├── .gitignore ├── CMakeLists.txt ├── DEV_GUIDE.md ├── INSTALL.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── USER_GUIDE.md ├── doc ├── Makefile ├── _img │ ├── color_dummy_atoms.png │ └── logo.jpg ├── api.rst ├── conf.py ├── developer_guide.md ├── env.yaml ├── examples.md ├── index.rst ├── install.md └── user_guide.md ├── environment.yaml ├── example ├── README.md ├── basic_run.py ├── basic_run_color.py ├── color_dummy_atoms.png ├── combine_h5s.py ├── custom_features.py ├── dataset.sdf ├── dataset_split_0.h5 ├── dataset_split_1.h5 ├── dataset_split_2.h5 ├── different_start_modes.py ├── example.smi ├── h5_to_sdf.py ├── large_run.py ├── large_scale_run.sh ├── minimal.fdef ├── modify_optimizer_settings.py ├── mulitgpu.py ├── prepare_from_rdkit.py ├── query.sdf ├── rdkit_integration.py ├── server_mode │ ├── README.md │ ├── config.yaml │ ├── config_node_1.yaml │ ├── config_node_2.yaml │ ├── config_node_3.yaml │ ├── search_multiple_servers.py │ └── search_server.py ├── simple_run.py └── visualize_color.py ├── pyproject.toml ├── roshambo2 ├── __init__.py ├── backends │ ├── __init__.py │ ├── _pytorch_backend.py │ ├── cpp_backend.py │ ├── cpp_src │ │ └── cpp_functions.cpp │ ├── cuda_backend.py │ └── cuda_src │ │ ├── cuda_functions.cu │ │ ├── cuda_functions.cuh │ │ └── cuda_interface.cpp ├── classes.py ├── client.py ├── pharmacophore.py ├── prepare.py ├── roshambo2.py ├── scripts │ ├── __init__.py │ ├── prepare_dataset_from_sdf.py │ └── roshambo2_server_app.py └── utils.py ├── setup.py └── test ├── confs.sdf ├── dataset.h5 ├── dataset.sdf ├── dataset_split_0.sdf ├── dataset_split_1.sdf ├── dataset_split_2.sdf ├── example.smi ├── make_large.py ├── query.sdf ├── querys.sdf ├── test_backends.py ├── test_best_fit_output.py ├── test_combine.py ├── test_large.py ├── test_multi_gpu.py ├── test_prepare.py ├── test_qname.py ├── test_rdkit_integration.py ├── test_roshambo2.py └── test_start_modes.py /.gitignore: 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