Index

_

__init__() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) (matchms.filtering.SpectraCollectionProcessor.SpectraCollectionProcessor method) (matchms.filtering.SpectrumProcessor.ProcessingReport method) (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.Fingerprints method) (matchms.Fingerprints.Fingerprints method) (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.Fragments method) (matchms.Fragments.Fragments method) (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection 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.ScoresMask method) (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) (matchms.similarity.Cosine method) (matchms.similarity.Cosine.Cosine method) (matchms.similarity.CosineBlink method) (matchms.similarity.CosineBlink.CosineBlink method) (matchms.similarity.CosineFlash method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.CosineLinear method) (matchms.similarity.CosineLinear.CosineLinear method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.FlashEntropy method) (matchms.similarity.FlashSimilarity.CosineFlash method) (matchms.similarity.FlashSimilarity.FlashEntropy method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) (matchms.SpectraCollectionProcessor method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) (matchms.SpectrumProcessor method)

A

abs() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) add() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) add_compound_name() (in module matchms.filtering) add_logging_to_file() (in module matchms.logging_functions) add_parent_mass() (in module matchms.filtering) add_precursor_formula() (in module matchms.filtering) add_precursor_mz() (in module matchms.filtering) add_prefix() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) add_retention_index() (in module matchms.filtering) add_retention_time() (in module matchms.filtering) add_suffix() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) add_to_report() (matchms.filtering.SpectrumProcessor.ProcessingReport method) agg() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) aggregate() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) align() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) all() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) any() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) apply() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

apply_metadata_row_filter() (in module matchms.filtering.filter_utils.metadata_conversions) apply_metadata_updates_to_spectrum() (in module matchms.filtering.filter_utils.metadata_conversions) apply_to_metadata_rows() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) apply_to_rows() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) as_float_or_none() (in module matchms.filtering.filter_utils.metadata_conversions) as_spectrum() (in module matchms.importing.load_from_json) as_string_or_none() (in module matchms.filtering.filter_utils.metadata_conversions) asfreq() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) asof() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) aspirin() (in module matchms.reference_spectra) (in module matchms.reference_spectra.aspirin) assign() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) astype() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) at (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) at_time() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) attrs (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) axes (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property)

B

BaseEmbeddingSimilarity (class in matchms.similarity.BaseEmbeddingSimilarity) BaseSimilarity (class in matchms.similarity.BaseSimilarity) BaseSimilarityWithSparse (class in matchms.similarity.BaseSimilarity) between_time() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) bfill() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) bin_to_mz() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method)

BinnedEmbeddingSimilarity (class in matchms.similarity) (class in matchms.similarity.BinnedEmbeddingSimilarity) boxplot() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) build_ann_index() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method)

C

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) clean() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method) clean_adduct() (in module matchms.filtering) 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) cleaned (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute) clip() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) clone() (matchms.Fragments method) (matchms.Fragments.Fragments method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) cocaine() (in module matchms.reference_spectra) (in module matchms.reference_spectra.cocaine) collect_peak_pairs() (in module matchms.similarity.spectrum_similarity_functions) columns (matchms.MetadataCollection attribute) (matchms.MetadataCollection.MetadataCollection attribute) combine() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) combine_first() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) compare() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) compute_combined_hashes() (in module matchms.hashing) compute_embeddings() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) compute_fingerprint() (matchms.Fingerprints method) (matchms.Fingerprints.Fingerprints method) compute_fingerprints() (matchms.Fingerprints method) (matchms.Fingerprints.Fingerprints method) compute_losses() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) compute_similarity_matrix_from_embeddings() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) config (matchms.Fingerprints attribute) (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints attribute) (matchms.Fingerprints.Fingerprints property) contains_metadata() (in module matchms.importing.load_from_msp)

convert_dtypes() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) 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) copy() (matchms.Fragments method) (matchms.Fragments.Fragments method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.Scores method) (matchms.Scores.Scores method) corr() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) correct_charge() (in module matchms.filtering) corrwith() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) Cosine (class in matchms.similarity) (class in matchms.similarity.Cosine) cosine_similarity() (in module matchms.similarity.vector_similarity_functions) cosine_similarity_matrix() (in module matchms.similarity.vector_similarity_functions) CosineBlink (class in matchms.similarity) (class in matchms.similarity.CosineBlink) CosineFlash (class in matchms.similarity) (class in matchms.similarity.FlashSimilarity) CosineGreedy (class in matchms.similarity) (class in matchms.similarity.CosineGreedy) CosineHungarian (class in matchms.similarity) (class in matchms.similarity.CosineHungarian) CosineLinear (class in matchms.similarity) (class in matchms.similarity.CosineLinear) count() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) count_peaks_above_relative_intensity() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) cov() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) create_network() (matchms.networking.SimilarityNetwork method) (matchms.networking.SimilarityNetwork.SimilarityNetwork method) create_partial_function() (in module matchms.filtering.SpectrumProcessor) create_spectrum_json_encoder() (in module matchms.exporting.save_as_json) create_workflow() (in module matchms.Pipeline) CSRFragmentCollection (class in matchms.FragmentCollection) cummax() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) cummin() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) cumprod() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) cumsum() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

D

default_filters() (in module matchms.filtering) (in module matchms.filtering.default_filters) derive_adduct_from_name() (in module matchms.filtering) derive_annotation_from_compound_name() (in module matchms.filtering) derive_formula_from_name() (in module matchms.filtering) derive_formula_from_smiles() (in module matchms.filtering) derive_inchi_from_smiles() (in module matchms.filtering) derive_inchikey_from_inchi() (in module matchms.filtering) derive_ionmode() (in module matchms.filtering) derive_parent_mass_from_metadata() (in module matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass) derive_smiles_from_inchi() (in module matchms.filtering) describe() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) 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) diff() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) dirty (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute) div() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

divide() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) dot() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) drop() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) drop_duplicates() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) drop_empty() (matchms.FragmentCollection.CSRFragmentCollection method) drop_empty_spectra() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) droplevel() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) dropna() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) dtypes (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) duplicated() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

E

empty (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) eq() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) equals() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) eval() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) ewm() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

expanding() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) explode() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) export_metadata_as_csv() (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

ffill() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) fillna() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) filter() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) filter_empty_spectra() (in module matchms.utils) filter_noise() (in module matchms.similarity.spectrum_similarity_functions) filter_none() (in module matchms.utils) find_by_key() (in module matchms.importing.parsing_utils) find_matches() (in module matchms.similarity.spectrum_similarity_functions) fingerprint_count (matchms.Fingerprints attribute) (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints attribute) (matchms.Fingerprints.Fingerprints property) fingerprint_export_warning() (in module matchms.utils) Fingerprints (class in matchms) (class in matchms.Fingerprints) fingerprints (matchms.Fingerprints attribute) (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints attribute) (matchms.Fingerprints.Fingerprints property)

FingerprintSimilarity (class in matchms.similarity) (class in matchms.similarity.FingerprintSimilarity) first_valid_index() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) flags (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) FlashEntropy (class in matchms.similarity) (class in matchms.similarity.FlashSimilarity) floordiv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) FragmentCollection (class in matchms.FragmentCollection) Fragments (class in matchms) (class in matchms.Fragments) fragments (matchms.Spectrum property) (matchms.Spectrum.Spectrum property) from_arrow() (matchms.MetadataCollection class method) (matchms.MetadataCollection.MetadataCollection class method) from_dict() (matchms.MetadataCollection class method) (matchms.MetadataCollection.MetadataCollection class method) from_records() (matchms.MetadataCollection class method) (matchms.MetadataCollection.MetadataCollection class method)

G

ge() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) get() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) get_anns() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) get_charge_of_adduct() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) get_common_keys() (in module matchms.utils) get_embeddings() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) get_fingerprint_by_inchikey() (matchms.Fingerprints method) (matchms.Fingerprints.Fingerprints method) get_fingerprint_by_spectrum() (matchms.Fingerprints method) (matchms.Fingerprints.Fingerprints method) get_first_common_element() (in module matchms.utils) get_index_anns() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method)

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_row() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) get_top_hits() (in module matchms.networking) (in module matchms.networking.networking_functions) get_top_hits_by_column() (in module matchms.networking.networking_functions) get_top_hits_by_row() (in module matchms.networking.networking_functions) get_unused_filters() (in module matchms.Pipeline) glucose() (in module matchms.reference_spectra) (in module matchms.reference_spectra.glucose) groupby() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) gt() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) guess_target() (matchms.filtering.SpeciesString method) (matchms.filtering.SpeciesString.SpeciesString method)

H

harmonize_columns() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) harmonize_keys() (matchms.Metadata method) (matchms.Metadata.Metadata method) harmonize_metadata_collection_columns() (in module matchms.MetadataCollection) harmonize_metadata_column_name() (in module matchms.MetadataCollection) harmonize_metadata_columns() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) harmonize_missing_entries() (in module matchms.filtering) 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) head() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) hist() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) hydroxy_cholesterol() (in module matchms.reference_spectra) (in module matchms.reference_spectra.hydroxy_cholesterol)

I

iat (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) idxmax() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) idxmin() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) iloc (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) import_spectra() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method) inchikeys (matchms.Fingerprints attribute) (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints attribute) (matchms.Fingerprints.Fingerprints property) index (matchms.MetadataCollection attribute) (matchms.MetadataCollection.MetadataCollection attribute) (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity attribute) index_backend (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity attribute) index_k (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity attribute) index_kwargs (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity attribute) infer_objects() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) info() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) insert() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) intensities (matchms.Fragments attribute) (matchms.Fragments property) (matchms.Fragments.Fragments attribute) (matchms.Fragments.Fragments property) interpolate() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) interpret_pepmass() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.interpret_pepmass) is_commutative (matchms.similarity.BaseSimilarity.BaseSimilarity attribute) is_missing_metadata_value() (in module matchms.filtering.filter_utils.metadata_conversions) is_sparse (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints property) is_structured_score (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity property) (matchms.similarity.BaseSimilarity.BaseSimilarity property) (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse property) (matchms.similarity.BinnedEmbeddingSimilarity property) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity property) (matchms.similarity.Cosine property) (matchms.similarity.Cosine.Cosine property) (matchms.similarity.CosineBlink property) (matchms.similarity.CosineBlink.CosineBlink property) (matchms.similarity.CosineFlash property) (matchms.similarity.CosineGreedy property) (matchms.similarity.CosineGreedy.CosineGreedy property) (matchms.similarity.CosineHungarian property) (matchms.similarity.CosineHungarian.CosineHungarian property) (matchms.similarity.CosineLinear property) (matchms.similarity.CosineLinear.CosineLinear property) (matchms.similarity.FingerprintSimilarity property) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity property) (matchms.similarity.FlashEntropy property) (matchms.similarity.FlashSimilarity.CosineFlash property) (matchms.similarity.FlashSimilarity.FlashEntropy property) (matchms.similarity.MetadataMatch property) (matchms.similarity.MetadataMatch.MetadataMatch property) (matchms.similarity.ModifiedCosine property) (matchms.similarity.ModifiedCosine.ModifiedCosine property) (matchms.similarity.ModifiedCosineGreedy property) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy property) (matchms.similarity.ModifiedCosineHungarian property) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian property) (matchms.similarity.NeutralLossesCosine property) (matchms.similarity.NeutralLossesCosine.NeutralLossesCosine property) (matchms.similarity.ParentMassMatch property) (matchms.similarity.ParentMassMatch.ParentMassMatch property) (matchms.similarity.PrecursorMzMatch property) (matchms.similarity.PrecursorMzMatch.PrecursorMzMatch property)

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) isetitem() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) isin() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) isna() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) isnull() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) items() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) iter_peak_arrays() (matchms.FragmentCollection.CSRFragmentCollection method) iterrows() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) itertuples() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

J

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

join() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

K

keep_score() (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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)

keep_top_k_per_row_variable() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) keys() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) kurt() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) kurtosis() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

L

last_valid_index() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) le() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) linear_cosine_score() (in module matchms.similarity.cosine_linear_functions) load() (matchms.Scores class method) (matchms.Scores.Scores class method) load_ann_index() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) load_embeddings() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity static method) (matchms.similarity.BinnedEmbeddingSimilarity static method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity static method) 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_matchms_filter_from_string() (in module matchms.filtering.SpectrumProcessor) load_ms2_dataset() (in module matchms.importing) (in module matchms.importing.load_spectra) load_spectra() (in module matchms.importing) (in module matchms.importing.load_spectra) load_workflow_from_yaml_file() (in module matchms.yaml_file_functions) loc (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) 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) lt() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

M

make_charge_int() (in module matchms.filtering) map() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) mask() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) 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_as_mzspeclib 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.metadata_conversions 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_parent_mass module matchms.filtering.metadata_processing.add_precursor_formula 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_formula_from_smiles 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_missing_entries 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_and_parent_mass_based_on_smiles module matchms.filtering.metadata_processing.repair_adduct_based_on_parent_mass 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_from_smiles module matchms.filtering.metadata_processing.repair_parent_mass_is_molar_mass module matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper module matchms.filtering.metadata_processing.repair_smiles_of_salts module matchms.filtering.metadata_processing.require_compound_name module matchms.filtering.metadata_processing.require_correct_ionmode module matchms.filtering.metadata_processing.require_correct_ms_level module matchms.filtering.metadata_processing.require_formula module matchms.filtering.metadata_processing.require_matching_adduct_and_ionmode module matchms.filtering.metadata_processing.require_matching_adduct_precursor_mz_parent_mass module matchms.filtering.metadata_processing.require_parent_mass_match_smiles module matchms.filtering.metadata_processing.require_precursor_mz module matchms.filtering.metadata_processing.require_retention_index module matchms.filtering.metadata_processing.require_retention_time module matchms.filtering.metadata_processing.require_valid_annotation module matchms.filtering.peak_processing module matchms.filtering.peak_processing.normalize_intensities module matchms.filtering.peak_processing.reduce_to_number_of_peaks module matchms.filtering.peak_processing.remove_noise_below_frequent_intensities 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.remove_peaks_relative_to_precursor_mz module matchms.filtering.peak_processing.remove_profiled_spectra module matchms.filtering.peak_processing.require_maximum_number_of_peaks 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.SpectraCollectionProcessor module matchms.filtering.SpectrumProcessor module matchms.Fingerprints module matchms.FragmentCollection 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_spectra module matchms.importing.parsing_utils module matchms.logging_functions module matchms.Metadata module matchms.MetadataCollection 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.reference_spectra module matchms.reference_spectra.aspirin module matchms.reference_spectra.cocaine module matchms.reference_spectra.glucose module matchms.reference_spectra.hydroxy_cholesterol module matchms.reference_spectra.phenylalanine module matchms.reference_spectra.salicin module matchms.Scores module matchms.similarity module matchms.similarity.BaseEmbeddingSimilarity module matchms.similarity.BaseSimilarity module matchms.similarity.BinnedEmbeddingSimilarity module matchms.similarity.Cosine module matchms.similarity.cosine_linear_functions module matchms.similarity.CosineBlink module matchms.similarity.CosineGreedy module matchms.similarity.CosineHungarian module matchms.similarity.CosineLinear module matchms.similarity.FingerprintSimilarity module matchms.similarity.flash_utils module matchms.similarity.FlashSimilarity module

matchms.similarity.MetadataMatch module matchms.similarity.ModifiedCosine module matchms.similarity.ModifiedCosineGreedy module matchms.similarity.ModifiedCosineHungarian 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.SpectraCollection module matchms.Spectrum module matchms.typing module matchms.utils module matchms.yaml_file_functions module matrix() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) (matchms.similarity.Cosine method) (matchms.similarity.Cosine.Cosine method) (matchms.similarity.CosineBlink method) (matchms.similarity.CosineBlink.CosineBlink method) (matchms.similarity.CosineFlash method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.CosineLinear method) (matchms.similarity.CosineLinear.CosineLinear method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.FlashEntropy method) (matchms.similarity.FlashSimilarity.CosineFlash method) (matchms.similarity.FlashSimilarity.FlashEntropy method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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) max() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) mean() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) median() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) melt() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) memory_usage() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) merge() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection 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) MetadataCollection (class in matchms) (class in matchms.MetadataCollection) MetadataMatch (class in matchms.similarity) (class in matchms.similarity.MetadataMatch) min() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) mod() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) mode() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) ModifiedCosine (class in matchms.similarity) (class in matchms.similarity.ModifiedCosine) ModifiedCosineGreedy (class in matchms.similarity) (class in matchms.similarity.ModifiedCosineGreedy) ModifiedCosineHungarian (class in matchms.similarity) (class in matchms.similarity.ModifiedCosineHungarian) 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_as_mzspeclib 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.metadata_conversions matchms.filtering.filter_utils.smile_inchi_inchikey_conversions matchms.filtering.metadata_processing matchms.filtering.metadata_processing.add_compound_name matchms.filtering.metadata_processing.add_parent_mass matchms.filtering.metadata_processing.add_precursor_formula 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_formula_from_smiles 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_missing_entries 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_and_parent_mass_based_on_smiles matchms.filtering.metadata_processing.repair_adduct_based_on_parent_mass matchms.filtering.metadata_processing.repair_inchi_inchikey_smiles matchms.filtering.metadata_processing.repair_not_matching_annotation matchms.filtering.metadata_processing.repair_parent_mass_from_smiles matchms.filtering.metadata_processing.repair_parent_mass_is_molar_mass matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper matchms.filtering.metadata_processing.repair_smiles_of_salts matchms.filtering.metadata_processing.require_compound_name matchms.filtering.metadata_processing.require_correct_ionmode matchms.filtering.metadata_processing.require_correct_ms_level matchms.filtering.metadata_processing.require_formula matchms.filtering.metadata_processing.require_matching_adduct_and_ionmode matchms.filtering.metadata_processing.require_matching_adduct_precursor_mz_parent_mass matchms.filtering.metadata_processing.require_parent_mass_match_smiles matchms.filtering.metadata_processing.require_precursor_mz matchms.filtering.metadata_processing.require_retention_index matchms.filtering.metadata_processing.require_retention_time matchms.filtering.metadata_processing.require_valid_annotation matchms.filtering.peak_processing matchms.filtering.peak_processing.normalize_intensities matchms.filtering.peak_processing.reduce_to_number_of_peaks matchms.filtering.peak_processing.remove_noise_below_frequent_intensities matchms.filtering.peak_processing.remove_peaks_around_precursor_mz matchms.filtering.peak_processing.remove_peaks_outside_top_k matchms.filtering.peak_processing.remove_peaks_relative_to_precursor_mz matchms.filtering.peak_processing.remove_profiled_spectra matchms.filtering.peak_processing.require_maximum_number_of_peaks 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.SpectraCollectionProcessor matchms.filtering.SpectrumProcessor matchms.Fingerprints matchms.FragmentCollection 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_spectra matchms.importing.parsing_utils matchms.logging_functions matchms.Metadata matchms.MetadataCollection matchms.networking matchms.networking.networking_functions matchms.networking.SimilarityNetwork matchms.Pipeline matchms.plotting matchms.plotting.spectrum_plots matchms.reference_spectra matchms.reference_spectra.aspirin matchms.reference_spectra.cocaine matchms.reference_spectra.glucose matchms.reference_spectra.hydroxy_cholesterol matchms.reference_spectra.phenylalanine matchms.reference_spectra.salicin matchms.Scores matchms.similarity matchms.similarity.BaseEmbeddingSimilarity matchms.similarity.BaseSimilarity matchms.similarity.BinnedEmbeddingSimilarity matchms.similarity.Cosine matchms.similarity.cosine_linear_functions matchms.similarity.CosineBlink matchms.similarity.CosineGreedy matchms.similarity.CosineHungarian matchms.similarity.CosineLinear matchms.similarity.FingerprintSimilarity matchms.similarity.flash_utils matchms.similarity.FlashSimilarity matchms.similarity.MetadataMatch matchms.similarity.ModifiedCosine matchms.similarity.ModifiedCosineGreedy matchms.similarity.ModifiedCosineHungarian matchms.similarity.NeutralLossesCosine matchms.similarity.ParentMassMatch matchms.similarity.PrecursorMzMatch matchms.similarity.spectrum_similarity_functions matchms.similarity.vector_similarity_functions matchms.SpectraCollection matchms.Spectrum matchms.typing matchms.utils matchms.yaml_file_functions mol_converter() (in module matchms.filtering.filter_utils.smile_inchi_inchikey_conversions) mul() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) multiply() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) mz (matchms.Fragments attribute) (matchms.Fragments property) (matchms.Fragments.Fragments attribute) (matchms.Fragments.Fragments property) mz_to_bin() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method)

N

n_bins (matchms.similarity.BinnedEmbeddingSimilarity property) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity property) ndim (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) ne() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) NeutralLossesCosine (class in matchms.similarity) (class in matchms.similarity.NeutralLossesCosine) nlargest() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) normalize_intensities() (in module matchms.filtering) (in module matchms.filtering.peak_processing.normalize_intensities)

notna() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) notnull() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) nsmallest() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) 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) nunique() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

O

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

ordered_dump() (in module matchms.yaml_file_functions) ordered_load() (in module matchms.yaml_file_functions)

P

pair() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) (matchms.similarity.Cosine method) (matchms.similarity.Cosine.Cosine method) (matchms.similarity.CosineBlink method) (matchms.similarity.CosineBlink.CosineBlink method) (matchms.similarity.CosineFlash method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.CosineLinear method) (matchms.similarity.CosineLinear.CosineLinear method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.FlashEntropy method) (matchms.similarity.FlashSimilarity.CosineFlash method) (matchms.similarity.FlashSimilarity.FlashEntropy method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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.SpectraCollectionProcessor.SpectraCollectionProcessor method) (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectraCollectionProcessor 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) pct_change() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) peaks (matchms.Spectrum attribute) (matchms.Spectrum.Spectrum attribute) phenylalanine() (in module matchms.reference_spectra) (in module matchms.reference_spectra.phenylalanine) pipe() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) Pipeline (class in matchms) (class in matchms.Pipeline) pivot() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) pivot_table() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) plot (matchms.MetadataCollection attribute) (matchms.MetadataCollection.MetadataCollection attribute) plot() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) plot_against() (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) 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) pop() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) pow() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) PrecursorMzMatch (class in matchms.similarity) (class in matchms.similarity.PrecursorMzMatch) process_collection() (matchms.filtering.SpectraCollectionProcessor.SpectraCollectionProcessor method) (matchms.SpectraCollectionProcessor method) process_spectra() (matchms.filtering.SpectraCollectionProcessor.SpectraCollectionProcessor method) (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectraCollectionProcessor method) (matchms.SpectrumProcessor method) process_spectrum() (matchms.filtering.SpectrumProcessor.SpectrumProcessor method) (matchms.SpectrumProcessor method) ProcessingReport (class in matchms.filtering.SpectrumProcessor) prod() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) product() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

Q

quantile() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

query() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

R

radd() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rank() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rdiv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) reduce_to_number_of_peaks() (in module matchms.filtering) (in module matchms.filtering.peak_processing.reduce_to_number_of_peaks) reindex() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) reindex_like() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) remove_noise_below_frequent_intensities() (in module matchms.filtering) (in module matchms.filtering.peak_processing.remove_noise_below_frequent_intensities) 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) remove_peaks_relative_to_precursor_mz() (in module matchms.filtering) (in module matchms.filtering.peak_processing.remove_peaks_relative_to_precursor_mz) remove_profiled_spectra() (in module matchms.filtering) (in module matchms.filtering.peak_processing.remove_profiled_spectra) rename() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rename_axis() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rename_deprecated_params() (in module matchms.utils) reorder() (matchms.FragmentCollection.CSRFragmentCollection method) reorder_levels() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) repair_adduct_and_parent_mass_based_on_smiles() (in module matchms.filtering) repair_adduct_based_on_parent_mass() (in module matchms.filtering) repair_inchi_inchikey_smiles() (in module matchms.filtering) repair_not_matching_annotation() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_not_matching_annotation) repair_parent_mass_from_smiles() (in module matchms.filtering) repair_parent_mass_is_molar_mass() (in module matchms.filtering) repair_parent_mass_match_smiles_wrapper() (in module matchms.filtering) (in module matchms.filtering.metadata_processing.repair_parent_mass_match_smiles_wrapper) repair_smiles_of_salts() (in module matchms.filtering) replace() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

replace_abbreviations() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) require_compound_name() (in module matchms.filtering) require_correct_ionmode() (in module matchms.filtering) require_correct_ms_level() (in module matchms.filtering) require_formula() (in module matchms.filtering) require_matching_adduct_and_ionmode() (in module matchms.filtering) require_matching_adduct_precursor_mz_parent_mass() (in module matchms.filtering) require_maximum_number_of_peaks() (in module matchms.filtering) (in module matchms.filtering.peak_processing.require_maximum_number_of_peaks) 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) require_precursor_mz() (in module matchms.filtering) require_retention_index() (in module matchms.filtering) require_valid_annotation() (in module matchms.filtering) resample() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) reset_index() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) reset_matchms_logger() (in module matchms.logging_functions) rfloordiv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rmod() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rmul() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rolling() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) round() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) row_to_dict() (matchms.MetadataCollection static method) (matchms.MetadataCollection.MetadataCollection static method) rpow() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rsub() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) rtruediv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) run() (matchms.Pipeline method) (matchms.Pipeline.Pipeline method)

S

salicin() (in module matchms.reference_spectra) (in module matchms.reference_spectra.salicin) sample() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) save() (matchms.Scores method) (matchms.Scores.Scores method) save_ann_index() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) 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_mzspeclib() (in module matchms.exporting) (in module matchms.exporting.save_as_mzspeclib) 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.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity attribute) (matchms.similarity.BaseSimilarity.BaseSimilarity attribute), [1] (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse attribute) (matchms.similarity.BinnedEmbeddingSimilarity attribute) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity attribute) (matchms.similarity.CosineBlink attribute) (matchms.similarity.CosineBlink.CosineBlink attribute) (matchms.similarity.CosineFlash attribute) (matchms.similarity.FingerprintSimilarity attribute) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity attribute) (matchms.similarity.FlashEntropy attribute) (matchms.similarity.FlashSimilarity.CosineFlash attribute) (matchms.similarity.FlashSimilarity.FlashEntropy 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) score_fields (matchms.similarity.BaseSimilarity.BaseSimilarity attribute) ScoreFilter (in module matchms.typing) Scores (class in matchms) (class in matchms.Scores) scores_json_decoder() (in module matchms.importing.load_from_json) ScoresMask (class in matchms.Scores) select_by_intensity() (in module matchms.filtering) (in module matchms.filtering.peak_processing.select_by_intensity) (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) 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) (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) select_dtypes() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) sem() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) set() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) set_axis() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) set_flags() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) set_index() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) set_key_replacements() (matchms.Metadata static method) (matchms.Metadata.Metadata static method) set_matchms_logger_level() (in module matchms) (in module matchms.logging_functions) set_rdkit_logger_level() (in module matchms.logging_functions) shape (matchms.FragmentCollection.CSRFragmentCollection property) (matchms.FragmentCollection.FragmentCollection property) (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) shift() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) SimilarityNetwork (class in matchms.networking) (class in matchms.networking.SimilarityNetwork) sirius_merge_close_peaks() (in module matchms.similarity.cosine_linear_functions) size (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property)

skew() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) slice_mz() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) slice_rows() (matchms.FragmentCollection.CSRFragmentCollection method) sort() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) sort_by_mz() (in module matchms.importing.parsing_utils) sort_index() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) sort_values() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) sparse (matchms.MetadataCollection attribute) (matchms.MetadataCollection.MetadataCollection attribute) sparse_matrix() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) (matchms.similarity.Cosine method) (matchms.similarity.Cosine.Cosine method) (matchms.similarity.CosineBlink method) (matchms.similarity.CosineBlink.CosineBlink method) (matchms.similarity.CosineFlash method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.CosineLinear method) (matchms.similarity.CosineLinear.CosineLinear method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.FlashEntropy method) (matchms.similarity.FlashSimilarity.CosineFlash method) (matchms.similarity.FlashSimilarity.FlashEntropy method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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) spectra_hashes() (in module matchms.hashing) SpectraCollection (class in matchms) (class in matchms.SpectraCollection) SpectraCollectionProcessor (class in matchms) (class in matchms.filtering.SpectraCollectionProcessor) Spectrum (class in matchms) (class in matchms.Spectrum) spectrum_hash() (in module matchms.hashing) (matchms.Spectrum method) (matchms.Spectrum.Spectrum method) spectrum_hash_arrays() (in module matchms.hashing) SpectrumProcessor (class in matchms) (class in matchms.filtering.SpectrumProcessor) split_ion() (in module matchms.filtering.filter_utils.interpret_unknown_adduct) squeeze() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) stack() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) std() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) store_embeddings() (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity static method) (matchms.similarity.BinnedEmbeddingSimilarity static method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity static method) style (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) sub() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) subtract() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) sum() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) swaplevel() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

T

T (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property) tail() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) take() (matchms.FragmentCollection.CSRFragmentCollection method) (matchms.FragmentCollection.FragmentCollection method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) target (matchms.filtering.SpeciesString attribute) (matchms.filtering.SpeciesString.SpeciesString attribute) to_camel_case() (in module matchms.utils) to_clipboard() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_csv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_dataframe (matchms.Fingerprints attribute) (matchms.Fingerprints property) (matchms.Fingerprints.Fingerprints attribute) (matchms.Fingerprints.Fingerprints property) to_dataframe() (matchms.filtering.SpectrumProcessor.ProcessingReport method) to_dict() (matchms.Metadata method) (matchms.Metadata.Metadata method) (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.similarity.BaseEmbeddingSimilarity.BaseEmbeddingSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarity method) (matchms.similarity.BaseSimilarity.BaseSimilarityWithSparse method) (matchms.similarity.BinnedEmbeddingSimilarity method) (matchms.similarity.BinnedEmbeddingSimilarity.BinnedEmbeddingSimilarity method) (matchms.similarity.Cosine method) (matchms.similarity.Cosine.Cosine method) (matchms.similarity.CosineBlink method) (matchms.similarity.CosineBlink.CosineBlink method) (matchms.similarity.CosineFlash method) (matchms.similarity.CosineGreedy method) (matchms.similarity.CosineGreedy.CosineGreedy method) (matchms.similarity.CosineHungarian method) (matchms.similarity.CosineHungarian.CosineHungarian method) (matchms.similarity.CosineLinear method) (matchms.similarity.CosineLinear.CosineLinear method) (matchms.similarity.FingerprintSimilarity method) (matchms.similarity.FingerprintSimilarity.FingerprintSimilarity method) (matchms.similarity.FlashEntropy method) (matchms.similarity.FlashSimilarity.CosineFlash method) (matchms.similarity.FlashSimilarity.FlashEntropy method) (matchms.similarity.MetadataMatch method) (matchms.similarity.MetadataMatch.MetadataMatch method) (matchms.similarity.ModifiedCosine method) (matchms.similarity.ModifiedCosine.ModifiedCosine method) (matchms.similarity.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineGreedy.ModifiedCosineGreedy method) (matchms.similarity.ModifiedCosineHungarian method) (matchms.similarity.ModifiedCosineHungarian.ModifiedCosineHungarian 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_excel() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_feather() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_hdf() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_html() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_iceberg() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_json() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) to_latex() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_markdown() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_mgf() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) to_msp() (matchms.SpectraCollection method) (matchms.SpectraCollection.SpectraCollection method) to_numpy (matchms.Fragments property) (matchms.Fragments.Fragments property) to_numpy() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_orc() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_parquet() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_peak_arrays() (matchms.FragmentCollection.CSRFragmentCollection method) to_period() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_pickle() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_records() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_sql() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_stata() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_string() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_timestamp() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_xarray() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) to_xml() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) transform() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) transpose() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) truediv() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) truncate() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) tz_convert() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) tz_localize() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

U

unstack() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) update() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

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

V

value_counts() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method) values (matchms.MetadataCollection property) (matchms.MetadataCollection.MetadataCollection property)

values() (matchms.Metadata method) (matchms.Metadata.Metadata method) var() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

W

where() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)

X

xs() (matchms.MetadataCollection method) (matchms.MetadataCollection.MetadataCollection method)