masskit package

Subpackages

• masskit.apps package
  • Subpackages
    • masskit.apps.process package
      • Subpackages
      • Module contents
    • masskit.apps.ui package
      • Submodules
      • masskit.apps.ui.pqview module
      • Module contents
  • Module contents
• masskit.conf package
  • Subpackages
    • masskit.conf.conversion package
      • Subpackages
      • Module contents
  • Module contents
• masskit.data_specs package
  • Submodules
  • masskit.data_specs.arrow_types module
    • JSONArrowArray
    • JSONArrowScalarType
      • JSONArrowScalarType.as_py()
    • JSONArrowType
      • JSONArrowType.to_pandas_dtype()
    • MasskitArrowArray
      • MasskitArrowArray.to_numpy()
      • MasskitArrowArray.to_pylist()
    • MasskitPandasArray
      • MasskitPandasArray.copy()
      • MasskitPandasArray.dtype
      • MasskitPandasArray.isna()
      • MasskitPandasArray.nbytes()
      • MasskitPandasArray.take()
      • MasskitPandasArray.to_mgf()
      • MasskitPandasArray.to_msp()
      • MasskitPandasArray.to_mzxml()
    • MasskitPandasDtype
      • MasskitPandasDtype.construct_array_type()
      • MasskitPandasDtype.na_value
      • MasskitPandasDtype.name
      • MasskitPandasDtype.type
    • MolArrowArray
    • MolArrowScalarType
      • MolArrowScalarType.as_py()
    • MolArrowType
      • MolArrowType.to_pandas_dtype()
    • MolPandasArray
      • MolPandasArray.dtype
    • MolPandasDtype
      • MolPandasDtype.construct_array_type()
      • MolPandasDtype.na_value
      • MolPandasDtype.name
    • PathArrowType
      • PathArrowType.to_pandas_dtype()
    • PathPandasArray
      • PathPandasArray.dtype
    • PathPandasDtype
      • PathPandasDtype.construct_array_type()
      • PathPandasDtype.na_value
      • PathPandasDtype.name
      • PathPandasDtype.type
    • SpectrumArrowArray
    • SpectrumArrowScalarType
      • SpectrumArrowScalarType.as_py()
    • SpectrumArrowType
      • SpectrumArrowType.to_pandas_dtype()
    • SpectrumPandasArray
      • SpectrumPandasArray.dtype
    • SpectrumPandasDtype
      • SpectrumPandasDtype.construct_array_type()
      • SpectrumPandasDtype.na_value
      • SpectrumPandasDtype.name
      • SpectrumPandasDtype.type
  • masskit.data_specs.file_schemas module
  • masskit.data_specs.schemas module
    • compose_fields()
    • create_array()
    • create_getter()
    • create_scalar()
    • create_setter()
    • get_field_int_metadata()
    • massinfo2struct()
    • name_to_type()
    • populate_properties()
    • set_field_int_metadata()
    • subtract_fields()
  • masskit.data_specs.spectral_library module
    • LibraryAccessor
      • LibraryAccessor.copy()
      • LibraryAccessor.display()
    • display_masskit_df()
  • Module contents
• masskit.peptide package
  • Submodules
  • masskit.peptide.encoding module
    • calc_ion_series()
    • calc_ions_mz()
    • calc_named_ions()
    • calc_precursor_mass()
    • calc_precursor_mz()
    • expand_mod_string()
    • mod_mass_pos()
    • parse_ion_type_tuple()
    • parse_modification_encoding()
    • protonate_mass()
  • masskit.peptide.spectrum_generator module
    • add_theoretical_spectra()
    • create_peptide_name()
    • generate_mods()
    • generate_peptide_library()
  • Module contents
• masskit.small_molecule package
  • Submodules
  • masskit.small_molecule.react module
    • Reactor
      • Reactor.apply_reactions()
      • Reactor.create_reactions()
      • Reactor.functional_group_names
      • Reactor.react()
      • Reactor.reactant_names
  • masskit.small_molecule.threed module
    • bounding_box()
    • create_conformer()
  • masskit.small_molecule.utils module
    • AdjustAromaticNs()
    • get_unspec_double_bonds()
    • is_transition_metal()
    • set_dative_bonds()
    • standardize_mol()
    • yang_polarizability()
  • Module contents
• masskit.spectra package
  • Submodules
  • masskit.spectra.ions module
    • HiResIons
      • HiResIons.cast_intensity()
      • HiResIons.cast_mz()
      • HiResIons.change_mass_info()
      • HiResIons.create_tolerance()
      • HiResIons.intersect()
      • HiResIons.starts
      • HiResIons.stops
      • HiResIons.tolerance
    • Ions
      • Ions.annotations
      • Ions.cast_intensity()
      • Ions.cast_mz()
      • Ions.clear_and_intersect()
      • Ions.clear_computed_properties()
      • Ions.copy()
      • Ions.copy_annot()
      • Ions.cosine_score()
      • Ions.evenly_space()
      • Ions.filter()
      • Ions.half_tolerance()
      • Ions.intensity
      • Ions.intersect()
      • Ions.ions2array()
      • Ions.join
      • Ions.mask()
      • Ions.mask_ions()
      • Ions.mass_type
      • Ions.merge()
      • Ions.mz
      • Ions.neutral_loss
      • Ions.neutral_loss_charge
      • Ions.norm()
      • Ions.num_ions()
      • Ions.parent_filter()
      • Ions.rank
      • Ions.rank_ions()
      • Ions.shift_mz()
      • Ions.stddev
      • Ions.tolerance
      • Ions.tolerance_type
      • Ions.total_intensity()
      • Ions.windowed_filter()
    • IonsIterator
    • MassInfo
    • cosine_score_calc()
    • dedup_matches()
    • intersect_hires()
    • my_intersect1d()
    • nce2ev()
  • masskit.spectra.ipython module
    • is_notebook()
  • masskit.spectra.join module
    • Join
      • Join.do_join()
      • Join.join_2_spectra()
      • Join.join_3_spectra()
      • Join.list2float32()
      • Join.list2float64()
      • Join.list2int16()
      • Join.list2uint16()
      • Join.list2uint32()
      • Join.list2uint64()
      • Join.to_pandas()
    • PairwiseJoin
      • PairwiseJoin.do_join()
    • ThreewayJoin
      • ThreewayJoin.do_join()
  • masskit.spectra.spectrum_plotting module
    • AnimateSpectrumPlot
      • AnimateSpectrumPlot.add_figure()
      • AnimateSpectrumPlot.create_animated_gif()
    • draw_spectrum()
    • error_bar_plot()
    • error_bar_plot_lines()
    • line_plot()
    • multiple_spectrum_plot()
    • normalize_intensity()
    • spectrum_plot()
    • unsparsify_spectrum()
  • masskit.spectra.theoretical_spectrum module
    • TheoreticalPeptideSpectrum
    • TheoreticalSpectrum
    • annotate_peptide_spectrum()
  • Module contents
• masskit.test_fixtures package
  • Submodules
  • masskit.test_fixtures.demo_fixtures module
    • cho_uniq_short_parquet()
  • Module contents
    • SRM1950_lumos_recordbatch()
    • SRM1950_lumos_short_parquet()
    • SRM1950_lumos_short_sdf()
    • SRM1950_lumos_structarray()
    • SRM1950_lumos_table()
    • batch_converted_csv_files()
    • batch_converted_csv_path_file()
    • batch_converted_plain_sdf_files()
    • batch_converted_pubchem_sdf_files()
    • batch_converted_sdf_files()
    • cho_uniq_short_msp()
    • cho_uniq_short_parquet()
    • cho_uniq_short_recordbatch()
    • cho_uniq_short_structarray()
    • cho_uniq_short_table()
    • config_batch_converter_csv()
    • config_batch_converter_plain_sdf()
    • config_batch_converter_pubchem_sdf()
    • config_batch_converter_sdf()
    • config_fasta2peptides()
    • config_reactor()
    • config_shortest_path_csv()
    • create_peptide_parquet_file()
    • data_dir()
    • human_uniprot_trunc_fasta()
    • human_uniprot_trunc_parquet()
    • plain_sdf()
    • pubchem_sdf()
    • reactants()
    • test_csv()
    • test_molecules()
    • test_new_sdf()
    • test_num_tautomers()
    • test_products()
    • test_reactants()
• masskit.utils package
  • Subpackages
    • masskit.utils.textalloc package
      • Submodules
      • masskit.utils.textalloc.candidates module
      • masskit.utils.textalloc.non_overlapping_boxes module
      • masskit.utils.textalloc.overlap_functions module
      • Module contents
  • Submodules
  • masskit.utils.accumulator module
    • Accumulator
      • Accumulator.add()
      • Accumulator.finalize()
    • AccumulatorProperty
      • AccumulatorProperty.add()
      • AccumulatorProperty.finalize()
  • masskit.utils.arrow module
    • create_object_id()
    • save_to_arrow()
  • masskit.utils.files module
    • BatchFileReader
      • BatchFileReader.iter_tables()
      • BatchFileReader.loaders
    • BatchFileWriter
      • BatchFileWriter.close()
      • BatchFileWriter.write_table()
    • BatchLoader
      • BatchLoader.ecfp4
      • BatchLoader.finalize()
      • BatchLoader.load()
      • BatchLoader.loop_end()
      • BatchLoader.mol2row()
      • BatchLoader.setup()
      • BatchLoader.tms
    • CSVLoader
      • CSVLoader.load()
    • MGFLoader
      • MGFLoader.load()
    • MSPLoader
      • MSPLoader.load()
    • MzTab_Reader
      • MzTab_Reader.get_hitlist()
      • MzTab_Reader.parse_metadata()
      • MzTab_Reader.parse_psm()
      • MzTab_Reader.parse_psm_row()
      • MzTab_Reader.read_sections()
    • SDFLoader
      • SDFLoader.load()
    • add_row_to_records()
    • create_table_with_mod_dict()
    • empty_records()
    • get_progress()
    • load_default_config_schema()
    • load_mzTab()
    • parse_energy()
    • parse_glycopeptide_annot()
    • read_parquet()
    • records2table()
    • seek_size()
    • spectra_to_array()
    • spectrum2mgf()
    • spectrum2msp()
    • write_parquet()
  • masskit.utils.fingerprints module
    • ECFPFingerprint
      • ECFPFingerprint.from_bitvec()
      • ECFPFingerprint.from_numpy()
      • ECFPFingerprint.object2fingerprint()
      • ECFPFingerprint.to_bitvec()
      • ECFPFingerprint.to_numpy()
    • Fingerprint
      • Fingerprint.bitvec2numpy()
      • Fingerprint.from_bitvec()
      • Fingerprint.from_numpy()
      • Fingerprint.get_num_on_bits()
      • Fingerprint.numpy2bitvec()
      • Fingerprint.object2fingerprint()
      • Fingerprint.size()
      • Fingerprint.to_bitvec()
      • Fingerprint.to_numpy()
    • MolFingerprint
      • MolFingerprint.from_bitvec()
      • MolFingerprint.from_numpy()
      • MolFingerprint.object2fingerprint()
      • MolFingerprint.to_bitvec()
      • MolFingerprint.to_numpy()
    • SpectrumFingerprint
      • SpectrumFingerprint.from_bitvec()
      • SpectrumFingerprint.from_numpy()
      • SpectrumFingerprint.object2fingerprint()
      • SpectrumFingerprint.to_bitvec()
      • SpectrumFingerprint.to_numpy()
    • SpectrumFloatFingerprint
      • SpectrumFloatFingerprint.from_bitvec()
      • SpectrumFloatFingerprint.from_numpy()
      • SpectrumFloatFingerprint.object2fingerprint()
      • SpectrumFloatFingerprint.to_bitvec()
      • SpectrumFloatFingerprint.to_numpy()
    • SpectrumTanimotoFingerPrint
      • SpectrumTanimotoFingerPrint.from_bitvec()
      • SpectrumTanimotoFingerPrint.from_numpy()
      • SpectrumTanimotoFingerPrint.object2fingerprint()
      • SpectrumTanimotoFingerPrint.to_bitvec()
      • SpectrumTanimotoFingerPrint.to_numpy()
    • calc_bit()
    • calc_dynamic_fingerprint()
    • calc_interval_fingerprint()
    • fingerprint_search_numpy()
  • masskit.utils.general module
    • MassKitSearchPathPlugin
      • MassKitSearchPathPlugin.manipulate_search_path()
    • class_for_name()
    • discounted_cumulative_gain()
    • expand_path()
    • expand_path_list()
    • get_file()
    • is_list_like()
    • open_if_compressed()
    • open_if_filename()
    • parse_filename()
    • read_arrow()
    • search_for_file()
    • write_arrow()
  • masskit.utils.hitlist module
    • CompareRecallDCG
      • CompareRecallDCG.compare()
    • CosineScore
      • CosineScore.score()
    • Hitlist
      • Hitlist.get_query_ids()
      • Hitlist.hitlist
      • Hitlist.load()
      • Hitlist.save()
      • Hitlist.sort()
      • Hitlist.to_pandas()
    • HitlistCompare
      • HitlistCompare.compare()
    • IdentityRecall
      • IdentityRecall.compare()
    • PeptideIdentityScore
      • PeptideIdentityScore.score()
    • Score
      • Score.score()
    • TanimotoScore
      • TanimotoScore.score()
  • masskit.utils.index module
    • BruteForceIndex
      • BruteForceIndex.create()
      • BruteForceIndex.load()
      • BruteForceIndex.optimize()
      • BruteForceIndex.save()
      • BruteForceIndex.search()
    • DescentIndex
      • DescentIndex.create()
      • DescentIndex.create_from_fingerprint()
      • DescentIndex.load()
      • DescentIndex.optimize()
      • DescentIndex.save()
      • DescentIndex.search()
    • DotProductIndex
      • DotProductIndex.create()
      • DotProductIndex.load()
      • DotProductIndex.optimize()
      • DotProductIndex.save()
      • DotProductIndex.search()
    • Index
      • Index.create()
      • Index.load()
      • Index.optimize()
      • Index.save()
      • Index.search()
      • Index.spectrum2array()
    • TanimotoIndex
      • TanimotoIndex.create()
      • TanimotoIndex.create_from_fingerprint()
      • TanimotoIndex.load()
      • TanimotoIndex.optimize()
      • TanimotoIndex.save()
      • TanimotoIndex.search()
    • dot_product()
  • masskit.utils.spectrum_writers module
    • spectra_to_mgf()
    • spectra_to_msp()
    • spectra_to_mzxml()
  • masskit.utils.tablemap module
    • ArrowLibraryMap
      • ArrowLibraryMap.create_dict()
      • ArrowLibraryMap.from_mgf()
      • ArrowLibraryMap.from_msp()
      • ArrowLibraryMap.from_parquet()
      • ArrowLibraryMap.from_sdf()
      • ArrowLibraryMap.get_ids()
      • ArrowLibraryMap.getitem_by_id()
      • ArrowLibraryMap.getitem_by_row()
      • ArrowLibraryMap.getrow_by_id()
      • ArrowLibraryMap.to_arrow()
      • ArrowLibraryMap.to_csv()
      • ArrowLibraryMap.to_mgf()
      • ArrowLibraryMap.to_mzxml()
      • ArrowLibraryMap.to_pandas()
      • ArrowLibraryMap.to_parquet()
    • ListLibraryMap
      • ListLibraryMap.create_dict()
      • ListLibraryMap.get_ids()
      • ListLibraryMap.getitem_by_id()
      • ListLibraryMap.getitem_by_row()
      • ListLibraryMap.getrow_by_id()
    • PandasLibraryMap
      • PandasLibraryMap.create_dict()
      • PandasLibraryMap.get_ids()
      • PandasLibraryMap.getitem_by_id()
      • PandasLibraryMap.getitem_by_row()
      • PandasLibraryMap.getrow_by_id()
    • TableMap
      • TableMap.create_dict()
      • TableMap.get_ids()
      • TableMap.getitem_by_id()
      • TableMap.getitem_by_row()
      • TableMap.getrow_by_id()
      • TableMap.to_msp()
  • masskit.utils.tables module
    • create_dataset()
    • is_struct_or_extstruct()
    • optimize_structarray()
    • optimize_table()
    • random_string()
    • row_view()
    • row_view_raw()
    • struct_view()
    • structarray_to_table()
    • table_add_structarray()
    • table_to_structarray()
  • Module contents

Submodules

masskit.data module

class masskit.data.Alphabet(chars, encoding=None, mask=False, missing=255)

Bases: object

decode(x)

decode index array, x, to byte string of this alphabet

encode(x, count=-1)

encode a string into alphabet indices

get_kmer(h, k)

retrieve byte string of length k decoded from integer h

unpack(h, k)

unpack integer h into array of this alphabet with length k

class masskit.data.MSDictionary

Bases: object

create_df()

create_dictionary(fill_value=None)

create a dictionary array

Parameters:

fill_value – pandas doesn’t allow None as a category value, so use the fill value

create_id2row()

create a dictionary that maps the unique id field to a row number

class masskit.data.SDM12(mask=False)

Bases: Alphabet

A D KER N TSQ YF LIVM C W H G P See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732308/#B33 “Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment” Peterson et al. 2009. Bioinformatics.

class masskit.data.Uniprot21(mask=False)

Bases: Alphabet

Module contents