Chemistry

Classes
class	AAIndex
	Representation of selected AAIndex properties. More...
class	AASequence::ConstIterator
	ConstIterator for AASequence. More...
class	AASequence::Iterator
	Iterator class for AASequence. 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...
struct	EnzymaticDigestion::BindingSite
struct	EnzymaticDigestion::CleavageModel
class	EnzymaticDigestion
	Class for the enzymatic digestion of proteins. 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...
struct	SvmTheoreticalSpectrumGenerator::IonType
	nested class More...
struct	SvmTheoreticalSpectrumGenerator::DescriptorSet
	A set of descriptors for a single training row. More...
struct	SvmTheoreticalSpectrumGenerator::SvmModelParameterSet
	Simple container storing the model parameters required for simulation. 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...

Enumerations
enum	Enzyme { ENZYME_TRYPSIN, SIZE_OF_ENZYMES }
	Possible enzymes for the digestion (adapt NamesOfEnzymes & nextCleavageSite_() if you add more enzymes here) More...
enum	Specificity { SPEC_FULL, SPEC_SEMI, SPEC_NONE, SIZE_OF_SPECIFICITY }
	when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important More...

Enums
enum	ResidueType {   Full = 0, Internal, NTerminal, CTerminal,   AIon, BIon, CIonMinusOne, CIon,   CIonPlusOne, CIonPlusTwo, XIon, YIon,   ZIonMinusOne, ZIon, ZIonPlusOne, ZIonPlusTwo,   SizeOfResidueType }

Detailed Description

Enumeration Type Documentation

enum Enzyme

Possible enzymes for the digestion (adapt NamesOfEnzymes & nextCleavageSite_() if you add more enzymes here)

Enumerator
ENZYME_TRYPSIN
SIZE_OF_ENZYMES

enum ResidueType

Enumerator
Full
Internal
NTerminal
CTerminal
AIon
BIon
CIonMinusOne
CIon
CIonPlusOne
CIonPlusTwo
XIon
YIon
ZIonMinusOne
ZIon
ZIonPlusOne
ZIonPlusTwo
SizeOfResidueType	Todo: add c+1, z+1, z+2 ion types (Andreas)

enum Specificity

when querying for valid digestion products, this determines if the specificity of the two peptide ends is considered important

Enumerator
SPEC_FULL
SPEC_SEMI
SPEC_NONE
SIZE_OF_SPECIFICITY