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OpenMS
|
Classes | |
| class | AAIndex |
| Representation of selected AAIndex properties. More... | |
| class | AASequence |
| Representation of a peptide/protein sequence. More... | |
| class | DigestionEnzyme |
| Base class for digestion enzymes. More... | |
| class | DigestionEnzymeDB< DigestionEnzymeType, InstanceType > |
| Digestion enzyme database (base class) More... | |
| class | DigestionEnzymeProtein |
| Representation of a digestion enzyme for proteins (protease) More... | |
| class | DigestionEnzymeRNA |
| Representation of a digestion enzyme for RNA (RNase) More... | |
| class | Element |
| Representation of an element. More... | |
| class | ElementDB |
| Singleton that stores elements and isotopes. More... | |
| class | EmpiricalFormula |
| Representation of an empirical formula. More... | |
| class | EnzymaticDigestion |
| Class for the enzymatic digestion of sequences. More... | |
| class | EnzymaticDigestionLogModel |
| Class for the Log L model of enzymatic digestion of proteins. More... | |
| class | CoarseIsotopePatternGenerator |
| Isotope pattern generator for coarse isotope distributions. More... | |
| class | FineIsotopePatternGenerator |
| Isotope pattern generator for fine isotope distributions. More... | |
| class | ModificationDefinition |
| Representation of modification definition. More... | |
| class | ModificationDefinitionsSet |
| Representation of a set of modification definitions. More... | |
| class | ModificationsDB |
| database which holds all residue modifications from UniMod More... | |
| class | NASequence |
| Representation of a nucleic acid sequence. More... | |
| class | NucleicAcidSpectrumGenerator |
| Generates theoretical spectra for nucleic acid sequences. More... | |
| class | ProteaseDB |
| Database for enzymes that digest proteins (proteases) More... | |
| class | ProteaseDigestion |
| Class for the enzymatic digestion of proteins represented as AASequence or String. More... | |
| class | Residue |
| Representation of an amino acid residue. More... | |
| class | ResidueDB |
| OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. More... | |
| class | Ribonucleotide |
| Representation of a ribonucleotide (modified or unmodified) More... | |
| class | RibonucleotideDB |
| Database of ribonucleotides (modified and unmodified) More... | |
| class | RNaseDB |
| Database for enzymes that digest RNA (RNases) More... | |
| class | RNaseDigestion |
| Class for the enzymatic digestion of RNAs. More... | |
| class | SimpleTSGXLMS |
| Generates theoretical spectra for cross-linked peptides. More... | |
| class | SpectrumAnnotator |
| Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More... | |
| class | SvmTheoreticalSpectrumGenerator |
| Simulates MS2 spectra with support vector machines. More... | |
| class | SvmTheoreticalSpectrumGeneratorSet |
| Loads SvmTheoreticalSpectrumGenerator instances for different charges. More... | |
| class | SvmTheoreticalSpectrumGeneratorTrainer |
| Train SVM models that are used by SvmTheoreticalSpectrumGenerator. More... | |
| class | TheoreticalSpectrumGenerator |
| Generates theoretical spectra for peptides with various options. More... | |
| class | TheoreticalSpectrumGeneratorXLMS |
| Generates theoretical spectra for cross-linked peptides. More... | |
1.9.1 
