├── .env ├── .github └── workflows │ └── lint_production.yaml ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── .project-root ├── LICENSE.md ├── Makefile ├── README.md ├── docs ├── _static │ ├── cover.png │ ├── image.png │ ├── prot_dna.png │ └── superimposed_80_residue_protein.png └── releases │ ├── rf3 │ └── examples │ │ ├── 3en2_from_file.cif │ │ ├── 3en2_from_json_with_msa.json │ │ ├── 5hkn_from_file.cif │ │ ├── 7o1r_from_json.json │ │ ├── 7xli_template_antigen_and_framework.json │ │ ├── 9dfn.cif │ │ ├── 9dfn_template_ligand_and_protein.json │ │ ├── ligands │ │ ├── HEM.sdf │ │ └── NAG.cif │ │ ├── msas │ │ ├── 3en2_A.a3m.gz │ │ ├── 7o1r_A.a3m.gz │ │ └── 8cdz_A.a3m.gz │ │ ├── multiple_examples_from_json.json │ │ └── templates │ │ ├── 7xli_chain_A.cif │ │ └── 7xli_chain_B.cif │ └── rfd3 │ └── examples │ └── README.md ├── examples ├── all.ipynb ├── enzymes.ipynb └── ipd_design_pipeline_collab.ipynb ├── models ├── mpnn │ ├── README.md │ ├── src │ │ └── mpnn │ │ │ ├── __init__.py │ │ │ ├── collate │ │ │ └── feature_collator.py │ │ │ ├── inference.py │ │ │ ├── inference_engines │ │ │ └── mpnn.py │ │ │ ├── loss │ │ │ └── nll_loss.py │ │ │ ├── metrics │ │ │ ├── nll.py │ │ │ └── sequence_recovery.py │ │ │ ├── model │ │ │ ├── layers │ │ │ │ ├── graph_embeddings.py │ │ │ │ ├── message_passing.py │ │ │ │ ├── position_wise_feed_forward.py │ │ │ │ └── positional_encoding.py │ │ │ └── mpnn.py │ │ │ ├── pipelines │ │ │ └── mpnn.py │ │ │ ├── samplers │ │ │ └── samplers.py │ │ │ ├── train.py │ │ │ ├── trainers │ │ │ └── mpnn.py │ │ │ ├── transforms │ │ │ ├── feature_aggregation │ │ │ │ ├── mpnn.py │ │ │ │ ├── polymer_ligand_interface.py │ │ │ │ ├── token_encodings.py │ │ │ │ └── user_settings.py │ │ │ └── polymer_ligand_interface.py │ │ │ └── utils │ │ │ ├── inference.py │ │ │ ├── probability.py │ │ │ └── weights.py │ └── tests │ │ ├── conftest.py │ │ ├── test_feature_collator.py │ │ ├── test_inference_engine.py │ │ ├── test_inference_utils.py │ │ ├── test_integration.py │ │ ├── test_loss.py │ │ ├── test_metrics.py │ │ ├── test_model.py │ │ ├── test_pipeline.py │ │ ├── test_polymer_ligand_interface.py │ │ ├── test_samplers.py │ │ └── test_utils.py ├── rf3 │ ├── README.md │ ├── configs │ │ ├── callbacks │ │ │ ├── default.yaml │ │ │ ├── dump_validation_structures.yaml │ │ │ ├── metrics_logging.yaml │ │ │ └── train_logging.yaml │ │ ├── dataloader │ │ │ └── default.yaml │ │ ├── datasets │ │ │ ├── base.yaml │ │ │ ├── pdb_and_distillation.yaml │ │ │ ├── pdb_only.yaml │ │ │ ├── train │ │ │ │ ├── disorder_distillation.yaml │ │ │ │ ├── domain_distillation.yaml │ │ │ │ ├── monomer_distillation.yaml │ │ │ │ ├── na_complex_distillation.yaml │ │ │ │ ├── pdb │ │ │ │ │ ├── af3_weighted_sampling.yaml │ │ │ │ │ ├── base.yaml │ │ │ │ │ ├── plinder.yaml │ │ │ │ │ ├── train_interface.yaml │ │ │ │ │ └── train_pn_unit.yaml │ │ │ │ └── rna_monomer_distillation.yaml │ │ │ └── val │ │ │ │ ├── af3_ab_set.yaml │ │ │ │ ├── af3_validation.yaml │ │ │ │ ├── base.yaml │ │ │ │ └── runs_and_poses.yaml │ │ ├── debug │ │ │ ├── default.yaml │ │ │ └── train_specific_examples.yaml │ │ ├── experiment │ │ │ ├── pretrained │ │ │ │ ├── rf3.yaml │ │ │ │ └── rf3_with_confidence.yaml │ │ │ ├── quick-rf3-with-confidence.yaml │ │ │ └── quick-rf3.yaml │ │ ├── hydra │ │ │ ├── default.yaml │ │ │ └── no_logging.yaml │ │ ├── inference.yaml │ │ ├── inference_engine │ │ │ ├── base.yaml │ │ │ └── rf3.yaml │ │ ├── logger │ │ │ ├── csv.yaml │ │ │ ├── default.yaml │ │ │ └── wandb.yaml │ │ ├── model │ │ │ ├── components │ │ │ │ ├── ema.yaml │ │ │ │ ├── rf3_net.yaml │ │ │ │ └── rf3_net_with_confidence_head.yaml │ │ │ ├── optimizers │ │ │ │ └── adam.yaml │ │ │ ├── rf3.yaml │ │ │ ├── rf3_with_confidence.yaml │ │ │ └── schedulers │ │ │ │ └── af3.yaml │ │ ├── paths │ │ │ ├── data │ │ │ │ └── default.yaml │ │ │ └── default.yaml │ │ ├── train.yaml │ │ ├── trainer │ │ │ ├── cpu.yaml │ │ │ ├── ddp.yaml │ │ │ ├── loss │ │ │ │ ├── losses │ │ │ │ │ ├── confidence_loss.yaml │ │ │ │ │ ├── diffusion_loss.yaml │ │ │ │ │ └── distogram_loss.yaml │ │ │ │ ├── structure_prediction.yaml │ │ │ │ └── structure_prediction_with_confidence.yaml │ │ │ ├── metrics │ │ │ │ └── structure_prediction.yaml │ │ │ ├── rf3.yaml │ │ │ └── rf3_with_confidence.yaml │ │ └── validate.yaml │ ├── src │ │ └── rf3 │ │ │ ├── __init__.py │ │ │ ├── _version.py │ │ │ ├── alignment.py │ │ │ ├── callbacks │ │ │ ├── dump_validation_structures.py │ │ │ └── metrics_logging.py │ │ │ ├── chemical.py │ │ │ ├── cli.py │ │ │ ├── data │ │ │ ├── cyclic_transform.py │ │ │ ├── extra_xforms.py │ │ │ ├── ground_truth_template.py │ │ │ ├── paired_msa.py │ │ │ ├── pipeline_utils.py │ │ │ └── pipelines.py │ │ │ ├── diffusion_samplers │ │ │ └── inference_sampler.py │ │ │ ├── inference.py │ │ │ ├── inference_engines │ │ │ ├── __init__.py │ │ │ └── rf3.py │ │ │ ├── kinematics.py │ │ │ ├── loss │ │ │ ├── af3_confidence_loss.py │ │ │ ├── af3_losses.py │ │ │ └── loss.py │ │ │ ├── metrics │ │ │ ├── chiral.py │ │ │ ├── clashing_chains.py │ │ │ ├── distogram.py │ │ │ ├── lddt.py │ │ │ ├── metadata.py │ │ │ ├── metric_utils.py │ │ │ ├── predicted_error.py │ │ │ ├── rasa.py │ │ │ └── selected_distances.py │ │ │ ├── model │ │ │ ├── RF3.py │ │ │ ├── RF3_blocks.py │ │ │ ├── RF3_structure.py │ │ │ └── layers │ │ │ │ ├── af3_auxiliary_heads.py │ │ │ │ ├── af3_diffusion_transformer.py │ │ │ │ ├── attention.py │ │ │ │ ├── layer_utils.py │ │ │ │ ├── mlff.py │ │ │ │ ├── outer_product.py │ │ │ │ ├── pairformer_layers.py │ │ │ │ └── structure_bias.py │ │ │ ├── scoring.py │ │ │ ├── symmetry │ │ │ └── resolve.py │ │ │ ├── train.py │ │ │ ├── trainers │ │ │ └── rf3.py │ │ │ ├── util_module.py │ │ │ ├── utils │ │ │ ├── frames.py │ │ │ ├── inference.py │ │ │ ├── io.py │ │ │ ├── loss.py │ │ │ ├── predict_and_score.py │ │ │ ├── predicted_error.py │ │ │ └── recycling.py │ │ │ └── validate.py │ └── tests │ │ ├── .gitkeep │ │ ├── conftest.py │ │ ├── data │ │ ├── 5vht_from_file.cif │ │ ├── 5vht_from_json.json │ │ ├── 8vkf_from_file.cif │ │ ├── example_from_pdb_with_inter_chain_bond.pdb │ │ ├── example_pdb_with_clashing_ligand_name.pdb │ │ ├── example_with_ncaa.json │ │ ├── inference_regression_tests │ │ │ ├── 5vht_from_file │ │ │ │ ├── 5vht_from_file_model.cif │ │ │ │ └── 5vht_from_file_summary_confidences.json │ │ │ └── 8vkf_from_file │ │ │ │ ├── 8vkf_from_file_model.cif │ │ │ │ └── 8vkf_from_file_summary_confidences.json │ │ ├── msas │ │ │ ├── 5vht_A.a3m │ │ │ └── 8vkf_A.a3m │ │ ├── multiple_examples_from_json.json │ │ ├── ncaa │ │ │ ├── create_cif_with_ligand_as_ncaa.ipynb │ │ │ ├── ligand_as_ncaa.cif │ │ │ └── penicillin_ts2_as_ncaa.cif │ │ └── nested_examples │ │ │ ├── example_from_json.json │ │ │ └── example_from_pdb_with_inter_chain_bonds.and.dots.pdb │ │ ├── test_chiral_metrics.py │ │ ├── test_inference_regression.py │ │ └── test_write_confidence.py └── rfd3 │ ├── .gitignore │ ├── README.md │ ├── configs │ ├── __init__.py │ ├── callbacks │ │ ├── design_callbacks.yaml │ │ ├── metrics_logging.yaml │ │ └── train_logging.yaml │ ├── dataloader │ │ ├── default.yaml │ │ └── fast.yaml │ ├── datasets │ │ ├── conditions │ │ │ ├── dna_condition.yaml │ │ │ ├── island.yaml │ │ │ ├── ppi.yaml │ │ │ ├── sequence_design.yaml │ │ │ ├── tipatom.yaml │ │ │ └── unconditional.yaml │ │ ├── design_base.yaml │ │ ├── train │ │ │ ├── pdb │ │ │ │ ├── af3_train_interface.yaml │ │ │ │ ├── af3_train_pn_unit.yaml │ │ │ │ ├── base.yaml │ │ │ │ ├── base_no_weights.yaml │ │ │ │ ├── base_transform_args.yaml │ │ │ │ ├── na_complex_distillation.yaml │ │ │ │ ├── pdb_base.yaml │ │ │ │ ├── rfd3_train_interface.yaml │ │ │ │ └── rfd3_train_pn_unit.yaml │ │ │ └── rfd3_monomer_distillation.yaml │ │ └── val │ │ │ ├── bcov_ppi_easy_medium.yaml │ │ │ ├── benchmarks │ │ │ ├── design_validation_base.yaml │ │ │ ├── dna_binder_design5.yaml │ │ │ ├── dna_binder_long.yaml │ │ │ ├── dna_binder_short.yaml │ │ │ ├── indexed.yaml │ │ │ ├── mcsa_41.yaml │ │ │ ├── mcsa_41_short_rigid.yaml │ │ │ ├── ppi_inference.yaml │ │ │ ├── sm_binder_hbonds.yaml │ │ │ ├── sm_binder_hbonds_short.yaml │ │ │ ├── unconditional.yaml │ │ │ ├── unconditional_deep.yaml │ │ │ ├── unindexed.yaml │ │ │ └── val_examples │ │ │ ├── bcov_ppi_easy_medium_with_ori.yaml │ │ │ ├── bcov_ppi_easy_medium_with_ori_spoof_helical_bundle.yaml │ │ │ ├── bcov_ppi_easy_medium_with_ori_varying_lengths.yaml │ │ │ └── bpem_ori_hb.yaml │ ├── debug │ │ ├── default.yaml │ │ └── train_specific_examples.yaml │ ├── dev.yaml │ ├── experiment │ │ ├── debug.yaml │ │ ├── pretrain.yaml │ │ ├── test-uncond.yaml │ │ └── test-unindexed.yaml │ ├── hydra │ │ ├── default.yaml │ │ └── no_logging.yaml │ ├── inference.yaml │ ├── inference_engine │ │ ├── base.yaml │ │ ├── dev.yaml │ │ └── rfdiffusion3.yaml │ ├── logger │ │ ├── csv.yaml │ │ ├── default.yaml │ │ └── wandb.yaml │ ├── model │ │ ├── components │ │ │ ├── ema.yaml │ │ │ └── rfd3_net.yaml │ │ ├── optimizers │ │ │ └── adam.yaml │ │ ├── rfd3_base.yaml │ │ ├── samplers │ │ │ ├── edm.yaml │ │ │ └── symmetry.yaml │ │ └── schedulers │ │ │ └── af3.yaml │ ├── paths │ │ ├── data │ │ │ └── default.yaml │ │ └── default.yaml │ ├── train.yaml │ ├── trainer │ │ ├── cpu.yaml │ │ ├── ddp.yaml │ │ ├── loss │ │ │ └── losses │ │ │ │ ├── diffusion_loss.yaml │ │ │ │ └── sequence_loss.yaml │ │ ├── metrics │ │ │ └── design_metrics.yaml │ │ └── rfd3_base.yaml │ └── validate.yaml │ ├── docs │ ├── .assets │ │ ├── conditioning.png │ │ ├── dna.png │ │ ├── enzyme.png │ │ ├── input_selection.png │ │ ├── input_selection_large.png │ │ ├── overview.png │ │ ├── partial_diff.png │ │ ├── ppi.png │ │ ├── sm.png │ │ ├── symm.png │ │ └── trajectory.png │ ├── demo.json │ ├── enzyme_design.json │ ├── enzyme_design.md │ ├── get_na_input.sh │ ├── input.md │ ├── input_pdbs │ │ ├── 1bna.pdb │ │ ├── 1q75.pdb │ │ ├── 2r5z.pdb │ │ ├── 4zxb_cropped.pdb │ │ ├── 5o45_cropped.pdb │ │ ├── 5o4d.pdb │ │ ├── 7v11.pdb │ │ ├── IAI.pdb │ │ ├── M0255_1mg5.pdb │ │ └── symmetry_examples │ │ │ ├── 1bfr_C2.pdb │ │ │ ├── 1e3v_C2.pdb │ │ │ ├── 1j79_C2.pdb │ │ │ └── 6t8h_C3.pdb │ ├── na_binder_design.json │ ├── na_binder_design.md │ ├── protein_binder_design.json │ ├── protein_binder_design.md │ ├── run_inf_tutorial.sh │ ├── sm_binder_design.json │ ├── sm_binder_design.md │ └── symmetry.md │ ├── src │ └── rfd3 │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── __init__.py │ │ ├── callbacks.py │ │ ├── cli.py │ │ ├── constants.py │ │ ├── engine.py │ │ ├── inference │ │ ├── datasets.py │ │ ├── input_parsing.py │ │ ├── legacy_input_parsing.py │ │ ├── parsing.py │ │ └── symmetry │ │ │ ├── atom_array.py │ │ │ ├── checks.py │ │ │ ├── contigs.py │ │ │ ├── frames.py │ │ │ └── symmetry_utils.py │ │ ├── metrics │ │ ├── design_metrics.py │ │ ├── hbonds_hbplus_metrics.py │ │ ├── hbonds_metrics.py │ │ ├── losses.py │ │ ├── metrics_utils.py │ │ └── sidechain_metrics.py │ │ ├── model │ │ ├── RFD3.py │ │ ├── RFD3_diffusion_module.py │ │ ├── cfg_utils.py │ │ ├── inference_sampler.py │ │ └── layers │ │ │ ├── attention.py │ │ │ ├── block_utils.py │ │ │ ├── blocks.py │ │ │ ├── chunked_pairwise.py │ │ │ ├── encoders.py │ │ │ ├── layer_utils.py │ │ │ └── pairformer_layers.py │ │ ├── run_inference.py │ │ ├── testing │ │ ├── debug.py │ │ ├── debug_utils.py │ │ └── testing_utils.py │ │ ├── train.py │ │ ├── trainer │ │ ├── dump_validation_structures.py │ │ ├── fabric_trainer.py │ │ ├── recycling.py │ │ ├── rfd3.py │ │ └── trainer_utils.py │ │ ├── transforms │ │ ├── conditioning_base.py │ │ ├── conditioning_utils.py │ │ ├── design_transforms.py │ │ ├── dna_crop.py │ │ ├── hbonds.py │ │ ├── hbonds_hbplus.py │ │ ├── ncaa_transforms.py │ │ ├── pipelines.py │ │ ├── ppi_transforms.py │ │ ├── rasa.py │ │ ├── symmetry.py │ │ ├── training_conditions.py │ │ ├── util_transforms.py │ │ └── virtual_atoms.py │ │ └── utils │ │ ├── inference.py │ │ ├── io.py │ │ └── vizualize.py │ └── tests │ ├── conftest.py │ ├── test_aa_design.py │ ├── test_conditioning.py │ ├── test_glycines.py │ ├── test_legacy_pipeline_equivalence.py │ ├── test_metrics.py │ ├── test_partial_diffusion.py │ ├── test_selections.py │ ├── test_subgraph_sampling.py │ ├── test_symmetry.py │ ├── test_tokenization.py │ ├── test_unindexing.py │ └── transforms │ ├── regression_test_data │ ├── 1p5d_0_inference_pretrain.pkl │ ├── 1p5d_0_train_pretrain.pkl │ ├── 1qys_0_inference_pretrain.pkl │ ├── 1qys_0_train_pretrain.pkl │ └── af2_122_train_test_unindexed.pkl │ └── test_pipeline_regression.py ├── pyproject.toml ├── refactor.sh ├── src ├── foundry │ ├── __init__.py │ ├── callbacks │ │ ├── __init__.py │ │ ├── callback.py │ │ ├── health_logging.py │ │ ├── metrics_logging.py │ │ ├── timing_logging.py │ │ └── train_logging.py │ ├── common.py │ ├── constants.py │ ├── hydra │ │ └── resolvers.py │ ├── inference_engines │ │ ├── base.py │ │ └── checkpoint_registry.py │ ├── metrics │ │ ├── __init__.py │ │ ├── losses.py │ │ └── metric.py │ ├── model │ │ └── layers │ │ │ └── blocks.py │ ├── testing │ │ ├── __init__.py │ │ ├── fixtures.py │ │ └── pytest_hooks.py 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