├── .gitignore ├── LICENSE ├── Model.png ├── README.md ├── byteff ├── __init__.py ├── data │ ├── __init__.py │ ├── mol_data.py │ └── mol_dataset.py ├── forcefield │ ├── __init__.py │ ├── classical_forcefield.py │ ├── ff_kernels.py │ ├── ffopt.py │ ├── gmxtools.py │ └── topparse.py ├── model │ ├── __init__.py │ ├── gnn.py │ ├── layers.py │ ├── mlparams.py │ └── swag.py ├── mol │ ├── __init__.py │ ├── conformer.py │ ├── molecule.py │ ├── moleculegraph.py │ ├── moltools.py │ ├── rkutil │ │ ├── __init__.py │ │ ├── conformer.py │ │ ├── helper.py │ │ ├── information.py │ │ ├── match_and_map.py │ │ ├── plot.py │ │ ├── resonance.py │ │ ├── sanitize.py │ │ ├── symmetry.py │ │ └── tables.py │ └── topology.py ├── tests │ ├── __init__.py │ ├── test_ffopt.py │ ├── test_mol_data.py │ ├── test_partial_hessian.py │ ├── test_symmetry.py │ ├── test_utils.py │ └── testdata │ │ ├── __init__.py │ │ ├── dataset_hessian │ │ └── meta.txt │ │ └── dataset_torsion │ │ └── meta.txt ├── train │ ├── __init__.py │ ├── loss.py │ ├── train_config_template.yaml │ └── trainer.py └── utils │ ├── __init__.py │ ├── definitions.py │ ├── logging.py │ ├── nested_data.py │ ├── simple_unit.py │ ├── tar.py │ └── utilities.py ├── data ├── BDTorsionInRing.h5 ├── BDTorsionInRing.json ├── BDTorsionNonRing.h5 ├── BDTorsionNonRing.json └── README.md ├── requirements.txt ├── scripts ├── prepare_data │ ├── README.md │ ├── prepare_shards_energyforce.py │ ├── prepare_shards_partial_hessian.py │ └── prepare_shards_torsion.py ├── train │ ├── README.md │ ├── train_ddp.py │ └── train_local.py └── write_itp │ ├── write_itp.py │ └── write_itp_ensemble.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bytedance/byteff/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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