libpappsomspp
Library for mass spectrometry
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32 #include "../pappsoexception.h"
42 #define CACHE_ARRAY_SIZE 500
57 for(
unsigned int d = 1; d <= k; ++d)
81 return (pow(abundance, heavy) * pow((
double)1 - abundance, (total - heavy)) *
201 PeptideNaturalIsotope::PeptideNaturalIsotope(
203 : m_peptide(peptide), m_mapIsotope(map_isotope)
218 int number_of_fixed_oxygen =
221 int number_of_fixed_sulfur =
239 number_of_fixed_oxygen,
244 number_of_fixed_oxygen,
249 number_of_fixed_sulfur,
254 number_of_fixed_sulfur,
259 number_of_fixed_sulfur,
279 : m_peptide(other.m_peptide), m_mapIsotope(other.m_mapIsotope)
313 return m_peptide.get()->getNumberOfAtom(atom);
320 m_peptide.get()->getNumberOfIsotope(isotope);
323 const std::map<Isotope, int> &
pappso_double ratioH2_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
double pappso_double
A type definition for doubles.
pappso_double isotopem_ratio_cache(Isotope isotope, unsigned int total, unsigned int heavy)
pappso_double ratioS34_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double ratioO17_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCEO17(0.000372)
const pappso_double ABUNDANCES36(0.00020)
virtual int getNumberOfIsotope(Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
const pappso_double ABUNDANCES33(0.00750)
const PeptideInterfaceSp m_peptide
const pappso_double ABUNDANCEH2(0.00015574)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN)
const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM)
pappso_double ratioC13_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double ABUNDANCEN15(0.003663)
const std::map< Isotope, int > & getIsotopeMap() const
uint64_t Combinations(unsigned int n, unsigned int k)
const pappso_double DIFFS32S33(32.97145876 - MASSSULFUR)
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
virtual const QString getSequence() const override
amino acid sequence without modification
virtual unsigned int size() const override
peptide natural isotope model
pappso_double isotopem_ratio(pappso_double abundance, unsigned int total, unsigned int heavy)
const pappso_double DIFFS32S34(33.96786690 - MASSSULFUR)
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
const pappso_double DIFFC12C13(1.0033548378)
uint64_t combinations_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
virtual bool isPalindrome() const override
tells if the peptide sequence is a palindrome
PeptideNaturalIsotope(const PeptideInterfaceSp &peptide, const std::map< Isotope, int > &map_isotope)
const pappso_double DIFFS32S36(35.96708076 - MASSSULFUR)
const pappso_double ABUNDANCES34(0.04215)
const pappso_double ABUNDANCEC13(0.011078)
pappso_double ratioS36_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double getMass() const override
virtual unsigned int getIsotopeNumber() const
pappso_double ratioN15_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double getIntensityRatio(unsigned int charge) const
const std::map< Isotope, int > m_mapIsotope
const pappso_double DIFFO16O17(16.99913150 - MASSOXYGEN)
const pappso_double ABUNDANCEO18(0.0020004)
pappso_double ratioO18_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
pappso_double ratioS33_cache[CACHE_ARRAY_SIZE][CACHE_ARRAY_SIZE]
const pappso_double DIFFO16O18(17.9991610 - MASSOXYGEN)