├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── applications ├── images │ ├── README.md │ ├── clip_eval.py │ ├── clip_eval.sh │ ├── img_examples.ipynb │ ├── parse_img_metric_files.py │ └── tifa_eval.py └── proteins │ ├── Proteus │ ├── ProteinMPNN │ │ ├── LICENSE │ │ ├── README.md │ │ ├── examples │ │ │ ├── submit_example_1.sh │ │ │ ├── submit_example_2.sh │ │ │ ├── submit_example_3.sh │ │ │ ├── submit_example_3_score_only.sh │ │ │ ├── submit_example_4.sh │ │ │ ├── submit_example_4_non_fixed.sh │ │ │ ├── submit_example_5.sh │ │ │ ├── submit_example_6.sh │ │ │ ├── submit_example_7.sh │ │ │ └── submit_example_8.sh │ │ ├── helper_scripts │ │ │ ├── assign_fixed_chains.py │ │ │ ├── make_bias_AA.py │ │ │ ├── make_bias_per_res_dict.py │ │ │ ├── make_fixed_positions_dict.py │ │ │ ├── make_pos_neg_tied_positions_dict.py │ │ │ ├── make_tied_positions_dict.py │ │ │ ├── other_tools │ │ │ │ ├── make_omit_AA.py │ │ │ │ └── make_pssm_dict.py │ │ │ ├── parse_multiple_chains.py │ │ │ ├── parse_multiple_chains.sh │ │ │ └── xml_scripts │ │ │ │ └── design.xml │ │ ├── protein_mpnn_pyrosetta.py │ │ ├── protein_mpnn_run.py │ │ ├── protein_mpnn_utils.py │ │ ├── pyrosetta_utils.py │ │ └── training │ │ │ ├── LICENSE │ │ │ ├── README.md │ │ │ ├── colab_training_example.ipynb │ │ │ ├── model_utils.py │ │ │ ├── plot_training_results.ipynb │ │ │ ├── training.py │ │ │ └── utils.py │ ├── config │ │ ├── base.yaml │ │ └── inference.yaml │ ├── environment.yml │ ├── proteus_analysis │ │ ├── metrics.py │ │ ├── plotting.py │ │ └── utils.py │ ├── proteus_data │ │ ├── all_atom.py │ │ ├── chemical.py │ │ ├── data_transforms.py │ │ ├── discrete_diffuser.py │ │ ├── errors.py │ │ ├── igso3.py │ │ ├── interpolant.py │ │ ├── mmcif_parsing.py │ │ ├── parsers.py │ │ ├── protein.py │ │ ├── r3_diffuser.py │ │ ├── residue_constants.py │ │ ├── se3_diffuser.py │ │ ├── so3_diffuser.py │ │ ├── so3_utils.py │ │ └── utils.py │ ├── proteus_experiments │ │ ├── inference_se3_diffusion.py │ │ └── utils.py │ ├── proteus_model │ │ ├── fold_module.py │ │ ├── heads.py │ │ ├── ipa_pytorch.py │ │ ├── layers.py │ │ ├── msa.py │ │ ├── score_network.py │ │ ├── strcture2seq.py │ │ └── utils.py │ ├── proteus_openfold │ │ ├── config.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── data_modules.py │ │ │ ├── data_pipeline.py │ │ │ ├── data_transforms.py │ │ │ ├── errors.py │ │ │ ├── feature_pipeline.py │ │ │ ├── input_pipeline.py │ │ │ ├── mmcif_parsing.py │ │ │ ├── parsers.py │ │ │ ├── templates.py │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── hhblits.py │ │ │ │ ├── hhsearch.py │ │ │ │ ├── jackhmmer.py │ │ │ │ ├── kalign.py │ │ │ │ └── utils.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── dropout.py │ │ │ ├── embedders.py │ │ │ ├── evoformer.py │ │ │ ├── heads.py │ │ │ ├── model.py │ │ │ ├── msa.py │ │ │ ├── outer_product_mean.py │ │ │ ├── pair_transition.py │ │ │ ├── primitives.py │ │ │ ├── structure_module.py │ │ │ ├── template.py │ │ │ ├── torchscript.py │ │ │ ├── triangular_attention.py │ │ │ └── triangular_multiplicative_update.py │ │ ├── np │ │ │ ├── __init__.py │ │ │ ├── protein.py │ │ │ ├── relax │ │ │ │ ├── __init__.py │ │ │ │ ├── amber_minimize.py │ │ │ │ ├── cleanup.py │ │ │ │ ├── relax.py │ │ │ │ └── utils.py │ │ │ └── residue_constants.py │ │ ├── resources │ │ │ ├── __init__.py │ │ │ └── stereo_chemical_props.txt │ │ └── utils │ │ │ ├── argparse.py │ │ │ ├── callbacks.py │ │ │ ├── checkpointing.py │ │ │ ├── exponential_moving_average.py │ │ │ ├── feats.py │ │ │ ├── import_weights.py │ │ │ ├── logger.py │ │ │ ├── loss.py │ │ │ ├── lr_schedulers.py │ │ │ ├── precision_utils.py │ │ │ ├── rigid_utils.py │ │ │ ├── seed.py │ │ │ ├── superimposition.py │ │ │ ├── suppress_output.py │ │ │ ├── tensor_utils.py │ │ │ └── validation_metrics.py │ ├── se3.yml │ └── setup.py │ ├── README.md │ ├── RFdiffusion │ ├── .rosetta-ci │ │ ├── .gitignore │ │ ├── benchmark.py │ │ ├── benchmark.template.ini │ │ ├── hpc_drivers │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── multicore.py │ │ │ └── slurm.py │ │ ├── test-sets.yaml │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── rfd.py │ │ │ ├── self.md │ │ │ └── self.py │ ├── config │ │ └── inference │ │ │ ├── base.yaml │ │ │ └── symmetry.yaml │ ├── examples │ │ ├── design_cyclic_oligos.sh │ │ ├── design_dihedral_oligos.sh │ │ ├── design_enzyme.sh │ │ ├── design_motifscaffolding.sh │ │ ├── design_motifscaffolding_inpaintseq.sh │ │ ├── design_motifscaffolding_with_target.sh │ │ ├── design_nickel.sh │ │ ├── design_partialdiffusion.sh │ │ ├── design_partialdiffusion_multipleseq.sh │ │ ├── design_partialdiffusion_withseq.sh │ │ ├── design_ppi.sh │ │ ├── design_ppi_flexible_peptide.sh │ │ ├── design_ppi_scaffolded.sh │ │ ├── design_tetrahedral_oligos.sh │ │ ├── design_timbarrel.sh │ │ ├── design_unconditional.sh │ │ ├── design_unconditional_w_contact_potential.sh │ │ ├── design_unconditional_w_monomer_ROG.sh │ │ ├── input_pdbs │ │ │ ├── 1YCR.pdb │ │ │ ├── 1qys.pdb │ │ │ ├── 2KL8.pdb │ │ │ ├── 3IOL.pdb │ │ │ ├── 5TPN.pdb │ │ │ ├── 5an7.pdb │ │ │ ├── insulin_target.pdb │ │ │ ├── nickel_symmetric_motif.pdb │ │ │ └── peptide_complex_ideal_helix.pdb │ │ ├── target_folds │ │ │ ├── insulin_target_adj.pt │ │ │ └── insulin_target_ss.pt │ │ └── tim_barrel_scaffold │ │ │ ├── 6WVS_adj.pt │ │ │ └── 6WVS_ss.pt │ ├── helper_scripts │ │ ├── 2KL8.pdb │ │ └── make_secstruc_adj.py │ ├── outputs │ │ └── 2024-08-27 │ │ │ ├── 14-09-12 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 14-17-33 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 14-18-55 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 14-52-05 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 14-56-37 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ └── 14-58-33 │ │ │ └── .hydra │ │ │ ├── config.yaml │ │ │ ├── hydra.yaml │ │ │ └── overrides.yaml │ ├── rfdiffusion │ │ ├── Attention_module.py │ │ ├── AuxiliaryPredictor.py │ │ ├── Embeddings.py │ │ ├── RoseTTAFoldModel.py │ │ ├── SE3_network.py │ │ ├── Track_module.py │ │ ├── __init__.py │ │ ├── chemical.py │ │ ├── contigs.py │ │ ├── coords6d.py │ │ ├── diffusion.py │ │ ├── igso3.py │ │ ├── inference │ │ │ ├── __init__.py │ │ │ ├── model_runners.py │ │ │ ├── sym_rots.npz │ │ │ ├── symmetry.py │ │ │ └── utils.py │ │ ├── kinematics.py │ │ ├── model_input_logger.py │ │ ├── potentials │ │ │ ├── __init__.py │ │ │ ├── manager.py │ │ │ └── potentials.py │ │ ├── scoring.py │ │ ├── util.py │ │ └── util_module.py │ ├── run_inference.sh │ ├── scripts │ │ ├── download_models.sh │ │ └── run_inference.py │ ├── setup.py │ └── tests │ │ └── test_diffusion.py │ ├── assets │ └── umap_superdiff_or_w_proteins.jpg │ ├── environment.yml │ ├── evaluation │ ├── analysis │ │ ├── metrics.py │ │ ├── plotting.py │ │ └── utils.py │ ├── config │ │ ├── base.yaml │ │ ├── icml_published.yaml │ │ ├── inference.yaml │ │ └── pure_dsm.yaml │ ├── data │ │ ├── all_atom.py │ │ ├── chemical.py │ │ ├── errors.py │ │ ├── igso3.py │ │ ├── mmcif_parsing.py │ │ ├── parsers.py │ │ ├── pdb_data_loader.py │ │ ├── process_pdb_dataset.py │ │ ├── process_pdb_files.py │ │ ├── protein.py │ │ ├── r3_diffuser.py │ │ ├── residue_constants.py │ │ ├── se3_diffuser.py │ │ ├── so3_diffuser.py │ │ ├── so3_utils.py │ │ └── utils.py │ ├── outputs │ │ └── 2024-09-20 │ │ │ ├── 12-40-23 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ └── 15-30-31 │ │ │ └── .hydra │ │ │ ├── config.yaml │ │ │ ├── hydra.yaml │ │ │ └── overrides.yaml │ ├── run_sc.sh │ ├── run_self_consistency.py │ └── sc_config │ │ ├── base.yaml │ │ ├── icml_published.yaml │ │ ├── inference.yaml │ │ └── pure_dsm.yaml │ ├── load_env.sh │ ├── requirements.txt │ ├── se3_diffusion │ ├── config │ │ ├── base.yaml │ │ ├── icml_published.yaml │ │ ├── inference.yaml │ │ └── pure_dsm.yaml │ ├── openfold │ │ ├── config.py │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── data_modules.py │ │ │ ├── data_pipeline.py │ │ │ ├── data_transforms.py │ │ │ ├── errors.py │ │ │ ├── feature_pipeline.py │ │ │ ├── input_pipeline.py │ │ │ ├── mmcif_parsing.py │ │ │ ├── parsers.py │ │ │ ├── templates.py │ │ │ └── tools │ │ │ │ ├── __init__.py │ │ │ │ ├── hhblits.py │ │ │ │ ├── hhsearch.py │ │ │ │ ├── jackhmmer.py │ │ │ │ ├── kalign.py │ │ │ │ └── utils.py │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── dropout.py │ │ │ ├── embedders.py │ │ │ ├── evoformer.py │ │ │ ├── heads.py │ │ │ ├── model.py │ │ │ ├── msa.py │ │ │ ├── outer_product_mean.py │ │ │ ├── pair_transition.py │ │ │ ├── primitives.py │ │ │ ├── structure_module.py │ │ │ ├── template.py │ │ │ ├── torchscript.py │ │ │ ├── triangular_attention.py │ │ │ └── triangular_multiplicative_update.py │ │ ├── np │ │ │ ├── __init__.py │ │ │ ├── protein.py │ │ │ ├── relax │ │ │ │ ├── __init__.py │ │ │ │ ├── amber_minimize.py │ │ │ │ ├── cleanup.py │ │ │ │ ├── relax.py │ │ │ │ └── utils.py │ │ │ └── residue_constants.py │ │ ├── resources │ │ │ ├── __init__.py │ │ │ └── stereo_chemical_props.txt │ │ └── utils │ │ │ ├── argparse.py │ │ │ ├── callbacks.py │ │ │ ├── checkpointing.py │ │ │ ├── exponential_moving_average.py │ │ │ ├── feats.py │ │ │ ├── import_weights.py │ │ │ ├── logger.py │ │ │ ├── loss.py │ │ │ ├── lr_schedulers.py │ │ │ ├── precision_utils.py │ │ │ ├── rigid_utils.py │ │ │ ├── seed.py │ │ │ ├── superimposition.py │ │ │ ├── suppress_output.py │ │ │ ├── tensor_utils.py │ │ │ └── validation_metrics.py │ ├── outputs │ │ ├── 2024-08-27 │ │ │ ├── 15-22-05 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 15-22-43 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ └── 21-14-16 │ │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ ├── 2024-08-28 │ │ │ ├── 13-31-03 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 13-36-06 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 13-40-33 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 13-52-43 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 13-58-15 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-00-13 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-00-54 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-01-14 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-04-17 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-04-34 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-04-50 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-05-06 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 14-05-24 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-29-19 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-29-56 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-32-09 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-33-54 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-34-39 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-37-31 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-42-54 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-42-56 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-42-59 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 18-43-01 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 19-06-17 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ ├── 19-06-19 │ │ │ │ └── .hydra │ │ │ │ │ ├── config.yaml │ │ │ │ │ ├── hydra.yaml │ │ │ │ │ └── overrides.yaml │ │ │ └── 19-06-21 │ │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ └── 2024-08-29 │ │ │ ├── 14-44-51 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 14-48-30 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-02-03 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-02-43 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-03-16 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-03-49 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-04-25 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-04-51 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ ├── 15-05-49 │ │ │ └── .hydra │ │ │ │ ├── config.yaml │ │ │ │ ├── hydra.yaml │ │ │ │ └── overrides.yaml │ │ │ └── 15-06-50 │ │ │ └── .hydra │ │ │ ├── config.yaml │ │ │ ├── hydra.yaml │ │ │ └── overrides.yaml │ ├── rename_package_dirs.sh │ ├── run_inference.sh │ ├── se3.yml │ ├── se3diff_analysis │ │ ├── metrics.py │ │ ├── plotting.py │ │ └── utils.py │ ├── se3diff_data │ │ ├── all_atom.py │ │ ├── chemical.py │ │ ├── errors.py │ │ ├── igso3.py │ │ ├── mmcif_parsing.py │ │ ├── parsers.py │ │ ├── pdb_data_loader.py │ │ ├── process_pdb_dataset.py │ │ ├── process_pdb_files.py │ │ ├── protein.py │ │ ├── r3_diffuser.py │ │ ├── residue_constants.py │ │ ├── se3_diffuser.py │ │ ├── so3_diffuser.py │ │ ├── so3_utils.py │ │ └── utils.py │ ├── se3diff_experiments │ │ ├── inference_se3_diffusion.py │ │ ├── train_se3_diffusion.py │ │ └── utils.py │ ├── se3diff_model │ │ ├── ipa_pytorch.py │ │ ├── layers.py │ │ └── score_network.py │ └── setup.py │ ├── superdiff │ ├── composition.py │ ├── config.yaml │ ├── config │ │ └── composition.yaml │ ├── inference.py │ └── run_inference.sh │ └── visualization │ ├── novel_proteins.ipynb │ └── protein_umap.ipynb ├── assets └── SD_examples.gif ├── cifar ├── configs │ ├── mnist_config.py │ └── sm │ │ └── cifar │ │ ├── vpsde.py │ │ ├── vpsdeA.py │ │ ├── vpsdeB.py │ │ ├── vpsde_less_5.py │ │ └── vpsde_more_5.py ├── datasets.py ├── dynamics.py ├── dynamics │ └── utils.py ├── eval_utils.py ├── evaluation.py ├── main.py ├── models │ ├── ddpm.py │ ├── layers.py │ ├── normalization.py │ └── utils.py ├── requirements.txt ├── run_lib.py └── train_utils.py └── notebooks ├── diffusion_edu.ipynb ├── eval_fld.ipynb ├── evals.ipynb ├── superposition_AND.ipynb ├── superposition_OR.ipynb ├── superposition_edu.ipynb └── visualizations.ipynb /.gitattributes: -------------------------------------------------------------------------------- 1 | *.ipynb linguist-vendored -------------------------------------------------------------------------------- /.gitignore: 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