libpappsomspp
Library for mass spectrometry
|
#include <aabase.h>
Public Member Functions | |
virtual pappso_double | getMass () const |
virtual const char & | getLetter () const |
const AminoAcidChar & | getAminoAcidChar () const |
virtual void | replaceLeucineIsoleucine () |
Static Public Member Functions | |
static const std::vector< AminoAcidChar > & | getAminoAcidCharList () |
Protected Member Functions | |
AaBase (char aa_letter) | |
AaBase (AminoAcidChar aa_char) | |
AaBase (const AaBase &aabase) | |
virtual | ~AaBase () |
virtual int | getNumberOfAtom (AtomIsotopeSurvey atom) const override |
get the number of atom C, O, N, H in the molecule | |
int | getNumberOfIsotope (Isotope isotope) const override |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule | |
Static Protected Member Functions | |
static pappso_double | getAaMass (char aa_letter) |
Protected Attributes | |
char | m_aaLetter |
Private Types | |
using | AaMassMap = std::map< char, pappso_double > |
using | AaIntMap = std::map< char, unsigned int > |
using | AminoAcidCharList = std::vector< AminoAcidChar > |
Static Private Attributes | |
static AaMassMap | m_aaMassMap |
static AaIntMap | m_aaNumberOfCarbonMap |
static AaIntMap | m_aaNumberOfSulfurMap |
static AaIntMap | m_aaNumberOfHydrogenMap |
static AaIntMap | m_aaNumberOfNitrogenMap |
static AaIntMap | m_aaNumberOfOxygenMap |
static AminoAcidCharList | m_aminoAcidCharList |
Friends | |
class | AaModification |
|
private |
|
private |
|
private |
|
protected |
Definition at line 42 of file aabase.cpp.
References m_aaMassMap.
|
protected |
Definition at line 56 of file aabase.cpp.
|
protected |
Definition at line 61 of file aabase.cpp.
|
protectedvirtual |
Definition at line 65 of file aabase.cpp.
|
staticprotected |
Definition at line 379 of file aabase.cpp.
References m_aaMassMap.
const AminoAcidChar & pappso::AaBase::getAminoAcidChar | ( | ) | const |
|
static |
Definition at line 445 of file aabase.cpp.
References m_aminoAcidCharList.
|
virtual |
Definition at line 433 of file aabase.cpp.
References m_aaLetter.
Referenced by pappso::specglob::PeptideModel::checkForAaModification(), pappso::specglob::PeptideModel::checkForMutation(), pappso::AaModification::createInstanceMutation(), pappso::AaStringCodeMassMatching::getAaCodeFromMassWearingModification(), pappso::Aa::toAbsoluteString(), pappso::Aa::toProForma(), and pappso::Aa::toString().
|
virtual |
Reimplemented in pappso::Aa.
Definition at line 386 of file aabase.cpp.
References m_aaLetter, and m_aaMassMap.
Referenced by pappso::Aa::getMass().
|
overrideprotectedvirtual |
get the number of atom C, O, N, H in the molecule
Implements pappso::AtomNumberInterface.
Reimplemented in pappso::Aa.
Definition at line 393 of file aabase.cpp.
References pappso::C, pappso::H, m_aaLetter, m_aaNumberOfCarbonMap, m_aaNumberOfHydrogenMap, m_aaNumberOfNitrogenMap, m_aaNumberOfOxygenMap, m_aaNumberOfSulfurMap, pappso::N, pappso::O, and pappso::S.
Referenced by pappso::Aa::getNumberOfAtom().
|
overrideprotectedvirtual |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 426 of file aabase.cpp.
|
virtual |
Definition at line 418 of file aabase.cpp.
References m_aaLetter.
|
friend |
|
protected |
Definition at line 68 of file aabase.h.
Referenced by getAminoAcidChar(), getLetter(), getMass(), getNumberOfAtom(), pappso::Aa::isAaEqual(), pappso::Aa::isLesser(), pappso::Aa::operator=(), and replaceLeucineIsoleucine().
|
staticprivate |
Definition at line 75 of file aabase.h.
Referenced by AaBase(), getAaMass(), and getMass().
|
staticprivate |
Definition at line 76 of file aabase.h.
Referenced by getNumberOfAtom().
|
staticprivate |
Definition at line 78 of file aabase.h.
Referenced by getNumberOfAtom().
|
staticprivate |
Definition at line 79 of file aabase.h.
Referenced by getNumberOfAtom().
|
staticprivate |
Definition at line 80 of file aabase.h.
Referenced by getNumberOfAtom().
|
staticprivate |
Definition at line 77 of file aabase.h.
Referenced by getNumberOfAtom().
|
staticprivate |
Definition at line 81 of file aabase.h.
Referenced by getAminoAcidCharList().