LICENSE
README.md
pyproject.toml
openfold3/__init__.py
openfold3/hacks.py
openfold3/run_openfold.py
openfold3/setup_openfold.py
openfold3.egg-info/PKG-INFO
openfold3.egg-info/SOURCES.txt
openfold3.egg-info/dependency_links.txt
openfold3.egg-info/entry_points.txt
openfold3.egg-info/requires.txt
openfold3.egg-info/top_level.txt
openfold3/core/__init__.py
openfold3/core/config/__init__.py
openfold3/core/config/config_utils.py
openfold3/core/config/default_linear_init_config.py
openfold3/core/config/msa_pipeline_configs.py
openfold3/core/data/__init__.py
openfold3/core/data/framework/__init__.py
openfold3/core/data/framework/data_module.py
openfold3/core/data/framework/lightning_utils.py
openfold3/core/data/framework/stochastic_sampler_dataset.py
openfold3/core/data/framework/single_datasets/__init__.py
openfold3/core/data/framework/single_datasets/abstract_single.py
openfold3/core/data/framework/single_datasets/base_of3.py
openfold3/core/data/framework/single_datasets/dataset_utils.py
openfold3/core/data/framework/single_datasets/inference.py
openfold3/core/data/framework/single_datasets/monomer.py
openfold3/core/data/framework/single_datasets/pdb.py
openfold3/core/data/framework/single_datasets/validation.py
openfold3/core/data/io/__init__.py
openfold3/core/data/io/dataset_cache.py
openfold3/core/data/io/s3.py
openfold3/core/data/io/utils.py
openfold3/core/data/io/sequence/__init__.py
openfold3/core/data/io/sequence/fasta.py
openfold3/core/data/io/sequence/msa.py
openfold3/core/data/io/sequence/template.py
openfold3/core/data/io/structure/__init__.py
openfold3/core/data/io/structure/atom_array.py
openfold3/core/data/io/structure/cif.py
openfold3/core/data/io/structure/mol.py
openfold3/core/data/io/structure/pdb.py
openfold3/core/data/pipelines/__init__.py
openfold3/core/data/pipelines/featurization/__init__.py
openfold3/core/data/pipelines/featurization/conformer.py
openfold3/core/data/pipelines/featurization/loss_weights.py
openfold3/core/data/pipelines/featurization/msa.py
openfold3/core/data/pipelines/featurization/structure.py
openfold3/core/data/pipelines/featurization/template.py
openfold3/core/data/pipelines/preprocessing/__init__.py
openfold3/core/data/pipelines/preprocessing/structure.py
openfold3/core/data/pipelines/preprocessing/template.py
openfold3/core/data/pipelines/preprocessing/utils.py
openfold3/core/data/pipelines/preprocessing/caches/RNA_monomer.py
openfold3/core/data/pipelines/preprocessing/caches/__init__.py
openfold3/core/data/pipelines/preprocessing/caches/pdb_disordered.py
openfold3/core/data/pipelines/preprocessing/caches/pdb_val.py
openfold3/core/data/pipelines/preprocessing/caches/pdb_weighted.py
openfold3/core/data/pipelines/preprocessing/caches/protein_monomer.py
openfold3/core/data/pipelines/sample_processing/__init__.py
openfold3/core/data/pipelines/sample_processing/conformer.py
openfold3/core/data/pipelines/sample_processing/msa.py
openfold3/core/data/pipelines/sample_processing/structure.py
openfold3/core/data/pipelines/sample_processing/template.py
openfold3/core/data/primitives/__init__.py
openfold3/core/data/primitives/caches/__init__.py
openfold3/core/data/primitives/caches/clustering.py
openfold3/core/data/primitives/caches/filtering.py
openfold3/core/data/primitives/caches/format.py
openfold3/core/data/primitives/caches/homology.py
openfold3/core/data/primitives/caches/lmdb.py
openfold3/core/data/primitives/featurization/__init__.py
openfold3/core/data/primitives/featurization/msa.py
openfold3/core/data/primitives/featurization/padding.py
openfold3/core/data/primitives/featurization/structure.py
openfold3/core/data/primitives/featurization/template.py
openfold3/core/data/primitives/permutation/__init__.py
openfold3/core/data/primitives/permutation/mol_labels.py
openfold3/core/data/primitives/quality_control/__init__.py
openfold3/core/data/primitives/quality_control/asserts.py
openfold3/core/data/primitives/quality_control/logging_datasets.py
openfold3/core/data/primitives/quality_control/logging_utils.py
openfold3/core/data/primitives/quality_control/worker_config.py
openfold3/core/data/primitives/sequence/__init__.py
openfold3/core/data/primitives/sequence/hash.py
openfold3/core/data/primitives/sequence/msa.py
openfold3/core/data/primitives/sequence/template.py
openfold3/core/data/primitives/structure/__init__.py
openfold3/core/data/primitives/structure/alignment.py
openfold3/core/data/primitives/structure/cleanup.py
openfold3/core/data/primitives/structure/component.py
openfold3/core/data/primitives/structure/conformer.py
openfold3/core/data/primitives/structure/cropping.py
openfold3/core/data/primitives/structure/interface.py
openfold3/core/data/primitives/structure/labels.py
openfold3/core/data/primitives/structure/metadata.py
openfold3/core/data/primitives/structure/query.py
openfold3/core/data/primitives/structure/template.py
openfold3/core/data/primitives/structure/tokenization.py
openfold3/core/data/primitives/structure/unresolved.py
openfold3/core/data/resources/__init__.py
openfold3/core/data/resources/lists.py
openfold3/core/data/resources/patches.py
openfold3/core/data/resources/residues.py
openfold3/core/data/resources/token_atom_constants.py
openfold3/core/data/tools/__init__.py
openfold3/core/data/tools/colabfold_msa_server.py
openfold3/core/data/tools/hhblits.py
openfold3/core/data/tools/hhsearch.py
openfold3/core/data/tools/hmmbuild.py
openfold3/core/data/tools/hmmsearch.py
openfold3/core/data/tools/jackhmmer.py
openfold3/core/data/tools/kalign.py
openfold3/core/data/tools/parse_msa_files.py
openfold3/core/data/tools/utils.py
openfold3/core/kernels/__init__.py
openfold3/core/kernels/cueq_utils.py
openfold3/core/kernels/triton/__init__.py
openfold3/core/kernels/triton/fused_softmax.py
openfold3/core/kernels/triton/swiglu.py
openfold3/core/kernels/triton/triton_softmax.py
openfold3/core/loss/__init__.py
openfold3/core/loss/confidence.py
openfold3/core/loss/diffusion.py
openfold3/core/loss/distogram.py
openfold3/core/loss/loss_module.py
openfold3/core/loss/loss_utils.py
openfold3/core/metrics/__init__.py
openfold3/core/metrics/aggregate_confidence_ranking.py
openfold3/core/metrics/confidence.py
openfold3/core/metrics/model_selection.py
openfold3/core/metrics/quality.py
openfold3/core/metrics/rasa.py
openfold3/core/metrics/sample_ranking.py
openfold3/core/model/__init__.py
openfold3/core/model/feature_embedders/__init__.py
openfold3/core/model/feature_embedders/input_embedders.py
openfold3/core/model/feature_embedders/template_embedders.py
openfold3/core/model/heads/__init__.py
openfold3/core/model/heads/head_modules.py
openfold3/core/model/heads/prediction_heads.py
openfold3/core/model/latent/__init__.py
openfold3/core/model/latent/base_blocks.py
openfold3/core/model/latent/base_stacks.py
openfold3/core/model/latent/evoformer.py
openfold3/core/model/latent/msa_module.py
openfold3/core/model/latent/pairformer.py
openfold3/core/model/latent/template_module.py
openfold3/core/model/layers/__init__.py
openfold3/core/model/layers/attention_pair_bias.py
openfold3/core/model/layers/diffusion_conditioning.py
openfold3/core/model/layers/diffusion_transformer.py
openfold3/core/model/layers/msa.py
openfold3/core/model/layers/outer_product_mean.py
openfold3/core/model/layers/sequence_local_atom_attention.py
openfold3/core/model/layers/transition.py
openfold3/core/model/layers/triangular_attention.py
openfold3/core/model/layers/triangular_multiplicative_update.py
openfold3/core/model/primitives/__init__.py
openfold3/core/model/primitives/activations.py
openfold3/core/model/primitives/attention.py
openfold3/core/model/primitives/dropout.py
openfold3/core/model/primitives/initialization.py
openfold3/core/model/primitives/linear.py
openfold3/core/model/primitives/normalization.py
openfold3/core/model/structure/__init__.py
openfold3/core/model/structure/diffusion_module.py
openfold3/core/runners/__init__.py
openfold3/core/runners/model_runner.py
openfold3/core/runners/writer.py
openfold3/core/utils/__init__.py
openfold3/core/utils/all_atom_multimer.py
openfold3/core/utils/atom_attention_block_utils.py
openfold3/core/utils/atomize_utils.py
openfold3/core/utils/callbacks.py
openfold3/core/utils/checkpoint_loading_utils.py
openfold3/core/utils/checkpointing.py
openfold3/core/utils/chunk_utils.py
openfold3/core/utils/exponential_moving_average.py
openfold3/core/utils/grad_manager.py
openfold3/core/utils/logging_utils.py
openfold3/core/utils/lr_schedulers.py
openfold3/core/utils/permutation_alignment.py
openfold3/core/utils/precision_utils.py
openfold3/core/utils/relpos.py
openfold3/core/utils/rigid_utils.py
openfold3/core/utils/s3.py
openfold3/core/utils/script_utils.py
openfold3/core/utils/superimposition.py
openfold3/core/utils/tensor_utils.py
openfold3/core/utils/timing.py
openfold3/core/utils/geometry/__init__.py
openfold3/core/utils/geometry/kabsch_alignment.py
openfold3/core/utils/geometry/rigid_matrix_vector.py
openfold3/core/utils/geometry/rotation_matrix.py
openfold3/core/utils/geometry/test_utils.py
openfold3/core/utils/geometry/utils.py
openfold3/core/utils/geometry/vector.py
openfold3/entry_points/__init__.py
openfold3/entry_points/experiment_runner.py
openfold3/entry_points/import_utils.py
openfold3/entry_points/parameters.py
openfold3/entry_points/validator.py
openfold3/projects/__init__.py
openfold3/projects/of3_all_atom/__init__.py
openfold3/projects/of3_all_atom/constants.py
openfold3/projects/of3_all_atom/model.py
openfold3/projects/of3_all_atom/project_entry.py
openfold3/projects/of3_all_atom/runner.py
openfold3/projects/of3_all_atom/config/__init__.py
openfold3/projects/of3_all_atom/config/dataset_config_components.py
openfold3/projects/of3_all_atom/config/dataset_configs.py
openfold3/projects/of3_all_atom/config/features.py
openfold3/projects/of3_all_atom/config/inference_query_format.py
openfold3/projects/of3_all_atom/config/linear_init_config.py
openfold3/projects/of3_all_atom/config/model_config.py
openfold3/projects/of3_all_atom/config/model_setting_presets.yml
openfold3/projects/of3_all_atom/config/runner_file_checks.py
openfold3/tests/__init__.py
openfold3/tests/compare_utils.py
openfold3/tests/config.py
openfold3/tests/conftest.py
openfold3/tests/custom_assert_utils.py
openfold3/tests/data_utils.py
openfold3/tests/test_atomize_utils.py
openfold3/tests/test_chain_pair_mask.py
openfold3/tests/test_colabfold_msa.py
openfold3/tests/test_confidence_loss.py
openfold3/tests/test_confidence_metrics.py
openfold3/tests/test_dataset_config.py
openfold3/tests/test_dataset_utils.py
openfold3/tests/test_diffusion_conditioning.py
openfold3/tests/test_diffusion_loss.py
openfold3/tests/test_diffusion_module.py
openfold3/tests/test_diffusion_transformer.py
openfold3/tests/test_distogram_loss.py
openfold3/tests/test_embedders.py
openfold3/tests/test_entry_points.py
openfold3/tests/test_evoformer.py
openfold3/tests/test_heads.py
openfold3/tests/test_inference_full.py
openfold3/tests/test_kernels.py
openfold3/tests/test_lmdb.py
openfold3/tests/test_model_checkpoint.py
openfold3/tests/test_model_runner.py
openfold3/tests/test_msa.py
openfold3/tests/test_msa_module.py
openfold3/tests/test_of3_model.py
openfold3/tests/test_outer_product_mean.py
openfold3/tests/test_pair_transition.py
openfold3/tests/test_pairformer.py
openfold3/tests/test_permutation_alignment.py
openfold3/tests/test_primitives.py
openfold3/tests/test_sequence_local_atom_attention.py
openfold3/tests/test_setup_openfold.py
openfold3/tests/test_structure_from_query.py
openfold3/tests/test_template.py
openfold3/tests/test_template_parsers.py
openfold3/tests/test_tokenizer.py
openfold3/tests/test_triangular_attention.py
openfold3/tests/test_triangular_multiplicative_update.py
openfold3/tests/test_utils.py
openfold3/tests/test_validation_metrics.py
openfold3/tests/test_writer.py
openfold3/tests/core/data/primitives/sequence/msa/test_find_pairing_indicies.py
openfold3/tests/core/data/primitives/sequence/msa/test_get_pairing_masks.py
openfold3/tests/core/data/primitives/structure/test_cleanup.py
openfold3/tests/core/data/primitives/structure/test_cleanup_bonds.py
openfold3/tests/core/data/primitives/structure/test_cleanup_waters.py
openfold3/tests/core/data/primitives/structure/test_labels.py
openfold3/tests/core/data/primitives/structure/test_query.py
openfold3/tests/scripts/__init__.py
openfold3/tests/scripts/data_preprocessing/__init__.py
openfold3/tests/scripts/data_preprocessing/test_preparse_alignments_of3.py
openfold3/tests/test_data/alignments/2q2k_A/bfd_uniclust_hits.a3m
openfold3/tests/test_data/alignments/2q2k_A/hmm_output.sto
openfold3/tests/test_data/alignments/2q2k_A/mgnify_hits.sto
openfold3/tests/test_data/alignments/2q2k_A/uniprot_hits.sto
openfold3/tests/test_data/alignments/2q2k_A/uniref90_hits.sto
openfold3/tests/test_data/alignments/2q2k_B/bfd_uniclust_hits.a3m
openfold3/tests/test_data/alignments/2q2k_B/hmm_output.sto
openfold3/tests/test_data/alignments/2q2k_B/mgnify_hits.sto
openfold3/tests/test_data/alignments/2q2k_B/uniprot_hits.sto
openfold3/tests/test_data/alignments/2q2k_B/uniref90_hits.sto
openfold3/tests/test_data/mmcifs/1hf9.cif
openfold3/tests/test_data/mmcifs/1kd8.cif
openfold3/tests/test_data/mmcifs/1psm.cif
openfold3/tests/test_data/mmcifs/2crb.cif
openfold3/tests/test_data/mmcifs/2q2k.cif
openfold3/tests/test_data/mmcifs/3u8v.cif
openfold3/tests/test_data/mmcifs/3zee.cif
openfold3/tests/test_data/mmcifs/4i6p.cif
openfold3/tests/test_data/mmcifs/4zey.cif
openfold3/tests/test_data/mmcifs/5kc1.cif
openfold3/tests/test_data/permutation_alignment/inputs/npz/7pbd/7pbd_subset.npz
openfold3/tests/test_data/permutation_alignment/outputs/npz/7pbd_subset_with-perm-ids.npz
openfold3/tests/test_data/structure_from_query/README.md
openfold3/tests/test_data/structure_from_query/structure-w-ref-mols_non-std-peptide.pkl
openfold3/tests/test_data/structure_from_query/structure-w-ref-mols_std-peptide.pkl
openfold3/tests/test_data/template_alignments/inputs/a3m_no_realign.a3m
openfold3/tests/test_data/template_alignments/inputs/a3m_realign.a3m
openfold3/tests/test_data/template_alignments/inputs/m8_cigar.m8
openfold3/tests/test_data/template_alignments/inputs/sto_hmmalign.sto
openfold3/tests/test_data/template_alignments/inputs/sto_hmmsearch_diff_seq.sto
openfold3/tests/test_data/template_alignments/inputs/sto_hmmsearch_same_seq.sto
openfold3/tests/test_data/template_alignments/outputs/a3m_no_realign.npz
openfold3/tests/test_data/template_alignments/outputs/a3m_realign.npz
openfold3/tests/test_data/template_alignments/outputs/m8_cigar.npz
openfold3/tests/test_data/template_alignments/outputs/m8_no_cigar.npz
openfold3/tests/test_data/template_alignments/outputs/sto_hmmalign.npz
openfold3/tests/test_data/template_alignments/outputs/sto_hmmsearch_diff_seq.npz
openfold3/tests/test_data/template_alignments/outputs/sto_hmmsearch_same_seq.npz
openfold3/tests/test_data/tokenization/README.md
openfold3/tests/test_data/tokenization/construct_tokenization_examples.py
openfold3/tests/test_data/tokenization/inputs/1ema_raw_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/inputs/1pwc_raw_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/inputs/5seb_raw_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/inputs/5tdj_raw_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/inputs/6znc_raw_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/outputs/1ema_tokenized_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/outputs/1pwc_tokenized_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/outputs/5seb_tokenized_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/outputs/5tdj_tokenized_bonds_unfiltered.npz
openfold3/tests/test_data/tokenization/outputs/6znc_tokenized_bonds_unfiltered.npz
scripts/__init__.py
scripts/validate_msas.py
scripts/analysis/run_ost.py
scripts/data_preprocessing/__init__.py
scripts/data_preprocessing/collect_preprocessed_fastas.py
scripts/data_preprocessing/convert_cache_to_lmdb.py
scripts/data_preprocessing/create_RNA-monomer_training_dataset_cache.py
scripts/data_preprocessing/create_pdb-disordered_training_dataset_cache.py
scripts/data_preprocessing/create_pdb-weighted_training_dataset_cache.py
scripts/data_preprocessing/create_pdb_validation_dataset_cache.py
scripts/data_preprocessing/create_protein-monomer_training_dataset_cache.py
scripts/data_preprocessing/cross_validate_atomarray_msa.py
scripts/data_preprocessing/preparse_alignments_of3.py
scripts/data_preprocessing/preparse_monomer_msas_from_s3.py
scripts/data_preprocessing/preparse_monomer_structures_from_s3.py
scripts/data_preprocessing/preprocess_ccd_biotite.py
scripts/data_preprocessing/preprocess_pdb_disordered_of3.py
scripts/data_preprocessing/preprocess_pdb_disordered_of3_compare_structures.py
scripts/data_preprocessing/preprocess_pdb_disordered_of3_count_unresolved.py
scripts/data_preprocessing/preprocess_pdb_of3.py
scripts/data_preprocessing/preprocess_rfam.py
scripts/data_preprocessing/preprocess_template_alignments_new_of3.py
scripts/data_preprocessing/preprocess_template_alignments_old_of3.py
scripts/data_preprocessing/preprocess_template_alignments_precache_of3.py
scripts/data_preprocessing/preprocess_template_structures_of3.py
scripts/data_preprocessing/run_data_pipeline_treadmill.py
scripts/dev/build_release_date_cache.py
scripts/dev/check_release_dates.py
scripts/dev/convert_ckpt_to_ema_only.py
scripts/dev/convert_compiled_weights.py
scripts/dev/update_ccd.py
scripts/snakemake_msa/download_of3_databases.py
scripts/snakemake_msa/test_download_of3_databases.py
scripts/utils/generate_representatives_from_msa_directory.py