Index

A

abs() (emzed.table.expressions.Expression method) ABSORPTION_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) add_column() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) add_column_from_expression() (in module emzed.table.add_column) add_column_with_constant_value() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) (in module emzed.table.add_column) add_column_with_values() (in module emzed.table.add_column) add_enumeration() (emzed.Table method) (emzed.table.table.Table method) add_or_replace_column() (emzed.Table method) (emzed.table.table.Table method) add_or_replace_column_with_constant_value() (emzed.Table method) (emzed.table.table.Table method) add_row() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) add_spectrum() (emzed.ms_data.peak_map.ImmutableSpectra method) (emzed.ms_data.peak_map.MutableSpectra method) (emzed.ms_data.peak_map.PeakMap method) (emzed.PeakMap method) aggregate() (emzed.table.group_by.GroupBy method) AggregateFunctionWrapper (class in emzed.table.group_by) align_peaks() (in module emzed.align) (in module emzed.align.sample_alignment)

all_false() (emzed.table.group_by.GroupBy method) all_none() (emzed.table.group_by.GroupBy method) all_true() (emzed.table.group_by.GroupBy method) annotate_adducts() (in module emzed.annotate.annotate_adducts) any_false() (emzed.table.group_by.GroupBy method) any_none() (emzed.table.group_by.GroupBy method) any_true() (emzed.table.group_by.GroupBy method) append() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) Apply (class in emzed.table.expressions) apply() (emzed.quantification.peak_shape_models.no_model.NoModel method) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel method) (emzed.Table method) (emzed.table.table.Table method) approx_equal() (emzed.table.expressions.Expression method) area (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel property) (emzed.quantification.peak_shape_models.base.PeakShapeModelBase property) (emzed.quantification.peak_shape_models.linear_interpolation_model.LinearInterpolationModel property) (emzed.quantification.peak_shape_models.no_model.NoModel property) (emzed.quantification.peak_shape_models.savgol_model.SavGolModel property) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel property) as_dict() (emzed.chemistry.molecular_formula.MolecularFormula method) (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) as_string() (emzed.chemistry.molecular_formula.MolecularFormula method) assemble_table() (in module emzed.chemistry.pubchem) assign() (emzed.r_connect.pyper.R method) AsymmetricGaussModel (class in emzed.quantification.peak_shape_models.asymmetric_gauss_model) attach_ms2_spectra() (in module emzed.ms2) (in module emzed.ms2.attach_ms2_spectra) available_types (emzed.ms_data.peak_map.MSChromatogram property)

B

BaseModel (class in emzed.table.base_models) BASEPEAK_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) best_convert() (in module emzed.table.table_utils) BinaryInfix (class in emzed.table.expressions) BinaryPrefix (class in emzed.table.expressions)

bool_formatter() (in module emzed.table.col_types) BoolStr() (in module emzed.r_connect.pyper) BoundSpectrum (class in emzed.ms_data.peak_map) busy_indicator() (in module emzed.utils.busy_indicator) bytes (emzed.table.pickle.Pickle attribute) ByteStr() (in module emzed.r_connect.pyper)

C

call_integrator() (in module emzed.quantification.utils) can_convert() (in module emzed.table.col_types) CentwaveFeatureDetector (class in emzed.r_connect.xcms_connector) check() (emzed.ms_data.peak_map.BoundSpectrum method) check_and_fix() (in module emzed.table.table) check_col_type() (in module emzed.table.col_types) check_columns() (in module emzed.quantification.utils) check_if_model_is_valid() (in module emzed.table.base_models) check_num_cores() (in module emzed.quantification.utils) check_pyopenms_linux() (in module emzed.check_pyopenms) check_pyopenms_win32() (in module emzed.check_pyopenms) check_update() (in module emzed.db) Chromatogram (class in emzed.ms_data.peak_map) chromatogram() (emzed.ms_data.peak_map.ImmutablePeakMap method) (in module emzed.ms_data.peak_map) chromatograms() (in module emzed.pyopenms.optimizations) ChromatogramType (class in emzed.ms_data.peak_map) cleanup_references() (in module emzed.table.table_utils) clear() (emzed.core.db_backed_dictionary.DbBackedDictionary method) (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) ClientObjectMapper (class in emzed.remote_package.object_handling) close() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) (emzed.utils.sqlite.Connection method) col_formats (emzed.Table property) (emzed.table.table.Table property) col_names (emzed.Table property) (emzed.table.table.Table property) col_types (emzed.Table property) (emzed.table.table.Table property) collapse() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.table.collapse) column_accessor() (emzed.table.base_models.BaseModel method) (in module emzed.table.expressions) ColumnAccessor (class in emzed.table.expressions) commit() (emzed.utils.sqlite.Connection method) compatible_with_sql_update (emzed.table.expressions.Expression attribute)

ComplexStr() (in module emzed.r_connect.pyper) compute_centroids() (in module emzed.chemistry.isotope_generator) compute_peakmap_hash() (in module emzed.ms_data.peak_map_hasher) compute_spectra_alignments() (in module emzed.utils.align_spectra) Connection (class in emzed.utils.sqlite) consolidate() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) consolidate_per_default() (in module emzed.table.table) Contains (class in emzed.table.expressions) contains() (emzed.table.expressions.Expression method) content_changed() (emzed.table.full_table_model.FullTableModel method) copy() (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) (emzed.Table method) (emzed.table.expressions.Expression method) (emzed.table.table.Table method) copy_all_refered_tables() (in module emzed.table.table_utils) copy_table() (in module emzed.utils.sqlite) copy_tables() (in module emzed.utils.sqlite) count() (emzed.table.base_models.BaseModel method) (emzed.table.group_by.GroupBy method) count_distinct() (emzed.table.base_models.BaseModel method) count_not_none() (emzed.table.expressions.ColumnAccessor method) create_abundance_dict() (in module emzed.chemistry.elements) create_db_table() (in module emzed.table.table_utils) create_elements_table() (in module emzed.chemistry.elements) create_function() (emzed.utils.sqlite.Connection method) create_index() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) create_indices() (in module emzed.ms_data.peak_map) create_mass_dict() (in module emzed.chemistry.elements) create_result_table() (in module emzed.quantification.chromatogram_integration) (in module emzed.quantification.peak_integration) create_row_class() (in module emzed.table.row_class) create_table() (emzed.Table static method) (emzed.table.table.Table static method) (in module emzed.ms_data.peak_map) (in module emzed.table.table) create_uid() (in module emzed.utils.sqlite) Cursor (class in emzed.utils.sqlite) cursor() (emzed.utils.sqlite.Connection method)

D

data_frame_col_types() (in module emzed.r_connect.r_executor) data_frame_to_table() (in module emzed.r_connect.r_executor) db_backed_property (in module emzed.ms_data.peak_map) DbBackedDictionary (class in emzed.core.db_backed_dictionary) DbBackedModel (class in emzed.core.db_backed_model) DbBackedProperty (class in emzed.ms_data.peak_map) debug() (in module emzed.utils.sqlite) decode() (in module emzed.pyopenms) (in module emzed.pyopenms.optimizations) DEFAULT_OFFSET (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) DelayedElementsTable (class in emzed.chemistry.elements) DelayedRemoteModule (class in emzed.remote_package) (class in emzed.remote_package.remote_module_wrapper) delete_rows() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (in module emzed.table.delete_rows)

deleted_callback() (emzed.remote_package.remote_module_wrapper.RemoteModule class method) (emzed.remote_package.RemoteModule class method) DictStr() (in module emzed.r_connect.pyper) DirWrapper (class in emzed.remote_package.remote_module_wrapper) download() (emzed.chemistry.pubchem.Downloader method) (in module emzed.utils.download) Downloader (class in emzed.chemistry.pubchem) drop_columns() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) drop_index() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method)

E

ELECTROMAGNETIC_RADIATION_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) EMISSION_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) emzed module emzed.align module emzed.align.mz_align module emzed.align.mz_align_routines module emzed.align.rt_align module emzed.align.sample_alignment module emzed.annotate module emzed.annotate.annotate_adducts module emzed.check_pyopenms module emzed.chemistry module emzed.chemistry.abundance module emzed.chemistry.adducts module emzed.chemistry.elements module emzed.chemistry.fetch_elements_pubchem module emzed.chemistry.fit_formula module emzed.chemistry.formula_parser module emzed.chemistry.isotope_generator module emzed.chemistry.mass module emzed.chemistry.molecular_formula module emzed.chemistry.pubchem module emzed.config module emzed.config.config module emzed.core module emzed.core.db_backed_dictionary module emzed.core.db_backed_model module emzed.core.exceptions module emzed.core.hashes module emzed.core.multiprocessing module emzed.db module emzed.ext module emzed.gui module emzed.io module emzed.ms2 module emzed.ms2.attach_ms2_spectra module emzed.ms2.merge_spectra module emzed.ms2.sirius_export module emzed.ms_data module emzed.ms_data.peak_map module emzed.ms_data.peak_map_hasher module emzed.optimized module emzed.optimized.formula_fit module emzed.peak_picking module emzed.peak_picking.extract_chromatograms module emzed.peak_picking.extract_ms_chromatograms module emzed.peak_picking.run_feature_finder_centwave module emzed.peak_picking.run_feature_finder_metabo module emzed.peak_picking.run_feature_finder_metabo_on_folder module emzed.pyopenms module emzed.pyopenms.optimizations module emzed.pyopenms.stderr_redirector module emzed.quantification module emzed.quantification.chromatogram_integration module emzed.quantification.peak_integration module emzed.quantification.peak_shape_models module emzed.quantification.peak_shape_models.asymmetric_gauss_model module emzed.quantification.peak_shape_models.base module emzed.quantification.peak_shape_models.linear_interpolation_model module emzed.quantification.peak_shape_models.no_model module emzed.quantification.peak_shape_models.savgol_model module emzed.quantification.peak_shape_models.simplified_emg module

emzed.quantification.utils module emzed.r_connect module emzed.r_connect.patched_pyper module emzed.r_connect.pyper module emzed.r_connect.r_executor module emzed.r_connect.xcms_connector module emzed.remote_package module emzed.remote_package.object_handling module emzed.remote_package.remote_module_wrapper module emzed.table module emzed.table.add_column module emzed.table.base_models module emzed.table.col_types module emzed.table.collapse module emzed.table.delete_rows module emzed.table.expressions module emzed.table.extract_columns_model module emzed.table.filter_model module emzed.table.full_table_model module emzed.table.group_by module emzed.table.immutable_table_model module emzed.table.join module emzed.table.load_into_from module emzed.table.pickle module emzed.table.prepare_table_cell_content module emzed.table.replace_column module emzed.table.row_class module emzed.table.select_model module emzed.table.sort_model module emzed.table.table module emzed.table.table_migrations module emzed.table.table_utils module emzed.targeted module emzed.targeted.solution_space module emzed.utils module emzed.utils.align_spectra module emzed.utils.busy_indicator module emzed.utils.download module emzed.utils.functools module emzed.utils.has_emzed_gui module emzed.utils.lookup module emzed.utils.numpy module emzed.utils.sqlite module emzed.utils.temp_file_handling module EmzedException encode() (in module emzed.pyopenms) (in module emzed.pyopenms.optimizations) EndsWith (class in emzed.table.expressions) endswith() (emzed.table.expressions.Expression method) equal() (in module emzed.quantification.peak_shape_models.base) eval() (emzed.table.expressions.Reduction method) (emzed.table.expressions.Unary method) execute() (emzed.r_connect.r_executor.RInterpreter method) (emzed.r_connect.RInterpreter method) (emzed.utils.sqlite.Connection method) (emzed.utils.sqlite.Cursor method) execute_file() (emzed.r_connect.r_executor.RInterpreter method) (emzed.r_connect.RInterpreter method) executemany() (emzed.utils.sqlite.Connection method) (emzed.utils.sqlite.Cursor method) export_sirius_files() (in module emzed.ms2) (in module emzed.ms2.sirius_export) Expression (class in emzed.table.expressions) extend() (emzed.Table method) (emzed.table.table.Table method) extend_function() (in module emzed.utils.functools) extract() (emzed.ms_data.peak_map.ImmutablePeakMap method) extract_chromatograms() (in module emzed.peak_picking.extract_chromatograms) extract_columns() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) extract_for_precursors() (emzed.ms_data.peak_map.ImmutablePeakMap method) extract_ms_chromatograms() (in module emzed.peak_picking.extract_ms_chromatograms) extract_spectrum() (in module emzed.ms_data.peak_map) (in module emzed.pyopenms.optimizations) ExtractColumnsModel (class in emzed.table.extract_columns_model)

F

fast_join() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.table.join) fast_left_join() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.table.join) fast_m0() (in module emzed.chemistry.pubchem) feature_finder() (in module emzed.pyopenms.optimizations) fetch() (in module emzed.chemistry.fetch_elements_pubchem) filter() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.table.Table method) FilterModel (class in emzed.table.filter_model) finalize() (emzed.table.group_by.AggregateFunctionWrapper method) (emzed.utils.sqlite.Md5HexDigestAggregate method) find_matches() (emzed.utils.lookup.NeighbourSearch method) find_matching_rows() (emzed.table.base_models.BaseModel method) find_r_exe_on_windows() (in module emzed.r_connect.r_executor) find_spectra() (emzed.ms2.attach_ms2_spectra.LookupMS2 method)

fit() (emzed.quantification.peak_shape_models.base.PeakShapeModelBase class method) (emzed.quantification.peak_shape_models.no_model.NoModel class method) fit_chromatogram() (emzed.quantification.peak_shape_models.base.PeakShapeModelBase class method) (emzed.quantification.peak_shape_models.no_model.NoModel class method) fix_names_right() (in module emzed.table.join) fix_pubchem_entries() (in module emzed.chemistry.elements) FloatStr() (in module emzed.r_connect.pyper) floor() (emzed.table.expressions.Expression method) flush() (emzed.core.multiprocessing.StreamToQueue method) formatter_from_format_str() (in module emzed.table.col_types) formula_table() (in module emzed.chemistry.fit_formula) (in module emzed.optimized.formula_fit) from_() (emzed.ms_data.peak_map.PeakMap class method) (emzed.PeakMap class method) from_db_tables() (emzed.table.full_table_model.FullTableModel static method) (emzed.table.immutable_table_model.ImmutableTableModel static method) from_pandas() (emzed.Table static method) (emzed.table.table.Table static method) FullTableModel (class in emzed.table.full_table_model) FunctionWrapper (class in emzed.table.expressions)

G

get() (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) (emzed.r_connect.pyper.R method) (in module emzed.chemistry.fetch_elements_pubchem) get_column() (emzed.Table method) (emzed.table.table.Table method) get_count() (emzed.chemistry.pubchem.PubChemAccessor method) get_df_as_table() (emzed.r_connect.r_executor.RInterpreter method) (emzed.r_connect.RInterpreter method) get_dominating_peak_map() (emzed.ms_data.peak_map.ImmutablePeakMap method) get_identifiers() (emzed.chemistry.pubchem.PubChemAccessor method) get_iter() (emzed.table.base_models.BaseModel method) get_iter_raw() (emzed.table.base_models.BaseModel method) get_precursors_mzs() (emzed.ms_data.peak_map.ImmutablePeakMap method) get_r_version() (in module emzed.r_connect.xcms_connector) get_raw() (emzed.r_connect.r_executor.RInterpreter method) (emzed.r_connect.RInterpreter method) get_references() (in module emzed.table.table_utils) get_registered() (emzed.remote_package.object_handling.ClientObjectMapper method)

get_row() (emzed.table.base_models.BaseModel method) get_summary_data() (emzed.chemistry.pubchem.PubChemAccessor method) get_title() (emzed.Table method) (emzed.table.table.Table method) get_version_number() (in module emzed.check_pyopenms) getVec() (in module emzed.r_connect.pyper) graph() (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel method) (emzed.quantification.peak_shape_models.base.PeakShapeModelBase method) (emzed.quantification.peak_shape_models.linear_interpolation_model.LinearInterpolationModel method) (emzed.quantification.peak_shape_models.no_model.NoModel method) (emzed.quantification.peak_shape_models.savgol_model.SavGolModel method) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel method) group_by() (emzed.Table method) (emzed.table.table.Table method) GroupBy (class in emzed.table.group_by) guess_col_format() (in module emzed.table.table_utils) guess_col_formats() (in module emzed.table.table_utils) guess_common_type() (in module emzed.table.table_utils)

H

has_emzed_gui() (in module emzed.utils.has_emzed_gui)

I

id() (emzed.table.group_by.GroupBy method) if_not_none_else() (emzed.table.expressions.Expression method) ignore_overflow() (in module emzed.utils.numpy) ImmutableDbBackedDictionary (class in emzed.core.db_backed_dictionary) ImmutableMSChromatograms (class in emzed.ms_data.peak_map) ImmutablePeakMap (class in emzed.ms_data.peak_map) ImmutableSpectra (class in emzed.ms_data.peak_map) ImmutableTableModel (class in emzed.table.immutable_table_model) in_range() (emzed.table.expressions.Expression method) indices (emzed.table.base_models.BaseModel property) indices_for_rows_matching() (emzed.table.base_models.BaseModel method) info (emzed.table.base_models.BaseModel property) initializer() (in module emzed.core.multiprocessing) inject_streams() (in module emzed.core.multiprocessing) insert_chromatogram() (in module emzed.ms_data.peak_map) insert_peaks() (in module emzed.ms_data.peak_map) insert_precursors() (in module emzed.ms_data.peak_map) install_del_callaback() (emzed.r_connect.pyper.R method) install_xcms() (emzed.r_connect.xcms_connector.CentwaveFeatureDetector static method) (in module emzed.peak_picking.run_feature_finder_centwave) integrate() (in module emzed.quantification) (in module emzed.quantification.peak_integration) integrate_chromatograms() (in module emzed.quantification) (in module emzed.quantification.chromatogram_integration) intensities (emzed.ms_data.peak_map.BoundSpectrum attribute) (emzed.ms_data.peak_map.MSChromatogram property)

inv_indices (emzed.table.base_models.BaseModel property) invalidate() (emzed.table.base_models.ViewModel method) invalidate_views() (emzed.table.full_table_model.FullTableModel method) irls_fit() (in module emzed.align.mz_align_routines) is_closed() (emzed.utils.sqlite.Connection method) is_in() (emzed.table.expressions.Expression method) is_in_memory() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.table.Table method) is_int() (in module emzed.table.table_utils) is_mutable() (emzed.Table method) (emzed.table.table.Table method) is_none() (emzed.table.expressions.Expression method) is_not_none() (emzed.table.expressions.Expression method) is_open() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.table.Table method) (emzed.utils.sqlite.Connection method) is_valid (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel property) (emzed.quantification.peak_shape_models.base.PeakShapeModelBase property) (emzed.quantification.peak_shape_models.linear_interpolation_model.LinearInterpolationModel property) (emzed.quantification.peak_shape_models.no_model.NoModel property) (emzed.quantification.peak_shape_models.savgol_model.SavGolModel property) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel property) is_xcms_installed() (emzed.r_connect.xcms_connector.CentwaveFeatureDetector method) IsIn (class in emzed.table.expressions) items() (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method)

J

join() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.table.join)

join_formula() (in module emzed.chemistry.formula_parser)

K

keys() (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method)

L

left_join() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.table.join) LIMITS_AREA (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) LIMITS_GRAPH (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) LinearInterpolationModel (class in emzed.quantification.peak_shape_models.linear_interpolation_model) list_data_tables() (in module emzed.table.table_utils) list_peakmap_tables() (in module emzed.table.table_utils) list_tables() (in module emzed.utils.sqlite) list_views() (in module emzed.utils.sqlite) load() (emzed.ms_data.peak_map.ImmutablePeakMap class method) (emzed.Table class method) (emzed.table.table.Table class method) load_csv() (emzed.Table static method) (emzed.table.table.Table static method) (in module emzed.io) load_csvs() (in module emzed.io) load_elements() (in module emzed.chemistry.elements) load_elements_pubchem() (in module emzed.chemistry.elements)

load_excel() (emzed.Table static method) (emzed.table.table.Table static method) (in module emzed.io) load_excels() (in module emzed.io) load_experiment() (in module emzed.pyopenms.optimizations) load_from() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) load_into_from() (in module emzed.table.load_into_from) load_optimizations() (emzed.remote_package.DelayedRemoteModule method) (emzed.remote_package.remote_module_wrapper.DelayedRemoteModule method) (emzed.remote_package.remote_module_wrapper.RemoteModule method) (emzed.remote_package.RemoteModule method) load_peak_map() (in module emzed.io) load_peak_maps() (in module emzed.io) load_table() (in module emzed.io) load_tables() (in module emzed.io) LongStr() (in module emzed.r_connect.pyper) Lookup (class in emzed.table.expressions) lookup() (emzed.table.expressions.ColumnAccessor method) LookupMS2 (class in emzed.ms2.attach_ms2_spectra)

M

main() (in module emzed.chemistry.fetch_elements_pubchem) mass() (emzed.chemistry.molecular_formula.MolecularFormula method) MASS_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) max() (emzed.table.expressions.Expression method) (emzed.table.group_by.GroupBy method) max_index (emzed.table.base_models.BaseModel property) md5_hexdigest() (in module emzed.core.hashes) Md5HexDigestAggregate (class in emzed.utils.sqlite) mean() (emzed.table.group_by.GroupBy method) measured_centroids() (in module emzed.chemistry.isotope_generator) median() (emzed.table.group_by.GroupBy method) merge() (emzed.ms_data.peak_map.PeakMap method) (emzed.PeakMap method) merge_spectra() (in module emzed.ms2) (in module emzed.ms2.merge_spectra) (in module emzed.pyopenms.optimizations) meta_data (emzed.Table property) (emzed.table.table.Table property) mf (in module emzed) migrate() (in module emzed.table.table_migrations) migrate_to_0_0_42() (in module emzed.table.table_migrations) min() (emzed.table.expressions.Expression method) (emzed.table.group_by.GroupBy method) mock_emzed_gui() (in module emzed.utils.has_emzed_gui) model_name (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) (emzed.quantification.peak_shape_models.base.PeakShapeModelBase property) (emzed.quantification.peak_shape_models.linear_interpolation_model.LinearInterpolationModel attribute) (emzed.quantification.peak_shape_models.no_model.NoModel attribute) (emzed.quantification.peak_shape_models.savgol_model.SavGolModel attribute) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel attribute) module emzed emzed.align emzed.align.mz_align emzed.align.mz_align_routines emzed.align.rt_align emzed.align.sample_alignment emzed.annotate emzed.annotate.annotate_adducts emzed.check_pyopenms emzed.chemistry emzed.chemistry.abundance emzed.chemistry.adducts emzed.chemistry.elements emzed.chemistry.fetch_elements_pubchem emzed.chemistry.fit_formula emzed.chemistry.formula_parser emzed.chemistry.isotope_generator emzed.chemistry.mass emzed.chemistry.molecular_formula emzed.chemistry.pubchem emzed.config emzed.config.config emzed.core emzed.core.db_backed_dictionary emzed.core.db_backed_model emzed.core.exceptions emzed.core.hashes emzed.core.multiprocessing emzed.db emzed.ext emzed.gui emzed.io emzed.ms2 emzed.ms2.attach_ms2_spectra emzed.ms2.merge_spectra emzed.ms2.sirius_export emzed.ms_data emzed.ms_data.peak_map emzed.ms_data.peak_map_hasher emzed.optimized emzed.optimized.formula_fit emzed.peak_picking emzed.peak_picking.extract_chromatograms emzed.peak_picking.extract_ms_chromatograms emzed.peak_picking.run_feature_finder_centwave emzed.peak_picking.run_feature_finder_metabo emzed.peak_picking.run_feature_finder_metabo_on_folder emzed.pyopenms emzed.pyopenms.optimizations emzed.pyopenms.stderr_redirector emzed.quantification emzed.quantification.chromatogram_integration emzed.quantification.peak_integration emzed.quantification.peak_shape_models emzed.quantification.peak_shape_models.asymmetric_gauss_model emzed.quantification.peak_shape_models.base emzed.quantification.peak_shape_models.linear_interpolation_model emzed.quantification.peak_shape_models.no_model emzed.quantification.peak_shape_models.savgol_model emzed.quantification.peak_shape_models.simplified_emg emzed.quantification.utils emzed.r_connect emzed.r_connect.patched_pyper emzed.r_connect.pyper emzed.r_connect.r_executor emzed.r_connect.xcms_connector emzed.remote_package emzed.remote_package.object_handling emzed.remote_package.remote_module_wrapper emzed.table emzed.table.add_column emzed.table.base_models emzed.table.col_types emzed.table.collapse emzed.table.delete_rows emzed.table.expressions emzed.table.extract_columns_model emzed.table.filter_model emzed.table.full_table_model emzed.table.group_by emzed.table.immutable_table_model emzed.table.join emzed.table.load_into_from emzed.table.pickle emzed.table.prepare_table_cell_content emzed.table.replace_column emzed.table.row_class emzed.table.select_model emzed.table.sort_model emzed.table.table emzed.table.table_migrations emzed.table.table_utils emzed.targeted emzed.targeted.solution_space emzed.utils emzed.utils.align_spectra emzed.utils.busy_indicator emzed.utils.download emzed.utils.functools emzed.utils.has_emzed_gui emzed.utils.lookup emzed.utils.numpy emzed.utils.sqlite emzed.utils.temp_file_handling

MolecularFormula (class in emzed.chemistry.molecular_formula) ms_level (emzed.ms_data.peak_map.BoundSpectrum attribute) ms_levels() (emzed.ms_data.peak_map.ImmutablePeakMap method) MSChromatogram (class in emzed.ms_data.peak_map) Multiprocessing (class in emzed.core.multiprocessing) MutableSpectra (class in emzed.ms_data.peak_map) mz (emzed.ms_data.peak_map.MSChromatogram property) mz_align() (in module emzed.align) (in module emzed.align.mz_align) mz_range() (emzed.ms_data.peak_map.ImmutablePeakMap method) mz_ranges() (emzed.ms_data.peak_map.ImmutablePeakMap method) mzs (emzed.ms_data.peak_map.BoundSpectrum attribute) MzType (class in emzed) (class in emzed.table.col_types)

N

NeighbourSearch (class in emzed.utils.lookup) NoModel (class in emzed.quantification.peak_shape_models.no_model) NonAlgebraicColumnAccessor (class in emzed.table.expressions) NoneStr() (in module emzed.r_connect.pyper) not_specified (class in emzed.table.table)

NPOINTS_GRAPH (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel attribute) NPOINTS_INTEGRAL (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel attribute) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel attribute) NumpyNdarrayStr() (in module emzed.r_connect.pyper)

O

ObjectMapper (class in emzed.remote_package.remote_module_wrapper) ObjectProxy (class in emzed.remote_package.remote_module_wrapper) on_die() (in module emzed.r_connect.patched_pyper) (in module emzed.r_connect.pyper)

open() (emzed.ms_data.peak_map.ImmutablePeakMap class method) (emzed.Table class method) (emzed.table.table.Table class method) OtherStr() (in module emzed.r_connect.pyper)

P

PandasDataFrameStr() (in module emzed.r_connect.pyper) PandasSerieStr() (in module emzed.r_connect.pyper) parse_float() (in module emzed.chemistry.elements) parse_formula() (in module emzed.chemistry.formula_parser) PatchedR (class in emzed.r_connect.patched_pyper) path (emzed.Table property) (emzed.table.table.Table property) PeakMap (class in emzed) (class in emzed.ms_data.peak_map) peaks (emzed.ms_data.peak_map.BoundSpectrum attribute) PeakShapeModelBase (class in emzed.quantification.peak_shape_models.base) Pickle (class in emzed.table.pickle) plot_profile() (in module emzed.chemistry.isotope_generator) polarities() (emzed.ms_data.peak_map.ImmutablePeakMap method) polarity (emzed.ms_data.peak_map.BoundSpectrum attribute)

Pool() (emzed.core.multiprocessing.Multiprocessing method) precursor_mz (emzed.ms_data.peak_map.MSChromatogram property) precursors (emzed.ms_data.peak_map.BoundSpectrum property) Predicate (class in emzed.table.expressions) prepare_table_cell_content() (in module emzed.table.prepare_table_cell_content) print_() (emzed.Table method) (emzed.table.table.Table method) print_report() (in module emzed.ms2.attach_ms2_spectra) print_table() (in module emzed.table.table_utils) proc_id() (in module emzed.utils.sqlite) process() (emzed.r_connect.xcms_connector.CentwaveFeatureDetector method) profile() (in module emzed.ms_data.peak_map) PubChemAccessor (class in emzed.chemistry.pubchem) python_exe_in() (in module emzed.remote_package) (in module emzed.remote_package.remote_module_wrapper)

R

R (class in emzed.r_connect.pyper) read_info() (emzed.table.base_models.BaseModel static method) ReadFromQueueAndPrint (class in emzed.core.multiprocessing) readLine() (in module emzed.r_connect.pyper) reconnect() (emzed.utils.sqlite.Connection method) reconstruct_all_function_args() (emzed.table.expressions.FunctionWrapper method) (emzed.table.group_by.AggregateFunctionWrapper method) Reduction (class in emzed.table.expressions) register() (emzed.remote_package.object_handling.ClientObjectMapper method) (in module emzed.remote_package.remote_module_wrapper) register_md5_hasher() (in module emzed.utils.sqlite) register_pubchem_api_key() (emzed.chemistry.pubchem.PubChemAccessor method) register_re_match_function() (in module emzed.utils.sqlite) register_view() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.immutable_table_model.ImmutableTableModel method) RemoteModule (class in emzed.remote_package) (class in emzed.remote_package.remote_module_wrapper) remove() (emzed.r_connect.pyper.R method) rename_columns() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.immutable_table_model.ImmutableTableModel method) (emzed.table.table.Table method) rename_postfixes() (emzed.Table method) (emzed.table.table.Table method) rename_table() (in module emzed.table.table_migrations) replace_column() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) replace_column_from_expression() (in module emzed.table.replace_column) replace_column_with_constant_value() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) (emzed.table.table.Table method) (in module emzed.table.replace_column) replace_column_with_values() (in module emzed.table.replace_column)

representing_mz_peak() (emzed.ms_data.peak_map.ImmutablePeakMap method) (in module emzed.ms_data.peak_map) ReprStr() (in module emzed.r_connect.pyper) reraise_exception_conn() (in module emzed.utils.sqlite) reraise_exception_cursor() (in module emzed.utils.sqlite) RError, [1] resolve_db_backed_dicts() (in module emzed.core.db_backed_dictionary) retry() (in module emzed.chemistry.pubchem) RInterpreter (class in emzed.r_connect) (class in emzed.r_connect.r_executor) rmse (emzed.quantification.peak_shape_models.asymmetric_gauss_model.AsymmetricGaussModel property) (emzed.quantification.peak_shape_models.base.PeakShapeModelBase property) (emzed.quantification.peak_shape_models.linear_interpolation_model.LinearInterpolationModel property) (emzed.quantification.peak_shape_models.no_model.NoModel property) (emzed.quantification.peak_shape_models.savgol_model.SavGolModel property) (emzed.quantification.peak_shape_models.simplified_emg.SimplifiedEmgModel property) round() (emzed.table.expressions.Expression method) Row (class in emzed.table.row_class) rows (emzed.Table property) (emzed.table.table.Table property) rt (emzed.ms_data.peak_map.BoundSpectrum attribute) rt_align() (in module emzed.align) (in module emzed.align.rt_align) rt_formatter() (in module emzed.table.col_types) rt_range() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.ms_data.peak_map.MSChromatogram method) rt_ranges() (emzed.ms_data.peak_map.ImmutablePeakMap method) rts (emzed.ms_data.peak_map.MSChromatogram property) RtType (class in emzed) (class in emzed.table.col_types) run() (emzed.core.multiprocessing.ReadFromQueueAndPrint method) (emzed.r_connect.pyper.R method) run_feature_finder_centwave() (in module emzed.peak_picking.run_feature_finder_centwave) run_feature_finder_metabo_on_folder() (in module emzed) (in module emzed.peak_picking.run_feature_finder_metabo_on_folder) RunFeatureFinderMetabo (class in emzed.peak_picking.run_feature_finder_metabo) runR() (in module emzed.r_connect.pyper)

S

save() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.table.Table method) save_csv() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) (in module emzed.io) save_excel() (emzed.Table method) (emzed.table.table.Table method) (in module emzed.io) save_info() (emzed.table.base_models.BaseModel method) save_peak_map() (in module emzed.io) save_table() (in module emzed.io) SavGolModel (class in emzed.quantification.peak_shape_models.savgol_model) scan_counts() (emzed.ms_data.peak_map.ImmutablePeakMap method) scan_number (emzed.ms_data.peak_map.BoundSpectrum property) schemata (emzed.utils.sqlite.Connection property) SELECTED_ION_CURRENT_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) SELECTED_ION_MONITORING_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) SELECTED_REACTION_MONITORING_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) SelectModel (class in emzed.table.select_model) sendAll() (in module emzed.r_connect.patched_pyper) (in module emzed.r_connect.pyper) seqstr() (in module emzed.r_connect.patched_pyper) SeqStr() (in module emzed.r_connect.pyper) set_col_format() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.immutable_table_model.ImmutableTableModel method) (emzed.table.table.Table method) set_col_type() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.immutable_table_model.ImmutableTableModel method) (emzed.table.table.Table method) set_exception() (emzed.utils.sqlite.Connection method) set_title() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) set_value() (emzed.table.full_table_model.FullTableModel method) set_values() (emzed.table.base_models.BaseModel method) (emzed.table.full_table_model.FullTableModel method) setup() (in module emzed.core.multiprocessing)

setup_col_formatters() (in module emzed.table.table_utils) setup_r_libs_variable() (in module emzed.r_connect.xcms_connector) setup_remote_venv() (in module emzed.remote_package) (in module emzed.remote_package.remote_module_wrapper) SimplifiedEmgModel (class in emzed.quantification.peak_shape_models.simplified_emg) size_changed() (emzed.table.full_table_model.FullTableModel method) solution_space() (in module emzed.targeted.solution_space) sort_by() (emzed.Table method) (emzed.table.table.Table method) sorting_permutation() (emzed.table.base_models.BaseModel method) SortModel (class in emzed.table.sort_model) spectra() (in module emzed.pyopenms.optimizations) spectra_for_modification() (emzed.ms_data.peak_map.PeakMap method) (emzed.PeakMap method) SpectraBase (class in emzed.ms_data.peak_map) Spectrum (class in emzed) (class in emzed.ms_data.peak_map) split_by() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) split_by_iter() (emzed.Table method) (emzed.table.base_models.BaseModel method) (emzed.table.table.Table method) split_by_precursors() (emzed.ms_data.peak_map.ImmutablePeakMap method) stack_tables() (emzed.Table static method) (emzed.table.table.Table static method) standard_config (emzed.r_connect.xcms_connector.CentwaveFeatureDetector attribute) start_remote_client() (in module emzed.remote_package.remote_module_wrapper) StartsWith (class in emzed.table.expressions) startswith() (emzed.table.expressions.Expression method) std() (emzed.table.group_by.GroupBy method) step() (emzed.table.group_by.AggregateFunctionWrapper method) (emzed.utils.sqlite.Md5HexDigestAggregate method) Str4R() (in module emzed.r_connect.pyper) StreamToQueue (class in emzed.core.multiprocessing) sum() (emzed.table.group_by.GroupBy method) summary() (emzed.ms_data.peak_map.ImmutablePeakMap method) (emzed.Table method) (emzed.table.table.Table method) supported_postfixes() (emzed.Table method) (emzed.table.table.Table method) suppress_stderr() (in module emzed.pyopenms.stderr_redirector)

T

Table (class in emzed) (class in emzed.table.table) table_exists() (in module emzed.utils.sqlite) table_hash() (in module emzed.utils.sqlite) table_to_html() (in module emzed.table.table_utils) temp_file_path() (in module emzed.utils.temp_file_handling) then_else() (emzed.table.expressions.Expression method) ThenElse (class in emzed.table.expressions) title (emzed.Table property) (emzed.table.table.Table property) to_list() (emzed.table.expressions.ColumnAccessor method) (in module emzed.table.full_table_model) to_openms_chromatogram() (in module emzed.pyopenms.optimizations)

to_openms_experiment() (in module emzed.pyopenms.optimizations) to_openms_feature_map() (in module emzed.table.table_utils) to_openms_spectrum() (in module emzed.ms_data.peak_map) (in module emzed.pyopenms.optimizations) to_pandas() (emzed.Table method) (emzed.table.table.Table method) to_pandas_type() (in module emzed.table.col_types) to_table() (in module emzed) (in module emzed.table.table) TOTAL_ION_CURRENT_CHROMATOGRAM (emzed.ms_data.peak_map.ChromatogramType attribute) transfer_functions() (emzed.utils.sqlite.Connection method) transform_rt_values() (in module emzed.pyopenms.optimizations) type (emzed.ms_data.peak_map.MSChromatogram property) type_to_str() (in module emzed.table.table_utils)

U

Unary (class in emzed.table.expressions) unbind() (emzed.ms_data.peak_map.BoundSpectrum method) (emzed.ms_data.peak_map.Spectrum method) (emzed.Spectrum method) unique_id (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary property) (emzed.core.db_backed_model.DbBackedModel property) (emzed.ms_data.peak_map.ImmutablePeakMap property) (emzed.Table property) (emzed.table.base_models.BaseModel property) (emzed.table.table.Table property) unique_value() (emzed.table.expressions.ColumnAccessor method)

unique_values() (emzed.table.expressions.ColumnAccessor method) UniStr() (in module emzed.r_connect.pyper) unpickle() (emzed.table.pickle.Pickle method) unwrap() (emzed.remote_package.object_handling.ClientObjectMapper method) (emzed.remote_package.remote_module_wrapper.ObjectMapper method) (in module emzed.remote_package.remote_module_wrapper) unzip() (in module emzed.table.collapse) update() (emzed.core.db_backed_dictionary.DbBackedDictionary method) (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) update_col_formatters() (emzed.table.base_models.BaseModel method) update_pubchem() (in module emzed.db)

V

Value (class in emzed.table.expressions)

values() (emzed.core.db_backed_dictionary.ImmutableDbBackedDictionary method) ViewModel (class in emzed.table.base_models)

W

wrap() (emzed.remote_package.object_handling.ClientObjectMapper method) (emzed.remote_package.remote_module_wrapper.ObjectMapper method) (in module emzed.remote_package.remote_module_wrapper)

write() (emzed.core.multiprocessing.StreamToQueue method)