├── .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_docker_image.yml │ └── publish_on_pypi.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ └── peptdeep.png ├── build_docs.sh ├── conf.py ├── index.rst ├── mass_spec │ ├── mass_calibration.rst │ ├── match.rst │ └── ms_reader.rst ├── model │ ├── building_block.rst │ ├── ccs.rst │ ├── featurize.rst │ ├── generic_property_prediction.rst │ ├── model_interface.rst │ ├── ms2.rst │ └── rt.rst ├── module_pipeline_api.rst ├── module_pretrained_models.rst ├── module_settings.rst ├── modules_mass_spec.rst ├── modules_model.rst ├── modules_protein.rst ├── modules_rescore.rst ├── modules_spec_lib.rst ├── nbs │ ├── alphapeptdeep_hdf_to_tsv.ipynb │ ├── tutorial.ipynb │ ├── tutorial_building_ccs_model.ipynb │ ├── tutorial_building_rt_model.ipynb │ ├── tutorial_model_manager.ipynb │ ├── tutorial_models_from_scratch.ipynb │ └── tutorial_speclib_from_fasta.ipynb ├── notebooks.rst ├── protein │ └── fasta.rst ├── rescore │ ├── fdr.rst │ ├── feature_extractor.rst │ └── percolator.rst ├── spec_lib │ ├── library_factory.rst │ ├── predict_lib.rst │ └── translate.rst └── tutorials │ ├── data │ ├── example.fasta │ ├── sample_openswath.tsv │ ├── sample_proteins.fasta │ └── timstof_speclib.tsv │ ├── tutorial_immunopeptidomics.ipynb │ └── tutorial_speclib.ipynb ├── misc ├── CLA.md ├── pip_install.sh └── screenshot.png ├── nbs_tests ├── .gitignore ├── hla │ └── hla_class1.ipynb ├── mass_spec │ ├── mass_calibration.ipynb │ ├── match.ipynb │ └── ms_reader.ipynb ├── model │ ├── building_block.ipynb │ ├── ccs.ipynb │ ├── charge.ipynb │ ├── featurize.ipynb │ ├── generic_property_prediction.ipynb │ ├── model_interface.ipynb │ ├── model_shop.ipynb │ ├── ms2.ipynb │ └── rt.ipynb ├── pipeline_api.ipynb ├── pretrained_models.ipynb ├── protein │ └── fasta.ipynb ├── psm_frag_reader │ ├── maxquant_frag_reader.ipynb │ ├── psm_frag_reader.ipynb │ └── psmlabel_reader.ipynb ├── settings.ipynb ├── spec_lib │ ├── library_factory.ipynb │ ├── predict_lib.ipynb │ └── test_translate_tsv.ipynb ├── test_ui.ipynb └── utils.ipynb ├── nbs_trials ├── precursor_table.csv ├── rescore │ ├── fdr.ipynb │ ├── feature_extractor.ipynb │ └── percolator.ipynb ├── speclib_from_dda.ipynb ├── test_argparse.ipynb ├── test_ccs_rt.ipynb ├── test_charge_model.ipynb ├── test_fasta_lib_gpu.ipynb ├── test_fasta_lib_precursor_lib.ipynb ├── test_multi_target.ipynb ├── test_new_ms2_weight_format.ipynb ├── test_percolator.ipynb ├── test_predict_mp.ipynb ├── test_predict_ms2.ipynb ├── test_rescore_api.ipynb ├── test_torch_jit.ipynb ├── test_transfer_api.ipynb └── test_transfer_ms2.ipynb ├── peptdeep ├── __init__.py ├── cli.py ├── cli_argparse.py ├── constants │ ├── __init__.py │ ├── _const.py │ ├── default_settings.yaml │ └── model_const.yaml ├── gui.py ├── hla │ ├── __init__.py │ ├── hla_class1.py │ └── hla_utils.py ├── mass_spec │ ├── __init__.py │ ├── mass_calibration.py │ ├── match.py │ └── ms_reader.py ├── model │ ├── __init__.py │ ├── base.py │ ├── building_block.py │ ├── ccs.py │ ├── charge.py │ ├── featurize.py │ ├── generic_property_prediction.py │ ├── model_interface.py │ ├── model_shop.py │ ├── ms2.py │ └── rt.py ├── pipeline_api.py ├── pretrained_models.py ├── protein │ ├── __init__.py │ └── fasta.py ├── psm_frag_reader │ ├── __init__.py │ ├── maxquant_frag_reader.py │ ├── psm_frag_reader.py │ └── psmlabel_reader.py ├── rescore │ ├── __init__.py │ ├── fdr.py │ ├── feature_extractor.py │ └── percolator.py ├── settings.py ├── spec_lib │ ├── __init__.py │ ├── library_factory.py │ ├── predict_lib.py │ └── translate.py ├── utils │ ├── __init__.py │ ├── _pyinstaller_hooks.py │ ├── deprecations.py │ ├── device_utils.py │ ├── logger.py │ └── regression.py └── webui │ ├── __init__.py │ ├── library_ui.py │ ├── logos │ ├── peptdeep.ico │ └── peptdeep.png │ ├── main_ui.py │ ├── model_ui.py │ ├── rescore_ui.py │ ├── server.py │ ├── server_ui.py │ ├── settings_ui.py │ ├── startpage.py │ ├── transfer_ui.py │ └── ui_utils.py ├── pyproject.toml ├── release ├── common │ └── build_wheel.sh ├── linux │ ├── build_installer_linux.sh │ ├── build_package_linux.sh │ └── control ├── logos │ ├── alpha_logo.icns │ ├── alpha_logo.ico │ └── alpha_logo.png ├── macos │ ├── Info.plist │ ├── Resources │ │ ├── conclusion.html │ │ └── welcome.html │ ├── build_installer_macos.sh │ ├── build_package_macos.sh │ ├── distribution.xml │ ├── peptdeep_terminal │ └── scripts │ │ ├── postinstall │ │ └── preinstall ├── pyinstaller │ ├── peptdeep.spec │ ├── peptdeep_cli_pyinstaller.py │ └── peptdeep_pyinstaller.py └── windows │ ├── build_installer_windows.ps1 │ ├── 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