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Classes | Enumerations
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, ENZYME_TRYPSIN_P, 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 
ENZYME_TRYPSIN_P 
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 

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:32 using doxygen 1.8.9.1