├── .gitattributes ├── .github └── workflows │ ├── CI_build.yml │ └── pypi_publish.yml ├── .gitignore ├── CHANGELOG.md ├── CITATION.cff ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── dummy_data ├── dummy_spectra.mgf └── expected_results_dummy_spectra.csv ├── environment.yml ├── images ├── features_used.png ├── ms2query_logo.png ├── ms2query_logo.svg ├── worflow_average_ms2deepscore.png └── workflow_ms2query.png ├── ms2query ├── __init__.py ├── __version__.py ├── benchmarking │ ├── __init__.py │ ├── collect_test_data_results.py │ ├── create_accuracy_vs_recall_plot.py │ ├── k_fold_cross_validation.py │ ├── visualize_mass_distribution.py │ └── visualize_tanimoto_score_distribution.py ├── clean_and_filter_spectra.py ├── create_new_library │ ├── __init__.py │ ├── add_classifire_classifications.py │ ├── calculate_tanimoto_scores.py │ ├── create_sqlite_database.py │ ├── library_files_creator.py │ ├── split_data_for_training.py │ ├── train_models.py │ └── train_ms2query_model.py ├── ms2library.py ├── old_query_from_sqlite_functions.py ├── query_from_sqlite_database.py ├── results_table.py ├── run_ms2query.py └── utils.py ├── notebooks ├── GNPS_15_12_2021 │ ├── Visualize example structures.ipynb │ ├── benchmarking │ │ ├── Generate_predictions_for_test_data.ipynb │ │ ├── benchmark_speed_ms2query.py │ │ ├── benchmarking_exact_matches_library_search.ipynb │ │ ├── benchmarking_visualization_analogue_search.ipynb │ │ ├── negative_mode │ │ │ ├── neg_Generate_predictions_for_test_data.ipynb │ │ │ ├── neg_benchmarking_exact_matches_library_search.ipynb │ │ │ └── neg_benchmarking_visualization_analogue_search.ipynb │ │ └── old_benchmarking_notebooks │ │ │ ├── Old_gnps_24_11_benchmarking_ms2query_random_forest.ipynb │ │ │ ├── benchmark_ms2query_random_forest_vs_MS2Deepscore.ipynb │ │ │ ├── cos_score_library_and_analog_search_testing.ipynb │ │ │ └── performance_dependent_on_molecular_size.ipynb │ ├── data_processing_and_training_models │ │ ├── 10_train_random_forest_ms2query.ipynb │ │ ├── 11_optional_create_classifier_classifications.ipynb │ │ ├── 1_Clean_GNPS_spectra.ipynb │ │ ├── 2_split_positive_and_negative_mode.ipynb │ │ ├── 3_split_train_val_test_sets.ipynb │ │ ├── 4_calculate_tanimoto_scores.ipynb │ │ ├── 5_train_ms2deepscore_model.py │ │ ├── 6_train_spec2vec_model.py │ │ ├── 7_create_library_files.py │ │ ├── 8_select_training_and_validation_spectra_ms2query.ipynb │ │ ├── 9_create_training_data_ms2query.py │ │ ├── negative_mode │ │ │ ├── 10_neg_train_random_forest_ms2query.ipynb │ │ │ ├── 3_neg_split_train_val_test_sets.ipynb │ │ │ ├── 4_neg_calculate_tanimoto_scores_negative_mode.ipynb │ │ │ ├── 5_neg_train_ms2deepscore_model.py │ │ │ ├── 6_neg_train_spec2vec_model.py │ │ │ ├── 7_neg_create_library_files.py │ │ │ ├── 8_neg_select_training_and_validation_spectra_ms2query.ipynb │ │ │ └── 9_neg_create_training_data_ms2query.py │ │ └── old_notebook_not_in_paper │ │ │ ├── changes_in_rerun.txt │ │ │ └── train_random_forest_ms2query_all_8_features.ipynb │ └── test_features_for_RF │ │ ├── Validate importance selected features.ipynb │ │ └── optimize_features_random_forest.ipynb └── older_gnps_datasets │ ├── Example structures and spectra for figures.ipynb │ ├── case_studies │ ├── Analyze case study robert jansen 2.ipynb │ ├── Case study huali.ipynb │ ├── Human_Urine_Metabolomics_Comparison.ipynb │ ├── Load_filter_and_select_analogs.ipynb │ ├── analyze results.ipynb │ └── select_analogs_with_high_ms2query.ipynb │ ├── create_library │ ├── MS2Query_import_clean_raw_data_data210409.ipynb │ ├── MS2Query_prepare_and_split_data_data210409.ipynb │ ├── MS2Query_prepare_tanimoto_scores_data210409.ipynb │ └── MS2Query_train_models_s2v_and_ms2ds_All_Spectrums_data210409.ipynb │ ├── old_tests_and_plots.ipynb │ ├── performance_analysis_internship │ ├── Plot_performance_analog_search.ipynb │ ├── Run_analog_search_for_test_and_validation_data.ipynb │ ├── compare_performance_to_ms2deepscore_with_parent_mass.ipynb │ └── test_speed_performance.ipynb │ ├── random_forest │ └── train_random_forest.ipynb │ ├── test_new_ms2deepscore_and_s2v_model.ipynb │ └── train_ms2query_model │ ├── Create_dataset_for_training_MS2Query_model.ipynb │ └── Train_MS2Query_model.ipynb ├── setup.cfg ├── setup.py ├── sonar-project.properties └── tests ├── __init__.py ├── conftest.py ├── test_add_classifier_annotations.py ├── test_calculate_tanimoto_scores.py ├── test_clean_and_filter_spectra.py ├── test_collect_test_data_results.py ├── test_files ├── 100_test_spectra.mgf ├── 100_test_spectra.sqlite ├── 100_test_spectra_ms2ds_embeddings.parquet ├── 100_test_spectra_s2v_embeddings.parquet ├── 100_test_spectra_s2v_model.model ├── 2000_negative_test_spectra.mgf ├── backwards_compatibility │ ├── 100_test_spectra_without_classes.sqlite │ ├── test_files_no_spectrum_id │ │ ├── 100_test_spectra.sqlite │ │ ├── 100_test_spectra_ms2ds_embeddings.pickle │ │ └── 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