Chemistry

Classes
class	AAIndex
	Representation of selected AAIndex properties. More...
class	AASequence
	Representation of a peptide/protein sequence. More...
class	Element
	Representation of an element. More...
class	ElementDB
	Stores elements. More...
class	EmpiricalFormula
	Representation of an empirical formula. More...
class	EnzymaticDigestion
	Class for the enzymatic digestion of proteins. More...
class	EnzymaticDigestionLogModel
	Class for the Log L model of enzymatic digestion of proteins. More...
class	Enzyme
	Representation of an enzyme. More...
class	EnzymesDB
	enzyme database which holds enzymes More...
class	IsotopeDistribution
	Isotope distribution class. 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	Residue
	Representation of a residue. More...
class	ResidueDB
	residue data base which holds residues 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 with various options. More...
class	TheoreticalSpectrumGeneratorXLMS
	Generates theoretical spectra for cross-linked peptides. More...

Detailed Description