │ └── generate_line_plot.py └── user_vars.py ├── blog ├── README.md └── fig │ ├── 3eml.png │ ├── 7l11.png │ ├── RGA.png │ ├── all_top100.png │ ├── results.png │ └── sns.png ├── demo_GAoperation.py ├── demo_docking.py ├── docker ├── Dockerfile ├── README.md ├── autogrow_in_docker.py ├── examples │ ├── example.bash │ └── sample_autogrow_docker_json.json ├── run_autogrow_in_container.bash ├── run_autogrow_in_container_windows.bash └── tests │ ├── QuickVina2Docking.json │ ├── QuickVina2NN1Docking.json │ ├── QuickVina2NN2Docking.json │ ├── README.md │ ├── VinaDocking.json │ ├── VinaNN1Docking.json │ ├── VinaNN2Docking.json │ └── run.sh ├── draw_crossover.py ├── draw_mutation.py ├── evaluate_baseline.py ├── model.py ├── pdb ├── 1iep.pdb ├── 1iep.pdbqt ├── 2rgp.pdb ├── 2rgp.pdbqt ├── 3eml.pdb ├── 3eml.pdbqt ├── 3ny8.pdb ├── 3ny8.pdbqt ├── 3pbl.pdb ├── 3pbl.pdbqt ├── 4r6e.pdb ├── 4rlu.pdb ├── 4rlu.pdbqt ├── 4unn.pdb ├── 4unn.pdbqt ├── 5mo4.pdb ├── 5mo4.pdbqt ├── 7l11.pdb └── 7l11.pdbqt ├── rga.yml ├── run.py ├── sample_sub_scripts ├── sample_submit_autogrow.json └── sample_submit_autogrow_docker.json ├── save_model ├── crossover_policy_net_1.ckpt ├── crossover_policy_net_2.ckpt ├── mutation_policy_net_1.ckpt └── mutation_policy_net_2.ckpt ├── smiles2dockscore.py ├── source_compounds ├── Example_source_compound_notes.txt ├── Fragment_MW_100_to_150.smi ├── Fragment_MW_150_to_200.smi ├── Fragment_MW_200_to_250.smi ├── Fragment_MW_up_to_100.smi ├── PARPI_BRICS_frags.smi ├── PARPi.smi └── naphthalene_smiles.smi ├── tutorial ├── PARP │ ├── 4r6eA_PARP1_prepared.pdb │ └── 4r6eA_PARP1_prepared.pdbqt ├── TUTORIAL.md ├── __init__.py └── install_dependencies.txt └── upload.sh /CHANGELOG.md: -------------------------------------------------------------------------------- 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