LICENSE
README.md
THIRD_PARTY_NOTICES.md
pyproject.toml
src/blocks/__init__.py
src/blocks/constants.py
src/blocks/metrics/__init__.py
src/blocks/metrics/aromatic_neighbors.py
src/blocks/metrics/chirality.py
src/blocks/metrics/clash.py
src/blocks/metrics/contact_ms.py
src/blocks/metrics/dssr_snap_metrics.py
src/blocks/metrics/foldseek.py
src/blocks/metrics/hbond.py
src/blocks/metrics/ipsae.py
src/blocks/metrics/ligand_clash.py
src/blocks/metrics/ligand_ddg.py
src/blocks/metrics/ligand_ddg_soft.py
src/blocks/metrics/ligand_pocket.py
src/blocks/metrics/metal3d.py
src/blocks/metrics/motif_confidence.py
src/blocks/metrics/motif_reference.py
src/blocks/metrics/mpnn_score.py
src/blocks/metrics/peppr.py
src/blocks/metrics/plip.py
src/blocks/metrics/pocket_coulomb.py
src/blocks/metrics/ppi_ddg.py
src/blocks/metrics/py_contact_ms.py
src/blocks/metrics/rasa.py
src/blocks/metrics/rmsd.py
src/blocks/metrics/rna_connectivity.py
src/blocks/metrics/rna_ss_f1_mcc.py
src/blocks/metrics/rna_thermo.py
src/blocks/metrics/rotamer.py
src/blocks/metrics/secondary_structure.py
src/blocks/metrics/sequence_identity_gate.py
src/blocks/metrics/symmetry.py
src/blocks/metrics/tm_score.py
src/blocks/metrics/tm_score_rna.py
src/blocks/metrics/utils/__init__.py
src/blocks/metrics/utils/dihedrals.py
src/blocks/networks/__init__.py
src/blocks/networks/mpnn.py
src/blocks/networks/mpnn_io.py
src/blocks/networks/rfdiffusion1.py
src/blocks/networks/rfdiffusion2.py
src/blocks/networks/rpxdock.py
src/blocks/networks/tmol.py
src/blocks/networks/design/bindcraft.py
src/blocks/networks/design/boltzgen.py
src/blocks/networks/design/bindcraft2/__init__.py
src/blocks/networks/design/bindcraft2/block.py
src/blocks/networks/design/bindcraft2/container.py
src/blocks/networks/design/bindcraft2/input.md
src/blocks/networks/design/disco/disco.py
src/blocks/networks/design/disco/input.md
src/blocks/networks/design/proteina_complexa/__init__.py
src/blocks/networks/design/proteina_complexa/container.py
src/blocks/networks/design/proteina_complexa/input.md
src/blocks/networks/design/proteina_complexa/proteina_complexa.py
src/blocks/networks/foundry/__init__.py
src/blocks/networks/foundry/_aw3_compat.py
src/blocks/networks/foundry/_rfd3_compat.py
src/blocks/networks/foundry/_rfd3na_compat.py
src/blocks/networks/foundry/atomworks3.patch
src/blocks/networks/foundry/container.py
src/blocks/networks/foundry/mpnn.py
src/blocks/networks/foundry/rfd3na.md
src/blocks/networks/foundry/rfd3na.py
src/blocks/networks/foundry/rfd3na_input.py
src/blocks/networks/foundry/rfdiffusion3.md
src/blocks/networks/foundry/rfdiffusion3.py
src/blocks/networks/foundry/.assets/input_selection.png
src/blocks/networks/foundry/.assets/input_selection_large.png
src/blocks/networks/foundry/.assets/partial_diff.png
src/blocks/networks/foundry/rfoptimization/__init__.py
src/blocks/networks/foundry/rfoptimization/block.py
src/blocks/networks/foundry/rfoptimization/container.py
src/blocks/networks/foundry/rfoptimization/input.md
src/blocks/networks/hallucination/__init__.py
src/blocks/networks/hallucination/boltz2_steered.py
src/blocks/networks/hallucination/protein_hunter.py
src/blocks/networks/plm/__init__.py
src/blocks/networks/plm/e1.py
src/blocks/networks/plm/esm2.py
src/blocks/networks/prediction/__init__.py
src/blocks/networks/prediction/af3_with_target_template.py
src/blocks/networks/prediction/alphafold3.py
src/blocks/networks/prediction/boltz2.py
src/blocks/networks/prediction/chai1.py
src/blocks/networks/prediction/colabfold.py
src/blocks/networks/prediction/esmfold2.py
src/blocks/networks/prediction/helpers.py
src/blocks/networks/prediction/monomer_reference.py
src/blocks/networks/prediction/openfold3.py
src/blocks/networks/prediction/protenix.py
src/blocks/networks/prediction/rosettafold3.py
src/blocks/networks/prediction/simplefold.py
src/blocks/networks/prediction/validation/__init__.py
src/blocks/networks/prediction/validation/lddt.py
src/blocks/networks/prediction/validation/manifest.py
src/blocks/networks/prediction/validation/remap.py
src/blocks/networks/prediction/validation/score.py
src/blocks/scripts/boltz2_steered_predict.py
src/blocks/scripts/ddg_protocol.xml
src/blocks/scripts/flags_rescore_genpot
src/blocks/scripts/install_usalign.sh
src/blocks/scripts/predict_stoichiometry.py
src/blocks/scripts/rpxdock_run.py
src/blocks/scripts/run_alphafold_AF.py
src/blocks/scripts/run_bindcraft.py
src/blocks/scripts/run_e1.py
src/blocks/scripts/run_esm2.py
src/blocks/scripts/run_esmfold2_runner.py
src/blocks/scripts/run_metal3d.py
src/blocks/scripts/run_simplefold.py
src/blocks/scripts/run_tmol.py
src/blocks/util_blocks/__init__.py
src/blocks/util_blocks/_sequence_resolution.py
src/blocks/util_blocks/annotate.py
src/blocks/util_blocks/filter.py
src/blocks/util_blocks/ingest.py
src/blocks/util_blocks/materialize.py
src/blocks/util_blocks/mutate_residues.py
src/blocks/util_blocks/nanoparticle.py
src/blocks/util_blocks/order_collection.py
src/blocks/util_blocks/package_submission.py
src/blocks/util_blocks/parse.py
src/blocks/util_blocks/remap_ligand.py
src/blocks/util_blocks/repack_sidechains.py
src/blocks/util_blocks/restore_sidechains.py
src/blocks/util_blocks/rna_designs.py
src/blocks/util_blocks/rotamer_relax.py
src/blocks/util_blocks/rotamer_sweep.py
src/blocks/util_blocks/select_chains.py
src/blocks/util_blocks/select_diverse.py
src/blocks/util_blocks/select_motif.py
src/blocks/util_blocks/testing.py
src/blocks/util_blocks/transform.py
src/blocks/utils/geometry.py
src/blocks/utils/hbonds.py
src/blocks/utils/ligand.py
src/blocks/utils/ligand_bias.py
src/blocks/utils/oracles.py
src/blocks/utils/ori_sweep.py
src/blocks/utils/params.py
src/blocks/utils/pyrosetta.py
src/blocks/utils/rasa.py
src/blocks/utils/params/FAD.params
src/blocks/utils/params/IAI.params
src/blocks/utils/params/OQO.params
src/blocks/utils/params/SAM.params
src/chaperone/__init__.py
src/chaperone/artifacts.py
src/chaperone/common.py
src/chaperone/containers.py
src/chaperone/evals.py
src/chaperone/execution_tracking.py
src/chaperone/io.py
src/chaperone/manifest.py
src/chaperone/settings.py
src/chaperone/smoke_defaults.py
src/chaperone/visualization_helper.py
src/chaperone/block_config/__init__.py
src/chaperone/block_config/_log_tee.py
src/chaperone/block_config/base.py
src/chaperone/block_config/compiled.py
src/chaperone/block_config/decorators.py
src/chaperone/block_config/inline.py
src/chaperone/block_config/inline_metric.py
src/chaperone/block_config/manifest.py
src/chaperone/block_config/prediction.py
src/chaperone/block_config/runner.py
src/chaperone/data/__init__.py
src/chaperone/data/catcif.py
src/chaperone/data/components.py
src/chaperone/data/handler.py
src/chaperone/data/schema.py
src/chaperone/data/structure.py
src/chaperone/engine/__init__.py
src/chaperone/engine/base.py
src/chaperone/engine/chunking.py
src/chaperone/engine/cleanup.py
src/chaperone/engine/resolve.py
src/chaperone/orchestration/__init__.py
src/chaperone/orchestration/annotations.py
src/chaperone/orchestration/base_runner.py
src/chaperone/orchestration/futures.py
src/chaperone/orchestration/gpu_local_taskrunner.py
src/chaperone/orchestration/job_args.py
src/chaperone/orchestration/modal_backend.py
src/chaperone/orchestration/slurm_executors.py
src/chaperone/orchestration/slurm_futures.py
src/chaperone/orchestration/slurm_taskrunner.py
src/chaperone/orchestration/thread_runner.py
src/chaperone/site_profiles/digs.env
src/chaperone_cli/args.py
src/chaperone_cli/artifact_cmd.py
src/chaperone_cli/campaign_inspect.py
src/chaperone_cli/install.py
src/chaperone_cli/job_wait.py
src/chaperone_cli/main.py
src/chaperone_cli/registry.py
src/chaperone_cli/warmup.py
src/chaperone_pipelines.egg-info/PKG-INFO
src/chaperone_pipelines.egg-info/SOURCES.txt
src/chaperone_pipelines.egg-info/dependency_links.txt
src/chaperone_pipelines.egg-info/entry_points.txt
src/chaperone_pipelines.egg-info/requires.txt
src/chaperone_pipelines.egg-info/top_level.txt
tests/test_bindcraft2.py
tests/test_biotin_dna_ports.py
tests/test_block_docs_internal_fields.py
tests/test_catcif_roundtrip.py
tests/test_ccd_detection.py
tests/test_chain_cache_invalidation.py
tests/test_chunk_recovery.py
tests/test_chunk_retry.py
tests/test_compiled_command_failures.py
tests/test_contained_input_staging.py
tests/test_container_dns.py
tests/test_container_gpu_resources.py
tests/test_container_install_dir.py
tests/test_container_install_registry.py
tests/test_container_portability.py
tests/test_core_gpu_batch_smoke.py
tests/test_data_model.py
tests/test_disco_cuda_arch.py
tests/test_distribution.py
tests/test_empty_chunk_chain.py
tests/test_enzyme_ports.py
tests/test_esmfold2_runner_failures.py
tests/test_example_ports.py
tests/test_foundry_mpnn_virtual_atoms.py
tests/test_foundry_native_inference.py
tests/test_full_install.py
tests/test_gpu_block_smoke.py
tests/test_mkdir_p.py
tests/test_modal_backend.py
tests/test_modal_foundry.py
tests/test_monitoring.py
tests/test_mpnn_download_recovery.py
tests/test_mpnn_packing_smoke.py
tests/test_naming.py
tests/test_nanoparticle.py
tests/test_network_blocks.py
tests/test_optional_annotations.py
tests/test_parse_config.py
tests/test_pdb_io.py
tests/test_plip_native.py
tests/test_portable_pipeline_smoke.py
tests/test_ported_fixes.py
tests/test_proteina_complexa.py
tests/test_remaining_example_ports.py
tests/test_rfd1_motif_mapping.py
tests/test_rfd3_compile.py
tests/test_rfd3na_compat.py
tests/test_rfoptimization.py
tests/test_ribozyme_ports.py
tests/test_rmsd_symmetry_annotations.py
tests/test_runtime.py
tests/test_sequence_workflows.py
tests/test_site_paths.py
tests/test_site_settings.py
tests/test_slurm_resources.py
tests/test_smoke_mode.py
tests/test_structure_functions.py
tests/test_visualization_helper.py