Index

A

AbstractCeramide (class in lipyd.lipid) AbstractGlycerol (class in lipyd.lipid) AbstractGlycerolipid (class in lipyd.lipid) AbstractMetabolite (class in lipyd.metabolite) AbstractMetaboliteComponent (class in lipyd.metabolite) AbstractMS2Identifier (class in lipyd.ms2) AbstractSphingolipid (class in lipyd.lipid) AbstractSubstituent (class in lipyd.metabolite) acurrent() (lipyd.sample.FeatureIdx method) add() (lipyd.formula.Formula method) (lipyd.fragment.AdductCalculator method) add_2h() (lipyd.mz.Mz method) add_3h() (lipyd.mz.Mz method) add_ac() (lipyd.mz.Mz method) add_annotations() (lipyd.moldb.SwissLipids static method) add_atoms() (lipyd.fragment.AdductCalculator method) add_constraints() (lipyd.fragdb.FragmentDatabaseAggregator method) add_fa1() (lipyd.ms2.MS2Scan method) add_fo() (lipyd.mz.Mz method) add_h() (lipyd.mz.Mz method) add_metabolite_series() (lipyd.moldb.MoleculeDatabaseAggregator method) add_na() (lipyd.mz.Mz method) add_nh4() (lipyd.mz.Mz method) add_oh() (lipyd.mz.Mz method) addToList() (in module lipyd.common) adduct() (lipyd.ms2.Scan method) (lipyd.mz.Mz method) adduct_annot() (lipyd.ms2.Scan method)

adduct_chain_list() (lipyd.ms2.Scan method) adduct_data() (lipyd.ms2.Scan method) adduct_lookup() (in module lipyd.moldb) (lipyd.moldb.MoleculeDatabaseAggregator method) adduct_lookup_many() (in module lipyd.moldb) (lipyd.moldb.MoleculeDatabaseAggregator method) adduct_str() (lipyd.fragment.FattyFragmentOld method) AdductCalculator (class in lipyd.fragment) annot_by_type() (lipyd.ms2.Scan method) annotate() (lipyd.fragdb.FragmentAnnotator method) (lipyd.ms2.ScanBase method) (lipyd.plot.SpectrumPlot method) annotate_distance() (lipyd.plot.SpectrumPlot method) annotate_point() (lipyd.plot.SpectrumPlot method) annots_default (lipyd.sdf.SdfReader attribute) aoriginal() (lipyd.sample.FeatureIdx method) apply() (lipyd.sample.Sample method) argsort_by_sample_id() (lipyd.sampleattrs.SampleSetAttrs method) as_mass() (lipyd.formula.Formula method) attr_proc() (lipyd.name.LipidNameProcessor class method) attrs_types() (lipyd.name.LipidNameProcessor method) auto_df() (lipyd.results.Results method) auto_fattyacids() (lipyd.moldb.MoleculeDatabaseAggregator method) auto_fractions() (lipyd.sec.SECReader method) auto_glycerolipids() (lipyd.moldb.MoleculeDatabaseAggregator method) auto_glycerophospholipids() (lipyd.moldb.MoleculeDatabaseAggregator method) auto_metabolites() (lipyd.moldb.MoleculeDatabaseAggregator method) auto_misc() (lipyd.moldb.MoleculeDatabaseAggregator method) auto_sphingolipids() (lipyd.moldb.MoleculeDatabaseAggregator method)

B

basic_filters() (lipyd.sample.Sample method) bind() (lipyd.formula.Formula method) (lipyd.formula.Mass method) BMP (class in lipyd.lipid) bmp_neg_1() (lipyd.ms2.MS2Scan method) BMP_Negative (class in lipyd.ms2) bmp_pos_1() (lipyd.ms2.MS2Scan method) BMP_Positive (class in lipyd.ms2) bubble_altair() (lipyd.results.Results method)

bubble_plotly() (lipyd.results.Results method) build() (lipyd.fragdb.FragmentDatabaseAggregator method) (lipyd.moldb.MoleculeDatabaseAggregator method) (lipyd.plot.SpectrumPlot method) build_chain_list() (lipyd.ms2.Scan method) build_fa_list() (lipyd.ms2.MS2Scan method) build_scans() (lipyd.ms2.MS2Feature method) by_name() (in module lipyd.fragdb) (lipyd.fragdb.FragmentDatabaseAggregator method)

C

c (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.ms2.ChainFragment attribute) calc_mass() (lipyd.mass.MassBase method) calculate() (in module lipyd.mass) carbon_counts() (lipyd.name.LipidNameProcessor method) cc2int() (lipyd.ms2.MS2Scan method) cc2str() (lipyd.ms2.MS2Scan method) ccs2int() (lipyd.ms2.MS2Scan method) ccs2str() (lipyd.ms2.MS2Scan method) cer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) cer1p() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) cer1p_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) cer1p_pos_1() (lipyd.ms2.MS2Scan method) cer_fa_test() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) cer_matching_fa() (lipyd.ms2.MS2Scan method) cer_missing_fa() (lipyd.ms2.MS2Scan method) cer_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) Cer_Negative (class in lipyd.ms2) cer_pos_1() (lipyd.ms2.MS2Scan method) Cer_Positive (class in lipyd.ms2) CeramideD (class in lipyd.lipid) CeramideD1OAcyl (class in lipyd.lipid) CeramideDihydro (class in lipyd.lipid) CeramideDihydro1OAcyl (class in lipyd.lipid) CeramideDihydroPE (class in lipyd.lipid) CeramideDihydroPhosphate (class in lipyd.lipid) CeramideDPE (class in lipyd.lipid) CeramideDPhosphate (class in lipyd.lipid) CeramideT (class in lipyd.lipid) CeramideT1OAcyl (class in lipyd.lipid) CeramideTPE (class in lipyd.lipid) CeramideTPhosphate (class in lipyd.lipid) cerp_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) cerp_pos_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) Chain (class in lipyd.lipproc) chain_among_most_abundant() (lipyd.ms2.Scan method) chain_combinations() (lipyd.ms2.Scan method) chain_fragment_type_among_most_abundant() (lipyd.ms2.Scan method) chain_fragment_type_is() (lipyd.ms2.Scan method) chain_percent_of_most_abundant() (lipyd.ms2.Scan method) ChainAttr (class in lipyd.lipproc) ChainFragment (class in lipyd.ms2) ChainFragParam (class in lipyd.fragment) ChainIdentificationDetails (class in lipyd.ms2) chains_of_type() (lipyd.ms2.Scan method) ChainSummary (class in lipyd.lipproc) chaintype (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.fragment.ChainFragParam attribute) (lipyd.fragment.FA attribute) (lipyd.fragment.FAL_mH attribute) (lipyd.fragment.FA_m3H attribute) (lipyd.fragment.FA_mCO_m3H attribute) (lipyd.fragment.FA_mH attribute) (lipyd.fragment.FA_mH2O attribute) (lipyd.fragment.FA_mH2O_mH attribute) (lipyd.fragment.FA_mH2O_mOH attribute) (lipyd.fragment.FA_mOH attribute) (lipyd.fragment.FA_mO_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2_pO attribute) (lipyd.fragment.FA_pC2H3_pNH2_m2H attribute) (lipyd.fragment.FA_pC2_pNH2 attribute) (lipyd.fragment.FA_pC2_pNH2_mO attribute) (lipyd.fragment.FA_pC2_pNH2_pO attribute) (lipyd.fragment.FA_pC2_pN_mO attribute) (lipyd.fragment.FA_pC3H2_pNH2 attribute) (lipyd.fragment.FA_pGlycerol_mOH attribute) (lipyd.fragment.FA_pN attribute) (lipyd.fragment.FA_pNH2_mH2O_mH attribute) (lipyd.fragment.FA_pNH2_mO attribute) (lipyd.fragment.FA_pNH_pC2H2_mOH attribute) (lipyd.fragment.FA_pO_mH attribute) (lipyd.fragment.FragConstraint attribute) (lipyd.fragment.LysoPA attribute) (lipyd.fragment.LysoPAAlkyl attribute) (lipyd.fragment.LysoPA_mH2O attribute) (lipyd.fragment.LysoPC attribute) (lipyd.fragment.LysoPCAlkyl attribute) (lipyd.fragment.LysoPE attribute) (lipyd.fragment.LysoPEAlkyl attribute) (lipyd.fragment.LysoPEAlkyl_mH2O attribute) (lipyd.fragment.LysoPG attribute) (lipyd.fragment.LysoPGAlkyl attribute) (lipyd.fragment.LysoPG_mH2O attribute) (lipyd.fragment.LysoPI attribute) (lipyd.fragment.LysoPIAlkyl attribute) (lipyd.fragment.LysoPI_mH2O attribute) (lipyd.fragment.NLFA attribute) (lipyd.fragment.NLFA_m2xH2O attribute) (lipyd.fragment.NLFA_mH2O attribute) (lipyd.fragment.NLFA_pNH3 attribute) (lipyd.fragment.NLFA_pOH attribute) (lipyd.fragment.Sph_m2xH2O_mH attribute) (lipyd.fragment.Sph_m2xH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_m2xH2O_pCH3 attribute) (lipyd.fragment.Sph_m2xH2O_pH attribute) (lipyd.fragment.Sph_mC2H2_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mC2H3_mNH2_mOH attribute) (lipyd.fragment.Sph_mC2H4_m3H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_m2H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_mH2O attribute) (lipyd.fragment.Sph_mCH2_m3H attribute) (lipyd.fragment.Sph_mCH2_mH2O_mH attribute) (lipyd.fragment.Sph_mCH2_mNH2_m4H attribute) (lipyd.fragment.Sph_mCH2_mOH attribute) (lipyd.fragment.Sph_mC_m2xH2O attribute) (lipyd.fragment.Sph_mC_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mH2O_mH attribute) (lipyd.fragment.Sph_mH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_mH2O_pCH3 attribute) (lipyd.fragment.Sph_mH2O_pH attribute) (lipyd.fragment.Sph_mH_N attribute) (lipyd.fragment.Sph_mH_P attribute) (lipyd.fragment.Sph_mNH2_m3H attribute) (lipyd.fragment.Sph_mNH2_mH2O_m2H attribute) (lipyd.fragment.Sph_mNH2_mOH attribute) (lipyd.fragment.Sph_mO_mH2O_pCH3_pH attribute) (lipyd.fragment.Sph_mO_pH attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3 attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pH2O attribute) (lipyd.fragment.Sph_pC2_pOH attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3 attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pH2O attribute) (lipyd.fragment.Sph_pH attribute) (lipyd.fragment.Sph_pH2O_mH attribute) (lipyd.fragment.Sph_pO attribute) (lipyd.fragment.Sph_pPCh_mCH3 attribute) (lipyd.ms2.ChainFragment attribute) charge (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.fragment.ChainFragParam attribute) charge_filter() (lipyd.sample.Sample method) charge_str() (in module lipyd.lipproc) (lipyd.fragment.FattyFragment method) (lipyd.fragment.FattyFragmentOld method)

charges() (lipyd.sample.FeatureAttributes method) check_lyso() (lipyd.ms2.AbstractMS2Identifier method) class_methods (lipyd.ms2.AbstractMS2Identifier attribute) (lipyd.ms2.Cer_Negative attribute) (lipyd.ms2.Cer_Positive attribute) (lipyd.ms2.GL_Positive attribute) class_name() (lipyd.lipid.SphingolipidFactory method) close_gzfile() (lipyd.moldb.SwissLipids method) close_logfile() (lipyd.log.Logger method) close_plainfile() (lipyd.moldb.SwissLipids method) col (lipyd.sec.Fraction attribute) collapse_attrs() (in module lipyd.lipproc) collect_mgf() (lipyd.sample.Sample method) collect_ms2() (lipyd.sample.Sample method) (lipyd.sample.SampleSet method) collect_mzml() (lipyd.sample.Sample method) combine_attrs() (in module lipyd.lipproc) combine_samples() (lipyd.sample.SampleSet class method) confirm_chains_explicit() (lipyd.ms2.AbstractMS2Identifier method) (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) confirm_chains_implicit() (lipyd.ms2.AbstractMS2Identifier method) confirm_class() (lipyd.ms2.AbstractMS2Identifier method) (lipyd.ms2.BMP_Positive method) (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) (lipyd.ms2.DAG_Negative method) (lipyd.ms2.DAG_Positive method) (lipyd.ms2.FA_Negative method) (lipyd.ms2.FA_Positive method) (lipyd.ms2.GL_Negative method) (lipyd.ms2.GL_Positive method) (lipyd.ms2.LysoPC_Positive method) (lipyd.ms2.LysoPE_Positive method) (lipyd.ms2.PA_Negative method) (lipyd.ms2.PA_Positive method) (lipyd.ms2.PC_Negative method) (lipyd.ms2.PC_Positive method) (lipyd.ms2.PE_Negative method) (lipyd.ms2.PE_Positive method) (lipyd.ms2.PG_Negative method) (lipyd.ms2.PG_Positive method) (lipyd.ms2.PI_Negative method) (lipyd.ms2.PI_Positive method) (lipyd.ms2.PS_Negative method) (lipyd.ms2.PS_Positive method) (lipyd.ms2.TAG_Negative method) (lipyd.ms2.TAG_Positive method) (lipyd.ms2.VA_Negative method) (lipyd.ms2.VA_Positive method) confirm_subclass() (lipyd.ms2.AbstractMS2Identifier method) constraints (lipyd.fragment.ChainFragParam attribute) (lipyd.fragment.FA attribute) (lipyd.fragment.FAL_mH attribute) (lipyd.fragment.FA_m3H attribute) (lipyd.fragment.FA_mCO_m3H attribute) (lipyd.fragment.FA_mH attribute) (lipyd.fragment.FA_mH2O attribute) (lipyd.fragment.FA_mH2O_mH attribute) (lipyd.fragment.FA_mH2O_mOH attribute) (lipyd.fragment.FA_mOH attribute) (lipyd.fragment.FA_mO_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2_pO attribute) (lipyd.fragment.FA_pC2H3_pNH2_m2H attribute) (lipyd.fragment.FA_pC2_pNH2 attribute) (lipyd.fragment.FA_pC2_pNH2_mO attribute) (lipyd.fragment.FA_pC2_pNH2_pO attribute) (lipyd.fragment.FA_pC2_pN_mO attribute) (lipyd.fragment.FA_pC3H2_pNH2 attribute) (lipyd.fragment.FA_pGlycerol_mOH attribute) (lipyd.fragment.FA_pN attribute) (lipyd.fragment.FA_pNH2_mH2O_mH attribute) (lipyd.fragment.FA_pNH2_mO attribute) (lipyd.fragment.FA_pNH_pC2H2_mOH attribute) (lipyd.fragment.FA_pO_mH attribute) (lipyd.fragment.LysoPA attribute) (lipyd.fragment.LysoPAAlkyl attribute) (lipyd.fragment.LysoPA_mH2O attribute) (lipyd.fragment.LysoPC attribute) (lipyd.fragment.LysoPCAlkyl attribute) (lipyd.fragment.LysoPE attribute) (lipyd.fragment.LysoPEAlkyl attribute) (lipyd.fragment.LysoPEAlkyl_mH2O attribute) (lipyd.fragment.LysoPG attribute) (lipyd.fragment.LysoPGAlkyl attribute) (lipyd.fragment.LysoPG_mH2O attribute) (lipyd.fragment.LysoPI attribute) (lipyd.fragment.LysoPIAlkyl attribute) (lipyd.fragment.LysoPI_mH2O attribute) (lipyd.fragment.NLFA attribute) (lipyd.fragment.NLFA_m2xH2O attribute) (lipyd.fragment.NLFA_mH2O attribute) (lipyd.fragment.NLFA_pNH3 attribute) (lipyd.fragment.NLFA_pOH attribute) (lipyd.fragment.Sph_m2xH2O_mH attribute) (lipyd.fragment.Sph_m2xH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_m2xH2O_pCH3 attribute) (lipyd.fragment.Sph_m2xH2O_pH attribute) (lipyd.fragment.Sph_mC2H2_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mC2H3_mNH2_mOH attribute) (lipyd.fragment.Sph_mC2H4_m3H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_m2H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_mH2O attribute) (lipyd.fragment.Sph_mCH2_m3H attribute) (lipyd.fragment.Sph_mCH2_mH2O_mH attribute) (lipyd.fragment.Sph_mCH2_mNH2_m4H attribute) (lipyd.fragment.Sph_mCH2_mOH attribute) (lipyd.fragment.Sph_mC_m2xH2O attribute) (lipyd.fragment.Sph_mC_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mH2O_mH attribute) (lipyd.fragment.Sph_mH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_mH2O_pCH3 attribute) (lipyd.fragment.Sph_mH2O_pH attribute) (lipyd.fragment.Sph_mH_N attribute) (lipyd.fragment.Sph_mH_P attribute) (lipyd.fragment.Sph_mNH2_m3H attribute) (lipyd.fragment.Sph_mNH2_mH2O_m2H attribute) (lipyd.fragment.Sph_mNH2_mOH attribute) (lipyd.fragment.Sph_mO_mH2O_pCH3_pH attribute) (lipyd.fragment.Sph_mO_pH attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3 attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pH2O attribute) (lipyd.fragment.Sph_pC2_pOH attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3 attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pH2O attribute) (lipyd.fragment.Sph_pH attribute) (lipyd.fragment.Sph_pH2O_mH attribute) (lipyd.fragment.Sph_pO attribute) (lipyd.fragment.Sph_pPCh_mCH3 attribute) constraints() (in module lipyd.fragdb) convert() (lipyd.sample.FeatureIdx method) cu_by_type() (lipyd.ms2.Scan method) cu_complete() (lipyd.ms2.Scan method) cu_str() (in module lipyd.lipproc) (lipyd.fragment.FattyFragment method) current() (lipyd.sample.FeatureIdx method)

D

dag_neg_1() (lipyd.ms2.MS2Scan method) DAG_Negative (class in lipyd.ms2) dag_pos_1() (lipyd.ms2.MS2Scan method) DAG_Positive (class in lipyd.ms2) database_lookup() (lipyd.sample.Sample method) db (lipyd.lipproc.LipidLabel attribute) db_id (lipyd.lipproc.LipidLabel attribute) default_args (lipyd.fragdb.FragmentDatabaseAggregator attribute) delEmpty() (in module lipyd.common) deltart (lipyd.ms2.ScanDetails attribute) DGCC (class in lipyd.lipid) dgcc() (lipyd.ms2.GL_Positive method) DGDG (class in lipyd.lipid)

dgdg() (lipyd.ms2.GL_Positive method) DGTA (class in lipyd.lipid) DGTS (class in lipyd.lipid) dgts() (lipyd.ms2.GL_Positive method) DiacylGlycerol (class in lipyd.lipid) DihexosylCeramideD (class in lipyd.lipid) DihexosylCeramideDihydro (class in lipyd.lipid) DihexosylCeramideT (class in lipyd.lipid) DihydroSphingosine (class in lipyd.substituent) DimethylSphingosineD (class in lipyd.lipid) DimethylSphingosineDihydro (class in lipyd.lipid) DimethylSphingosineT (class in lipyd.lipid) docs (lipyd.fragment.FattyFragmentFactory attribute)

E

e (in module lipyd.mass) electron (in module lipyd.mass) empty_chain() (in module lipyd.lipproc) empty_chainsum() (in module lipyd.lipproc) end (lipyd.sec.Fraction attribute) ether (lipyd.lipproc.ChainAttr attribute) EtherBMP (class in lipyd.lipid) EtherPA (class in lipyd.lipid) EtherPC (class in lipyd.lipid) EtherPE (class in lipyd.lipid) EtherPG (class in lipyd.lipid)

EtherPGP (class in lipyd.lipid) EtherPI (class in lipyd.lipid) EtherPIP (class in lipyd.lipid) EtherPIP2 (class in lipyd.lipid) EtherPIP3 (class in lipyd.lipid) EtherPS (class in lipyd.lipid) export_db() (lipyd.moldb.MoleculeDatabaseAggregator method) export_db_lipidblast() (lipyd.moldb.MoleculeDatabaseAggregator method) export_df() (lipyd.results.Results static method) export_names() (lipyd.moldb.SwissLipids method) export_table() (lipyd.sample.Sample method) expr() (in module lipyd.mass)

F

FA (class in lipyd.fragment) fa_among_most_abundant() (lipyd.ms2.MS2Scan method) fa_cc_agrees_ms1() (lipyd.ms2.MS2Scan method) fa_cc_among_most_abundant() (lipyd.ms2.MS2Scan method) fa_ccs_agree_ms1() (lipyd.ms2.MS2Scan method) fa_combinations() (lipyd.ms2.MS2Scan method) fa_combinations3() (lipyd.ms2.MS2Scan method) fa_combinations_old() (lipyd.ms2.MS2Scan method) fa_combinations_preprocess() (lipyd.ms2.MS2Scan method) fa_combinations_tuples() (lipyd.ms2.MS2Scan method) fa_greek_cc() (lipyd.name.LipidNameProcessor method) FA_m3H (class in lipyd.fragment) FA_mCO_m3H (class in lipyd.fragment) FA_mH (class in lipyd.fragment) FA_mH2O (class in lipyd.fragment) FA_mH2O_mH (class in lipyd.fragment) FA_mH2O_mOH (class in lipyd.fragment) FA_mO_pNH2 (class in lipyd.fragment) FA_mOH (class in lipyd.fragment) fa_neg_1() (lipyd.ms2.MS2Scan method) FA_Negative (class in lipyd.ms2) FA_pC2_pN_mO (class in lipyd.fragment) FA_pC2_pNH2 (class in lipyd.fragment) FA_pC2_pNH2_mO (class in lipyd.fragment) FA_pC2_pNH2_pO (class in lipyd.fragment) FA_pC2H2_pNH2 (class in lipyd.fragment) FA_pC2H2_pNH2_pO (class in lipyd.fragment) FA_pC2H3_pNH2_m2H (class in lipyd.fragment) FA_pC3H2_pNH2 (class in lipyd.fragment) fa_percent_of_most_abundant() (lipyd.ms2.MS2Scan method) FA_pGlycerol_mOH (class in lipyd.fragment) FA_pN (class in lipyd.fragment) FA_pNH2_mH2O_mH (class in lipyd.fragment) FA_pNH2_mO (class in lipyd.fragment) FA_pNH_pC2H2_mOH (class in lipyd.fragment) FA_pO_mH (class in lipyd.fragment) fa_pos_1() (lipyd.ms2.MS2Scan method) FA_Positive (class in lipyd.ms2) fa_type_is() (lipyd.ms2.MS2Scan method) FAFragSeries (class in lipyd.fragment) FAL_mH (class in lipyd.fragment) family (lipyd.fragment.FragConstraint attribute) fatty_acyl() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) FattyAcid (class in lipyd.lipid) FattyAcyl (class in lipyd.substituent)

FattyAlkoxy (class in lipyd.substituent) FattyFragment (class in lipyd.fragment) FattyFragmentFactory (class in lipyd.fragment) FattyFragmentOld (class in lipyd.fragment) feature_data() (lipyd.sample.FeatureBase method) (lipyd.sample.Sample method) FeatureAnalyzer (class in lipyd.feature) FeatureAttributes (class in lipyd.sample) FeatureBase (class in lipyd.sample) FeatureIdx (class in lipyd.sample) FeatureSelection (class in lipyd.sample) figdpi (lipyd.plot.SpectrumPlot attribute) filetype (lipyd.plot.SpectrumPlot attribute) filter() (lipyd.sample.FeatureBase method) filter_selection() (lipyd.sample.FeatureBase method) find() (in module lipyd.lookup) findall() (in module lipyd.lookup) first_isotope_mass() (in module lipyd.mass) first_record() (lipyd.ms2.Scan method) flatList() (in module lipyd.common) flush() (lipyd.log.Logger method) Formula (class in lipyd.formula) formula (lipyd.lipproc.LipidLabel attribute) formula2atoms() (in module lipyd.formula) formula2counts() (lipyd.fragment.AdductCalculator method) formula_from_dict() (lipyd.mass.MassBase method) Fraction (class in lipyd.sec) fraction_mean() (lipyd.sec.SECReader method) frag_name_present() (lipyd.ms2.MS2Scan method) FragConstraint (class in lipyd.fragment) fragment_among_most_abundant() (lipyd.ms2.Scan method) fragment_by_name() (lipyd.ms2.Scan method) fragment_percent_of_most_abundant() (lipyd.ms2.Scan method) FragmentAnnotation (class in lipyd.fragdb) FragmentAnnotator (class in lipyd.fragdb) FragmentDatabaseAggregator (class in lipyd.fragdb) fragments_by_chain_type() (lipyd.ms2.Scan method) frags_for_positions() (lipyd.ms2.Scan method) fragtype (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.ms2.ChainFragment attribute) (lipyd.ms2.ChainIdentificationDetails attribute) from_mgf() (lipyd.ms2.Scan class method) full_list_str() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) full_str() (in module lipyd.lipproc) (lipyd.lipproc.LipidRecord method) (lipyd.ms2.MS2Identity method)

G

gen_fa_greek() (lipyd.name.LipidNameProcessor method) gen_session_id() (lipyd.session.Session static method) generate_massspectra_plot_automatic_labels() (lipyd.plot.SpectrumPlot method) generate_massspectra_two_plot_manual_annotation() (lipyd.plot.SpectrumPlot method) generate_series() (lipyd.fragdb.FragmentDatabaseAggregator method) get() (in module lipyd.settings) get_annot() (lipyd.ms2.ScanBase method) get_attributes() (in module lipyd.lipproc) (lipyd.sample.SampleReader method) get_by_rank() (lipyd.ms2.MS2Scan method) get_cc() (lipyd.ms2.MS2Scan method) get_chain() (lipyd.metabolite.AbstractSubstituent method) get_constraints() (lipyd.fragdb.FragmentDatabaseAggregator method) get_database_records() (lipyd.sample.Sample method) get_db() (in module lipyd.fragdb) (in module lipyd.moldb) get_default() (in module lipyd.settings) get_default_file() (lipyd.fragdb.FragmentDatabaseAggregator method) get_desc() (lipyd.progress.Progress method) get_fa_combinations() (lipyd.ms2.MS2Scan method) get_file() (lipyd.mgf.MgfReader method) get_fraction() (lipyd.sec.SECReader method) get_fragline() (lipyd.fragment.FattyFragmentOld method) get_header_div() (lipyd.ms2.MS2FeatureOld method) get_hg() (lipyd.moldb.SwissLipids method) (lipyd.ms2.MS2Scan method) get_hg_obmol() (lipyd.moldb.SwissLipids method) get_intensity() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) get_isomer() (lipyd.moldb.SwissLipids method) get_isomer_obmol() (lipyd.moldb.SwissLipids method) get_log() (in module lipyd.session) get_logdir() (lipyd.log.Logger method) get_mass() (in module lipyd.mass) get_mol() (lipyd.sdf.SdfReader static method) get_most_abundant_chain() (lipyd.ms2.Scan method) get_most_abundant_fa() (lipyd.ms2.MS2Scan method) get_ms1_records() (lipyd.ms2.Scan method) get_name() (lipyd.fragment.FattyFragment method) get_nl_intensity() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method)

get_obmol() (lipyd.moldb.SwissLipids method) (lipyd.sdf.SdfReader method) get_prefix() (lipyd.metabolite.AbstractSubstituent method) (lipyd.substituent.Sphingosine method) get_record() (lipyd.moldb.SwissLipids method) (lipyd.sdf.SdfReader method) get_sample() (lipyd.sample.SampleSet method) get_sample_attrs() (lipyd.sample.SampleSet method) get_sample_data() (lipyd.sample.SampleSet method) get_sample_id() (lipyd.sampleattrs.SampleSetAttrs method) get_sample_index() (lipyd.sampleattrs.SampleSetAttrs method) get_samples() (lipyd.sample.SampleReader method) get_sampleset() (lipyd.sample.SampleReader method) get_scan() (lipyd.mgf.MgfReader method) get_scans() (lipyd.mgf.MgfReader method) get_selection() (lipyd.sample.SampleSet method) (lipyd.sampleattrs.SampleSorter method) get_series_args() (lipyd.fragdb.FragmentDatabaseAggregator method) get_session() (in module lipyd.session) get_species() (lipyd.moldb.SwissLipids method) get_species_obmol() (lipyd.moldb.SwissLipids method) get_subspec() (lipyd.moldb.SwissLipids method) get_subspec_obmol() (lipyd.moldb.SwissLipids method) get_substituent() (lipyd.metabolite.AbstractMetabolite static method) get_type() (lipyd.name.LipidNameProcessor static method) get_url() (lipyd.moldb.MoleculeDatabaseAggregator static method) get_weight() (in module lipyd.mass) getFreqIso() (in module lipyd.mass) getMasses() (in module lipyd.mass) getMassFirstIso() (in module lipyd.mass) getMassMonoIso() (in module lipyd.mass) getname() (lipyd.formula.Formula method) getWeightStd() (in module lipyd.mass) gl_class_name() (lipyd.lipid.GlycerolipidFactory static method) GL_Negative (class in lipyd.ms2) GL_Positive (class in lipyd.ms2) GlycerolipidFactory (class in lipyd.lipid) gpl_class_name() (lipyd.lipid.GlycerolipidFactory static method) guess_format() (lipyd.sec.SECReader method) guess_ionmode() (in module lipyd.common) guess_resouce_type() (lipyd.ms2.MS2Feature static method)

H

has_chain_combination() (lipyd.ms2.Scan method) has_chain_combinations() (lipyd.ms2.Scan method) has_chain_fragment_type() (lipyd.ms2.Scan method) has_formula() (lipyd.mass.MassBase method) has_fragment() (lipyd.ms2.Scan method) has_mass() (lipyd.mass.MassBase method) has_mz() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) has_nl() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) has_sph_prefix() (lipyd.name.LipidNameProcessor static method) has_variable_aliphatic_chain() (lipyd.metabolite.AbstractMetabolite method) Headgroup (class in lipyd.lipproc) headgroup_from_lipid_name() (lipyd.name.LipidNameProcessor method) headgroups_cross_screening() (lipyd.results.Results method) hex2cer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) hexcer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) hexcer_chain_combination() (lipyd.ms2.Cer_Positive method) hexcer_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) hexcer_pos_1() (lipyd.ms2.MS2Scan method) hexceroh_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) hexceroh_pos_1() (lipyd.ms2.MS2Scan method) HexosylCeramideD (class in lipyd.lipid) HexosylCeramideDihydro (class in lipyd.lipid) HexosylCeramideT (class in lipyd.lipid) hg (lipyd.fragment.FragConstraint attribute) highest_fragment_by_chain_type() (lipyd.ms2.Scan method) html_table() (lipyd.ms2.MS2FeatureOld method) (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) html_table_b64() (lipyd.ms2.MS2FeatureOld method) HydroxyacylCeramideD (class in lipyd.lipid) HydroxyacylCeramideD1OAcyl (class in lipyd.lipid) HydroxyacylCeramideDihydro (class in lipyd.lipid) HydroxyacylCeramideDihydro1OAcyl (class in lipyd.lipid) HydroxyacylCeramideDihydroPE (class in lipyd.lipid) HydroxyacylCeramideDihydroPhosphate (class in lipyd.lipid)

HydroxyacylCeramideDPE (class in lipyd.lipid) HydroxyacylCeramideDPhosphate (class in lipyd.lipid) HydroxyacylCeramideT (class in lipyd.lipid) HydroxyacylCeramideT1OAcyl (class in lipyd.lipid) HydroxyacylCeramideTPE (class in lipyd.lipid) HydroxyacylCeramideTPhosphate (class in lipyd.lipid) HydroxyacylDihexosylCeramideD (class in lipyd.lipid) HydroxyacylDihexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylDihexosylCeramideT (class in lipyd.lipid) HydroxyacylHexosylCeramideD (class in lipyd.lipid) HydroxyacylHexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylHexosylCeramideT (class in lipyd.lipid) HydroxyacylLysoCeramideDihydroPE (class in lipyd.lipid) HydroxyacylLysoCeramideDPE (class in lipyd.lipid) HydroxyacylLysoCeramideTPE (class in lipyd.lipid) HydroxyacylLysoDihexosylCeramideD (class in lipyd.lipid) HydroxyacylLysoDihexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylLysoDihexosylCeramideT (class in lipyd.lipid) HydroxyacylLysoHexosylCeramideD (class in lipyd.lipid) HydroxyacylLysoHexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylLysoHexosylCeramideT (class in lipyd.lipid) HydroxyacylLysoSphingomyelinD (class in lipyd.lipid) HydroxyacylLysoSphingomyelinDihydro (class in lipyd.lipid) HydroxyacylLysoSphingomyelinT (class in lipyd.lipid) HydroxyacylLysoSulfoDihexosylCeramideD (class in lipyd.lipid) HydroxyacylLysoSulfoDihexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylLysoSulfoDihexosylCeramideT (class in lipyd.lipid) HydroxyacylLysoSulfoHexosylCeramideD (class in lipyd.lipid) HydroxyacylLysoSulfoHexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylLysoSulfoHexosylCeramideT (class in lipyd.lipid) HydroxyacylSphingomyelinD (class in lipyd.lipid) HydroxyacylSphingomyelinDihydro (class in lipyd.lipid) HydroxyacylSphingomyelinT (class in lipyd.lipid) HydroxyacylSulfoDihexosylCeramideD (class in lipyd.lipid) HydroxyacylSulfoDihexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylSulfoDihexosylCeramideT (class in lipyd.lipid) HydroxyacylSulfoHexosylCeramideD (class in lipyd.lipid) HydroxyacylSulfoHexosylCeramideDihydro (class in lipyd.lipid) HydroxyacylSulfoHexosylCeramideT (class in lipyd.lipid) HydroxyFattyAcyl (class in lipyd.substituent) HydroxySphingosine (class in lipyd.substituent)

I

i (lipyd.ms2.ChainFragment attribute) (lipyd.ms2.ChainIdentificationDetails attribute) i_by_id() (lipyd.mgf.MgfReader method) id_next() (lipyd.sampleattrs.SampleSorter method) id_previous() (lipyd.sampleattrs.SampleSorter method) identify() (lipyd.ms2.AbstractMS2Identifier method) (lipyd.ms2.MS2Feature method) (lipyd.ms2.MS2FeatureOld method) (lipyd.ms2.Scan method) identify2() (lipyd.ms2.MS2FeatureOld method) identities_str() (lipyd.ms2.MS2Scan method) identity_summary() (lipyd.ms2.MS2Feature method) ilookup() (lipyd.moldb.MoleculeDatabaseAggregator method) in_ipython() (lipyd.progress.OldProgress method) index() (lipyd.mgf.MgfReader method) (lipyd.sdf.SdfReader method) index_info() (lipyd.sdf.SdfReader method) index_next() (lipyd.sampleattrs.SampleSorter method) index_previous() (lipyd.sampleattrs.SampleSorter method) init_counts() (lipyd.fragment.AdductCalculator method) init_db() (in module lipyd.fragdb) (in module lipyd.moldb) init_name_processor() (lipyd.moldb.SwissLipids method) init_rebuild() (lipyd.moldb.MoleculeDatabaseAggregator method) init_tqdm() (lipyd.progress.Progress method) intensity (lipyd.ms2.ChainFragment attribute) intensity_filter() (lipyd.sample.Sample method) intensity_ratios() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) intensity_sorted (class in lipyd.ms2) ionmode (lipyd.fragment.FA attribute) (lipyd.fragment.FAL_mH attribute) (lipyd.fragment.FA_m3H attribute) (lipyd.fragment.FA_mCO_m3H attribute) (lipyd.fragment.FA_mH attribute) (lipyd.fragment.FA_mH2O attribute) (lipyd.fragment.FA_mH2O_mH attribute) (lipyd.fragment.FA_mH2O_mOH attribute) (lipyd.fragment.FA_mOH attribute) (lipyd.fragment.FA_mO_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2_pO attribute) (lipyd.fragment.FA_pC2H3_pNH2_m2H attribute) (lipyd.fragment.FA_pC2_pNH2 attribute) (lipyd.fragment.FA_pC2_pNH2_mO attribute) (lipyd.fragment.FA_pC2_pNH2_pO attribute) (lipyd.fragment.FA_pC2_pN_mO attribute) (lipyd.fragment.FA_pC3H2_pNH2 attribute) (lipyd.fragment.FA_pGlycerol_mOH attribute) (lipyd.fragment.FA_pN attribute) (lipyd.fragment.FA_pNH2_mH2O_mH attribute) (lipyd.fragment.FA_pNH2_mO attribute) (lipyd.fragment.FA_pNH_pC2H2_mOH attribute) (lipyd.fragment.FA_pO_mH attribute) (lipyd.fragment.LysoPA attribute) (lipyd.fragment.LysoPAAlkyl attribute) (lipyd.fragment.LysoPA_mH2O attribute) (lipyd.fragment.LysoPC attribute) (lipyd.fragment.LysoPCAlkyl attribute) (lipyd.fragment.LysoPE attribute) (lipyd.fragment.LysoPEAlkyl attribute) (lipyd.fragment.LysoPEAlkyl_mH2O attribute) (lipyd.fragment.LysoPG attribute) (lipyd.fragment.LysoPGAlkyl attribute) (lipyd.fragment.LysoPG_mH2O attribute) (lipyd.fragment.LysoPI attribute) (lipyd.fragment.LysoPIAlkyl attribute) (lipyd.fragment.LysoPI_mH2O attribute) (lipyd.fragment.NLFA attribute) (lipyd.fragment.NLFA_m2xH2O attribute) (lipyd.fragment.NLFA_mH2O attribute) (lipyd.fragment.NLFA_pNH3 attribute) (lipyd.fragment.NLFA_pOH attribute) (lipyd.fragment.Sph_m2xH2O_mH attribute) (lipyd.fragment.Sph_m2xH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_m2xH2O_pCH3 attribute) (lipyd.fragment.Sph_m2xH2O_pH attribute) (lipyd.fragment.Sph_mC2H2_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mC2H3_mNH2_mOH attribute) (lipyd.fragment.Sph_mC2H4_m3H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_m2H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_mH2O attribute) (lipyd.fragment.Sph_mCH2_m3H attribute) (lipyd.fragment.Sph_mCH2_mH2O_mH attribute) (lipyd.fragment.Sph_mCH2_mNH2_m4H attribute) (lipyd.fragment.Sph_mCH2_mOH attribute) (lipyd.fragment.Sph_mC_m2xH2O attribute) (lipyd.fragment.Sph_mC_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mH2O_mH attribute) (lipyd.fragment.Sph_mH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_mH2O_pCH3 attribute) (lipyd.fragment.Sph_mH2O_pH attribute) (lipyd.fragment.Sph_mH_N attribute) (lipyd.fragment.Sph_mH_P attribute) (lipyd.fragment.Sph_mNH2_m3H attribute) (lipyd.fragment.Sph_mNH2_mH2O_m2H attribute) (lipyd.fragment.Sph_mNH2_mOH attribute) (lipyd.fragment.Sph_mO_mH2O_pCH3_pH attribute) (lipyd.fragment.Sph_mO_pH attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3 attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pH2O attribute) (lipyd.fragment.Sph_pC2_pOH attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3 attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pH2O attribute) (lipyd.fragment.Sph_pH attribute) (lipyd.fragment.Sph_pH2O_mH attribute) (lipyd.fragment.Sph_pO attribute) (lipyd.fragment.Sph_pPCh_mCH3 attribute)

is_chain() (lipyd.ms2.Scan method) is_chain_type() (lipyd.ms2.Scan method) is_ether() (lipyd.name.LipidNameProcessor static method) is_fa() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) is_fal() (lipyd.ms2.Scan method) is_pa() (lipyd.ms2.MS2Scan method) is_pc() (lipyd.ms2.MS2Scan method) is_pe() (lipyd.ms2.MS2Scan method) is_pg() (lipyd.ms2.MS2Scan method) is_ps() (lipyd.ms2.MS2Scan method) is_sph() (lipyd.ms2.Scan method) is_type() (lipyd.ms2.Scan method) isomer_str() (lipyd.lipproc.Chain method) isomeric_carbon_counts() (lipyd.name.LipidNameProcessor method) isotope_mass() (in module lipyd.mass) iter_obmol() (lipyd.sdf.SdfReader method) iter_records() (lipyd.sdf.SdfReader method) iterator_insert() (in module lipyd.common) iterfile() (lipyd.moldb.SwissLipids method) iterfraglines() (lipyd.fragment.FAFragSeries method) (lipyd.fragment.FattyFragment method) iterlines() (lipyd.metabolite.AbstractMetabolite method) itermass() (lipyd.fragment.FAFragSeries method) itermol() (lipyd.moldb.SwissLipids method) iterrecords() (lipyd.ms2.Scan method) iterrows() (lipyd.moldb.Reader method) iterscans() (lipyd.ms2.MS2Feature method) itersubs() (lipyd.metabolite.AbstractMetabolite method) itersum() (lipyd.metabolite.AbstractMetabolite method)

L

lcb_name (lipyd.lipid.SphingolipidFactory attribute) LipidLabel (class in lipyd.lipproc) LipidMaps (class in lipyd.moldb) LipidNameProcessor (class in lipyd.name) LipidRecord (class in lipyd.lipproc) lipyd (module) lipyd.common (module) lipyd.data (module) lipyd.data.ms2_examples (module) lipyd.feature (module) lipyd.formula (module) lipyd.fragdb (module) lipyd.fragment (module) lipyd.lipid (module) lipyd.lipproc (module) lipyd.log (module) lipyd.lookup (module) lipyd.mass (module) lipyd.metabolite (module) lipyd.mgf (module) lipyd.moldb (module) lipyd.ms2 (module) lipyd.mz (module) lipyd.mzml (module) lipyd.name (module) lipyd.plot (module) lipyd.progress (module) lipyd.results (module) lipyd.sample (module) lipyd.sampleattrs (module) lipyd.sdf (module) lipyd.sec (module) lipyd.session (module) lipyd.settings (module) lipyd.substituent (module) load() (lipyd.moldb.SwissLipids method) load_databases() (lipyd.moldb.MoleculeDatabaseAggregator method) Logger (class in lipyd.log) logical_and() (lipyd.sampleattrs.SampleSelection method) logical_not() (lipyd.sampleattrs.SampleSelection method) logical_or() (lipyd.sampleattrs.SampleSelection method) lookup() (in module lipyd.fragdb) (in module lipyd.moldb) (lipyd.fragdb.FragmentDatabaseAggregator method) (lipyd.mgf.MgfReader method) (lipyd.moldb.MoleculeDatabaseAggregator method) lookup_accuracy() (lipyd.moldb.MoleculeDatabaseAggregator method) lookup_neg() (in module lipyd.fragdb) lookup_neg_nl() (in module lipyd.fragdb) lookup_nl() (in module lipyd.fragdb) (lipyd.fragdb.FragmentDatabaseAggregator method) lookup_pos() (in module lipyd.fragdb) lookup_pos_nl() (in module lipyd.fragdb) lookup_scan_ids() (lipyd.mgf.MgfReader method) LysoBMP (class in lipyd.lipid) LysoCeramideDihydroPE (class in lipyd.lipid) LysoCeramideDPE (class in lipyd.lipid) LysoCeramideTPE (class in lipyd.lipid) LysoDGCC (class in lipyd.lipid)

LysoDGDG (class in lipyd.lipid) LysoDGTA (class in lipyd.lipid) LysoDGTS (class in lipyd.lipid) LysoDihexosylCeramideD (class in lipyd.lipid) LysoDihexosylCeramideDihydro (class in lipyd.lipid) LysoDihexosylCeramideT (class in lipyd.lipid) LysoEtherBMP (class in lipyd.lipid) LysoEtherPA (class in lipyd.lipid) LysoEtherPC (class in lipyd.lipid) LysoEtherPE (class in lipyd.lipid) LysoEtherPG (class in lipyd.lipid) LysoEtherPGP (class in lipyd.lipid) LysoEtherPI (class in lipyd.lipid) LysoEtherPIP (class in lipyd.lipid) LysoEtherPIP2 (class in lipyd.lipid) LysoEtherPIP3 (class in lipyd.lipid) LysoEtherPS (class in lipyd.lipid) LysoHexosylCeramideD (class in lipyd.lipid) LysoHexosylCeramideDihydro (class in lipyd.lipid) LysoHexosylCeramideT (class in lipyd.lipid) LysoMGDG (class in lipyd.lipid) LysoPA (class in lipyd.fragment) (class in lipyd.lipid) LysoPA_mH2O (class in lipyd.fragment) LysoPAAlkyl (class in lipyd.fragment) LysoPC (class in lipyd.fragment) (class in lipyd.lipid) lysopc_pos_1() (lipyd.ms2.MS2Scan method) LysoPC_Positive (class in lipyd.ms2) LysoPCAlkyl (class in lipyd.fragment) LysoPE (class in lipyd.fragment) (class in lipyd.lipid) lysope_neg_1() (lipyd.ms2.MS2Scan method) lysope_pos_1() (lipyd.ms2.MS2Scan method) LysoPE_Positive (class in lipyd.ms2) LysoPEAlkyl (class in lipyd.fragment) LysoPEAlkyl_mH2O (class in lipyd.fragment) LysoPG (class in lipyd.fragment) (class in lipyd.lipid) LysoPG_mH2O (class in lipyd.fragment) LysoPGAlkyl (class in lipyd.fragment) LysoPGP (class in lipyd.lipid) LysoPI (class in lipyd.fragment) (class in lipyd.lipid) LysoPI_mH2O (class in lipyd.fragment) LysoPIAlkyl (class in lipyd.fragment) LysoPIP (class in lipyd.lipid) LysoPIP2 (class in lipyd.lipid) LysoPIP3 (class in lipyd.lipid) LysoPS (class in lipyd.lipid) LysoSphingomyelinD (class in lipyd.lipid) LysoSphingomyelinDihydro (class in lipyd.lipid) LysoSphingomyelinT (class in lipyd.lipid) LysoSQDG (class in lipyd.lipid) LysoSulfoDihexosylCeramideD (class in lipyd.lipid) LysoSulfoDihexosylCeramideDihydro (class in lipyd.lipid) LysoSulfoDihexosylCeramideT (class in lipyd.lipid) LysoSulfoHexosylCeramideD (class in lipyd.lipid) LysoSulfoHexosylCeramideDihydro (class in lipyd.lipid) LysoSulfoHexosylCeramideT (class in lipyd.lipid)

M

m1() (lipyd.ms2.Cer_Positive method) m2() (lipyd.ms2.Cer_Positive method) m3() (lipyd.ms2.Cer_Positive method) main (lipyd.lipproc.Headgroup attribute) main() (lipyd.ms2.MS2Feature method) make_index() (lipyd.moldb.SwissLipids method) make_selection() (lipyd.sampleattrs.SampleSorter method) manual_df() (lipyd.results.Results method) Mass (class in lipyd.formula) mass_data_arrays() (lipyd.moldb.MoleculeDatabaseAggregator method) MassBase (class in lipyd.mass) match() (in module lipyd.lookup) match_annot() (lipyd.ms2.Scan class method) match_chattr() (lipyd.ms2.Scan static method) match_chtype() (lipyd.ms2.Scan class method) match_constraint() (in module lipyd.lipproc) match_constraints() (in module lipyd.lipproc) matching_chain_combinations() (lipyd.ms2.AbstractMS2Identifier method) (lipyd.ms2.Scan method) matching_fa_frags_of_type() (lipyd.ms2.MS2Scan method) mean (lipyd.sec.Fraction attribute) method_hg (lipyd.ms2.Scan attribute) MethylSphingosineD (class in lipyd.lipid) MethylSphingosineDihydro (class in lipyd.lipid) MethylSphingosineT (class in lipyd.lipid) MGDG (class in lipyd.lipid) mgdg() (lipyd.ms2.GL_Positive method) mgf_iterscans() (lipyd.ms2.MS2Feature method) MgfReader (class in lipyd.mgf) minus (lipyd.fragment.ChainFragParam attribute) missing_chain() (lipyd.ms2.Scan method) MoleculeDatabaseAggregator (class in lipyd.moldb) MonoacylGlycerol (class in lipyd.lipid) MonoalkylDiacylGlycerol (class in lipyd.lipid) MonoalkylGlycerol (class in lipyd.lipid)

MonoalkylMonoacylGlycerol (class in lipyd.lipid) most_abundant_fa() (lipyd.ms2.MS2Scan method) most_abundant_fa_cc() (lipyd.ms2.MS2Scan method) most_abundant_fragment_is() (lipyd.ms2.Scan method) most_abundant_mz() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) most_abundant_mz_is() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) ms1_cc() (lipyd.ms2.MS2Scan method) ms1_lookup() (lipyd.ms2.MS2Feature method) ms1_mz() (lipyd.ms2.MS2Scan method) ms2_analysis() (lipyd.sample.Sample method) ms2_collection_methods (lipyd.sample.Sample attribute) ms2_identify() (lipyd.sample.Sample method) MS2Feature (class in lipyd.ms2) MS2FeatureOld (class in lipyd.ms2) MS2Identity (class in lipyd.ms2) MS2Scan (class in lipyd.ms2) msg() (lipyd.log.Logger method) (lipyd.ms2.MS2FeatureOld method) Mz (class in lipyd.mz) mz (lipyd.fragdb.FragmentAnnotation attribute) mz_among_most_abundant() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) mz_by_name() (in module lipyd.fragdb) (lipyd.fragdb.FragmentDatabaseAggregator method) mz_lookup() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) mz_match() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) mz_most_abundant_fold() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) mz_percent_of_most_abundant() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) mz_sorted (class in lipyd.ms2) mzml_iterscans() (lipyd.ms2.MS2Feature method)

N

n (in module lipyd.mass) name (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.fragment.ChainFragParam attribute) (lipyd.fragment.FA attribute) (lipyd.fragment.FAL_mH attribute) (lipyd.fragment.FA_m3H attribute) (lipyd.fragment.FA_mCO_m3H attribute) (lipyd.fragment.FA_mH attribute) (lipyd.fragment.FA_mH2O attribute) (lipyd.fragment.FA_mH2O_mH attribute) (lipyd.fragment.FA_mH2O_mOH attribute) (lipyd.fragment.FA_mOH attribute) (lipyd.fragment.FA_mO_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2 attribute) (lipyd.fragment.FA_pC2H2_pNH2_pO attribute) (lipyd.fragment.FA_pC2H3_pNH2_m2H attribute) (lipyd.fragment.FA_pC2_pNH2 attribute) (lipyd.fragment.FA_pC2_pNH2_mO attribute) (lipyd.fragment.FA_pC2_pNH2_pO attribute) (lipyd.fragment.FA_pC2_pN_mO attribute) (lipyd.fragment.FA_pC3H2_pNH2 attribute) (lipyd.fragment.FA_pGlycerol_mOH attribute) (lipyd.fragment.FA_pN attribute) (lipyd.fragment.FA_pNH2_mH2O_mH attribute) (lipyd.fragment.FA_pNH2_mO attribute) (lipyd.fragment.FA_pNH_pC2H2_mOH attribute) (lipyd.fragment.FA_pO_mH attribute) (lipyd.fragment.LysoPA attribute) (lipyd.fragment.LysoPAAlkyl attribute) (lipyd.fragment.LysoPA_mH2O attribute) (lipyd.fragment.LysoPC attribute) (lipyd.fragment.LysoPCAlkyl attribute) (lipyd.fragment.LysoPE attribute) (lipyd.fragment.LysoPEAlkyl attribute) (lipyd.fragment.LysoPEAlkyl_mH2O attribute) (lipyd.fragment.LysoPG attribute) (lipyd.fragment.LysoPGAlkyl attribute) (lipyd.fragment.LysoPG_mH2O attribute) (lipyd.fragment.LysoPI attribute) (lipyd.fragment.LysoPIAlkyl attribute) (lipyd.fragment.LysoPI_mH2O attribute) (lipyd.fragment.NLFA attribute) (lipyd.fragment.NLFA_m2xH2O attribute) (lipyd.fragment.NLFA_mH2O attribute) (lipyd.fragment.NLFA_pNH3 attribute) (lipyd.fragment.NLFA_pOH attribute) (lipyd.fragment.Sph_m2xH2O_mH attribute) (lipyd.fragment.Sph_m2xH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_m2xH2O_pCH3 attribute) (lipyd.fragment.Sph_m2xH2O_pH attribute) (lipyd.fragment.Sph_mC2H2_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mC2H3_mNH2_mOH attribute) (lipyd.fragment.Sph_mC2H4_m3H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_m2H attribute) (lipyd.fragment.Sph_mC2H4_mNH2_mH2O attribute) (lipyd.fragment.Sph_mCH2_m3H attribute) (lipyd.fragment.Sph_mCH2_mH2O_mH attribute) (lipyd.fragment.Sph_mCH2_mNH2_m4H attribute) (lipyd.fragment.Sph_mCH2_mOH attribute) (lipyd.fragment.Sph_mC_m2xH2O attribute) (lipyd.fragment.Sph_mC_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mH attribute) (lipyd.fragment.Sph_mC_mO_mH2O_mNH attribute) (lipyd.fragment.Sph_mH2O_mH attribute) (lipyd.fragment.Sph_mH2O_p2xCH3_pH attribute) (lipyd.fragment.Sph_mH2O_pCH3 attribute) (lipyd.fragment.Sph_mH2O_pH attribute) (lipyd.fragment.Sph_mH_N attribute) (lipyd.fragment.Sph_mH_P attribute) (lipyd.fragment.Sph_mNH2_m3H attribute) (lipyd.fragment.Sph_mNH2_mH2O_m2H attribute) (lipyd.fragment.Sph_mNH2_mOH attribute) (lipyd.fragment.Sph_mO_mH2O_pCH3_pH attribute) (lipyd.fragment.Sph_mO_pH attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3 attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC12O10H18_pSO3_pH2O attribute) (lipyd.fragment.Sph_pC2_pOH attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3 attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pCO_pH2O attribute) (lipyd.fragment.Sph_pC6O5H8_pSO3_pH2O attribute) (lipyd.fragment.Sph_pH attribute) (lipyd.fragment.Sph_pH2O_mH attribute) (lipyd.fragment.Sph_pO attribute) (lipyd.fragment.Sph_pPCh_mCH3 attribute)

names (lipyd.lipproc.LipidLabel attribute) names() (lipyd.moldb.SwissLipids static method) names_default (lipyd.sdf.SdfReader attribute) negative (lipyd.sample.FeatureSelection attribute) neutron (in module lipyd.mass) new_session() (in module lipyd.session) nl() (lipyd.ms2.Scan method) nl_among_most_abundant() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) nl_lookup() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) NLFA (class in lipyd.fragment) NLFA_m2xH2O (class in lipyd.fragment) NLFA_mH2O (class in lipyd.fragment) NLFA_pNH3 (class in lipyd.fragment) NLFA_pOH (class in lipyd.fragment) non_hex() (lipyd.ms2.Cer_Positive method) normalize_intensities() (lipyd.ms2.ScanBase method) (lipyd.plot.SpectrumPlot method) numof_samples (lipyd.sample.SampleSet attribute)

O

oh (lipyd.fragment.FragConstraint attribute) (lipyd.lipproc.ChainAttr attribute)

OldProgress (class in lipyd.progress) open_logfile() (lipyd.log.Logger method) original() (lipyd.sample.FeatureIdx method)

P

p (in module lipyd.mass) PA (class in lipyd.lipid) PA_Negative (class in lipyd.ms2) pa_pe_ps_pg_pos() (lipyd.ms2.MS2Scan method) PA_Positive (class in lipyd.ms2) pa_ps_neg() (lipyd.ms2.MS2Scan method) param_neg (lipyd.fragment.FattyFragmentFactory attribute) param_pos (lipyd.fragment.FattyFragmentFactory attribute) params (lipyd.plot.SpectrumPlot attribute) PC (class in lipyd.lipid) pc() (lipyd.ms2.Cer_Positive method) pc_neg_1() (lipyd.ms2.MS2Scan method) PC_Negative (class in lipyd.ms2) pc_pos() (lipyd.ms2.MS2Scan method) pc_pos_1() (lipyd.ms2.MS2Scan method) PC_Positive (class in lipyd.ms2) PE (class in lipyd.lipid) pe_cer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) pe_neg_1() (lipyd.ms2.MS2Scan method) PE_Negative (class in lipyd.ms2) pe_pc_pg_neg() (lipyd.ms2.MS2Scan method) pe_pos_1() (lipyd.ms2.MS2Scan method) PE_Positive (class in lipyd.ms2) peak_size() (lipyd.feature.PeakSize method) peak_size_filter() (lipyd.sample.SampleSet method) PeakSize (class in lipyd.feature) percent_score() (lipyd.ms2.AbstractMS2Identifier method) PG (class in lipyd.lipid) pg_neg_1() (lipyd.ms2.MS2Scan method) PG_Negative (class in lipyd.ms2) pg_pos_1() (lipyd.ms2.MS2Scan method) PG_Positive (class in lipyd.ms2) PGP (class in lipyd.lipid)

Phosphatidylethanolamine (class in lipyd.lipid) PI (class in lipyd.lipid) pi_neg_1() (lipyd.ms2.MS2Scan method) PI_Negative (class in lipyd.ms2) pi_pos_1() (lipyd.ms2.MS2Scan method) PI_Positive (class in lipyd.ms2) piecharts_plotly() (lipyd.results.Results method) PIP (class in lipyd.lipid) PIP2 (class in lipyd.lipid) PIP3 (class in lipyd.lipid) plate_sample_id_processor() (in module lipyd.sampleattrs) plus (lipyd.fragment.ChainFragParam attribute) positions_for_frag_type() (lipyd.ms2.Scan method) possible_classes() (in module lipyd.moldb) post_subclass_name (lipyd.lipid.SphingolipidFactory attribute) ppm_tolerance() (in module lipyd.lookup) pre_subclass_name (lipyd.lipid.SphingolipidFactory attribute) precursor_by_id() (lipyd.mgf.MgfReader method) print_db_species() (lipyd.ms2.MS2FeatureOld method) print_identities() (lipyd.ms2.MS2Scan method) print_scan() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) process() (lipyd.name.LipidNameProcessor method) (lipyd.sample.Sample method) process_db_keywords() (lipyd.name.LipidNameProcessor static method) process_fa_name() (lipyd.name.LipidNameProcessor method) profile() (lipyd.sec.SECReader method) Progress (class in lipyd.progress) protein_containing_samples() (lipyd.sampleattrs.SECProfile method) proton (in module lipyd.mass) PS (class in lipyd.lipid) ps_neg_1() (lipyd.ms2.MS2Scan method) PS_Negative (class in lipyd.ms2) ps_pos_1() (lipyd.ms2.MS2Scan method) PS_Positive (class in lipyd.ms2)

Q

quality_filter() (lipyd.sample.Sample method)

R

random_string() (in module lipyd.common) rank (lipyd.ms2.ChainIdentificationDetails attribute) read() (lipyd.sample.SampleReader method) (lipyd.sdf.SdfReader method) (lipyd.sec.SECReader method) read_asc() (lipyd.sec.SECReader method) read_file() (lipyd.fragdb.FragmentDatabaseAggregator method) read_files() (lipyd.fragdb.FragmentDatabaseAggregator method) read_lipid_names() (lipyd.name.LipidNameProcessor method) read_manual() (lipyd.results.Results method) read_manual2() (lipyd.results.Results method) read_mzml() (lipyd.mzml.Reader method) read_sec() (lipyd.sampleattrs.SECProfile method) read_xls() (lipyd.sec.SECReader method) Reader (class in lipyd.moldb) (class in lipyd.mzml) reader_classes (lipyd.sample.SampleReader attribute) record_to_obmol() (lipyd.sdf.SdfReader method) record_to_obmol_mol() (lipyd.sdf.SdfReader method) records_by_type() (lipyd.ms2.Scan method) records_string() (in module lipyd.moldb) (lipyd.moldb.MoleculeDatabaseAggregator static method) register() (lipyd.sample.FeatureIdx method) (lipyd.sampleattrs.SampleSorter method) reln (lipyd.mgf.MgfReader attribute) reload() (lipyd.fragdb.FragmentAnnotator method) (lipyd.fragdb.FragmentDatabaseAggregator method) (lipyd.mass.MassBase method) (lipyd.mgf.MgfReader method) (lipyd.moldb.MoleculeDatabaseAggregator method) (lipyd.moldb.Reader method) (lipyd.ms2.MS2FeatureOld method) (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) (lipyd.ms2.ScanBase method) (lipyd.mz.Mz method) (lipyd.name.LipidNameProcessor method) (lipyd.plot.SpectrumPlot method) (lipyd.progress.Progress method) (lipyd.sample.FeatureBase method) (lipyd.sample.Sample method) (lipyd.sample.SampleReader method) (lipyd.sdf.SdfReader method) (lipyd.sec.SECReader method)

remove() (lipyd.fragment.AdductCalculator method) remove_ac() (lipyd.mz.Mz method) remove_fo() (lipyd.mz.Mz method) remove_h() (lipyd.mz.Mz method) remove_na() (lipyd.mz.Mz method) remove_nh4() (lipyd.mz.Mz method) remove_oh() (lipyd.mz.Mz method) reset() (in module lipyd.settings) reset_all() (in module lipyd.settings) reset_atoms() (lipyd.formula.Formula method) Results (class in lipyd.results) RetinoicAcid (class in lipyd.lipid) Retinol (class in lipyd.lipid) row (lipyd.sec.Fraction attribute) rt_filter() (lipyd.sample.Sample method) run() (lipyd.feature.FeatureAnalyzer method)

S

Sample (class in lipyd.sample) sample_id (lipyd.ms2.ScanDetails attribute) sample_id_processor() (in module lipyd.sampleattrs) sample_ids_selected() (lipyd.sampleattrs.SampleSelection method) SampleAttrs (class in lipyd.sampleattrs) SampleData (class in lipyd.sampleattrs) SampleReader (class in lipyd.sample) SampleSelection (class in lipyd.sampleattrs) SampleSet (class in lipyd.sample) SampleSetAttrs (class in lipyd.sampleattrs) SampleSorter (class in lipyd.sampleattrs) Scan (class in lipyd.ms2) scan_by_id() (lipyd.mgf.MgfReader method) scan_id (lipyd.ms2.ScanDetails attribute) scan_methods (lipyd.ms2.MS2Feature attribute) scan_str() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) ScanBase (class in lipyd.ms2) ScanDetails (class in lipyd.ms2) SdfReader (class in lipyd.sdf) SECProfile (class in lipyd.sampleattrs) SECReader (class in lipyd.sec) select() (lipyd.sample.Sample method) select_best_scan() (lipyd.ms2.MS2FeatureOld method) Session (class in lipyd.session) set_attr() (lipyd.metabolite.AbstractSubstituent method) set_chlens() (lipyd.metabolite.AbstractSubstituent method) set_done() (lipyd.progress.OldProgress method) (lipyd.progress.Progress method) set_filenames() (lipyd.fragdb.FragmentDatabaseAggregator method) set_levels() (lipyd.moldb.SwissLipids method) set_ms2_sources() (lipyd.sample.Sample method) (lipyd.sample.SampleSet method) set_name() (lipyd.fragment.FattyFragmentOld method) set_series() (lipyd.fragdb.FragmentDatabaseAggregator method) set_status() (lipyd.progress.OldProgress method) (lipyd.progress.Progress method) set_total() (lipyd.progress.OldProgress method) (lipyd.progress.Progress method) set_unsats() (lipyd.metabolite.AbstractSubstituent method) settings (in module lipyd.settings) setup() (in module lipyd.settings) shex2cer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) shexcer() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) show() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) Slope (class in lipyd.feature) slope() (lipyd.feature.Slope method) sm() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) sm_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) sm_pos_1() (lipyd.ms2.MS2Scan method) sort() (lipyd.moldb.MoleculeDatabaseAggregator method) (lipyd.ms2.ScanBase method) (lipyd.sampleattrs.SampleSorter method) sort_all() (lipyd.sample.FeatureBase method) (lipyd.sample.FeatureIdx method) (lipyd.sample.Sample method) sort_by() (lipyd.sampleattrs.SampleSetAttrs method) (lipyd.sampleattrs.SampleSorter method) sort_by_i() (lipyd.ms2.MS2Scan method) sort_by_index() (lipyd.sampleattrs.SampleSetAttrs method) sort_by_mz() (lipyd.ms2.MS2Scan method) sort_by_sample_id() (lipyd.sampleattrs.SampleSetAttrs method) sort_by_sample_ids() (lipyd.sampleattrs.SampleSorter method) sort_intensity() (lipyd.ms2.ScanBase method) sort_mz() (lipyd.ms2.ScanBase method) sort_scans() (lipyd.ms2.MS2FeatureOld method) sort_to() (lipyd.sampleattrs.SampleSorter method) source (lipyd.ms2.ScanDetails attribute) SpectrumPlot (class in lipyd.plot) sph (lipyd.fragment.FragConstraint attribute) (lipyd.lipproc.ChainAttr attribute) sph() (lipyd.ms2.Cer_Positive method) sph1p_neg_1() (lipyd.ms2.MS2Scan method) (lipyd.ms2.Scan method) Sph_m2xH2O_mH (class in lipyd.fragment) Sph_m2xH2O_p2xCH3_pH (class in lipyd.fragment) Sph_m2xH2O_pCH3 (class in lipyd.fragment) Sph_m2xH2O_pH (class in lipyd.fragment) Sph_mC2H2_mO_mH2O_mNH (class in lipyd.fragment) Sph_mC2H3_mNH2_mOH (class in lipyd.fragment) Sph_mC2H4_m3H (class in lipyd.fragment) Sph_mC2H4_mNH2_m2H (class in lipyd.fragment) Sph_mC2H4_mNH2_mH2O (class in lipyd.fragment) Sph_mC_m2xH2O (class in lipyd.fragment) Sph_mC_mH2O_mH (class in lipyd.fragment) Sph_mC_mO_mH2O_mH (class in lipyd.fragment) Sph_mC_mO_mH2O_mNH (class in lipyd.fragment)

Sph_mCH2_m3H (class in lipyd.fragment) Sph_mCH2_mH2O_mH (class in lipyd.fragment) Sph_mCH2_mNH2_m4H (class in lipyd.fragment) Sph_mCH2_mOH (class in lipyd.fragment) Sph_mH2O_mH (class in lipyd.fragment) Sph_mH2O_p2xCH3_pH (class in lipyd.fragment) Sph_mH2O_pCH3 (class in lipyd.fragment) Sph_mH2O_pH (class in lipyd.fragment) Sph_mH_N (class in lipyd.fragment) Sph_mH_P (class in lipyd.fragment) Sph_mNH2_m3H (class in lipyd.fragment) Sph_mNH2_mH2O_m2H (class in lipyd.fragment) Sph_mNH2_mOH (class in lipyd.fragment) Sph_mO_mH2O_pCH3_pH (class in lipyd.fragment) Sph_mO_pH (class in lipyd.fragment) Sph_pC12O10H18_pSO3 (class in lipyd.fragment) Sph_pC12O10H18_pSO3_pCO_pH2O (class in lipyd.fragment) Sph_pC12O10H18_pSO3_pH2O (class in lipyd.fragment) Sph_pC2_pOH (class in lipyd.fragment) Sph_pC6O5H8_pSO3 (class in lipyd.fragment) Sph_pC6O5H8_pSO3_pCO_pH2O (class in lipyd.fragment) Sph_pC6O5H8_pSO3_pH2O (class in lipyd.fragment) Sph_pH (class in lipyd.fragment) Sph_pH2O_mH (class in lipyd.fragment) Sph_pO (class in lipyd.fragment) Sph_pPCh_mCH3 (class in lipyd.fragment) SphingolipidFactory (class in lipyd.lipid) SphingomyelinD (class in lipyd.lipid) SphingomyelinDihydro (class in lipyd.lipid) SphingomyelinT (class in lipyd.lipid) Sphingosine (class in lipyd.substituent) sphingosine_base() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) sphingosine_d() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) sphingosine_d_dh() (lipyd.ms2.Cer_Negative method) sphingosine_dh() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) sphingosine_k() (lipyd.ms2.Cer_Positive method) sphingosine_t() (lipyd.ms2.Cer_Negative method) (lipyd.ms2.Cer_Positive method) SphingosineD (class in lipyd.lipid) SphingosineDihydro (class in lipyd.lipid) SphingosineDihydroPC (class in lipyd.lipid) SphingosineDihydroPhosphate (class in lipyd.lipid) SphingosineDPC (class in lipyd.lipid) SphingosineDPhosphate (class in lipyd.lipid) SphingosineKeto (class in lipyd.lipid) SphingosineT (class in lipyd.lipid) SphingosineTPC (class in lipyd.lipid) SphingosineTPhosphate (class in lipyd.lipid) split() (lipyd.formula.Formula method) SQDG (class in lipyd.lipid) sqdg() (lipyd.ms2.GL_Positive method) start (lipyd.sec.Fraction attribute) start_logger() (lipyd.session.Session method) step() (lipyd.progress.OldProgress method) (lipyd.progress.Progress method) str2hg() (in module lipyd.lipproc) stRbe (lipyd.mgf.MgfReader attribute) stRch (lipyd.mgf.MgfReader attribute) stRcharge (lipyd.mgf.MgfReader attribute) stRempty (lipyd.mgf.MgfReader attribute) stRen (lipyd.mgf.MgfReader attribute) strftime() (lipyd.log.Logger method) stRpepmass (lipyd.mgf.MgfReader attribute) stRrtinseconds (lipyd.mgf.MgfReader attribute) stRtitle (lipyd.mgf.MgfReader attribute) sub (lipyd.fragment.FragConstraint attribute) (lipyd.lipproc.Headgroup attribute) sub() (lipyd.formula.Formula method) subclass_methods (lipyd.ms2.AbstractMS2Identifier attribute) (lipyd.ms2.Cer_Negative attribute) (lipyd.ms2.Cer_Positive attribute) subclass_str() (in module lipyd.lipproc) (lipyd.lipproc.LipidRecord method) subsproduct() (lipyd.metabolite.AbstractMetabolite method) SulfoDihexosylCeramideD (class in lipyd.lipid) SulfoDihexosylCeramideDihydro (class in lipyd.lipid) SulfoDihexosylCeramideT (class in lipyd.lipid) SulfoHexosylCeramideD (class in lipyd.lipid) SulfoHexosylCeramideDihydro (class in lipyd.lipid) SulfoHexosylCeramideT (class in lipyd.lipid) sum_cc() (lipyd.ms2.MS2Scan method) sum_cc2() (lipyd.ms2.MS2Scan method) sum_cc2str() (lipyd.ms2.MS2Scan method) sum_cc_is() (lipyd.ms2.MS2Scan method) sum_cc_str() (lipyd.ms2.MS2Scan method) sum_chains() (in module lipyd.lipproc) summary() (lipyd.ms2.MS2Identity method) summary_str() (in module lipyd.lipproc) (lipyd.lipproc.LipidRecord method) SwissLipids (class in lipyd.moldb)

T

table() (lipyd.sample.Sample method) tag_neg_1() (lipyd.ms2.MS2Scan method) TAG_Negative (class in lipyd.ms2) tag_pos_1() (lipyd.ms2.MS2Scan method) TAG_Positive (class in lipyd.ms2) terminate() (lipyd.progress.OldProgress method) (lipyd.progress.Progress method) test_branched() (lipyd.name.LipidNameProcessor method) threshold_filter() (lipyd.sample.FeatureBase method)

threshold_select() (lipyd.sample.FeatureBase method) timestamp() (lipyd.log.Logger class method) to_float() (in module lipyd.common) to_int() (in module lipyd.common) to_obmol() (lipyd.moldb.SwissLipids static method) TriacylGlycerol (class in lipyd.lipid) TrimethylSphingosineD (class in lipyd.lipid) TrimethylSphingosineDihydro (class in lipyd.lipid) TrimethylSphingosineT (class in lipyd.lipid)

U

u (lipyd.fragdb.FragmentAnnotation attribute) (lipyd.ms2.ChainFragment attribute) uniqList() (in module lipyd.common) uniqOrdList() (in module lipyd.common) unregister() (lipyd.sample.FeatureIdx method)

update() (lipyd.formula.Formula method) update_core() (lipyd.metabolite.AbstractSubstituent method) update_mz() (lipyd.formula.Formula method) urlAbundances (in module lipyd.mass) urlMasses (in module lipyd.mass) urlWeights (in module lipyd.mass)

V

VA_Negative (class in lipyd.ms2) va_pos_1() (lipyd.ms2.MS2Scan method)

VA_Positive (class in lipyd.ms2) vd_pos_1() (lipyd.ms2.MS2Scan method)

W

warn_with_traceback() (in module lipyd.common)

weight() (lipyd.mz.Mz method) write_mol() (lipyd.sdf.SdfReader method)