Index

_

__init__() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) (matchms.filtering.SpectrumProcessor.ProcessingReport method) (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.Fragments method) (matchms.Fragments.Fragments method) (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.networking.SimilarityNetwork method) (matchms.networking.SimilarityNetwork.SimilarityNetwork method) (matchms.Pipeline method) (matchms.Pipeline.Pipeline method) (matchms.Scores method) (matchms.Scores.Scores method) (matchms.Scores.ScoresBuilder method) (matchms.Scores.ScoresJSONEncoder method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) (matchms.SpectrumProcessor method) (matchms.Spikes.Spikes method)

A

add_compound_name() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_compound_name) add_fingerprint() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_fingerprint) add_logging_to_file() (in module matchms.logging_functions) add_losses() (in module matchms.filtering) (in module matchms.filtering.peak_processing.add_losses) add_parent_mass() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_parent_mass)

add_precursor_mz() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_precursor_mz) add_retention_index() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_retention) add_retention_time() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.add_retention) add_to_report() (matchms.filtering.SpectrumProcessor.ProcessingReport method) as_spectrum() (in module matchms.importing.load_from_json)

B

BaseSimilarity (class in matchms.similarity.BaseSimilarity)

build() (matchms.Scores.ScoresBuilder method)

C

calculate() (matchms.Scores method) (matchms.Scores.Scores method) calculate_scores() (in module matchms) (in module matchms.calculate_scores) check_all_parameters_given() (in module matchms.filtering.SpectrumProcessor) check_score_computation() (in module matchms.Pipeline) check_workflow() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method) clean() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) clean_adduct() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.clean_adduct) clean_as_inchi() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) clean_as_inchikey() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) clean_as_smiles() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) clean_compound_name() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.clean_compound_name)

cleaned (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute) clone() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) collect_peak_pairs() (in module matchms.similarity.spectrum_similarity_functions) contains_metadata() (in module matchms.importing.load_from_msp) convert_inchi_to_inchikey() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) convert_inchi_to_smiles() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) convert_smiles_to_inchi() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) correct_charge() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.correct_charge) cosine_similarity() (in module matchms.similarity.vector_similarity_functions) cosine_similarity_matrix() (in module matchms.similarity.vector_similarity_functions) CosineGreedy (class in matchms.similarity) (class in matchms.similarity.CosineGreedy) CosineHungarian (class in matchms.similarity) (class in matchms.similarity.CosineHungarian) create_network() (matchms.networking.SimilarityNetwork method) (matchms.networking.SimilarityNetwork.SimilarityNetwork method) create_partial_function() (in module matchms.filtering.SpectrumProcessor) create_workflow() (in module matchms.Pipeline)

D

default() (matchms.Scores.ScoresJSONEncoder method) default_filters() (in module matchms.filtering) (in module matchms.filtering.default_filters) derive_adduct_from_name() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_adduct_from_name) derive_annotation_from_compound_name() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_annotation_from_compound_name) derive_formula_from_name() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_formula_from_name) derive_inchi_from_smiles() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_inchi_from_smiles) derive_inchikey_from_inchi() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_inchikey_from_inchi)

derive_ionmode() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_ionmode) derive_parent_mass_from_precursor_mz() (in module matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass) derive_precursor_mz_from_parent_mass() (in module matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass) derive_smiles_from_inchi() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.derive_smiles_from_inchi) dice_similarity() (in module matchms.similarity.vector_similarity_functions) dice_similarity_matrix() (in module matchms.similarity.vector_similarity_functions) dict2spectrum() (in module matchms.importing.load_from_json) dirty (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute)

E

encode() (matchms.Scores.ScoresJSONEncoder method) export_metadata_as_csv() (in module matchms.exporting.metadata_export) export_metadata_as_json() (in module matchms.exporting.metadata_export)

export_to_file() (matchms.networking.SimilarityNetwork method) (matchms.networking.SimilarityNetwork.SimilarityNetwork method) export_to_graphml() (matchms.networking.SimilarityNetwork method) (matchms.networking.SimilarityNetwork.SimilarityNetwork method)

F

filter_by_range() (matchms.Scores method) (matchms.Scores.Scores method) filter_none() (in module matchms.utils) find_by_key() (in module matchms.importing.parsing_utils) find_matches() (in module matchms.similarity.spectrum_similarity_functions)

FingerprintSimilarity (class in matchms.similarity) (class in matchms.similarity.FingerprintSimilarity) Fragments (class in matchms) (class in matchms.Fragments) from_json() (matchms.Scores.ScoresBuilder method)

G

get() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) get_charge_of_adduct() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_common_keys() (in module matchms.utils) get_first_common_element() (in module matchms.utils) get_ions_from_adduct() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_mass_of_formula() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_mass_of_ion() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_metadata_as_array() (in module matchms.exporting.metadata_export)

get_molecular_weight_neutral_mass() (in module matchms.filtering.filter_utils.get_neutral_mass_from_smiles) get_monoisotopic_neutral_mass() (in module matchms.filtering.filter_utils.get_neutral_mass_from_smiles) get_multiplier_and_mass_from_adduct() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_parameter_settings() (in module matchms.filtering.SpectrumProcessor) get_peak_comment() (in module matchms.importing.load_from_msp) get_peak_values() (in module matchms.importing.load_from_msp) get_top_hits() (in module matchms.networking.networking_functions) get_unused_filters() (in module matchms.Pipeline) graph (matchms.networking.SimilarityNetwork attribute) (matchms.networking.SimilarityNetwork.SimilarityNetwork attribute) guess_target() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method)

H

harmonize_keys() (matchms.Metadata method) (matchms.Metadata.Metadata method) harmonize_undefined_inchi() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.harmonize_undefined_inchi) harmonize_undefined_inchikey() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.harmonize_undefined_inchikey)

harmonize_undefined_smiles() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.harmonize_undefined_smiles) harmonize_values() (matchms.Metadata method) (matchms.Metadata.Metadata method)

I

import_spectrums() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method) intensities (matchms.Fragments attribute) (matchms.Fragments property) (matchms.Fragments.Fragments attribute) (matchms.Fragments.Fragments property) (matchms.Spikes.Spikes property) interpret_pepmass() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.interpret_pepmass)

IntersectMz (class in matchms.similarity) (class in matchms.similarity.IntersectMz) is_commutative (matchms.similarity.BaseSimilarity.BaseSimilarity attribute) is_valid_inchi() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) is_valid_inchikey() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) is_valid_smiles() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) items() (matchms.Metadata method) (matchms.Metadata.Metadata method) iterencode() (matchms.Scores.ScoresJSONEncoder method)

J

jaccard_index() (in module matchms.similarity.vector_similarity_functions)

jaccard_similarity_matrix() (in module matchms.similarity.vector_similarity_functions)

K

keep_score() (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method)

keys() (matchms.Metadata method) (matchms.Metadata.Metadata method)

L

load_export_key_conversions() (in module matchms.utils) load_from_json() (in module matchms.importing) (in module matchms.importing.load_from_json) load_from_mgf() (in module matchms.importing) (in module matchms.importing.load_from_mgf) load_from_msp() (in module matchms.importing) (in module matchms.importing.load_from_msp) load_from_mzml() (in module matchms.importing) (in module matchms.importing.load_from_mzml) load_from_mzxml() (in module matchms.importing) (in module matchms.importing.load_from_mzxml) load_from_pickle() (in module matchms.importing) (in module matchms.importing.load_from_pickle) load_from_usi() (in module matchms.importing) (in module matchms.importing.load_from_usi)

load_known_adduct_conversions() (in module matchms.filtering.filter_utils.load_known_adducts) load_known_adducts() (in module matchms.filtering.filter_utils.load_known_adducts) load_known_key_conversions() (in module matchms.utils) load_list_of_spectrum_files() (in module matchms.importing.load_spectra) load_spectra() (in module matchms.importing) (in module matchms.importing.load_spectra) looks_like_a_smiles() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) looks_like_an_inchi() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) looks_like_an_inchikey() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) losses (matchms.Spectrum attribute) (matchms.Spectrum.Spectrum attribute)

M

make_charge_int() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.make_charge_int) matchms module matchms.calculate_scores module matchms.constants module matchms.exporting module matchms.exporting.metadata_export module matchms.exporting.save_as_json module matchms.exporting.save_as_mgf module matchms.exporting.save_as_msp module matchms.exporting.save_spectra module matchms.filtering module matchms.filtering.default_filters module matchms.filtering.default_pipelines module matchms.filtering.filter_order module matchms.filtering.filter_utils module matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass module matchms.filtering.filter_utils.get_neutral_mass_from_smiles module matchms.filtering.filter_utils.interpret_unknown_adduct module matchms.filtering.filter_utils.load_known_adducts module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions module matchms.filtering.metadata_processing module matchms.filtering.metadata_processing.add_compound_name module matchms.filtering.metadata_processing.add_fingerprint module matchms.filtering.metadata_processing.add_parent_mass module matchms.filtering.metadata_processing.add_precursor_mz module matchms.filtering.metadata_processing.add_retention module matchms.filtering.metadata_processing.clean_adduct module matchms.filtering.metadata_processing.clean_compound_name module matchms.filtering.metadata_processing.correct_charge module matchms.filtering.metadata_processing.derive_adduct_from_name module matchms.filtering.metadata_processing.derive_annotation_from_compound_name module matchms.filtering.metadata_processing.derive_formula_from_name module matchms.filtering.metadata_processing.derive_inchi_from_smiles module matchms.filtering.metadata_processing.derive_inchikey_from_inchi module matchms.filtering.metadata_processing.derive_ionmode module matchms.filtering.metadata_processing.derive_smiles_from_inchi module matchms.filtering.metadata_processing.harmonize_undefined_inchi module matchms.filtering.metadata_processing.harmonize_undefined_inchikey module matchms.filtering.metadata_processing.harmonize_undefined_smiles module matchms.filtering.metadata_processing.interpret_pepmass module matchms.filtering.metadata_processing.make_charge_int module matchms.filtering.metadata_processing.repair_adduct_based_on_smiles module matchms.filtering.metadata_processing.repair_inchi_inchikey_smiles module matchms.filtering.metadata_processing.repair_not_matching_annotation module matchms.filtering.metadata_processing.repair_parent_mass_is_mol_wt module matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper module matchms.filtering.metadata_processing.repair_precursor_is_parent_mass module matchms.filtering.metadata_processing.repair_smiles_of_salts module matchms.filtering.metadata_processing.require_correct_ionmode module matchms.filtering.metadata_processing.require_parent_mass_match_smiles module matchms.filtering.metadata_processing.require_precursor_below_mz module matchms.filtering.metadata_processing.require_precursor_mz module matchms.filtering.metadata_processing.require_valid_annotation module matchms.filtering.peak_processing module matchms.filtering.peak_processing.add_losses module matchms.filtering.peak_processing.normalize_intensities module matchms.filtering.peak_processing.reduce_to_number_of_peaks module matchms.filtering.peak_processing.remove_peaks_around_precursor_mz module matchms.filtering.peak_processing.remove_peaks_outside_top_k module matchms.filtering.peak_processing.require_minimum_number_of_high_peaks module matchms.filtering.peak_processing.require_minimum_number_of_peaks module matchms.filtering.peak_processing.select_by_intensity module matchms.filtering.peak_processing.select_by_mz module matchms.filtering.peak_processing.select_by_relative_intensity module matchms.filtering.SpeciesString module matchms.filtering.SpectrumProcessor module matchms.Fragments module matchms.hashing module matchms.importing module matchms.importing.load_from_json module matchms.importing.load_from_mgf module matchms.importing.load_from_msp module matchms.importing.load_from_mzml module matchms.importing.load_from_mzxml module matchms.importing.load_from_pickle module matchms.importing.load_from_usi module matchms.importing.load_scores module matchms.importing.load_spectra module matchms.importing.parsing_utils module matchms.logging_functions module matchms.Metadata module matchms.networking module matchms.networking.networking_functions module matchms.networking.SimilarityNetwork module matchms.Pipeline module matchms.plotting module matchms.plotting.spectrum_plots module matchms.Scores module matchms.similarity module

matchms.similarity.BaseSimilarity module matchms.similarity.CosineGreedy module matchms.similarity.CosineHungarian module matchms.similarity.FingerprintSimilarity module matchms.similarity.IntersectMz module matchms.similarity.MetadataMatch module matchms.similarity.ModifiedCosine module matchms.similarity.NeutralLossesCosine module matchms.similarity.ParentMassMatch module matchms.similarity.PrecursorMzMatch module matchms.similarity.spectrum_similarity_functions module matchms.similarity.vector_similarity_functions module matchms.Spectrum module matchms.Spikes module matchms.typing module matchms.utils module matchms.yaml_file_functions module matrix() (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method) Metadata (class in matchms) (class in matchms.Metadata) metadata (matchms.Spectrum attribute) (matchms.Spectrum.Spectrum attribute) metadata_dict() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) metadata_hash() (in module matchms.hashing) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) MetadataMatch (class in matchms.similarity) (class in matchms.similarity.MetadataMatch) ModifiedCosine (class in matchms.similarity) (class in matchms.similarity.ModifiedCosine) module matchms matchms.calculate_scores matchms.constants matchms.exporting matchms.exporting.metadata_export matchms.exporting.save_as_json matchms.exporting.save_as_mgf matchms.exporting.save_as_msp matchms.exporting.save_spectra matchms.filtering matchms.filtering.default_filters matchms.filtering.default_pipelines matchms.filtering.filter_order matchms.filtering.filter_utils matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass matchms.filtering.filter_utils.get_neutral_mass_from_smiles matchms.filtering.filter_utils.interpret_unknown_adduct matchms.filtering.filter_utils.load_known_adducts matchms.filtering.filter_utils.smile_inchi_inchikey_conversions matchms.filtering.metadata_processing matchms.filtering.metadata_processing.add_compound_name matchms.filtering.metadata_processing.add_fingerprint matchms.filtering.metadata_processing.add_parent_mass matchms.filtering.metadata_processing.add_precursor_mz matchms.filtering.metadata_processing.add_retention matchms.filtering.metadata_processing.clean_adduct matchms.filtering.metadata_processing.clean_compound_name matchms.filtering.metadata_processing.correct_charge matchms.filtering.metadata_processing.derive_adduct_from_name matchms.filtering.metadata_processing.derive_annotation_from_compound_name matchms.filtering.metadata_processing.derive_formula_from_name matchms.filtering.metadata_processing.derive_inchi_from_smiles matchms.filtering.metadata_processing.derive_inchikey_from_inchi matchms.filtering.metadata_processing.derive_ionmode matchms.filtering.metadata_processing.derive_smiles_from_inchi matchms.filtering.metadata_processing.harmonize_undefined_inchi matchms.filtering.metadata_processing.harmonize_undefined_inchikey matchms.filtering.metadata_processing.harmonize_undefined_smiles matchms.filtering.metadata_processing.interpret_pepmass matchms.filtering.metadata_processing.make_charge_int matchms.filtering.metadata_processing.repair_adduct_based_on_smiles matchms.filtering.metadata_processing.repair_inchi_inchikey_smiles matchms.filtering.metadata_processing.repair_not_matching_annotation matchms.filtering.metadata_processing.repair_parent_mass_is_mol_wt matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper matchms.filtering.metadata_processing.repair_precursor_is_parent_mass matchms.filtering.metadata_processing.repair_smiles_of_salts matchms.filtering.metadata_processing.require_correct_ionmode matchms.filtering.metadata_processing.require_parent_mass_match_smiles matchms.filtering.metadata_processing.require_precursor_below_mz matchms.filtering.metadata_processing.require_precursor_mz matchms.filtering.metadata_processing.require_valid_annotation matchms.filtering.peak_processing matchms.filtering.peak_processing.add_losses matchms.filtering.peak_processing.normalize_intensities matchms.filtering.peak_processing.reduce_to_number_of_peaks matchms.filtering.peak_processing.remove_peaks_around_precursor_mz matchms.filtering.peak_processing.remove_peaks_outside_top_k matchms.filtering.peak_processing.require_minimum_number_of_high_peaks matchms.filtering.peak_processing.require_minimum_number_of_peaks matchms.filtering.peak_processing.select_by_intensity matchms.filtering.peak_processing.select_by_mz matchms.filtering.peak_processing.select_by_relative_intensity matchms.filtering.SpeciesString matchms.filtering.SpectrumProcessor matchms.Fragments matchms.hashing matchms.importing matchms.importing.load_from_json matchms.importing.load_from_mgf matchms.importing.load_from_msp matchms.importing.load_from_mzml matchms.importing.load_from_mzxml matchms.importing.load_from_pickle matchms.importing.load_from_usi matchms.importing.load_scores matchms.importing.load_spectra matchms.importing.parsing_utils matchms.logging_functions matchms.Metadata matchms.networking matchms.networking.networking_functions matchms.networking.SimilarityNetwork matchms.Pipeline matchms.plotting matchms.plotting.spectrum_plots matchms.Scores matchms.similarity matchms.similarity.BaseSimilarity matchms.similarity.CosineGreedy matchms.similarity.CosineHungarian matchms.similarity.FingerprintSimilarity matchms.similarity.IntersectMz matchms.similarity.MetadataMatch matchms.similarity.ModifiedCosine matchms.similarity.NeutralLossesCosine matchms.similarity.ParentMassMatch matchms.similarity.PrecursorMzMatch matchms.similarity.spectrum_similarity_functions matchms.similarity.vector_similarity_functions matchms.Spectrum matchms.Spikes matchms.typing matchms.utils matchms.yaml_file_functions mol_converter() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) mz (matchms.Fragments attribute) (matchms.Fragments property) (matchms.Fragments.Fragments attribute) (matchms.Fragments.Fragments property) (matchms.Spikes.Spikes property)

N

NeutralLossesCosine (class in matchms.similarity) (class in matchms.similarity.NeutralLossesCosine) normalize_intensities() (in module matchms.filtering) (in module matchms.filtering.peak_processing.normalize_intensities)

number_matching() (in module matchms.similarity.spectrum_similarity_functions) number_matching_ppm() (in module matchms.similarity.spectrum_similarity_functions) number_matching_symmetric() (in module matchms.similarity.spectrum_similarity_functions) number_matching_symmetric_ppm() (in module matchms.similarity.spectrum_similarity_functions)

O

objects_differ() (in module matchms.filtering.SpectrumProcessor)

ordered_load() (in module matchms.yaml_file_functions)

P

pair() (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method) ParentMassMatch (class in matchms.similarity) (class in matchms.similarity.ParentMassMatch) parse_and_add_filter() (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectrumProcessor method) parse_metadata() (in module matchms.importing.load_from_msp)

parse_msp_file() (in module matchms.importing.load_from_msp) parse_mzml_mzxml_metadata() (in module matchms.importing.parsing_utils) parse_spectrum_dict() (in module matchms.importing.parsing_utils) peaks (matchms.Spectrum attribute) (matchms.Spectrum.Spectrum attribute) Pipeline (class in matchms) (class in matchms.Pipeline) plot() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) plot_against() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) plot_spectra_array() (in module matchms.plotting) (in module matchms.plotting.spectrum_plots) plot_spectra_mirror() (in module matchms.plotting) (in module matchms.plotting.spectrum_plots) plot_spectrum() (in module matchms.plotting) (in module matchms.plotting.spectrum_plots) PrecursorMzMatch (class in matchms.similarity) (class in matchms.similarity.PrecursorMzMatch) process_spectrum() (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectrumProcessor method) process_spectrums() (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectrumProcessor method) ProcessingReport (class in matchms.filtering.SpectrumProcessor)

R

reduce_to_number_of_peaks() (in module matchms.filtering) (in module matchms.filtering.peak_processing.reduce_to_number_of_peaks) ReferencesType (in module matchms.typing) remove_peaks_around_precursor_mz() (in module matchms.filtering) (in module matchms.filtering.peak_processing.remove_peaks_around_precursor_mz) remove_peaks_outside_top_k() (in module matchms.filtering) (in module matchms.filtering.peak_processing.remove_peaks_outside_top_k) repair_adduct_based_on_smiles() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_adduct_based_on_smiles) repair_inchi_inchikey_smiles() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_inchi_inchikey_smiles) repair_not_matching_annotation() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_not_matching_annotation) repair_parent_mass_is_mol_wt() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_parent_mass_is_mol_wt) repair_parent_mass_match_smiles_wrapper() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper) repair_precursor_is_parent_mass() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_precursor_is_parent_mass)

repair_smiles_of_salts() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_smiles_of_salts) replace_abbreviations() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) require_correct_ionmode() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.require_correct_ionmode) require_minimum_number_of_high_peaks() (in module matchms.filtering) (in module matchms.filtering.peak_processing.require_minimum_number_of_high_peaks) require_minimum_number_of_peaks() (in module matchms.filtering) (in module matchms.filtering.peak_processing.require_minimum_number_of_peaks) require_parent_mass_match_smiles() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.require_parent_mass_match_smiles) require_precursor_below_mz() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.require_precursor_below_mz) require_precursor_mz() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.require_precursor_mz) require_valid_annotation() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.require_valid_annotation) reset_matchms_logger() (in module matchms.logging_functions) run() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method)

S

save_as_json() (in module matchms.exporting) (in module matchms.exporting.save_as_json) save_as_mgf() (in module matchms.exporting) (in module matchms.exporting.save_as_mgf) save_as_msp() (in module matchms.exporting) (in module matchms.exporting.save_as_msp) save_as_pickled_file() (in module matchms.exporting.save_spectra) save_spectra() (in module matchms.exporting) (in module matchms.exporting.save_spectra) score_best_matches() (in module matchms.similarity.spectrum_similarity_functions) score_datatype (matchms.similarity.BaseSimilarity.BaseSimilarity attribute) (matchms.similarity.FingerprintSimilarity attribute) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity attribute) (matchms.similarity.IntersectMz attribute) (matchms.similarity.IntersectMz.IntersectMz attribute) (matchms.similarity.MetadataMatch attribute) (matchms.similarity.MetadataMatch.MetadataMatch attribute) (matchms.similarity.ParentMassMatch attribute) (matchms.similarity.ParentMassMatch.ParentMassMatch attribute) (matchms.similarity.PrecursorMzMatch attribute) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch attribute) Scores (class in matchms) (class in matchms.Scores) scores_by_query() (matchms.Scores method) (matchms.Scores.Scores method) scores_by_reference() (matchms.Scores method) (matchms.Scores.Scores method) scores_from_json() (in module matchms.importing) (in module matchms.importing.load_scores) scores_from_pickle() (in module matchms.importing) (in module matchms.importing.load_scores) scores_json_decoder() (in module matchms.importing.load_from_json) ScoresBuilder (class in matchms.Scores) ScoresJSONEncoder (class in matchms.Scores) select_by_intensity() (in module matchms.filtering) (in module matchms.filtering.peak_processing.select_by_intensity) select_by_mz() (in module matchms.filtering) (in module matchms.filtering.peak_processing.select_by_mz) select_by_relative_intensity() (in module matchms.filtering) (in module matchms.filtering.peak_processing.select_by_relative_intensity) set() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method)

set_key_replacements() (matchms.Metadata static method) (matchms.Metadata.Metadata static method) set_logging() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method) set_matchms_logger_level() (in module matchms) (in module matchms.logging_functions) SimilarityNetwork (class in matchms.networking) (class in matchms.networking.SimilarityNetwork) sort_by_mz() (in module matchms.importing.parsing_utils) sparse_array() (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method) SpeciesString (class in matchms.filtering) (class in matchms.filtering.SpeciesString) Spectrum (class in matchms) (class in matchms.Spectrum) spectrum_hash() (in module matchms.hashing) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) SpectrumProcessor (class in matchms) (class in matchms.filtering.SpectrumProcessor) Spikes (class in matchms.Spikes) split_ion() (in module matchms.filtering.filter_utils.interpret_unknown_adduct)

T

target (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute) to_array() (matchms.Scores method) (matchms.Scores.Scores method) to_coo() (matchms.Scores method) (matchms.Scores.Scores method) to_dataframe() (matchms.filtering.SpectrumProcessor.ProcessingReport method) to_dict() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.Scores method) (matchms.Scores.Scores method) (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.IntersectMz method) (matchms.similarity.IntersectMz.IntersectMz method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.NeutralLossesCosine method) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine method) (matchms.similarity.ParentMassMatch method) (matchms.similarity.ParentMassMatch.ParentMassMatch method) (matchms.similarity.PrecursorMzMatch method) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method)

to_json() (matchms.Scores method) (matchms.Scores.Scores method) to_numpy (matchms.Fragments property) (matchms.Fragments.Fragments property) (matchms.Spikes.Spikes property) to_pickle() (matchms.Scores method) (matchms.Scores.Scores method)

U

update_peak_comments_mz_tolerance() (matchms.Spectrum class method) (matchms.Spectrum.Spectrum class method)

V

values() (matchms.Metadata method) (matchms.Metadata.Metadata method)

W

write_to_logfile() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method)