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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/snapshots/test_conformer/test_compute_conformer_snapshot_benzene_default_no_hs_.npz
openfold3/tests/test_data/snapshots/test_conformer/test_compute_conformer_snapshot_ethanol_default_keep_hs_.npz
openfold3/tests/test_data/snapshots/test_conformer/test_compute_conformer_snapshot_ethanol_default_no_hs_.npz
openfold3/tests/test_data/snapshots/test_conformer/test_compute_conformer_snapshot_ethanol_random_init_no_hs_.npz
openfold3/tests/test_data/snapshots/test_conformer/test_compute_conformer_snapshot_paracetamol_default_no_hs_.npz
openfold3/tests/test_data/snapshots/test_structure_from_query/test_structure_from_query_non_canonical_peptide_.npz
openfold3/tests/test_data/snapshots/test_structure_from_query/test_structure_from_query_standard_peptide_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/nvidia/_snapshot_env.json
openfold3/tests/test_data/snapshots/test_triangular_attention/nvidia/test_shape_cpu_False_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/nvidia/test_shape_cpu_True_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/nvidia/test_shape_cuda_False_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/nvidia/test_shape_cuda_True_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/rocm/_snapshot_env.json
openfold3/tests/test_data/snapshots/test_triangular_attention/rocm/test_shape_cpu_False_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/rocm/test_shape_cpu_True_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/rocm/test_shape_cuda_False_.npz
openfold3/tests/test_data/snapshots/test_triangular_attention/rocm/test_shape_cuda_True_.npz
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/nvidia/_snapshot_env.json
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/nvidia/test_shape_cpu_.npz
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/nvidia/test_shape_cuda_.npz
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/rocm/_snapshot_env.json
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/rocm/test_shape_cpu_.npz
openfold3/tests/test_data/snapshots/test_triangular_multiplicative_update/rocm/test_shape_cuda_.npz
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
openfold3/tests/utils/__init__.py
openfold3/tests/utils/test_utils.py
openfold3/tests/utils/geometry/__init__.py
openfold3/tests/utils/geometry/helpers.py
openfold3/tests/utils/geometry/test_rigid_matrix_vector.py
openfold3/tests/utils/geometry/test_rotation_matrix.py
openfold3/tests/utils/geometry/test_vector.py
scripts/__init__.py
scripts/install_third_party_dependencies.sh
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/download_pdb_mmcif.sh
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/MSA_Snakefile
scripts/snakemake_msa/aln_env.yml
scripts/snakemake_msa/download_of3_databases.py
scripts/snakemake_msa/example_fasta_RNA.fasta
scripts/snakemake_msa/example_fasta_protein.fasta
scripts/snakemake_msa/example_msa_config_RNA.json
scripts/snakemake_msa/example_msa_config_protein.json
scripts/snakemake_msa/test_download_of3_databases.py
scripts/utils/generate_representatives_from_msa_directory.py