OpenMS
Chemistry

Classes

class  AAIndex
 Representation of selected AAIndex properties. More...
 
class  AASequence
 Representation of a peptide/protein sequence. More...
 
class  DigestionEnzyme
 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
 Singleton that stores elements and isotopes. 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 represented as AASequence or String. More...
 
class  Residue
 Representation of an amino acid residue. More...
 
class  ResidueDB
 OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. 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