├── LICENSE ├── README.md ├── configs ├── sample │ ├── confidence │ │ ├── flex_cfd.yml │ │ └── tuned_cfd.yml │ ├── examples │ │ ├── dock_pep.yml │ │ ├── dock_pep_fix_some.yml │ │ ├── dock_pep_know_some.yml │ │ ├── dock_smallmol.yml │ │ ├── dock_smallmol_84663.yml │ │ ├── dock_smallmol_flex.yml │ │ ├── growing_fixed_frag.yml │ │ ├── growing_unfixed_frag.yml │ │ ├── pepdesign.yml │ │ ├── pepdesign_hot136E │ │ │ ├── fixed_CCOOH.yml │ │ │ ├── fixed_CCOOH_init0.9.yml │ │ │ ├── fixed_Glu_CCOOH.yml │ │ │ ├── unfixed_CCOOH.yml │ │ │ ├── unfixed_CCOOH_from_inputs.yml │ │ │ └── unfixed_Glu.yml │ │ ├── sbdd.yml │ │ └── sbdd_simple.yml │ ├── pxm.yml │ ├── pxm_use.yml │ └── test │ │ ├── conf_geom │ │ └── base.yml │ │ ├── denovo_geom │ │ ├── ar.yml │ │ ├── base.yml │ │ ├── shape │ │ │ ├── C.yml │ │ │ ├── E.yml │ │ │ ├── K.yml │ │ │ ├── L.yml │ │ │ ├── M.yml │ │ │ ├── O.yml │ │ │ ├── P.yml │ │ │ ├── T.yml │ │ │ └── X.yml │ │ └── simple.yml │ │ ├── dock_pepbdb │ │ ├── base.yml │ │ ├── base_flex.yml │ │ ├── prior_fix_anchor.yml │ │ ├── prior_fix_backbone.yml │ │ ├── prior_fix_first_residue.yml │ │ └── prior_fix_terminal_residue.yml │ │ ├── dock_poseboff │ │ ├── base.yml │ │ ├── base_flex.yml │ │ ├── prior_anchor.yml │ │ ├── prior_bond_length.yml │ │ ├── prior_center.yml │ │ ├── prior_chirality.yml │ │ └── prior_fix_anchor.yml │ │ ├── growing_csd │ │ └── base.yml │ │ ├── linking_moad │ │ ├── known_connect.yml │ │ └── unknown_connect.yml │ │ ├── linking_protacdb │ │ ├── fixed_fragpos.yml │ │ ├── unfixed_lv0.yml │ │ ├── unfixed_lv1.yml │ │ ├── unfixed_lv2.yml │ │ ├── unfixed_lv3.yml │ │ └── unfixed_lv4.yml │ │ ├── pepdesign_pepbdb │ │ └── base.yml │ │ ├── pepinv_pepbdb │ │ └── base.yml │ │ └── sbdd_csd │ │ ├── ar.yml │ │ ├── base.yml │ │ ├── base_mol_size.yml │ │ └── simple.yml └── train │ └── train_pxm_reduced.yml ├── data └── examples │ ├── dock │ ├── 8C7Y_TXV_ligand.sdf │ ├── 8C7Y_TXV_ligand_start_conf.sdf │ ├── 8C7Y_TXV_protein.pdb │ ├── casp9_align_rec.pdb │ └── casp9_pocket_coord.sdf │ ├── hot136E │ ├── PDL1_3bik_pro.pdb │ ├── PDL1_pephot136E_pep.pdb │ └── center_hot136E.sdf │ ├── peptide │ ├── 3bik_A.pdb │ ├── 3bik_A_pocket_coord.sdf │ └── P73.pdb │ └── smallmol │ ├── 2ar9_A.pdb │ ├── fragment.sdf │ └── pocket_coord.sdf ├── environment.yml ├── evaluate ├── apply_openmm.py ├── apply_vina.py ├── evaluate_by_buster.py ├── evaluate_by_buster_linking.py ├── evaluate_by_buster_sbdd.py ├── evaluate_conf.py ├── evaluate_denovo.py ├── evaluate_dock.py ├── evaluate_dockpep.py ├── evaluate_for_ranking.py ├── evaluate_growing.py ├── evaluate_linking.py ├── evaluate_mols.py ├── evaluate_pepfull.py ├── evaluate_pepsc.py ├── evaluate_sbdd.py ├── evaluate_sbdd_add.py ├── foldx │ ├── foldx_energy.py │ ├── foldx_pipeline.py │ ├── foldx_repair.py │ └── foldx_stability.py ├── from_delinker.py ├── get_cfd.py ├── parse_openmm_outs.py ├── prepare_cpx.py ├── rosetta.py ├── rosetta_pack.py ├── structure_consistency.py ├── structure_consistency_af.py └── utils_eval.py ├── models ├── common.py ├── corrector.py ├── diffusion.py ├── embedding.py ├── encoders │ ├── __init__.py │ └── cftfm.py ├── fields │ ├── __init__.py │ └── classifier.py ├── graph.py ├── graph_context.py ├── graph_gvp.py ├── invariant.py ├── ipa.py ├── loss.py ├── maskfill.py ├── position.py ├── sample.py └── transition.py ├── notebooks ├── PXM_Dock.ipynb ├── PXM_PeptideDesign.ipynb └── PXM_SmallMoleculeDesign.ipynb ├── process ├── csd │ ├── extract_pockets.py │ ├── process_pocmol.py │ └── process_torsional_info.py ├── extract_pockets.py ├── geom │ ├── process_mols.py │ └── process_torsional_info.py ├── make_assembly_lmdb.py ├── make_mol_meta.py ├── moad │ ├── extract_pockets.py │ └── process_pocmol.py ├── pbdock │ ├── extract_pockets.py │ ├── process_pocmol.py │ └── process_torsional_info.py ├── process_decompose_info.py ├── process_mols.py ├── process_peptide_allinone.py ├── process_pocmol.py ├── process_pocmol_allinone.py ├── process_raw_steps.md ├── process_torsional_info.py ├── qm9 │ └── process_mols.py ├── unmi │ ├── preprocess_db.py │ └── process_mols.py └── utils_process.py ├── scripts ├── believe.py ├── believe_use_pdb.py ├── eval_rdkit.py ├── parse_pdb_data.py ├── rank_pose.py ├── refine_dataset.py ├── sample_drug3d.py ├── sample_pdb.py ├── sample_use.py ├── sample_use_pdb.py ├── split_pl_dataset.py ├── split_test.py └── train_pl.py └── utils ├── buster_tools.py ├── data.py ├── dataset.py ├── difflinker_decom.py ├── docking_aux_scores.py ├── docking_qvina.py ├── docking_vina.py ├── evaluation.py ├── fpscores.pkl.gz ├── fragment.py ├── graph.py ├── graph_decom.py ├── info_level.py ├── linker ├── calc_SC_RDKit.py └── frag_utils.py ├── lmdb_legacy.py ├── misc.py ├── motion.py ├── parser.py ├── pdb_fix.py ├── prior.py ├── reconstruct.py ├── requirements.txt ├── sample_noise.py ├── sascorer.py ├── scoring_func.py ├── shape.py ├── similarity.py ├── train.py ├── train_noise.py ├── transforms.py ├── vina.py ├── visualization.py └── 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