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class | AAIndex |
| Representation of selected AAIndex properties. More...
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class | AASequence |
| Representation of a peptide/protein sequence. More...
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class | Element |
| Representation of an element. More...
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class | ElementDB |
| Stores elements. More...
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class | EmpiricalFormula |
| Representation of an empirical formula. More...
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class | EnzymaticDigestion |
| Class for the enzymatic digestion of proteins. More...
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class | EnzymaticDigestionLogModel |
| Class for the Log L model of enzymatic digestion of proteins. More...
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class | Enzyme |
| Representation of an enzyme. More...
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class | EnzymesDB |
| enzyme database which holds enzymes More...
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class | IsotopeDistribution |
| Isotope distribution class. More...
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class | ModificationDefinition |
| Representation of modification definition. More...
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class | ModificationDefinitionsSet |
| Representation of a set of modification definitions. More...
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class | ModificationsDB |
| database which holds all residue modifications from UniMod More...
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class | Residue |
| Representation of a residue. More...
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class | ResidueDB |
| residue data base which holds residues More...
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class | SpectrumAnnotator |
| Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...
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class | SvmTheoreticalSpectrumGenerator |
| Simulates MS2 spectra with support vector machines. More...
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class | SvmTheoreticalSpectrumGeneratorSet |
| Loads SvmTheoreticalSpectrumGenerator instances for different charges. More...
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class | SvmTheoreticalSpectrumGeneratorTrainer |
| Train SVM models that are used by SvmTheoreticalSpectrumGenerator. More...
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class | TheoreticalSpectrumGenerator |
| Generates theoretical spectra with various options. More...
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class | TheoreticalSpectrumGeneratorXLMS |
| Generates theoretical spectra for cross-linked peptides. More...
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