LICENSE
MANIFEST.in
NOTICE
README.md
pyproject.toml
tests/test_accurate_softmax_defaults.py
tests/test_batch_position_gate.py
tests/test_batched_matmul_hw.py
tests/test_boltz2_sample_chunk.py
tests/test_boltzgen.py
tests/test_boltzgen_designability.py
tests/test_boltzgen_regression.py
tests/test_cache_contract.py
tests/test_concat_host_budget.py
tests/test_constraints.py
tests/test_design_info_requires_design_residue.py
tests/test_device_lease.py
tests/test_device_lease_hw.py
tests/test_edm_sample_multiplicity.py
tests/test_envflags.py
tests/test_esmc.py
tests/test_esmfold2.py
tests/test_esmfold2_cif_write.py
tests/test_esmfold2_modifications.py
tests/test_esmfold2_msa_depth_cap.py
tests/test_fp32_softmax_l1_backoff.py
tests/test_full_parity_gate.py
tests/test_input_validation.py
tests/test_l1_budget_gate.py
tests/test_l1_out_rung_backoff.py
tests/test_lever_census_reasons.py
tests/test_msa_cache_key.py
tests/test_msa_default.py
tests/test_opendde_covalent_ligand.py
tests/test_openfold3_atom_transformer.py
tests/test_openfold3_cli.py
tests/test_openfold3_confidence.py
tests/test_openfold3_diffusion_conditioning.py
tests/test_openfold3_diffusion_decoder.py
tests/test_openfold3_diffusion_module_xlout.py
tests/test_openfold3_diffusion_transformer.py
tests/test_openfold3_fold_rmsd.py
tests/test_openfold3_input_embedder.py
tests/test_openfold3_msa.py
tests/test_openfold3_msa_embedder.py
tests/test_openfold3_noisy_position_embedder.py
tests/test_openfold3_pairformer.py
tests/test_openfold3_ref_atom_feat.py
tests/test_openfold3_sample_diffusion.py
tests/test_openfold3_template.py
tests/test_openfold3_trunk.py
tests/test_pair_l1_consumer_reserve.py
tests/test_parity_gate_workdir_provenance.py
tests/test_pdb_bfactor.py
tests/test_perf_citations.py
tests/test_pharma_parity.py
tests/test_predict_exit_code.py
tests/test_predict_progress.py
tests/test_protenix.py
tests/test_protenix_atomfeat.py
tests/test_protenix_atomtx.py
tests/test_protenix_confidence.py
tests/test_protenix_data.py
tests/test_protenix_diffusion.py
tests/test_protenix_diffusion_cond.py
tests/test_protenix_dit_consistent.py
tests/test_protenix_fold.py
tests/test_protenix_ife.py
tests/test_protenix_largeN.py
tests/test_protenix_ligand.py
tests/test_protenix_msa.py
tests/test_protenix_na.py
tests/test_protenix_seqfold.py
tests/test_protenix_traj.py
tests/test_protenix_trunk_class.py
tests/test_protenix_trunk_msa.py
tests/test_protenix_trunk_pairformer.py
tests/test_protenix_trunk_template.py
tests/test_protenix_trunkin.py
tests/test_recycling_default.py
tests/test_release_gate_msa_preflight.py
tests/test_repo_root_clean.py
tests/test_repo_size_guard.py
tests/test_rf3_featurizer.py
tests/test_rf3_partial_and_earlystop.py
tests/test_rf3_progress_events.py
tests/test_runtime.py
tests/test_sampling_default.py
tests/test_saturation_crossover.py
tests/test_shared_outputs.py
tests/test_size_ladder_gate.py
tests/test_structure.py
tests/test_template_l1_consumer_margin.py
tests/test_tenstorrent.py
tests/test_trimul_chunk_budget.py
tests/test_visible_devices.py
tests/test_weights_registry.py
tests/test_windowing_m_shapes.py
tests/test_windowing_multiplicity.py
tests/test_worker_liveness.py
tt_bio/__init__.py
tt_bio/boltz2.py
tt_bio/cache.py
tt_bio/device_lease.py
tt_bio/distributed.py
tt_bio/energy.py
tt_bio/envflags.py
tt_bio/esmc.py
tt_bio/esmfold2.py
tt_bio/esmfold2_runtime.py
tt_bio/install_system_deps.py
tt_bio/main.py
tt_bio/mm_dualnoc.py
tt_bio/mm_generic.py
tt_bio/msa_server.py
tt_bio/opendde.py
tt_bio/opendde_data.py
tt_bio/openfold3.py
tt_bio/openfold3_atom_transformer.py
tt_bio/openfold3_confidence.py
tt_bio/openfold3_data.py
tt_bio/openfold3_diffusion.py
tt_bio/openfold3_diffusion_decoder.py
tt_bio/openfold3_diffusion_module.py
tt_bio/openfold3_diffusion_transformer.py
tt_bio/openfold3_fold.py
tt_bio/openfold3_host_prep.py
tt_bio/openfold3_msa_embedder.py
tt_bio/openfold3_sample_diffusion.py
tt_bio/openfold3_template.py
tt_bio/openfold3_trunk.py
tt_bio/openfold3_weights.py
tt_bio/progress.py
tt_bio/protenix.py
tt_bio/protenix_data.py
tt_bio/protenix_weights.py
tt_bio/reblock_permute.py
tt_bio/reference.py
tt_bio/rfd3_bias.py
tt_bio/runtime.py
tt_bio/saprot.py
tt_bio/sdpa_generic.py
tt_bio/softmax_generic.py
tt_bio/tenstorrent.py
tt_bio/triatt_qkv.py
tt_bio/triatt_sdpa.py
tt_bio/trimul_tail.py
tt_bio/weights.py
tt_bio/worker.py
tt_bio.egg-info/PKG-INFO
tt_bio.egg-info/SOURCES.txt
tt_bio.egg-info/dependency_links.txt
tt_bio.egg-info/entry_points.txt
tt_bio.egg-info/requires.txt
tt_bio.egg-info/top_level.txt
tt_bio/_vendor/__init__.py
tt_bio/_vendor/atomworks/__init__.py
tt_bio/_vendor/atomworks/_compat.py
tt_bio/_vendor/atomworks/biotite_patch.py
tt_bio/_vendor/atomworks/common.py
tt_bio/_vendor/atomworks/constants.py
tt_bio/_vendor/atomworks/enums.py
tt_bio/_vendor/atomworks/py.typed
tt_bio/_vendor/atomworks/io/__init__.py
tt_bio/_vendor/atomworks/io/parser.py
tt_bio/_vendor/atomworks/io/template.py
tt_bio/_vendor/atomworks/io/tools/chembl_transformations.smirks
tt_bio/_vendor/atomworks/io/tools/fasta.py
tt_bio/_vendor/atomworks/io/tools/inference.py
tt_bio/_vendor/atomworks/io/tools/rdkit.py
tt_bio/_vendor/atomworks/io/transforms/atom_array.py
tt_bio/_vendor/atomworks/io/transforms/categories.py
tt_bio/_vendor/atomworks/io/utils/__init__.py
tt_bio/_vendor/atomworks/io/utils/assembly.py
tt_bio/_vendor/atomworks/io/utils/atom_array.py
tt_bio/_vendor/atomworks/io/utils/atom_array_plus.py
tt_bio/_vendor/atomworks/io/utils/bonds.py
tt_bio/_vendor/atomworks/io/utils/ccd.py
tt_bio/_vendor/atomworks/io/utils/chain.py
tt_bio/_vendor/atomworks/io/utils/compression.py
tt_bio/_vendor/atomworks/io/utils/error.py
tt_bio/_vendor/atomworks/io/utils/io_utils.py
tt_bio/_vendor/atomworks/io/utils/non_rcsb.py
tt_bio/_vendor/atomworks/io/utils/query.py
tt_bio/_vendor/atomworks/io/utils/scatter.py
tt_bio/_vendor/atomworks/io/utils/selection.py
tt_bio/_vendor/atomworks/io/utils/sequence.py
tt_bio/_vendor/atomworks/io/utils/testing.py
tt_bio/_vendor/atomworks/io/utils/visualize.py
tt_bio/_vendor/atomworks/ml/__init__.py
tt_bio/_vendor/atomworks/ml/encoding_definitions.py
tt_bio/_vendor/atomworks/ml/example_id.py
tt_bio/_vendor/atomworks/ml/samplers.py
tt_bio/_vendor/atomworks/ml/conditions/__init__.py
tt_bio/_vendor/atomworks/ml/conditions/annotator.py
tt_bio/_vendor/atomworks/ml/conditions/base.py
tt_bio/_vendor/atomworks/ml/conditions/conditions.py
tt_bio/_vendor/atomworks/ml/datasets/README.md
tt_bio/_vendor/atomworks/ml/datasets/__init__.py
tt_bio/_vendor/atomworks/ml/datasets/base.py
tt_bio/_vendor/atomworks/ml/datasets/concat_dataset.py
tt_bio/_vendor/atomworks/ml/datasets/file_dataset.py
tt_bio/_vendor/atomworks/ml/datasets/pandas_dataset.py
tt_bio/_vendor/atomworks/ml/datasets/loaders/__init__.py
tt_bio/_vendor/atomworks/ml/datasets/loaders/base.py
tt_bio/_vendor/atomworks/ml/datasets/loaders/cif.py
tt_bio/_vendor/atomworks/ml/datasets/parsers/__init__.py
tt_bio/_vendor/atomworks/ml/datasets/parsers/base.py
tt_bio/_vendor/atomworks/ml/datasets/parsers/custom_metadata_row_parsers.py
tt_bio/_vendor/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py
tt_bio/_vendor/atomworks/ml/executables/__init__.py
tt_bio/_vendor/atomworks/ml/executables/hbplus.py
tt_bio/_vendor/atomworks/ml/executables/hhfilter.py
tt_bio/_vendor/atomworks/ml/executables/mmseqs2.py
tt_bio/_vendor/atomworks/ml/executables/x3dna.py
tt_bio/_vendor/atomworks/ml/pipelines/__init__.py
tt_bio/_vendor/atomworks/ml/pipelines/af3.py
tt_bio/_vendor/atomworks/ml/pipelines/rf2aa.py
tt_bio/_vendor/atomworks/ml/preprocessing/__init__.py
tt_bio/_vendor/atomworks/ml/preprocessing/constants.py
tt_bio/_vendor/atomworks/ml/preprocessing/get_pn_unit_data_from_structure.py
tt_bio/_vendor/atomworks/ml/preprocessing/msa/filtering.py
tt_bio/_vendor/atomworks/ml/preprocessing/msa/finding.py
tt_bio/_vendor/atomworks/ml/preprocessing/msa/generating.py
tt_bio/_vendor/atomworks/ml/preprocessing/msa/organizing.py
tt_bio/_vendor/atomworks/ml/preprocessing/utils/fasta.py
tt_bio/_vendor/atomworks/ml/preprocessing/utils/structure_utils.py
tt_bio/_vendor/atomworks/ml/transforms/_checks.py
tt_bio/_vendor/atomworks/ml/transforms/af3_reference_molecule.py
tt_bio/_vendor/atomworks/ml/transforms/atom_array.py
tt_bio/_vendor/atomworks/ml/transforms/atom_frames.py
tt_bio/_vendor/atomworks/ml/transforms/atom_level_embeddings.py
tt_bio/_vendor/atomworks/ml/transforms/atomize.py
tt_bio/_vendor/atomworks/ml/transforms/base.py
tt_bio/_vendor/atomworks/ml/transforms/bfactor_conditioned_transforms.py
tt_bio/_vendor/atomworks/ml/transforms/bonds.py
tt_bio/_vendor/atomworks/ml/transforms/cached_residue_data.py
tt_bio/_vendor/atomworks/ml/transforms/center_random_augmentation.py
tt_bio/_vendor/atomworks/ml/transforms/chirals.py
tt_bio/_vendor/atomworks/ml/transforms/covalent_modifications.py
tt_bio/_vendor/atomworks/ml/transforms/crop.py
tt_bio/_vendor/atomworks/ml/transforms/design_task.py
tt_bio/_vendor/atomworks/ml/transforms/encoding.py
tt_bio/_vendor/atomworks/ml/transforms/featurize_unresolved_residues.py
tt_bio/_vendor/atomworks/ml/transforms/filters.py
tt_bio/_vendor/atomworks/ml/transforms/mask_generator.py
tt_bio/_vendor/atomworks/ml/transforms/masks.py
tt_bio/_vendor/atomworks/ml/transforms/mirror_transform.py
tt_bio/_vendor/atomworks/ml/transforms/openbabel_utils.py
tt_bio/_vendor/atomworks/ml/transforms/random_atomize_residues.py
tt_bio/_vendor/atomworks/ml/transforms/rdkit_utils.py
tt_bio/_vendor/atomworks/ml/transforms/rf2aa_assumptions.py
tt_bio/_vendor/atomworks/ml/transforms/sasa.py
tt_bio/_vendor/atomworks/ml/transforms/symmetry.py
tt_bio/_vendor/atomworks/ml/transforms/template.py
tt_bio/_vendor/atomworks/ml/transforms/diffusion/batch_structures.py
tt_bio/_vendor/atomworks/ml/transforms/diffusion/edm.py
tt_bio/_vendor/atomworks/ml/transforms/dna/pad_dna.py
tt_bio/_vendor/atomworks/ml/transforms/feature_aggregation/af3.py
tt_bio/_vendor/atomworks/ml/transforms/feature_aggregation/confidence.py
tt_bio/_vendor/atomworks/ml/transforms/feature_aggregation/rf2aa.py
tt_bio/_vendor/atomworks/ml/transforms/msa/_msa_constants.py
tt_bio/_vendor/atomworks/ml/transforms/msa/_msa_featurizing_utils.py
tt_bio/_vendor/atomworks/ml/transforms/msa/_msa_loading_utils.py
tt_bio/_vendor/atomworks/ml/transforms/msa/_msa_pairing_utils.py
tt_bio/_vendor/atomworks/ml/transforms/msa/msa.py
tt_bio/_vendor/atomworks/ml/utils/__init__.py
tt_bio/_vendor/atomworks/ml/utils/condition.py
tt_bio/_vendor/atomworks/ml/utils/debug.py
tt_bio/_vendor/atomworks/ml/utils/error.py
tt_bio/_vendor/atomworks/ml/utils/geometry.py
tt_bio/_vendor/atomworks/ml/utils/io.py
tt_bio/_vendor/atomworks/ml/utils/misc.py
tt_bio/_vendor/atomworks/ml/utils/nested_dict.py
tt_bio/_vendor/atomworks/ml/utils/numpy.py
tt_bio/_vendor/atomworks/ml/utils/rng.py
tt_bio/_vendor/atomworks/ml/utils/testing.py
tt_bio/_vendor/atomworks/ml/utils/timer.py
tt_bio/_vendor/atomworks/ml/utils/token.py
tt_bio/_vendor/esm/LICENSE
tt_bio/_vendor/esm/__init__.py
tt_bio/_vendor/esm/models/__init__.py
tt_bio/_vendor/esm/models/esmfold2/__init__.py
tt_bio/_vendor/esm/models/esmfold2/conformers.py
tt_bio/_vendor/esm/models/esmfold2/constants.py
tt_bio/_vendor/esm/models/esmfold2/output.py
tt_bio/_vendor/esm/models/esmfold2/paired_msa.py
tt_bio/_vendor/esm/models/esmfold2/prepare_input.py
tt_bio/_vendor/esm/models/esmfold2/processor.py
tt_bio/_vendor/esm/models/esmfold2/types.py
tt_bio/_vendor/esm/utils/__init__.py
tt_bio/_vendor/esm/utils/misc.py
tt_bio/_vendor/esm/utils/parsing.py
tt_bio/_vendor/esm/utils/residue_constants.py
tt_bio/_vendor/esm/utils/sequential_dataclass.py
tt_bio/_vendor/esm/utils/system.py
tt_bio/_vendor/esm/utils/types.py
tt_bio/_vendor/esm/utils/constants/__init__.py
tt_bio/_vendor/esm/utils/constants/esm3.py
tt_bio/_vendor/esm/utils/msa/__init__.py
tt_bio/_vendor/esm/utils/msa/filter_sequences.py
tt_bio/_vendor/esm/utils/msa/msa.py
tt_bio/_vendor/esm/utils/structure/__init__.py
tt_bio/_vendor/esm/utils/structure/affine3d.py
tt_bio/_vendor/esm/utils/structure/aligner.py
tt_bio/_vendor/esm/utils/structure/atom_indexer.py
tt_bio/_vendor/esm/utils/structure/input_builder.py
tt_bio/_vendor/esm/utils/structure/metrics.py
tt_bio/_vendor/esm/utils/structure/mmcif_parsing.py
tt_bio/_vendor/esm/utils/structure/molecular_complex.py
tt_bio/_vendor/esm/utils/structure/normalize_coordinates.py
tt_bio/_vendor/esm/utils/structure/protein_chain.py
tt_bio/_vendor/esm/utils/structure/protein_complex.py
tt_bio/_vendor/esm/utils/structure/protein_structure.py
tt_bio/_vendor/esmfold2_hf/LICENSE
tt_bio/_vendor/esmfold2_hf/__init__.py
tt_bio/_vendor/esmfold2_hf/configuration_esmfold2.py
tt_bio/_vendor/esmfold2_hf/modeling_esmfold2.py
tt_bio/_vendor/esmfold2_hf/modeling_esmfold2_common.py
tt_bio/_vendor/foundry/__init__.py
tt_bio/_vendor/foundry/common.py
tt_bio/_vendor/foundry/model/__init__.py
tt_bio/_vendor/foundry/model/layers/__init__.py
tt_bio/_vendor/foundry/model/layers/blocks.py
tt_bio/_vendor/foundry/training/__init__.py
tt_bio/_vendor/foundry/training/checkpoint.py
tt_bio/_vendor/foundry/utils/__init__.py
tt_bio/_vendor/foundry/utils/alignment.py
tt_bio/_vendor/foundry/utils/ddp.py
tt_bio/_vendor/foundry/utils/rigid.py
tt_bio/_vendor/foundry/utils/rotation_augmentation.py
tt_bio/_vendor/foundry/utils/torch.py
tt_bio/_vendor/openfold3/LICENSE
tt_bio/_vendor/openfold3/__init__.py
tt_bio/_vendor/openfold3/core/__init__.py
tt_bio/_vendor/openfold3/core/config/__init__.py
tt_bio/_vendor/openfold3/core/config/config_utils.py
tt_bio/_vendor/openfold3/core/config/msa_pipeline_configs.py
tt_bio/_vendor/openfold3/core/data/__init__.py
tt_bio/_vendor/openfold3/core/data/io/__init__.py
tt_bio/_vendor/openfold3/core/data/io/utils.py
tt_bio/_vendor/openfold3/core/data/io/sequence/__init__.py
tt_bio/_vendor/openfold3/core/data/io/sequence/fasta.py
tt_bio/_vendor/openfold3/core/data/io/sequence/msa.py
tt_bio/_vendor/openfold3/core/data/io/structure/__init__.py
tt_bio/_vendor/openfold3/core/data/io/structure/atom_array.py
tt_bio/_vendor/openfold3/core/data/io/structure/cif.py
tt_bio/_vendor/openfold3/core/data/io/structure/mol.py
tt_bio/_vendor/openfold3/core/data/pipelines/__init__.py
tt_bio/_vendor/openfold3/core/data/pipelines/featurization/__init__.py
tt_bio/_vendor/openfold3/core/data/pipelines/featurization/conformer.py
tt_bio/_vendor/openfold3/core/data/pipelines/featurization/msa.py
tt_bio/_vendor/openfold3/core/data/pipelines/featurization/structure.py
tt_bio/_vendor/openfold3/core/data/pipelines/featurization/template.py
tt_bio/_vendor/openfold3/core/data/pipelines/preprocessing/__init__.py
tt_bio/_vendor/openfold3/core/data/pipelines/preprocessing/template.py
tt_bio/_vendor/openfold3/core/data/pipelines/sample_processing/__init__.py
tt_bio/_vendor/openfold3/core/data/pipelines/sample_processing/conformer.py
tt_bio/_vendor/openfold3/core/data/pipelines/sample_processing/msa.py
tt_bio/_vendor/openfold3/core/data/pipelines/sample_processing/template.py
tt_bio/_vendor/openfold3/core/data/primitives/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/caches/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/caches/format.py
tt_bio/_vendor/openfold3/core/data/primitives/featurization/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/featurization/msa.py
tt_bio/_vendor/openfold3/core/data/primitives/featurization/padding.py
tt_bio/_vendor/openfold3/core/data/primitives/featurization/structure.py
tt_bio/_vendor/openfold3/core/data/primitives/featurization/template.py
tt_bio/_vendor/openfold3/core/data/primitives/quality_control/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/quality_control/logging_utils.py
tt_bio/_vendor/openfold3/core/data/primitives/sequence/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/sequence/msa.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/__init__.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/cleanup.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/component.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/conformer.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/interface.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/labels.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/metadata.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/query.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/template.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/tokenization.py
tt_bio/_vendor/openfold3/core/data/primitives/structure/unresolved.py
tt_bio/_vendor/openfold3/core/data/resources/__init__.py
tt_bio/_vendor/openfold3/core/data/resources/lists.py
tt_bio/_vendor/openfold3/core/data/resources/patches.py
tt_bio/_vendor/openfold3/core/data/resources/residues.py
tt_bio/_vendor/openfold3/core/data/resources/token_atom_constants.py
tt_bio/_vendor/openfold3/core/data/tools/__init__.py
tt_bio/_vendor/openfold3/core/data/tools/utils.py
tt_bio/_vendor/openfold3/core/model/__init__.py
tt_bio/_vendor/openfold3/core/model/structure/__init__.py
tt_bio/_vendor/openfold3/core/model/structure/augmentation.py
tt_bio/_vendor/openfold3/core/utils/__init__.py
tt_bio/_vendor/openfold3/core/utils/all_atom_multimer.py
tt_bio/_vendor/openfold3/core/utils/atom_attention_block_utils.py
tt_bio/_vendor/openfold3/core/utils/atomize_utils.py
tt_bio/_vendor/openfold3/core/utils/relpos.py
tt_bio/_vendor/openfold3/core/utils/rigid_utils.py
tt_bio/_vendor/openfold3/core/utils/tensor_utils.py
tt_bio/_vendor/openfold3/core/utils/geometry/__init__.py
tt_bio/_vendor/openfold3/core/utils/geometry/rigid_matrix_vector.py
tt_bio/_vendor/openfold3/core/utils/geometry/rotation_matrix.py
tt_bio/_vendor/openfold3/core/utils/geometry/utils.py
tt_bio/_vendor/openfold3/core/utils/geometry/vector.py
tt_bio/_vendor/openfold3/projects/__init__.py
tt_bio/_vendor/openfold3/projects/of3_all_atom/__init__.py
tt_bio/_vendor/openfold3/projects/of3_all_atom/config/__init__.py
tt_bio/_vendor/openfold3/projects/of3_all_atom/config/dataset_config_components.py
tt_bio/_vendor/openfold3/projects/of3_all_atom/config/inference_query_format.py
tt_bio/_vendor/rf3/__init__.py
tt_bio/_vendor/rf3/util_module.py
tt_bio/_vendor/rf3/data/__init__.py
tt_bio/_vendor/rf3/data/cyclic_transform.py
tt_bio/_vendor/rf3/data/extra_xforms.py
tt_bio/_vendor/rf3/data/ground_truth_template.py
tt_bio/_vendor/rf3/data/pipeline_utils.py
tt_bio/_vendor/rf3/data/pipelines.py
tt_bio/_vendor/rf3/diffusion_samplers/__init__.py
tt_bio/_vendor/rf3/diffusion_samplers/inference_sampler.py
tt_bio/_vendor/rf3/loss/__init__.py
tt_bio/_vendor/rf3/loss/loss.py
tt_bio/_vendor/rf3/model/RF3.py
tt_bio/_vendor/rf3/model/RF3_blocks.py
tt_bio/_vendor/rf3/model/RF3_structure.py
tt_bio/_vendor/rf3/model/__init__.py
tt_bio/_vendor/rf3/model/layers/__init__.py
tt_bio/_vendor/rf3/model/layers/af3_auxiliary_heads.py
tt_bio/_vendor/rf3/model/layers/af3_diffusion_transformer.py
tt_bio/_vendor/rf3/model/layers/attention.py
tt_bio/_vendor/rf3/model/layers/layer_utils.py
tt_bio/_vendor/rf3/model/layers/mlff.py
tt_bio/_vendor/rf3/model/layers/outer_product.py
tt_bio/_vendor/rf3/model/layers/pairformer_layers.py
tt_bio/_vendor/rf3/model/layers/structure_bias.py
tt_bio/_vendor/rf3/utils/__init__.py
tt_bio/_vendor/rf3/utils/inference.py
tt_bio/_vendor/rf3/utils/io.py
tt_bio/boltzgen/LICENSE
tt_bio/boltzgen/__init__.py
tt_bio/boltzgen/_config.py
tt_bio/boltzgen/adapter.py
tt_bio/boltzgen/progress.py
tt_bio/boltzgen/cli/__init__.py
tt_bio/boltzgen/cli/boltzgen.py
tt_bio/boltzgen/data/__init__.py
tt_bio/boltzgen/data/cropper.py
tt_bio/boltzgen/data/data.py
tt_bio/boltzgen/data/featurizer.py
tt_bio/boltzgen/data/rmsd_computation.py
tt_bio/boltzgen/data/selector.py
tt_bio/boltzgen/data/template.py
tt_bio/boltzgen/data/tokenizer.py
tt_bio/boltzgen/data/write_mmcif.py
tt_bio/boltzgen/data/write_pdb.py
tt_bio/boltzgen/data/parse/__init__.py
tt_bio/boltzgen/data/parse/a3m.py
tt_bio/boltzgen/data/parse/mmcif.py
tt_bio/boltzgen/data/parse/pdb_parser.py
tt_bio/boltzgen/data/parse/schema.py
tt_bio/boltzgen/model/__init__.py
tt_bio/boltzgen/model/geometry.py
tt_bio/boltzgen/model/layers/__init__.py
tt_bio/boltzgen/model/layers/attention.py
tt_bio/boltzgen/model/layers/confidence_utils.py
tt_bio/boltzgen/model/layers/dropout.py
tt_bio/boltzgen/model/layers/initialize.py
tt_bio/boltzgen/model/layers/relative.py
tt_bio/boltzgen/model/layers/transition.py
tt_bio/boltzgen/model/models/__init__.py
tt_bio/boltzgen/model/models/boltz.py
tt_bio/boltzgen/model/modules/__init__.py
tt_bio/boltzgen/model/modules/affinity.py
tt_bio/boltzgen/model/modules/confidence.py
tt_bio/boltzgen/model/modules/diffusion.py
tt_bio/boltzgen/model/modules/diffusion_conditioning.py
tt_bio/boltzgen/model/modules/encoders.py
tt_bio/boltzgen/model/modules/inverse_fold.py
tt_bio/boltzgen/model/modules/masker.py
tt_bio/boltzgen/model/modules/scatter_utils.py
tt_bio/boltzgen/model/modules/transformers.py
tt_bio/boltzgen/model/modules/trunk.py
tt_bio/boltzgen/model/modules/utils.py
tt_bio/boltzgen/resources/metrics_normalization.json
tt_bio/boltzgen/resources/config/affinity.yaml
tt_bio/boltzgen/resources/config/analysis.yaml
tt_bio/boltzgen/resources/config/design.yaml
tt_bio/boltzgen/resources/config/filtering.yaml
tt_bio/boltzgen/resources/config/fold.yaml
tt_bio/boltzgen/resources/config/inverse_fold.yaml
tt_bio/boltzgen/resources/config/inverse_fold_only.yaml
tt_bio/boltzgen/resources/splits/val_ccd_pdb_pairs_boltzgen.txt
tt_bio/boltzgen/resources/splits/val_monomers_boltzgen_min50_max220.txt
tt_bio/boltzgen/resources/splits/validation_ids_boltz2_all.txt
tt_bio/boltzgen/task/__init__.py
tt_bio/boltzgen/task/task.py
tt_bio/boltzgen/task/analyze/analyze.py
tt_bio/boltzgen/task/analyze/analyze_utils.py
tt_bio/boltzgen/task/filter/__init__.py
tt_bio/boltzgen/task/filter/filter.py
tt_bio/boltzgen/task/filter/seqplot_utils.py
tt_bio/boltzgen/task/predict/__init__.py
tt_bio/boltzgen/task/predict/data_from_generated.py
tt_bio/boltzgen/task/predict/data_from_yaml.py
tt_bio/boltzgen/task/predict/data_ligands.py
tt_bio/boltzgen/task/predict/data_protein_binder.py
tt_bio/boltzgen/task/predict/loading_utils.py
tt_bio/boltzgen/task/predict/predict.py
tt_bio/boltzgen/task/predict/writer.py
tt_bio/boltzgen/utils/__init__.py
tt_bio/boltzgen/utils/quiet.py
tt_bio/data/__init__.py
tt_bio/data/const.py
tt_bio/data/featurizer.py
tt_bio/data/mol.py
tt_bio/data/msa.py
tt_bio/data/pad.py
tt_bio/data/parse.py
tt_bio/data/protein_ref_conformers.json
tt_bio/data/tokenize.py
tt_bio/data/types.py
tt_bio/data/write.py
tt_bio/kernels/mm_split/dm_in0_sender.cpp
tt_bio/kernels/mm_split/dm_in1_sender_out.cpp
tt_bio/kernels/mm_split/matmul_dataflow_common.hpp
tt_bio/kernels/mm_split/patch_mm_split.py
tt_bio/kernels/reblock_permute/compute_reblock_permute.cpp
tt_bio/kernels/reblock_permute/reader_reblock_permute.cpp
tt_bio/kernels/reblock_permute/writer_reblock_permute.cpp
tt_bio/kernels/reblock_permute_back/reader_reblock_permute_back.cpp
tt_bio/kernels/reblock_permute_back/writer_reblock_permute_back.cpp
tt_bio/kernels/reblock_permute_gated/compute_reblock_permute_gated.cpp
tt_bio/kernels/reblock_permute_gated/reader_reblock_permute_gated.cpp
tt_bio/kernels/reblock_permute_gated/writer_reblock_permute_gated.cpp
tt_bio/kernels/rfd3_bias/compute_fused_scores.cpp
tt_bio/kernels/rfd3_bias/reader_dense_scores.cpp
tt_bio/kernels/rfd3_bias/reader_fused_scores.cpp
tt_bio/kernels/rfd3_bias/writer_dense_scores.cpp
tt_bio/kernels/rfd3_bias/writer_fused_scores.cpp
tt_bio/kernels/rfd3_bias/writer_sparse_bias.cpp
tt_bio/kernels/rfd3_softmax/softmax.cpp
tt_bio/kernels/rfd3_softmax/softmax_large_tensor.cpp
tt_bio/kernels/triatt/dm_in0_sender.cpp
tt_bio/kernels/triatt/dm_in1_sender_out.cpp
tt_bio/kernels/triatt/matmul_dataflow_common.hpp
tt_bio/kernels/triatt/patch_head_major.py
tt_bio/kernels/triatt/patch_head_major2.py
tt_bio/kernels/triatt_sdpa/patch_persistent_mask.py
tt_bio/kernels/triatt_sdpa/compute/compute_common.hpp
tt_bio/kernels/triatt_sdpa/compute/compute_streaming.hpp
tt_bio/kernels/triatt_sdpa/compute/joint_sdpa.cpp
tt_bio/kernels/triatt_sdpa/compute/ring_joint_sdpa.cpp
tt_bio/kernels/triatt_sdpa/compute/sdpa.cpp
tt_bio/kernels/triatt_sdpa/dataflow/dataflow_common.hpp
tt_bio/kernels/triatt_sdpa/dataflow/fused_op_indexer.hpp
tt_bio/kernels/triatt_sdpa/dataflow/fused_op_receiver.hpp
tt_bio/kernels/triatt_sdpa/dataflow/joint_reader.cpp
tt_bio/kernels/triatt_sdpa/dataflow/joint_writer.cpp
tt_bio/kernels/triatt_sdpa/dataflow/reader_interleaved.cpp
tt_bio/kernels/triatt_sdpa/dataflow/ring_joint_reader.cpp
tt_bio/kernels/triatt_sdpa/dataflow/ring_joint_writer.cpp
tt_bio/kernels/triatt_sdpa/dataflow/ring_utils.hpp
tt_bio/kernels/triatt_sdpa/dataflow/writer_interleaved.cpp
tt_bio/kernels/trimul_tail/compute.cpp
tt_bio/kernels/trimul_tail/dm_in0_sender.cpp
tt_bio/kernels/trimul_tail/dm_in1_sender_out.cpp
tt_bio/kernels/trimul_tail/matmul_dataflow_common.hpp
tt_bio/kernels/trimul_tail/patch_trimul_tail.py
tt_bio/rf3/__init__.py
tt_bio/rf3/atom_encoder.py
tt_bio/rf3/atom_encoder_host.py
tt_bio/rf3/confidence.py
tt_bio/rf3/confidence_head.py
tt_bio/rf3/diffusion_atom_decoder.py
tt_bio/rf3/diffusion_atom_encoder.py
tt_bio/rf3/diffusion_conditioning.py
tt_bio/rf3/distogram_head.py
tt_bio/rf3/feature_init.py
tt_bio/rf3/feature_initializer.py
tt_bio/rf3/featurize.py
tt_bio/rf3/host.py
tt_bio/rf3/model.py
tt_bio/rf3/msa.py
tt_bio/rf3/remap.py
tt_bio/rf3/remap_encoder.py
tt_bio/rf3/sampler.py
tt_bio/rf3/template.py
tt_bio/rf3/token_dit.py
tt_bio/rf3/weights.py
tt_bio/rfd3/__init__.py
tt_bio/rfd3/design.py
tt_bio/rfd3/featurize.py
tt_bio/rfd3/input.py
tt_bio/rfd3/model.py
tt_bio/rfd3/sampler.py