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pwiz::proteome::Peptide Class Reference

represents a peptide or polypeptide (a sequence of amino acids) More...

#include <Peptide.hpp>

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

Public Member Functions

 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
 
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
 
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
 
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
 
ModificationMapmodifications ()
 the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map
 
const ModificationMapmodifications () const
 the map of sequence offsets (0-based) to modifications
 
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
 
bool operator== (const Peptide &rhs) const
 returns true iff peptide sequences and modifications are equal
 
bool operator< (const Peptide &rhs) const
 returns true iff this peptide has a lesser sequence length, sequence, modifications length, or modifications
 

Private Attributes

boost::shared_ptr< Impl > impl_
 

Friends

class ModificationMap
 
class Fragmentation
 

Detailed Description

represents a peptide or polypeptide (a sequence of amino acids)

Definition at line 61 of file Peptide.hpp.

Constructor & Destructor Documentation

◆ Peptide() [1/5]

pwiz::proteome::Peptide::Peptide ( const std::string &  sequence = "",
MODIFICATION_PARSING_ARGUMENTS   
)

◆ Peptide() [2/5]

pwiz::proteome::Peptide::Peptide ( const char *  sequence,
MODIFICATION_PARSING_ARGUMENTS   
)

◆ Peptide() [3/5]

pwiz::proteome::Peptide::Peptide ( std::string::const_iterator  begin,
std::string::const_iterator  end,
MODIFICATION_PARSING_ARGUMENTS   
)

◆ Peptide() [4/5]

pwiz::proteome::Peptide::Peptide ( const char *  begin,
const char *  end,
MODIFICATION_PARSING_ARGUMENTS   
)

◆ Peptide() [5/5]

pwiz::proteome::Peptide::Peptide ( const Peptide )

◆ ~Peptide()

virtual pwiz::proteome::Peptide::~Peptide ( )
virtual

Member Function Documentation

◆ operator=()

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

◆ sequence()

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

◆ formula()

chemistry::Formula pwiz::proteome::Peptide::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

Referenced by modificationTest(), peptideTest(), and test().

◆ monoisotopicMass()

double pwiz::proteome::Peptide::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

Referenced by fragmentTest(), modificationTest(), and peptideTest().

◆ molecularWeight()

double pwiz::proteome::Peptide::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

Referenced by modificationTest(), and peptideTest().

◆ modifications() [1/2]

ModificationMap & pwiz::proteome::Peptide::modifications ( )

the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map

Referenced by fragmentTest(), modificationTest(), pwiz::tradata::TextWriter::operator()(), operatorTest(), and testConversion().

◆ modifications() [2/2]

const ModificationMap & pwiz::proteome::Peptide::modifications ( ) const

the map of sequence offsets (0-based) to modifications

◆ fragmentation()

Fragmentation pwiz::proteome::Peptide::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

Referenced by fragmentTest().

◆ operator==()

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

returns true iff peptide sequences and modifications are equal

◆ operator<()

bool pwiz::proteome::Peptide::operator< ( const Peptide rhs) const

returns true iff this peptide has a lesser sequence length, sequence, modifications length, or modifications

Friends And Related Symbol Documentation

◆ ModificationMap

friend class ModificationMap
friend

Definition at line 112 of file Peptide.hpp.

◆ Fragmentation

friend class Fragmentation
friend

Definition at line 113 of file Peptide.hpp.

Member Data Documentation

◆ impl_

boost::shared_ptr<Impl> pwiz::proteome::Peptide::impl_
private

Definition at line 115 of file Peptide.hpp.


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