├── .coveragerc ├── .github └── workflows │ ├── docker.yaml │ ├── pythonpublish.yaml │ └── test.yaml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── docker └── Dockerfile ├── docs ├── .gitignore ├── Makefile ├── _ext │ ├── exec_directive.py │ ├── rst_table.py │ ├── sphinx_clickx.py │ └── unimod_table.py ├── _static │ ├── css │ │ └── custom.css │ └── img │ │ └── logo.png ├── _templates │ └── sidebar.html ├── _theme │ └── custom_theme │ │ ├── layout.html │ │ ├── static │ │ ├── alert_info_32.png │ │ ├── alert_warning_32.png │ │ ├── bg-page.png │ │ ├── bullet_orange.png │ │ └── haiku.css_t │ │ └── theme.conf ├── cli-apps │ ├── database │ │ ├── combinatorial-glycan.rst │ │ ├── fasta-glycopeptide.rst │ │ ├── glycan-networks.rst │ │ ├── glyspace-glycan.rst │ │ ├── index.rst │ │ └── text-glycan.rst │ ├── index.rst │ ├── output │ │ ├── export-glycan.rst │ │ ├── export-glycopeptide.rst │ │ ├── export-hypothesis.rst │ │ └── index.rst │ └── search │ │ ├── index.rst │ │ ├── mzml-preprocess.rst │ │ ├── retention-time-model.rst │ │ ├── search-glycan.rst │ │ └── search-glycopeptide.rst ├── conf.py ├── index.rst ├── installing.rst ├── topics │ ├── glycan-classes.rst │ ├── index.rst │ ├── iupaclite.rst │ └── peptide-mods.rst └── tutorials │ ├── combined_mouse_nglycans.txt │ ├── glycoproteomics-sce-tutorial.rst │ ├── glycoproteomics-tutorial.rst │ ├── index.rst │ └── rules-file.txt ├── external-requirements.txt ├── makefile ├── pyinstaller ├── .gitignore ├── glycresoft-cli.py ├── hooks │ ├── _hook-rdflib.py │ ├── hook-brainpy.py │ ├── hook-glycopeptide_feature_learning.py │ ├── hook-glycopeptidepy.py │ ├── hook-glycresoft.py │ ├── hook-glycresoft_app.py │ ├── hook-glypy.py │ ├── hook-ms_deisotope.py │ ├── hook-ms_peak_picker.py │ ├── hook-psims.py │ └── hook-sklearn.py ├── img │ └── logo.ico ├── install-from-git.py ├── make-pyinstaller.sh └── readme ├── pyproject.toml ├── requirements.txt ├── scripts └── intracluster_similarity.py ├── setup.py ├── src ├── glycan_profiling │ └── __init__.py └── glycresoft │ ├── __init__.py │ ├── _c │ ├── __init__.py │ ├── chromatogram_tree │ │ ├── __init__.py │ │ ├── chromatogram.pxd │ │ ├── chromatogram.pyx │ │ ├── index.pxd │ │ ├── index.pyx │ │ ├── mass_shift.pxd │ │ └── mass_shift.pyx │ ├── composition_distribution_model │ │ ├── __init__.py │ │ ├── utils.pxd │ │ └── utils.pyx │ ├── composition_network │ │ ├── __init__.py │ │ ├── graph.pxd │ │ └── graph.pyx │ ├── cythonizer.py │ ├── database │ │ ├── __init__.py │ │ ├── mass_collection.pxd │ │ └── mass_collection.pyx │ ├── scoring │ │ ├── __init__.py │ │ ├── elution_time_grouping.pyx │ │ └── shape_fitter.pyx │ ├── structure │ │ ├── __init__.py │ │ ├── fragment_match_map.pxd │ │ ├── fragment_match_map.pyx │ │ ├── intervals.pyx │ │ ├── lru.pyx │ │ ├── probability.pyx │ │ ├── structure_loader.pxd │ │ └── structure_loader.pyx │ └── tandem │ │ ├── __init__.py │ │ ├── core_search.pyx │ │ ├── oxonium_ions.pxd │ │ ├── oxonium_ions.pyx │ │ ├── peptide_graph.pyx │ │ ├── spectrum_match.pxd │ │ ├── spectrum_match.pyx │ │ ├── tandem_scoring_helpers.pyx │ │ └── target_decoy.pyx │ ├── chromatogram_tree │ ├── __init__.py │ ├── chromatogram.py │ ├── generic.py │ ├── grouping.py │ ├── index.py │ ├── mass_shift.py │ ├── mass_shift_tree.py │ ├── relation_graph.py │ └── utils.py │ ├── cli │ ├── __init__.py │ ├── __main__.py │ ├── analyze.py │ ├── base.py │ ├── build_db.py │ ├── config.py │ ├── export.py │ ├── logger_config.py │ ├── mzml.py │ ├── tools.py │ ├── utils.py │ └── validators.py │ ├── composition_distribution_model │ ├── __init__.py │ ├── constants.py │ ├── glycome_network_smoothing.py │ ├── graph.py │ ├── grid_search.py │ ├── laplacian_smoothing.py │ ├── observation.py │ ├── prior_distribution.py │ ├── site_model │ │ ├── __init__.py │ │ ├── builder.py │ │ ├── glycoprotein_model.py │ │ ├── glycoproteome_model.py │ │ └── glycosite_model.py │ └── utils.py │ ├── config │ ├── __init__.py │ ├── colors.py │ ├── config_file.py │ ├── mass_shift.py │ ├── peptide_modification.py │ └── substituent.py │ ├── database │ ├── __init__.py │ ├── analysis │ │ ├── __init__.py │ │ └── analysis_migration.py │ ├── builder │ │ ├── __init__.py │ │ ├── base.py │ │ ├── glycan │ │ │ ├── __init__.py │ │ │ ├── constrained_combinatorics.py │ │ │ ├── convert_analysis.py │ │ │ ├── glycan_combinator.py │ │ │ ├── glycan_permutations.py │ │ │ ├── glycan_source.py │ │ │ ├── glycosaminoglycan_linker_generation.py │ │ │ ├── glyspace.py │ │ │ ├── migrate.py │ │ │ └── synthesis.py │ │ └── glycopeptide │ │ │ ├── __init__.py │ │ │ ├── common.py │ │ │ ├── extending_glycopeptide.py │ │ │ ├── informed_glycopeptide.py │ │ │ ├── migrate.py │ │ │ ├── naive_glycopeptide.py │ │ │ └── proteomics │ │ │ ├── __init__.py │ │ │ ├── fasta.py │ │ │ ├── mzid_parser.py │ │ │ ├── mzid_proteome.py │ │ │ ├── peptide_permutation.py │ │ │ ├── proteome.py │ │ │ ├── remove_duplicate_peptides.py │ │ │ ├── sequence_tree.py │ │ │ ├── share_peptides.py │ │ │ ├── uniprot.py │ │ │ └── utils.py │ ├── composition_aggregation.py │ ├── composition_network │ │ ├── __init__.py │ │ ├── graph.py │ │ ├── neighborhood.py │ │ ├── rule.py │ │ └── space.py │ ├── disk_backed_database.py │ ├── glycan_composition_filter.py │ ├── index.py │ ├── intervals.py │ ├── mass_collection.py │ └── prebuilt │ │ ├── __init__.py │ │ ├── biosynthesis_human_n_linked.py │ │ ├── biosynthesis_mammalian_n_linked.py │ │ ├── combinatorial_human_n_linked.py │ │ ├── combinatorial_mammalian_n_linked.py │ │ ├── data │ │ ├── __init__.py │ │ ├── human_composition_enzyme_graph.json │ │ ├── mammalian_composition_enzyme_graph.json │ │ └── mucin_compositions.txt │ │ ├── glycosaminoglycan_linkers.py │ │ ├── heparin.py │ │ ├── human_mucin_o_linked.py │ │ └── utils.py │ ├── models │ ├── __init__.py │ ├── charge_models.py │ ├── data │ │ ├── __init__.py │ │ ├── ammonium_adduct_model.json │ │ ├── asialo_formate_adduct_model.json │ │ ├── disialo_formate_adduct_model.json │ │ ├── methyl_loss_adduct_model.json │ │ ├── monosialo_formate_adduct_model.json │ │ ├── sialylated_charge_model.json │ │ ├── tetrasialo_formate_adduct_model.json │ │ ├── trisialo_formate_adduct_model.json │ │ └── unsialylated_charge_model.json │ ├── features.py │ ├── mass_shift_models.py │ └── utils.py │ ├── output │ ├── __init__.py │ ├── annotate_spectra.py │ ├── csv_format.py │ ├── report │ │ ├── __init__.py │ │ ├── base.py │ │ ├── glycan_lcms │ │ │ ├── __init__.py │ │ │ ├── behaviors.js │ │ │ ├── overview.templ │ │ │ ├── render.py │ │ │ └── style.css │ │ └── glycopeptide_lcmsms │ │ │ ├── __init__.py │ │ │ ├── behaviors.js │ │ │ ├── glycopeptide-detail-entry.templ │ │ │ ├── glycopeptide-table.templ │ │ │ ├── overview.templ │ │ │ ├── protein-heading.templ │ │ │ ├── render.py │ │ │ └── style.css │ ├── text_format.py │ └── xml.py │ ├── piped_deconvolve.py │ ├── plotting │ ├── __init__.py │ ├── base.py │ ├── chromatogram_artist.py │ ├── colors.py │ ├── diagnostics.py │ ├── entity_bar_chart.py │ ├── glycan_visual_classification.py │ ├── lcms_map.py │ ├── lcms_surface.py │ ├── map_glycan_network.py │ ├── plot_glycoforms.py │ ├── sequence_fragment_logo.py │ ├── spectral_annotation.py │ ├── summaries.py │ ├── svg_utils.py │ └── utils.py │ ├── profiler.py │ ├── scan_cache.py │ ├── scoring │ ├── __init__.py │ ├── base.py │ ├── charge_state.py │ ├── chromatogram_solution.py │ ├── elution_time_grouping │ │ ├── __init__.py │ │ ├── cross_run.py │ │ ├── linear_regression.py │ │ ├── model.py │ │ ├── pipeline.py │ │ ├── recalibrator.py │ │ ├── reviser.py │ │ └── structure.py │ ├── isotopic_fit.py │ ├── mass_shift_scoring.py │ ├── shape_fitter.py │ ├── spacing_fitter.py │ └── utils.py │ ├── serialize │ ├── __init__.py │ ├── analysis.py │ ├── base.py │ ├── chromatogram.py │ ├── config.py │ ├── connection.py │ ├── hypothesis │ │ ├── __init__.py │ │ ├── generic.py │ │ ├── glycan.py │ │ ├── hypothesis.py │ │ └── peptide.py │ ├── identification.py │ ├── migration.py │ ├── param.py │ ├── serializer.py │ ├── spectrum.py │ ├── tandem.py │ └── utils.py │ ├── structure │ ├── __init__.py │ ├── denovo.py │ ├── enums.py │ ├── fragment_match_map.py │ ├── lru.py │ ├── probability.py │ ├── scan.py │ ├── structure_loader.py │ └── utils.py │ ├── symbolic_expression.py │ ├── tandem │ ├── __init__.py │ ├── chromatogram_mapping │ │ ├── __init__.py │ │ ├── aggregation.py │ │ ├── base.py │ │ ├── chromatogram.py │ │ ├── graph.py │ │ ├── mapper.py │ │ ├── representer.py │ │ └── revision.py │ ├── coelute.py │ ├── evaluation_dispatch │ │ ├── __init__.py │ │ ├── evaluation.py │ │ ├── process.py │ │ ├── task.py │ │ └── utils.py │ ├── glycan │ │ ├── __init__.py │ │ ├── composition_matching.py │ │ ├── denovo.py │ │ └── scoring │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── binomial_coverage │ │ │ ├── __init__.py │ │ │ ├── matcher.py │ │ │ └── score_components.py │ │ │ └── signature_ion_scoring.py │ ├── glycopeptide │ │ ├── __init__.py │ │ ├── chromatogram_graph.py │ │ ├── core_search.py │ │ ├── dynamic_generation │ │ │ ├── __init__.py │ │ │ ├── journal.py │ │ │ ├── mixture.py │ │ │ ├── multipart_fdr.py │ │ │ ├── peptide_graph.py │ │ │ ├── search_space.py │ │ │ ├── searcher.py │ │ │ └── workflow.py │ │ ├── glycopeptide_matcher.py │ │ ├── identified_structure.py │ │ ├── matcher.py │ │ └── scoring │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── binomial_score.py │ │ │ ├── coverage_weighted_binomial.py │ │ │ ├── glycan_signature_ions.py │ │ │ ├── intensity_scorer.py │ │ │ ├── pair_amino_acids_scoring.py │ │ │ ├── peak_vector.py │ │ │ ├── precursor_mass_accuracy.py │ │ │ └── simple_score.py │ ├── identified_structure.py │ ├── localize.py │ ├── match_between_runs │ │ ├── __init__.py │ │ ├── dataset.py │ │ └── match_between.py │ ├── oxonium_ions.py │ ├── peptide │ │ ├── __init__.py │ │ └── scoring │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── intensity_score.py │ │ │ ├── localize.py │ │ │ └── simple_score.py │ ├── process_dispatcher.py │ ├── ref.py │ ├── reporter.py │ ├── spectrum_evaluation.py │ ├── spectrum_graph.py │ ├── spectrum_match │ │ ├── __init__.py │ │ ├── solution_set.py │ │ └── spectrum_match.py │ ├── target_decoy │ │ ├── __init__.py │ │ ├── base.py │ │ └── svm.py │ ├── temp_store.py │ ├── workflow.py │ └── workload.py │ ├── task.py │ ├── trace │ ├── __init__.py │ ├── evaluate.py │ ├── extract.py │ ├── match.py │ ├── process.py │ └── sink.py │ └── version.py └── tests ├── __init__.py ├── fixtures.py ├── test_composition_network.py ├── test_constrained_combinatorics.py ├── test_core_search.py ├── test_data ├── .gitignore ├── 20150710_3um_AGP_001_29_30.mzML ├── 20150710_3um_AGP_001_29_30.preprocessed.mzML ├── 20150710_3um_AGP_001_29_30.preprocessed.mzML-idx.json ├── AGP_Glycomics_20150930_06.centroid-byte-offsets.json ├── AGP_Glycomics_20150930_06.centroid.mzML ├── AGP_Glycomics_20150930_06.deconvoluted.mzML ├── AGP_Glycomics_20150930_06.deconvoluted.mzML-idx.json ├── AGP_Proteomics2.mzid ├── IAV_matched_glycans.txt ├── __init__.py ├── agp.db ├── agp.fa ├── agp_glycans.txt ├── agp_indexed.db ├── agp_indexed_decoy.db ├── build_refs.sh ├── classic_agp_search.db ├── classic_agp_search_empty.db ├── compositions.txt ├── example_glycopeptide_spectra.mzML ├── example_glycopeptide_spectra.mzML-idx.json ├── glycan_composition_records_for_smoothing_test.txt ├── human_n_glycan_rules.txt ├── indexed_agp_search.db ├── indexed_agp_search_empty.db ├── numpairs.txt ├── phil-82-proteins.fasta ├── serum_gp_chromatograms.csv.gz └── yeast_glycoproteins.fa ├── test_fasta_glycopeptide.py ├── test_glycan_chromatogram_analyzer.py ├── test_glycan_combinator.py ├── test_glycan_prebuilt.py ├── test_glycan_source.py ├── test_glycopeptide_scorers.py ├── test_glycopeptide_search.py ├── test_mzid_glycopeptide.py ├── test_rt_model.py ├── test_sample_consumer.py ├── test_structure_loader.py ├── test_symbolic_expression.py ├── test_target_decoy.py └── test_task_execution_sequence.py /.coveragerc: 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