.gitignore
License.md
MANIFEST.in
PSM.png
README.md
config.ini
proteorift_env.yml
pyproject.toml
read_spectra.py
readme_pypi.md
requirements.txt
run_ooc_search.py
run_search.py
run_train.py
setup.py
validate.py
examples/basic_search.py
examples/custom_parameters.py
examples/search_with_sample_data.py
proteorift/__init__.py
proteorift/cli.py
proteorift/models.py
proteorift/read_spectra.py
proteorift/run_search.py
proteorift/search.py
proteorift.egg-info/PKG-INFO
proteorift.egg-info/SOURCES.txt
proteorift.egg-info/dependency_links.txt
proteorift.egg-info/entry_points.txt
proteorift.egg-info/requires.txt
proteorift.egg-info/top_level.txt
proteorift/src/__init__.py
proteorift/src/atlesconfig/__init__.py
proteorift/src/atlesconfig/arg_parse.py
proteorift/src/atlesconfig/config.py
proteorift/src/atlesconfig/wandbsetup.py
proteorift/src/atlespredict/__init__.py
proteorift/src/atlespredict/dbsearch.py
proteorift/src/atlespredict/filter.py
proteorift/src/atlespredict/ooc_filtered_search.py
proteorift/src/atlespredict/ooc_unfiltered_search.py
proteorift/src/atlespredict/pepdataset.py
proteorift/src/atlespredict/postprocess.py
proteorift/src/atlespredict/preprocess.py
proteorift/src/atlespredict/specdataset.py
proteorift/src/atlespredict/specollate_model.py
proteorift/src/atlestrain/__init__.py
proteorift/src/atlestrain/dataset.py
proteorift/src/atlestrain/model.py
proteorift/src/atlestrain/process.py
proteorift/src/atlestrain/sampler.py
proteorift/src/atlestrain/trainmodel.py
proteorift/src/atlesutils/__init__.py
proteorift/src/atlesutils/preprocess.py
proteorift/src/atlesutils/reader.py
proteorift/src/atlesutils/simulatespectra.py
proteorift/src/atlesutils/utils.py
proteorift/src/test/__init__.py
proteorift/src/test/test_reader.py
sample_data/peptide_database/human-peptidome-subset.fasta
sample_data/spectra/1DLC012615QE_RRAG_006B_rep2.mgf
sample_data/spectra/1DLC012615QE_RRAG_014B_rep1.mgf
src/__init__.py
src/atlesconfig/__init__.py
src/atlesconfig/arg_parse.py
src/atlesconfig/config.py
src/atlesconfig/wandbsetup.py
src/atlespredict/__init__.py
src/atlespredict/dbsearch.py
src/atlespredict/filter.py
src/atlespredict/ooc_filtered_search.py
src/atlespredict/ooc_unfiltered_search.py
src/atlespredict/pepdataset.py
src/atlespredict/postprocess.py
src/atlespredict/preprocess.py
src/atlespredict/specdataset.py
src/atlespredict/specollate_model.py
src/atlestrain/__init__.py
src/atlestrain/dataset.py
src/atlestrain/model.py
src/atlestrain/process.py
src/atlestrain/sampler.py
src/atlestrain/trainmodel.py
src/atlesutils/__init__.py
src/atlesutils/preprocess.py
src/atlesutils/reader.py
src/atlesutils/simulatespectra.py
src/atlesutils/utils.py
src/test/__init__.py
src/test/test_reader.py