Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

EnzymaticDigestion Class Reference
[Chemistry]

#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>

List of all members.


Detailed Description

Class for the enzymatic digestion of proteins.

Public Types

enum  Enzyme { TRYPSIN, SIZE_OF_ENZYMES }
 Possible enzymes for the digestion. More...

Public Member Functions

 EnzymaticDigestion ()
 Deafult constructor.
UInt getMissedCleavages () const
 Returns the number of missed cleavages for the digestion.
void setMissedCleavages (UInt missed_cleavages)
 Sets the number of missed cleavages for the digestion (default is 0).
Enzyme getEnzyme () const
 Returns the enzyme for the digestion.
void setEnzyme (Enzyme enzyme)
 Sets the enzyme for the digestion (default is TRYPSIN).
void digest (const AASequence &protein, std::vector< AASequence > &output)
 Performs the enzymatic digestion of a protein.
UInt peptideCount (const AASequence &protein)
 Returns the number of peptides a digestion of protein would yield.

Static Public Attributes

static const std::string NamesOfEnzymes [SIZE_OF_ENZYMES]
 Names of the Enzymes.

Protected Member Functions

void nextCleavageSite_ (const AASequence &sequence, AASequence::ConstIterator &iterator)
 moves the iterator it after the next cleavage site of the sequence

Protected Attributes

UInt missed_cleavages_
 Number of missed cleavages.
Enzyme enzyme_
 Used enzyme.

Member Enumeration Documentation

enum Enzyme

Possible enzymes for the digestion.

Enumerator:
TRYPSIN 
SIZE_OF_ENZYMES 


Constructor & Destructor Documentation

EnzymaticDigestion (  ) 

Deafult constructor.


Member Function Documentation

UInt getMissedCleavages (  )  const

Returns the number of missed cleavages for the digestion.

void setMissedCleavages ( UInt  missed_cleavages  ) 

Sets the number of missed cleavages for the digestion (default is 0).

Enzyme getEnzyme (  )  const

Returns the enzyme for the digestion.

void setEnzyme ( Enzyme  enzyme  ) 

Sets the enzyme for the digestion (default is TRYPSIN).

void digest ( const AASequence protein,
std::vector< AASequence > &  output 
)

Performs the enzymatic digestion of a protein.

UInt peptideCount ( const AASequence protein  ) 

Returns the number of peptides a digestion of protein would yield.

void nextCleavageSite_ ( const AASequence sequence,
AASequence::ConstIterator iterator 
) [protected]

moves the iterator it after the next cleavage site of the sequence


Member Data Documentation

const std::string NamesOfEnzymes[SIZE_OF_ENZYMES] [static]

Names of the Enzymes.

UInt missed_cleavages_ [protected]

Number of missed cleavages.

Enzyme enzyme_ [protected]

Used enzyme.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1