├── .gitignore ├── License ├── README.md ├── architecture ├── README.md ├── generation_scheme.png ├── model_architecture.png └── training_scheme.png ├── config ├── generator.yaml └── model.yaml ├── data ├── 3CL_ZINC.tar.gz ├── LIT-PCBA.tar.gz ├── README.md └── ZINC.tar.gz ├── download-weights.sh ├── images └── TOC.png ├── notebook ├── BBAR_Tutorial.ipynb └── images │ ├── logp.png │ ├── logp_tpsa.png │ ├── mw.png │ ├── qed.png │ ├── reference_ligand.png │ └── tpsa.png ├── pyproject.toml ├── script ├── preprocess.py ├── sample_denovo.py ├── sample_scaffold.py ├── train.py └── utils │ ├── __init__.py │ ├── logger.py │ └── seed.py ├── src └── bbar │ ├── __init__.py │ ├── fragmentation │ ├── __init__.py │ ├── brics.py │ ├── fragmentation.py │ ├── library.py │ └── utils.py │ ├── generate │ ├── __init__.py │ ├── generator.py │ └── utils.py │ ├── model │ ├── __init__.py │ ├── layers │ │ ├── __init__.py │ │ ├── atom_selection.py │ │ ├── block │ │ │ ├── __init__.py │ │ │ ├── activation.py │ │ │ ├── fc.py │ │ │ ├── graph_conv.py │ │ │ ├── norm.py │ │ │ └── readout.py │ │ ├── block_selection.py │ │ ├── condition_embedding.py │ │ ├── graph_embedding.py │ │ ├── property_prediction.py │ │ └── termination_prediction.py │ └── network.py │ ├── options │ ├── __init__.py │ ├── generation_options.py │ └── train_options.py │ ├── train │ ├── __init__.py │ ├── dataset.py │ └── trainer.py │ ├── transform │ ├── __init__.py │ ├── base.py │ ├── block.py │ ├── core.py │ └── feature │ │ ├── __init__.py │ │ ├── _atom.py │ │ ├── _bond.py │ │ ├── _edge_index.py │ │ └── getter.py │ └── utils │ ├── __init__.py │ ├── common.py │ └── typing.py └── test ├── builtin_model └── .gitkeep ├── generation_config ├── 3cl_affinity.yaml ├── logp.yaml ├── logp_tpsa.yaml ├── mw.yaml ├── mw_logp.yaml ├── qed.yaml └── tpsa.yaml └── start_scaffolds.smi /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SeonghwanSeo/BBAR/HEAD/.gitignore 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