LICENSE
MANIFEST.in
NOTICE
README.md
pyproject.toml
tests/test_boltz2_sample_chunk.py
tests/test_boltzgen.py
tests/test_boltzgen_designability.py
tests/test_boltzgen_regression.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_esmc.py
tests/test_esmfold2.py
tests/test_esmfold2_cif_write.py
tests/test_input_validation.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_pharma_parity.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_runtime.py
tests/test_sampling_default.py
tests/test_saturation_crossover.py
tests/test_shared_outputs.py
tests/test_structure.py
tests/test_tenstorrent.py
tests/test_windowing_m_shapes.py
tests/test_windowing_multiplicity.py
tt_bio/__init__.py
tt_bio/boltz2.py
tt_bio/device_lease.py
tt_bio/distributed.py
tt_bio/energy.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/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/reference.py
tt_bio/runtime.py
tt_bio/saprot.py
tt_bio/tenstorrent.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/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/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/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/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