├── .github └── workflows │ └── stale.yml ├── .gitignore ├── LICENSE ├── README.md ├── assets └── cover.png ├── configs ├── pretrain_ldm.yaml ├── setup_latent_guidance.yaml ├── test.yaml ├── train_autoencoder.yaml ├── train_ifencoder.yaml └── train_ldm.yaml ├── data ├── __init__.py ├── codesign.py ├── confidence.py ├── converter │ ├── blocks_interface.py │ ├── blocks_to_data.py │ ├── list_blocks_to_pdb.py │ └── pdb_to_list_blocks.py ├── dataset_wrapper.py ├── extend.py ├── format.py ├── mimicry.py ├── mmap_dataset.py └── resample.py ├── env_cu117.yaml ├── env_cu124.yaml ├── evaluation ├── analyzer │ ├── select_final.py │ └── tools.py ├── dG │ ├── base.py │ ├── energy.py │ ├── foldx_energy.py │ └── openmm_relaxer.py ├── diversity.py ├── dockq.py ├── interface_hit.py ├── rmsd.py ├── runner │ ├── base.py │ ├── foldx_dG.py │ ├── interface_hit.py │ ├── pyrosetta_dG.py │ └── relax.py └── seq_metric.py ├── example_data └── CD38 │ ├── 4cmh.pdb │ ├── 5f1o.pdb │ ├── config.yaml │ └── index.txt ├── globals.py ├── mimic_design.py ├── models ├── LDM │ ├── diffusion │ │ ├── dpm_full.py │ │ ├── transition.py │ │ └── vlb.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 └── ifencoder │ ├── ept.py │ ├── model.py │ └── tools.py ├── scripts ├── data_process │ ├── process.py │ └── split.py ├── mimic.sh ├── run_exp_pipe.sh └── train.sh ├── setup_latent_guidance.py ├── train.py ├── trainer ├── __init__.py ├── abs_trainer.py ├── autoencoder_trainer.py ├── if_trainer.py └── ldm_trainer.py └── utils ├── config_utils.py ├── const.py ├── decorators.py ├── file_utils.py ├── logger.py ├── network.py ├── nn_utils.py ├── 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