.gitignore
.readthedocs.yaml
LICENSE.md
README.md
pyproject.toml
setup.cfg
setup.py
.github/workflows/linux-build.yml
.github/workflows/publish.yml
.github/workflows/windows-build.yml
docs/Makefile
docs/make.bat
docs/source/cli.rst
docs/source/conf.py
docs/source/index.rst
docs/source/api/index.rst
docs/source/api/modified_peptides.rst
docs/source/api/parsing.rst
docs/source/api/scoring.rst
pyascore/__init__.py
pyascore/__main__.py
pyascore/config.py
pyascore.egg-info/PKG-INFO
pyascore.egg-info/SOURCES.txt
pyascore.egg-info/dependency_links.txt
pyascore.egg-info/entry_points.txt
pyascore.egg-info/requires.txt
pyascore.egg-info/top_level.txt
pyascore/parsing/__init__.py
pyascore/parsing/id_parsers.py
pyascore/parsing/spec_parsers.py
pyascore/ptm_scoring/Ascore.pxd
pyascore/ptm_scoring/Ascore.pyx
pyascore/ptm_scoring/ModifiedPeptide.pxd
pyascore/ptm_scoring/ModifiedPeptide.pyx
pyascore/ptm_scoring/PTMScoring.cpp
pyascore/ptm_scoring/PTMScoring.pyx
pyascore/ptm_scoring/Spectra.pxd
pyascore/ptm_scoring/Spectra.pyx
pyascore/ptm_scoring/Util.pxd
pyascore/ptm_scoring/Util.pyx
pyascore/ptm_scoring/cpp/Ascore.cpp
pyascore/ptm_scoring/cpp/Ascore.h
pyascore/ptm_scoring/cpp/ModifiedPeptide.cpp
pyascore/ptm_scoring/cpp/ModifiedPeptide.h
pyascore/ptm_scoring/cpp/Spectra.cpp
pyascore/ptm_scoring/cpp/Spectra.h
pyascore/ptm_scoring/cpp/Types.h
pyascore/ptm_scoring/cpp/Util.cpp
pyascore/ptm_scoring/cpp/Util.h
static/logo.png
test/__init__.py
test/test_ascore.py
test/test_id_parsers.py
test/test_modified_peptide_container.py
test/test_spec_parsers.py
test/test_spectra_container.py
test/test_util.py
test/example_inputs/psms/test_psms.mzid
test/example_inputs/psms/test_psms.pep.xml
test/example_inputs/spectra/test_spectra.mzML
test/example_inputs/spectra/test_spectra.mzXML
test/match_spectra_pairs/velos_matches_1_mods.pkl
test/match_spectra_pairs/velos_matches_2_mods.pkl
test/match_spectra_pairs/velos_matches_3_mods.pkl
test/match_spectra_pairs/velos_matches_aux.pkl
test/match_spectra_pairs/velos_spectra_1_mods.pkl
test/match_spectra_pairs/velos_spectra_2_mods.pkl
test/match_spectra_pairs/velos_spectra_3_mods.pkl
test/match_spectra_pairs/velos_spectra_aux.pkl
test/pyteomics_examples/mzml/qexactive_mzml_examples.pkl
test/pyteomics_examples/mzml/velos_mzml_examples.pkl
test/pyteomics_examples/pepxml/comet_qexactive_pepxml_examples.pkl
test/pyteomics_examples/pepxml/comet_velos_pepxml_examples.pkl
test/pyteomics_examples/pepxml/percolator_qexactive_pepxml_examples.pkl
test/pyteomics_examples/pepxml/percolator_velos_pepxml_examples.pkl