Chemistry

Classes
class	AAIndex
	Representation of selected AAIndex properties. More...
class	AASequence
	Representation of a peptide/protein sequence. More...
class	DigestionEnzyme
	Abstract 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
	Stores elements. 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. More...
class	Residue
	Representation of a residue. More...
class	ResidueDB
	residue data base which holds residues 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...

Detailed Description