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30 #include <boost/shared_ptr.hpp>
36 class ModificationMap;
45 ModificationParsing_Auto
53 ModificationDelimiter_Braces
56 #define MODIFICATION_PARSING_ARGUMENTS \
57 ModificationParsing mp = ModificationParsing_Off, \
58 ModificationDelimiter md = ModificationDelimiter_Parentheses
134 double a(
size_t length,
size_t charge = 0)
const;
140 double b(
size_t length,
size_t charge = 0)
const;
146 double c(
size_t length,
size_t charge = 0)
const;
152 double x(
size_t length,
size_t charge = 0)
const;
158 double y(
size_t length,
size_t charge = 0)
const;
164 double z(
size_t length,
size_t charge = 0)
const;
170 double zRadical(
size_t length,
size_t charge = 0)
const;
186 #endif // _PEPTIDE_HPP_
maps peptide/protein sequence indexes (0-based) to a modification list
chemistry::Formula formula(bool modified=false) const
if modified = false: returns the composition formula of sequence()+water if modified = true: returns ...
double c(size_t length, size_t charge=0) const
returns the c ion of length <length> example: c(1) returns the c1 ion if <charge> = 0: returns neutra...
Peptide & operator=(const Peptide &)
ModificationDelimiter_Parentheses
double a(size_t length, size_t charge=0) const
returns the a ion of length <length>; example: a(1) returns the a1 ion if <charge> = 0: returns neutr...
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 t...
represents a peptide or polypeptide (a sequence of amino acids)
bool operator==(const Peptide &rhs) const
returns true iff peptide sequences and modifications are equal
Peptide(const char *begin, const char *end, MODIFICATION_PARSING_ARGUMENTS)
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 t...
Peptide(const char *sequence, MODIFICATION_PARSING_ARGUMENTS)
double zRadical(size_t length, size_t charge=0) const
returns the z radical ion of length <length> example: zRadical(1) returns the z1* ion if <charge> = 0...
ModificationDelimiter_Brackets
'(' and ')'
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
Fragmentation(const Fragmentation &)
bool operator<(const Peptide &rhs) const
returns true iff this peptide has a lesser sequence length, sequence, modifications length,...
double y(size_t length, size_t charge=0) const
returns the y ion of length <length> example: y(1) returns the y1 ion if <charge> = 0: returns neutra...
double x(size_t length, size_t charge=0) const
returns the x ion of length <length> example: x(1) returns the x1 ion if <charge> = 0: returns neutra...
boost::shared_ptr< Impl > impl_
Peptide(std::string::const_iterator begin, std::string::const_iterator end, MODIFICATION_PARSING_ARGUMENTS)
ModificationParsing_ByMass
oxidized P in peptide: PEP(O)TIDE
const std::string & sequence() const
returns the sequence of amino acids making up the peptide
boost::shared_ptr< Impl > impl_
const ModificationMap & modifications() const
the map of sequence offsets (0-based) to modifications
Fragmentation(const Peptide &peptide, bool monoisotopic, bool modified)
double z(size_t length, size_t charge=0) const
returns the z ion of length <length> example: z(1) returns the z1 ion if <charge> = 0: returns neutra...
ModificationParsing_ByFormula
any non-AA characters will cause an exception
ModificationMap & modifications()
the map of sequence offsets (0-based) to modifications; modifications can be added or removed from th...
Peptide(const std::string &sequence="", MODIFICATION_PARSING_ARGUMENTS)
provides fragment ion masses for a peptide
double b(size_t length, size_t charge=0) const
returns the b ion of length <length> example: b(1) returns the b1 ion if <charge> = 0: returns neutra...
#define MODIFICATION_PARSING_ARGUMENTS
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 modi...