LICENSE.md
README.md
pyproject.toml
src/pdbe_sifts/__init__.py
src/pdbe_sifts/cli.py
src/pdbe_sifts/seq2seq.py
src/pdbe_sifts/sifts_database_loader.py
src/pdbe_sifts/sifts_fasta_builder.py
src/pdbe_sifts/sifts_segments_generation.py
src/pdbe_sifts/sifts_sequence_match.py
src/pdbe_sifts/taxonomy_fix_pkl.py
src/pdbe_sifts.egg-info/PKG-INFO
src/pdbe_sifts.egg-info/SOURCES.txt
src/pdbe_sifts.egg-info/dependency_links.txt
src/pdbe_sifts.egg-info/entry_points.txt
src/pdbe_sifts.egg-info/requires.txt
src/pdbe_sifts.egg-info/top_level.txt
src/pdbe_sifts/base/__init__.py
src/pdbe_sifts/base/exceptions.py
src/pdbe_sifts/base/log.py
src/pdbe_sifts/base/paths.py
src/pdbe_sifts/base/utils.py
src/pdbe_sifts/config/__init__.py
src/pdbe_sifts/data/__init__.py
src/pdbe_sifts/data/default_config.yaml
src/pdbe_sifts/data/nf90_taxid.pkl.gz
src/pdbe_sifts/data/three_to_one_letter_mapping.csv
src/pdbe_sifts/database/__init__.py
src/pdbe_sifts/database/sifts_db_wrapper.py
src/pdbe_sifts/mmcif/__init__.py
src/pdbe_sifts/mmcif/chain.py
src/pdbe_sifts/mmcif/chem_comp.py
src/pdbe_sifts/mmcif/entity.py
src/pdbe_sifts/mmcif/entry.py
src/pdbe_sifts/mmcif/generate_ccd_mapping.py
src/pdbe_sifts/mmcif/mmcif_helper.py
src/pdbe_sifts/mmcif/poly_seq_scheme.py
src/pdbe_sifts/mmcif/residue.py
src/pdbe_sifts/mmcif/curator/__init__.py
src/pdbe_sifts/mmcif/curator/cif_sequence_update.py
src/pdbe_sifts/mmcif/curator/pdbx_connectivity.py
src/pdbe_sifts/segments_generation/__init__.py
src/pdbe_sifts/segments_generation/generate_xref_csv.py
src/pdbe_sifts/segments_generation/get_list_of_mappings.py
src/pdbe_sifts/segments_generation/alignment/__init__.py
src/pdbe_sifts/segments_generation/alignment/helper.py
src/pdbe_sifts/segments_generation/connectivity/__init__.py
src/pdbe_sifts/segments_generation/connectivity/ccd_parser.py
src/pdbe_sifts/segments_generation/connectivity/process_connectivity.py
src/pdbe_sifts/sequence_match/__init__.py
src/pdbe_sifts/sequence_match/base_alignment_search.py
src/pdbe_sifts/sequence_match/blastp.py
src/pdbe_sifts/sequence_match/database.py
src/pdbe_sifts/sequence_match/makeblastdb.py
src/pdbe_sifts/sequence_match/mmseqs_search.py
src/pdbe_sifts/sequence_match/scoring_function_helper.py
src/pdbe_sifts/sequence_match/sequence_match_parser.py
src/pdbe_sifts/sequence_match/target_database.py
src/pdbe_sifts/sifts_to_mmcif/__init__.py
src/pdbe_sifts/sifts_to_mmcif/comm_utils.py
src/pdbe_sifts/sifts_to_mmcif/def_mmcif_cat.py
src/pdbe_sifts/sifts_to_mmcif/delta_mappings.py
src/pdbe_sifts/sifts_to_mmcif/main.py
src/pdbe_sifts/sifts_to_mmcif/read_sifts_csv.py
src/pdbe_sifts/unp/__init__.py
src/pdbe_sifts/unp/unp.py
tests/test_ccd_parser.py
tests/test_chem_comp.py
tests/test_def_mmcif_cat.py
tests/test_entry_id_security.py
tests/test_exceptions.py
tests/test_extract_entities.py
tests/test_fasta_builder.py
tests/test_mmcif_helper.py
tests/test_paths.py
tests/test_process_connectivity.py
tests/test_residue.py
tests/test_score_formulas.py
tests/test_scoring_function_helper.py
tests/test_sequence_match_parser.py
tests/test_sifts_align.py
tests/test_sifts_db_wrapper.py
tests/test_utils_pure.py