├── .gitignore ├── LICENSE ├── README.md ├── assets └── overview.png ├── configs ├── sampling │ ├── protac │ │ ├── protac_all_gui.yml │ │ ├── protac_anchor.yml │ │ ├── protac_dist.yml │ │ └── protac_no_gui.yml │ └── zinc.yml └── training │ ├── nn_variants │ ├── pos_eps_rot_eps.yml │ ├── pos_eps_rot_euler.yml │ └── pos_newton_rot_eps.yml │ ├── warhead_protac.yml │ └── zinc.yml ├── data ├── .gitignore └── protac │ ├── 3d_index.pkl │ ├── e3_ligand.csv │ ├── index.pkl │ ├── linker.csv │ ├── protac.csv │ ├── smi_protac.txt │ └── warhead.csv ├── datasets ├── __init__.py ├── linker_data.py └── linker_dataset.py ├── models ├── common.py ├── diff_protac_bond.py ├── encoders │ ├── __init__.py │ └── node_edge_net.py ├── eps_net.py └── transition.py ├── playground └── check_data.ipynb ├── scripts ├── baselines │ ├── eval_3dlinker.py │ ├── eval_delinker.py │ └── eval_difflinker.py ├── eval_protac.py ├── prepare_data.py ├── sample_protac.py └── train_protac.py └── utils ├── calc_SC_RDKit.py ├── const.py ├── data.py ├── eval_bond.py ├── evaluation.py ├── fpscores.pkl.gz ├── frag_utils.py ├── geometry.py ├── guidance_funcs.py ├── misc.py ├── prior_num_atoms.py ├── reconstruct_linker.py ├── sascorer.py ├── so3.py ├── train.py ├── train_linker_smiles.pkl ├── transforms.py ├── visualize.py └── wehi_pains.csv /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guanjq/LinkerNet/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guanjq/LinkerNet/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guanjq/LinkerNet/HEAD/README.md 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