├── .DS_Store ├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── analysis ├── SA_Score │ ├── README.md │ ├── __pycache__ │ │ ├── sascorer.cpython-310.pyc │ │ └── sascorer.cpython-38.pyc │ └── sascorer.py ├── all_pdbs_to_pdbqts.py ├── bond_angle_config.py ├── bond_length_config.py ├── docking.py ├── docking_py27.py ├── eval_bond_angles.py ├── eval_bond_length.py ├── get_atom_types_dist.py ├── get_empirical_angles.py ├── get_empirical_dists.py ├── get_volume.py ├── metrics.py ├── qvina_docking.py ├── reconstruct_mol.py ├── scoring_func.py ├── similarity.py ├── utils.py └── vina_docking.py ├── analyze_generated_pocket_mols.py ├── analyze_scaffolds_generated.py ├── assets ├── .DS_Store ├── movie.gif └── scaffold_optim.png ├── data ├── CROSSDOCK │ ├── __init__.py │ ├── fragment_hierarchy.py │ ├── prepare_fragments.py │ ├── process_crossdock.py │ ├── process_ligands.py │ ├── process_pockets.py │ └── sascorer.py ├── __init__.py └── sascorer.py ├── extend_scaffold_crossdock.py ├── fpscores.pkl.gz ├── generate_pocket_molecules.py ├── notebooks ├── 2z3h.pdb ├── 2z3h_H.pdb ├── 2z3h_out │ ├── 2z3h.pml │ ├── 2z3h.tcl │ ├── 2z3h_PYMOL.sh │ ├── 2z3h_VMD.sh │ ├── 2z3h_info.txt │ ├── 2z3h_out.pdb │ ├── 2z3h_pockets.pqr │ └── pockets │ │ ├── pocket1_atm.pdb │ │ ├── pocket1_vert.pqr │ │ ├── pocket2_atm.pdb │ │ └── pocket2_vert.pqr ├── __init__.py └── sample_for_pocket.ipynb ├── sample_crossdock_mols.py ├── sample_from_pocket.py ├── sampling ├── rejection_sampling.py ├── sample_mols.py └── scaffold_extension.py ├── src ├── __init__.py ├── anchor_gnn.py ├── const.py ├── conv_layer.py ├── datasets.py ├── dropout.py ├── dynamics_gvp.py ├── edm.py ├── egnn.py ├── extension_size.py ├── fragment_size_gnn.py ├── gvp.py ├── gvp_model.py ├── layer_norm.py ├── lightning.py ├── lightning_anchor_gnn.py ├── noise.py └── utils.py ├── train_anchor_predictor.py ├── train_frag_diffuser.py └── utils ├── sample_frag_size.py ├── templates.py ├── visuals.py └── volume_sampling.py /.DS_Store: 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