represents a peptide or polypeptide (a sequence of amino acids) More...
#include <Peptide.hpp>
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 &) | |
| Peptide & | operator= (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 | |
| ModificationMap & | modifications () |
| the map of sequence offsets (0-based) to modifications; modifications can be added or removed from the peptide with this map | |
| const ModificationMap & | modifications () 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
| pwiz::proteome::Peptide::Peptide | ( | const std::string & | sequence = "", |
| MODIFICATION_PARSING_ARGUMENTS | |||
| ) |
| pwiz::proteome::Peptide::Peptide | ( | const char * | sequence, |
| MODIFICATION_PARSING_ARGUMENTS | |||
| ) |
| pwiz::proteome::Peptide::Peptide | ( | std::string::const_iterator | begin, |
| std::string::const_iterator | end, | ||
| MODIFICATION_PARSING_ARGUMENTS | |||
| ) |
| pwiz::proteome::Peptide::Peptide | ( | const char * | begin, |
| const char * | end, | ||
| MODIFICATION_PARSING_ARGUMENTS | |||
| ) |
| pwiz::proteome::Peptide::Peptide | ( | const Peptide & | ) |
|
virtual |
Member Function Documentation
| const std::string& pwiz::proteome::Peptide::sequence | ( | ) | const |
returns the sequence of amino acids making up the peptide
Referenced by fragmentTest(), modificationTest(), pwiz::proteome::TextWriter::operator()(), DigestedPeptideLessThan::operator()(), pwiz::tradata::TextWriter::operator()(), peptideTest(), test(), testConversion(), testDigestionMetadata(), testNontrypticBSA(), testPeptide(), testProtein(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), testTrypticBSA(), and writeFragmentation().
| 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().
| 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().
| 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().
| 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().
| const ModificationMap& pwiz::proteome::Peptide::modifications | ( | ) | const |
the map of sequence offsets (0-based) to modifications
| 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().
| bool pwiz::proteome::Peptide::operator== | ( | const Peptide & | rhs | ) | const |
returns true iff peptide sequences and modifications are equal
| 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 Function Documentation
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friend |
Definition at line 112 of file Peptide.hpp.
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friend |
Definition at line 113 of file Peptide.hpp.
Member Data Documentation
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private |
Definition at line 114 of file Peptide.hpp.
The documentation for this class was generated from the following file:
- /Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/proteome/Peptide.hpp
