ProteoWizard
Public Member Functions | Public Attributes
pwiz::proteome::Protein Struct Reference

#include <ProteomeData.hpp>

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

List of all members.

Public Member Functions

 Protein (const std::string &id, size_t index, const std::string &description, const std::string &sequence)
bool empty () const
- 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
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

Public Attributes

std::string id
size_t index
std::string description

Detailed Description

Definition at line 36 of file ProteomeData.hpp.


Constructor & Destructor Documentation

pwiz::proteome::Protein::Protein ( const std::string &  id,
size_t  index,
const std::string &  description,
const std::string &  sequence 
)

Member Function Documentation

bool pwiz::proteome::Protein::empty ( ) const

Member Data Documentation

std::string pwiz::proteome::Protein::id
size_t pwiz::proteome::Protein::index
std::string pwiz::proteome::Protein::description

Definition at line 44 of file ProteomeData.hpp.

Referenced by pwiz::proteome::TextWriter::operator()().


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