├── .github └── workflows │ └── stale.yml ├── .gitignore ├── LICENSE ├── README.md ├── api ├── detect_pocket.py └── run.py ├── assets ├── 1ssc_A_B.pdb ├── 1ssc_A_pocket.json └── cover.png ├── cal_metrics.py ├── configs ├── pepbdb │ ├── autoencoder │ │ ├── train_codesign.yaml │ │ └── train_fixseq.yaml │ ├── ldm │ │ ├── setup_latent_guidance.yaml │ │ ├── train_codesign.yaml │ │ └── train_fixseq.yaml │ ├── test_codesign.yaml │ └── test_fixseq.yaml └── pepbench │ ├── autoencoder │ ├── train_codesign.yaml │ └── train_fixseq.yaml │ ├── ldm │ ├── setup_latent_guidance.yaml │ ├── train_codesign.yaml │ └── train_fixseq.yaml │ ├── test_codesign.yaml │ └── test_fixseq.yaml ├── data ├── __init__.py ├── codesign.py ├── converter │ ├── blocks_interface.py │ ├── blocks_to_data.py │ ├── list_blocks_to_pdb.py │ └── pdb_to_list_blocks.py ├── dataset_wrapper.py ├── format.py ├── mmap_dataset.py └── resample.py ├── datasets └── pepbdb │ ├── test.cluster │ ├── test.txt │ ├── train.cluster │ ├── train.txt │ ├── valid.cluster │ └── valid.txt ├── env.yaml ├── evaluation ├── __init__.py ├── dG │ ├── RosettaFastRelaxUtil.xml │ ├── base.py │ ├── energy.py │ ├── openmm_relaxer.py │ └── run.py ├── diversity.py ├── dockq.py ├── rmsd.py └── seq_metric.py ├── generate.py ├── globals.py ├── models ├── LDM │ ├── diffusion │ │ ├── dpm_full.py │ │ └── transition.py │ ├── energies │ │ └── dist.py │ └── ldm.py ├── __init__.py ├── autoencoder │ ├── backbone │ │ ├── api.py │ │ └── backbone.py │ ├── model.py │ └── sidechain │ │ ├── api.py │ │ ├── constants │ │ ├── __init__.py │ │ ├── geometry.py │ │ └── sequence.py │ │ ├── sidechain.py │ │ └── structure │ │ └── geometry.py └── dyMEAN │ ├── model.py │ ├── modules │ ├── am_egnn.py │ ├── am_enc.py │ └── radial_basis.py │ └── nn_utils.py ├── scripts ├── data_process │ ├── aug_from_monomer.py │ ├── monomer.py │ ├── pepbdb.py │ ├── process.py │ └── split.py ├── run_exp_pipe.sh └── train.sh ├── setup_latent_guidance.py ├── train.py ├── trainer ├── __init__.py ├── 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