├── .bumpversion.toml ├── .github ├── ISSUE_TEMPLATE │ └── bug-report.md ├── release.yml └── workflows │ ├── _run_tests.yml │ ├── branch-checks.yaml │ ├── bump_version.yml │ ├── code-review.yml │ ├── create_release.yml │ ├── pip_installation.yml │ └── publish_on_pypi.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── alphabase ├── __init__.py ├── constants │ ├── __init__.py │ ├── _const.py │ ├── aa.py │ ├── atom.py │ ├── const_files │ │ ├── __emass_element.yaml │ │ ├── amino_acid.tsv │ │ ├── common_constants.yaml │ │ ├── contaminants.fasta │ │ ├── modification.tsv │ │ ├── nist_element.yaml │ │ ├── pg_reader.yaml │ │ ├── protease.yaml │ │ ├── psm_reader.yaml │ │ └── quant_reader_config.yaml │ ├── element.py │ ├── isotope.py │ ├── modification.py │ └── spectral_library.py ├── io │ ├── __init__.py │ ├── hdf.py │ └── tempmmap.py ├── peptide │ ├── __init__.py │ ├── fragment.py │ ├── mass_calc.py │ ├── mobility.py │ └── precursor.py ├── pg_reader │ ├── __init__.py │ ├── alphadia_pg_reader.py │ ├── alphapept_pg_reader.py │ ├── diann_pg_reader.py │ ├── directlfq_pg_reader.py │ ├── fragpipe_pg_reader.py │ ├── keys.py │ ├── maxquant_pg_reader.py │ ├── mztab_pg_reader.py │ ├── pg_reader.py │ └── spectronaut_reader.py ├── protein │ ├── __init__.py │ ├── fasta.py │ ├── inference.py │ ├── lcp_digest.py │ └── protein_level_decoy.py ├── psm_reader │ ├── __init__.py │ ├── alphadia_reader.py │ ├── alphapept_reader.py │ ├── dia_psm_reader.py │ ├── keys.py │ ├── maxquant_reader.py │ ├── modification_mapper.py │ ├── msfragger_reader.py │ ├── pfind_reader.py │ ├── psm_reader.py │ ├── sage_reader.py │ └── utils.py ├── quantification │ └── quant_reader │ │ ├── config_dict_loader.py │ │ ├── longformat_reader.py │ │ ├── plexdia_reformatter.py │ │ ├── quant_reader_manager.py │ │ ├── quantreader_utils.py │ │ ├── table_reformatter.py │ │ └── wideformat_reader.py ├── smiles │ ├── __init__.py │ ├── adding_smiles.py │ ├── peptide.py │ └── smiles.py ├── spectral_library │ ├── __init__.py │ ├── annotate.py │ ├── base.py │ ├── decoy.py │ ├── flat.py │ ├── metrics.py │ ├── reader.py │ ├── translate.py │ └── validate.py ├── tools │ ├── __init__.py │ └── data_downloader.py ├── utils.py └── yaml_utils.py ├── docs ├── Makefile ├── _static │ ├── css │ │ └── custom.css │ └── diagrams │ │ ├── loader_classes.drawio │ │ ├── loader_classes.drawio.svg │ │ ├── loader_classes_new.drawio │ │ └── loader_classes_new.drawio.svg ├── api.rst ├── conf.py ├── constants │ ├── aa.rst │ ├── atom.rst │ ├── isotope.rst │ └── modification.rst ├── index.rst ├── installation.rst ├── io │ ├── hdf.rst │ └── tempmmap.rst ├── modules_constants.rst ├── modules_io.rst ├── modules_peptide.rst ├── modules_pg_reader.rst ├── modules_protein.rst ├── modules_psm_reader.rst ├── modules_spectral_library.rst ├── nbs │ ├── library_from_fasta.ipynb │ ├── library_reader.ipynb │ ├── peptide_smiles.ipynb │ ├── psm_readers.ipynb │ └── tutorial_smiles.ipynb ├── notebooks.rst ├── peptide │ ├── fragment.rst │ ├── mass_calc.rst │ ├── mobility.rst │ └── precursor.rst ├── pg_reader │ ├── alphadia_pg_reader.rst │ ├── alphapept_pg_reader.rst │ ├── diann_pg_reader.rst │ ├── fragpipe_pg_reader.rst │ ├── maxquant_pg_reader.rst │ ├── mztab_pg_reader.rst │ ├── pg_base.rst │ └── spectronaut_pg_reader.rst ├── protein │ ├── fasta.rst │ └── protein_level_decoy.rst ├── psm_reader │ ├── alphapept_reader.rst │ ├── dia_psm_reader.rst │ ├── maxquant_reader.rst │ ├── msfragger_reader.rst │ ├── pfind_reader.rst │ └── psm_reader.rst ├── references.rst ├── spectral_library │ ├── base.rst │ ├── decoy.rst │ ├── flat.rst │ ├── reader.rst │ └── translate.rst └── tutorials │ ├── adding_smiles.rst │ ├── atom-to-peptides.png │ ├── peptide-fragment-dataframe.png │ ├── tutorial_basic_definitions.ipynb │ ├── tutorial_dataframe_structures.ipynb │ ├── tutorial_pg_reader.ipynb │ ├── tutorial_scverse_compatibility.ipynb │ └── tutorial_spectral_libraries.ipynb ├── misc ├── CLA.md └── pip_install.sh ├── nbs_tests ├── io │ └── hdf.ipynb ├── peptide │ ├── fragment.ipynb │ ├── mass_calc.ipynb │ ├── mobility.ipynb │ └── precursor.ipynb ├── protein │ ├── annotate_fasta.ipynb │ ├── fasta.ipynb │ ├── test_fasta.ipynb │ └── test_lcp.ipynb ├── psm_reader │ ├── alphapept_reader.ipynb │ ├── dia_psm_reader.ipynb │ ├── maxquant_reader.ipynb │ ├── msfragger_reader.ipynb │ ├── pfind_reader.ipynb │ ├── psm_reader.ipynb │ ├── sage_reader.ipynb │ └── speclib_tsv_reader.ipynb ├── quantification │ └── test_table_loading.ipynb ├── spectral_library │ ├── decoy_library.ipynb │ ├── flat_library.ipynb │ ├── library_base.ipynb │ ├── library_reader.ipynb │ ├── raw_library_generator.ipynb │ ├── translate.ipynb │ └── validate.ipynb ├── test_isotope_calc.ipynb ├── test_isotope_mp.ipynb ├── test_thread.ipynb ├── utils.ipynb └── yaml_utils.ipynb ├── pyproject.toml ├── requirements ├── requirements.txt ├── requirements_dask.txt ├── requirements_dask_loose.txt ├── requirements_development.txt ├── requirements_docs.txt ├── requirements_hdf_loose.txt ├── requirements_loose.txt └── requirements_tests.txt ├── ruff-lint-psm-readers.toml ├── scripts ├── README.md ├── emass_element.yaml ├── nist_chem_to_yaml.ipynb ├── nist_element.yaml ├── unimod.xml └── unimod_to_tsv.ipynb └── tests ├── __init__.py ├── integration ├── __init__.py ├── conftest.py ├── reference_data │ ├── reference_alphadia.parquet │ ├── reference_alphadia_1.8.1_tsv.parquet │ ├── reference_alphadia_2.0.0_tsv.parquet │ ├── reference_diann.parquet │ ├── reference_diann_1.8.1_tsv.parquet │ ├── reference_diann_1.9.0_tsv.parquet │ ├── reference_diann_speclib.parquet │ ├── reference_directlfq_0.3.2_tsv.parquet │ ├── reference_maxquant.parquet │ ├── reference_msfragger_psm_tsv.parquet │ ├── reference_msfragger_speclib.parquet │ ├── reference_openswath.parquet │ ├── reference_pfind.parquet │ ├── reference_pg_alphadia_1.10.0.tsv.parquet │ ├── reference_pg_alphapept_0.5.3.tsv.parquet │ ├── reference_pg_diann_1.8.1.tsv.parquet │ ├── reference_pg_fragpipe.parquet │ ├── reference_pg_maxquant.2024.tsv.parquet │ ├── reference_pg_mztab_minimal.parquet │ ├── reference_pg_spectronaut_18.0.tsv.parquet │ ├── reference_sage.parquet │ ├── reference_spectronaut.parquet │ └── reference_spectronaut_report.parquet ├── test_pg_reader_provider.py ├── test_pg_readers.py └── test_psm_readers.py ├── run_tests.sh ├── test_cli.py ├── test_fragment.py ├── test_gui.py ├── test_peptide_smiles.py ├── test_smiles.py └── unit ├── __init__.py ├── constants ├── test_aa.py ├── test_atom.py ├── test_isotope.py ├── test_modification.py └── test_modification_functions.py ├── io └── test_tempmmap.py ├── peptide └── test_fragment.py ├── pg_reader ├── __init__.py ├── test_alphadia_reader.py ├── test_alphapept_pg_reader.py ├── test_pg_reader.py └── test_pg_reader_provider.py ├── protein ├── __init__.py └── test_fasta.py ├── psm_reader ├── __init__.py ├── 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