├── .codecov.yml ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ └── CI.yaml ├── .gitignore ├── .lgtm.yml ├── .readthedocs.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── USING-NEW-DOCKING-METHODS.md ├── colab_example └── helper_ligands.csv ├── config ├── description ├── devtools ├── README.md ├── conda-envs │ └── test_env.yaml ├── legacy-miniconda-setup │ └── before_install.sh └── scripts │ └── create_conda_env.py ├── docs ├── Makefile ├── README.md ├── _static │ └── README.md ├── _templates │ └── README.md ├── api │ ├── dock.rst │ ├── features.rst │ ├── index.rst │ ├── pymol.rst │ ├── score.rst │ └── utils.rst ├── conf.py ├── index.rst ├── intro │ ├── getting_started.rst │ └── installation.rst ├── make.bat └── requirements.yaml ├── hooks ├── applypatch-msg.sample ├── commit-msg.sample ├── fsmonitor-watchman.sample ├── post-update.sample ├── pre-applypatch.sample ├── pre-commit.sample ├── pre-merge-commit.sample ├── pre-push.sample ├── pre-rebase.sample ├── pre-receive.sample ├── prepare-commit-msg.sample └── update.sample ├── info └── exclude ├── open_combind ├── __init__.py ├── _version.py ├── chembl │ ├── chembl.py │ ├── chembl_proc.py │ └── split_chembl.py ├── cli │ └── cli.py ├── data │ ├── README.md │ └── look_and_say.dat ├── dock │ ├── __init__.py │ ├── crossdock_atom_types.txt │ ├── dock.py │ ├── grid.py │ ├── ligand_handling.py │ ├── ligprep.py │ ├── postprocessing.py │ ├── struct_align.py │ ├── struct_process.py │ └── struct_sort.py ├── features │ ├── features.py │ ├── ifp.py │ ├── ifp_similarity.py │ ├── mcss.py │ └── shape.py ├── open_combind.py ├── pymol │ ├── .DS_Store │ ├── interactions.py │ └── view_complexes.py ├── score │ ├── density_estimate.py │ ├── pose_prediction.py │ ├── screen.py │ └── statistics.py ├── stats_data │ ├── benchmarking.py │ ├── combind_default │ │ ├── ._stats.pdf │ │ ├── native_contact.txt │ │ ├── native_hbond.txt │ │ ├── native_mcss.txt │ │ ├── native_saltbridge.txt │ │ ├── native_shape.txt │ │ ├── reference_contact.txt │ │ ├── reference_hbond.txt │ │ ├── reference_mcss.txt │ │ ├── reference_saltbridge.txt │ │ ├── reference_shape.txt │ │ └── stats.pdf │ ├── default │ │ ├── native_contact.txt │ │ ├── native_hbond.txt │ │ ├── native_mcss.txt │ │ ├── native_saltbridge.txt │ │ ├── reference_contact.txt │ │ ├── reference_hbond.txt │ │ ├── reference_mcss.txt │ │ ├── reference_saltbridge.txt │ │ └── stats.pdf │ ├── docked_to_alpha.py │ ├── features_to_stats.py │ ├── helper_best_affinity_diverse.csv │ ├── helper_best_mcss.csv │ ├── mcss_sizes.pkl │ ├── pdbs_for_benchmark.csv │ └── systems.txt ├── tests │ ├── 3ZPR_lig-to-2VT4_ifp.csv │ ├── 3ZPR_lig-to-2VT4_ifp_raw.csv │ ├── 3ZPR_lig-to-2VT4_pv.maegz │ ├── 6IBL-to-2VT4_pv.maegz │ ├── __init__.py │ ├── ifp_test.py │ ├── structures │ │ ├── aligned │ │ │ ├── 1FKN_complex_truth.pdb │ │ │ ├── 3UDH_complex_truth.pdb │ │ │ └── 3UDH_lig_truth.sdf │ │ ├── ligands │ │ │ ├── 1FKN_lig_truth.sdf │ 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