├── .gitignore ├── LICENSE ├── README.md ├── assets └── overview.png ├── bin └── .gitignore ├── configs ├── test │ ├── abopt_singlecdr.yml │ ├── codesign_multicdrs.yml │ ├── codesign_single.yml │ ├── codesign_single_ddg.yml │ ├── codesign_single_ddg_and_hydro.yml │ ├── codesign_single_hydro.yml │ ├── fixbb.yml │ └── strpred.yml └── train │ ├── codesign_fv.yml │ ├── codesign_multicdrs.yml │ ├── codesign_single.yml │ ├── fixbb.yml │ └── strpred.yml ├── data ├── .gitignore ├── examples │ ├── 3QHF_Fv.pdb │ ├── 7DK2_AB_C.pdb │ └── Omicron_RBD.pdb └── sabdab_summary_all.tsv ├── design_dock.py ├── design_pdb.py ├── design_testset.py ├── diffab ├── datasets │ ├── __init__.py │ ├── _base.py │ ├── custom.py │ └── sabdab.py ├── models │ ├── __init__.py │ ├── _base.py │ └── diffab.py ├── modules │ ├── common │ │ ├── geometry.py │ │ ├── layers.py │ │ ├── so3.py │ │ ├── structure.py │ │ └── topology.py │ ├── diffusion │ │ ├── dpm_full.py │ │ └── transition.py │ └── encoders │ │ ├── ga.py │ │ ├── pair.py │ │ └── residue.py ├── tools │ ├── ddg │ │ ├── data │ │ │ └── model.pt │ │ ├── models │ │ │ ├── attention.py │ │ │ ├── common.py │ │ │ ├── predictor.py │ │ │ └── residue.py │ │ ├── predictor.py │ │ └── utils │ │ │ ├── data.py │ │ │ ├── misc.py │ │ │ └── protein.py │ ├── dock │ │ ├── base.py │ │ └── hdock.py │ ├── eval │ │ ├── __main__.py │ │ ├── base.py │ │ ├── energy.py │ │ ├── hydropathy.py │ │ ├── run.py │ │ └── similarity.py │ ├── relax │ │ ├── __main__.py │ │ ├── base.py │ │ ├── openmm_relaxer.py │ │ ├── pyrosetta_relaxer.py │ │ └── run.py │ ├── renumber │ │ ├── __init__.py │ │ ├── __main__.py │ │ └── run.py │ └── runner │ │ ├── design_for_pdb.py │ │ └── design_for_testset.py └── utils │ ├── data.py │ ├── inference.py │ ├── misc.py │ ├── potentials.py │ ├── protein │ ├── constants.py │ ├── parsers.py │ └── writers.py │ ├── train.py │ └── transforms │ ├── __init__.py │ ├── _base.py │ ├── mask.py │ ├── merge.py │ ├── patch.py │ └── select_atom.py ├── env.yaml ├── eval.py ├── 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