ProteoWizard
Public Member Functions | Private Attributes | List of all members
pwiz::proteome::DigestedPeptide Class Reference

peptide subclass that contains extra metadata provided by digestion More...

#include <Digestion.hpp>

Inheritance diagram for pwiz::proteome::DigestedPeptide:
pwiz::proteome::Peptide

Public Member Functions

 DigestedPeptide (const std::string &sequence)
 
 DigestedPeptide (const char *sequence)
 
 DigestedPeptide (std::string::const_iterator begin, std::string::const_iterator end, size_t offset, size_t missedCleavages, bool NTerminusIsSpecific, bool CTerminusIsSpecific, std::string NTerminusPrefix="", std::string CTerminusSuffix="")
 
 DigestedPeptide (const Peptide &peptide, size_t offset, size_t missedCleavages, bool NTerminusIsSpecific, bool CTerminusIsSpecific, std::string NTerminusPrefix="", std::string CTerminusSuffix="")
 
 DigestedPeptide (const DigestedPeptide &)
 
DigestedPeptideoperator= (const DigestedPeptide &)
 
virtual ~DigestedPeptide ()
 
size_t offset () const
 returns the zero-based offset of the N terminus of the peptide in the polypeptide from which it was digested More...
 
size_t missedCleavages () const
 returns the number of missed cleavage sites in the peptide More...
 
size_t specificTermini () const
 returns the number of termini that matched to the digestion rules More...
 
bool NTerminusIsSpecific () const
 returns true iff the N terminus matched the digestion rules More...
 
bool CTerminusIsSpecific () const
 returns true iff the C terminus matched the digestion rules More...
 
std::string NTerminusPrefix () const
 returns residue preceding digestion site More...
 
std::string CTerminusSuffix () const
 returns residue following digestion site More...
 
bool operator== (const DigestedPeptide &rhs) const
 returns true iff peptide sequences, masses, and all digestion metadata are equal More...
 
- Public Member Functions inherited from pwiz::proteome::Peptide
 Peptide (const std::string &sequence="", MODIFICATION_PARSING_ARGUMENTS)
 
 Peptide (const char *sequence, MODIFICATION_PARSING_ARGUMENTS)
 
 Peptide (std::string::const_iterator begin, std::string::const_iterator end, MODIFICATION_PARSING_ARGUMENTS)
 
 Peptide (const char *begin, const char *end, MODIFICATION_PARSING_ARGUMENTS)
 
 Peptide (const Peptide &)
 
Peptideoperator= (const Peptide &)
 
virtual ~Peptide ()
 
const std::string & sequence () const
 returns the sequence of amino acids making up the peptide More...
 
chemistry::Formula formula (bool modified=false) const
 if modified = false: returns the composition formula of sequence()+water if modified = true: returns the composition formula of sequence()+modifications()+water throws an exception if modified = true and any modification has only mass information More...
 
double monoisotopicMass (int charge=0, bool modified=true) const
 if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the monoisotopic mass of sequence()+water if modified = true: returns the monoisotopic mass of sequence()+modifications()+water More...
 
double molecularWeight (int charge=0, bool modified=true) const
 if charge = 0: returns neutral mass if charge > 0: returns charged m/z if modified = false: returns the molecular weight of sequence()+water if modified = true: returns the molecular weight of sequence()+modifications()+water More...
 
ModificationMapmodifications ()
 the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map More...
 
const ModificationMapmodifications () const
 the map of sequence offsets (0-based) to modifications More...
 
Fragmentation fragmentation (bool monoisotopic=true, bool modified=true) const
 returns a fragmentation model for the peptide; fragment masses can calculated as mono/avg and as modified/unmodified More...
 
bool operator== (const Peptide &rhs) const
 returns true iff peptide sequences and modifications are equal More...
 
bool operator< (const Peptide &rhs) const
 returns true iff this peptide has a lesser sequence length, sequence, modifications length, or modifications More...
 

Private Attributes

size_t offset_
 
size_t missedCleavages_
 
bool NTerminusIsSpecific_
 
bool CTerminusIsSpecific_
 
std::string NTerminusPrefix_
 
std::string CTerminusSuffix_
 

Detailed Description

peptide subclass that contains extra metadata provided by digestion

Definition at line 47 of file Digestion.hpp.

Constructor & Destructor Documentation

§ DigestedPeptide() [1/5]

pwiz::proteome::DigestedPeptide::DigestedPeptide ( const std::string &  sequence)

§ DigestedPeptide() [2/5]

pwiz::proteome::DigestedPeptide::DigestedPeptide ( const char *  sequence)

§ DigestedPeptide() [3/5]

pwiz::proteome::DigestedPeptide::DigestedPeptide ( std::string::const_iterator  begin,
std::string::const_iterator  end,
size_t  offset,
size_t  missedCleavages,
bool  NTerminusIsSpecific,
bool  CTerminusIsSpecific,
std::string  NTerminusPrefix = "",
std::string  CTerminusSuffix = "" 
)

§ DigestedPeptide() [4/5]

pwiz::proteome::DigestedPeptide::DigestedPeptide ( const Peptide peptide,
size_t  offset,
size_t  missedCleavages,
bool  NTerminusIsSpecific,
bool  CTerminusIsSpecific,
std::string  NTerminusPrefix = "",
std::string  CTerminusSuffix = "" 
)

§ DigestedPeptide() [5/5]

pwiz::proteome::DigestedPeptide::DigestedPeptide ( const DigestedPeptide )

§ ~DigestedPeptide()

virtual pwiz::proteome::DigestedPeptide::~DigestedPeptide ( )
virtual

Member Function Documentation

§ operator=()

DigestedPeptide& pwiz::proteome::DigestedPeptide::operator= ( const DigestedPeptide )

§ offset()

size_t pwiz::proteome::DigestedPeptide::offset ( ) const

returns the zero-based offset of the N terminus of the peptide in the polypeptide from which it was digested

Referenced by testDigestionMetadata(), testNontrypticBSA(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), and testTrypticBSA().

§ missedCleavages()

size_t pwiz::proteome::DigestedPeptide::missedCleavages ( ) const

returns the number of missed cleavage sites in the peptide

Referenced by testDigestionMetadata(), testNontrypticBSA(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), and testTrypticBSA().

§ specificTermini()

size_t pwiz::proteome::DigestedPeptide::specificTermini ( ) const

returns the number of termini that matched to the digestion rules

Referenced by testDigestionMetadata(), testNontrypticBSA(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), and testTrypticBSA().

§ NTerminusIsSpecific()

bool pwiz::proteome::DigestedPeptide::NTerminusIsSpecific ( ) const

returns true iff the N terminus matched the digestion rules

§ CTerminusIsSpecific()

bool pwiz::proteome::DigestedPeptide::CTerminusIsSpecific ( ) const

returns true iff the C terminus matched the digestion rules

§ NTerminusPrefix()

std::string pwiz::proteome::DigestedPeptide::NTerminusPrefix ( ) const

returns residue preceding digestion site

Referenced by testDigestionMetadata().

§ CTerminusSuffix()

std::string pwiz::proteome::DigestedPeptide::CTerminusSuffix ( ) const

returns residue following digestion site

Referenced by testDigestionMetadata().

§ operator==()

bool pwiz::proteome::DigestedPeptide::operator== ( const DigestedPeptide rhs) const

returns true iff peptide sequences, masses, and all digestion metadata are equal

Member Data Documentation

§ offset_

size_t pwiz::proteome::DigestedPeptide::offset_
private

Definition at line 101 of file Digestion.hpp.

§ missedCleavages_

size_t pwiz::proteome::DigestedPeptide::missedCleavages_
private

Definition at line 102 of file Digestion.hpp.

§ NTerminusIsSpecific_

bool pwiz::proteome::DigestedPeptide::NTerminusIsSpecific_
private

Definition at line 103 of file Digestion.hpp.

§ CTerminusIsSpecific_

bool pwiz::proteome::DigestedPeptide::CTerminusIsSpecific_
private

Definition at line 104 of file Digestion.hpp.

§ NTerminusPrefix_

std::string pwiz::proteome::DigestedPeptide::NTerminusPrefix_
private

Definition at line 105 of file Digestion.hpp.

§ CTerminusSuffix_

std::string pwiz::proteome::DigestedPeptide::CTerminusSuffix_
private

Definition at line 106 of file Digestion.hpp.


The documentation for this class was generated from the following file: