--- name: "IsoSpec_Iso" section: "3" platform: "linux" package: "libisospec++-dev" version: "2.2.1-4.1+b3" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/IsoSpec_Iso" --- # IsoSpec\_Iso(3) The Iso class for the calculation of the isotopic distribution. ## NAME IsoSpec::Iso - The **Iso** class for the calculation of the isotopic distribution. ## SYNOPSIS `#include ` Inherited by **IsoSpec::IsoGenerator**. ### Public Member Functions **Iso** (int \_dimNumber, const int \*\_isotopeNumbers, const int \*\_atomCounts, const double \*\_isotopeMasses, const double \*\_isotopeProbabilities)\ General constructror. **Iso** (int \_dimNumber, const int \*\_isotopeNumbers, const int \*\_atomCounts, const double \*const \*\_isotopeMasses, const double \*const \*\_isotopeProbabilities)\ **Iso** (const char \*formula, bool use\_nominal\_masses=false)\ Constructor from the formula object. **Iso** (const std::string &formula, bool use\_nominal\_masses=false)\ Constructor from C++ std::string chemical formula. **Iso** (**Iso** &&other)\ The move constructor. **Iso** & **operator=** (const **Iso** &other)=delete\ **Iso** (const **Iso** &other, bool fullcopy)\ The copy constructor. virtual **~Iso** ()\ Destructor. double **getLightestPeakMass** () const\ Get the mass of the lightest peak in the isotopic distribution. double **getHeaviestPeakMass** () const\ Get the mass of the heaviest peak in the isotopic distribution. double **getMonoisotopicPeakMass** () const\ double **getModeLProb** () const\ Get the log-probability of the mode-configuration (if there are many modes, they share this value). double **getUnlikeliestPeakLProb** () const\ Get the logprobability of the least probable subisotopologue. double **getModeMass** () const\ Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected). double **getTheoreticalAverageMass** () const\ Get the theoretical average mass of the molecule. double **variance** () const\ Get the theoretical variance of the distribution. double **stddev** () const\ Get the standard deviation of the theoretical distribution. int **getDimNumber** () const\ Get the number of elements in the chemical formula of the molecule. int **getAllDim** () const\ Get the total number of isotopes of elements present in a chemical formula. void **addElement** (int atomCount, int noIsotopes, const double \*isotopeMasses, const double \*isotopeProbabilities)\ Add an element to the molecule. Note: this method can only be used BEFORE **Iso** is used to construct an **IsoGenerator** instance. void **saveMarginalLogSizeEstimates** (double \*priorities, double target\_total\_prob) const\ Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array. Array priorities must have length equal to dimNumber. ### Static Public Member Functions static **Iso** **FromFASTA** (const char \*fasta, bool use\_nominal\_masses=false, bool add\_water=true)\ Constructor (named) from aminoacid FASTA sequence as C string. static **Iso** **FromFASTA** (const std::string &fasta, bool use\_nominal\_masses=false, bool add\_water=true)\ Constructor (named) from aminoacid FASTA sequence as C++ std::string. See above for details. ### Protected Member Functions bool **doMarginalsNeedSorting** () const\ ### Protected Attributes int **dimNumber**\ int \* **isotopeNumbers**\ int \* **atomCounts**\ unsigned int **confSize**\ int **allDim**\ **Marginal** \*\* **marginals**\ ## Detailed Description The **Iso** class for the calculation of the isotopic distribution. It contains full description of the molecule for which one would like to calculate the isotopic distribution. Definition at line **49** of file **isoSpec++.h**. ## Constructor & Destructor Documentation ### IsoSpec::Iso::Iso () Definition at line **50** of file **isoSpec++.cpp**. ### IsoSpec::Iso::Iso (int \_dimNumber, const int \* \_isotopeNumbers, const int \* \_atomCounts, const double \* \_isotopeMasses, const double \* \_isotopeProbabilities) General constructror. **Parameters** *\_dimNumber* The number of elements in the formula, e.g. for C100H202 it would be 2, as there are only carbon and hydrogen atoms. \ *\_isotopeNumbers* A table with numbers of isotopes for each element, e.g. for C100H202 it would be {2, 2}, because both C and H have two stable isotopes. \ *\_atomCounts* Number of atoms of each element in the formula, e.g. for C100H202 corresponds to {100, 202}. \ *\_isotopeMasses* A table of tables of masses of isotopes of the elements in the chemical formula, e.g. {{12.0, 13.003355}, {1.007825, 2.014102}} for C100H202. \ *\_isotopeProbabilities* A table of tables of isotope frequencies of the elements in the chemical formula, e.g. {{.989212, .010788}, {.999885, .000115}} for C100H202. Definition at line **109** of file **isoSpec++.cpp**. ### IsoSpec::Iso::Iso (int \_dimNumber, const int \* \_isotopeNumbers, const int \* \_atomCounts, const double \*const \* \_isotopeMasses, const double \*const \* \_isotopeProbabilities) Definition at line **61** of file **isoSpec++.cpp**. ### IsoSpec::Iso::Iso (const char \* formula, bool use\_nominal\_masses = `false`) Constructor from the formula object. Definition at line **310** of file **isoSpec++.cpp**. ### IsoSpec::Iso::Iso (const std::string & formula, bool use\_nominal\_masses = `false`)` [inline]` Constructor from C++ std::string chemical formula. Definition at line **102** of file **isoSpec++.h**. ### IsoSpec::Iso::Iso (Iso && other) The move constructor. Definition at line **140** of file **isoSpec++.cpp**. ### IsoSpec::Iso::Iso (const Iso & other, bool fullcopy) The copy constructor. **Parameters** *other* The other instance of the **Iso** class. \ *fullcopy* If false, copy only the number of atoms in the formula, the size of the configuration, the total number of isotopes, and the probability of the mode isotopologue. Definition at line **153** of file **isoSpec++.cpp**. ### IsoSpec::Iso::~Iso ()` [virtual]` Destructor. Definition at line **221** of file **isoSpec++.cpp**. ## Member Function Documentation ### void IsoSpec::Iso::addElement (int atomCount, int noIsotopes, const double \* isotopeMasses, const double \* isotopeProbabilities) Add an element to the molecule. Note: this method can only be used BEFORE **Iso** is used to construct an **IsoGenerator** instance. Definition at line **324** of file **isoSpec++.cpp**. ### bool IsoSpec::Iso::doMarginalsNeedSorting () const` [protected]` Definition at line **232** of file **isoSpec++.cpp**. ### Iso IsoSpec::Iso::FromFASTA (const char \* fasta, bool use\_nominal\_masses = `false`, bool add\_water = `true`)` [static]` Constructor (named) from aminoacid FASTA sequence as C string. **Parameters** *fasta* An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain selenocystein (U) or xleucine (J). Other characters, including FASTA codes of indeterminate chemical formula (X, \*, -, B, ...) are silently ignored. That means 'AEDA', 'AE-DA', 'EAXXDA', 'AE DA' will all result in the same chemical formula. Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present. \\use\_nominal\_masses Whether to use nucleon number instead of the real mass of each isotope during calculations. \\add\_water Whether the chain should have the terminating -H and -OH groups at the N and C terminus, respectively. Definition at line **169** of file **isoSpec++.cpp**. ### static Iso IsoSpec::Iso::FromFASTA (const std::string & fasta, bool use\_nominal\_masses = `false`, bool add\_water = `true`)` [inline]`, ` [static]` Constructor (named) from aminoacid FASTA sequence as C++ std::string. See above for details. Definition at line **116** of file **isoSpec++.h**. ### int IsoSpec::Iso::getAllDim () const` [inline]` Get the total number of isotopes of elements present in a chemical formula. Definition at line **169** of file **isoSpec++.h**. ### int IsoSpec::Iso::getDimNumber () const` [inline]` Get the number of elements in the chemical formula of the molecule. Definition at line **166** of file **isoSpec++.h**. ### double IsoSpec::Iso::getHeaviestPeakMass () const Get the mass of the heaviest peak in the isotopic distribution. Definition at line **253** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getLightestPeakMass () const Get the mass of the lightest peak in the isotopic distribution. Definition at line **245** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getModeLProb () const Get the log-probability of the mode-configuration (if there are many modes, they share this value). Definition at line **285** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getModeMass () const Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected). Definition at line **277** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getMonoisotopicPeakMass () const Get the mass of the monoisotopic peak in the isotopic distribution. Monoisotopc molecule is defined as consisting only of the most frequent isotopes of each element. These are often (but not always) the lightest ones, making this often (but again, not always) equal to **getLightestPeakMass()** Definition at line **261** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getTheoreticalAverageMass () const Get the theoretical average mass of the molecule. Definition at line **293** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::getUnlikeliestPeakLProb () const Get the logprobability of the least probable subisotopologue. Definition at line **269** of file **isoSpec++.cpp**. ### void IsoSpec::Iso::saveMarginalLogSizeEstimates (double \* priorities, double target\_total\_prob) const Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array. Array priorities must have length equal to dimNumber. Definition at line **335** of file **isoSpec++.cpp**. ### double IsoSpec::Iso::stddev () const` [inline]` Get the standard deviation of the theoretical distribution. Definition at line **163** of file **isoSpec++.h**. ### double IsoSpec::Iso::variance () const Get the theoretical variance of the distribution. Definition at line **301** of file **isoSpec++.cpp**. ## Member Data Documentation ### int IsoSpec::Iso::allDim` [protected]` The total number of isotopes of elements present in a chemical formula, e.g. for H20 it is 2+3=5. Definition at line **67** of file **isoSpec++.h**. ### int\* IsoSpec::Iso::atomCounts` [protected]` A table with numbers of isotopes for each element. Definition at line **65** of file **isoSpec++.h**. ### unsigned int IsoSpec::Iso::confSize` [protected]` The number of bytes needed to represent the counts of isotopes present in the extended chemical formula. Definition at line **66** of file **isoSpec++.h**. ### int IsoSpec::Iso::dimNumber` [protected]` The number of elements in the chemical formula of the molecule. Definition at line **63** of file **isoSpec++.h**. ### int\* IsoSpec::Iso::isotopeNumbers` [protected]` A table with numbers of isotopes for each element. Definition at line **64** of file **isoSpec++.h**. ### Marginal\*\* IsoSpec::Iso::marginals` [protected]` The table of pointers to the distributions of individual subisotopologues. Definition at line **68** of file **isoSpec++.h**. ## Author Generated automatically by Doxygen for IsoSpec from the source code.