--- name: "IsoSpec_IsoGenerator" 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_IsoGenerator" --- # IsoSpec\_IsoGenerator(3) The generator of isotopologues. ## NAME IsoSpec::IsoGenerator - The generator of isotopologues. ## SYNOPSIS `#include ` Inherits **IsoSpec::Iso**. Inherited by **IsoSpec::IsoLayeredGenerator**, **IsoSpec::IsoOrderedGenerator**, **IsoSpec::IsoStochasticGenerator**, and **IsoSpec::IsoThresholdGenerator**. ### Public Member Functions virtual bool **advanceToNextConfiguration** ()=0\ Advance to the next, not yet visited, most probable isotopologue. virtual double **lprob** () const\ Get the log-probability of the current isotopologue. virtual double **mass** () const\ Get the mass of the current isotopologue. virtual double **prob** () const\ Get the probability of the current isotopologue. virtual void **get\_conf\_signature** (int \*space) const =0\ Write the signature of configuration into target memory location. It must be large enough to accomodate it. **IsoGenerator** (**Iso** &&iso, bool alloc\_partials=true)\ Move constructor. virtual **~IsoGenerator** ()\ Destructor. Public Member Functions inherited from **IsoSpec::Iso** **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. ### Public Attributes const double **mode\_lprob**\ ### Protected Attributes double \* **partialLProbs**\ double \* **partialMasses**\ double \* **partialProbs**\ Protected Attributes inherited from **IsoSpec::Iso** int **dimNumber**\ int \* **isotopeNumbers**\ int \* **atomCounts**\ unsigned int **confSize**\ int **allDim**\ **Marginal** \*\* **marginals**\ ### Additional Inherited Members Static Public Member Functions inherited from **IsoSpec::Iso** 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 inherited from **IsoSpec::Iso** bool **doMarginalsNeedSorting** () const\ ## Detailed Description The generator of isotopologues. This class provides the common interface for all isotopic generators. Definition at line **183** of file **isoSpec++.h**. ## Constructor & Destructor Documentation ### IsoSpec::IsoGenerator::IsoGenerator (Iso && iso, bool alloc\_partials = `true`) Move constructor. Definition at line **442** of file **isoSpec++.cpp**. ### IsoSpec::IsoGenerator::~IsoGenerator ()` [virtual]` Destructor. Definition at line **460** of file **isoSpec++.cpp**. ## Member Function Documentation ### virtual bool IsoSpec::IsoGenerator::advanceToNextConfiguration ()` [pure virtual]` Advance to the next, not yet visited, most probable isotopologue. **Returns** Return false if it is not possible to advance. Implemented in **IsoSpec::IsoOrderedGenerator**, **IsoSpec::IsoThresholdGenerator**, **IsoSpec::IsoLayeredGenerator**, and **IsoSpec::IsoStochasticGenerator**. ### virtual void IsoSpec::IsoGenerator::get\_conf\_signature (int \* space) const` [pure virtual]` Write the signature of configuration into target memory location. It must be large enough to accomodate it. Implemented in **IsoSpec::IsoOrderedGenerator**, **IsoSpec::IsoThresholdGenerator**, **IsoSpec::IsoLayeredGenerator**, and **IsoSpec::IsoStochasticGenerator**. ### virtual double IsoSpec::IsoGenerator::lprob () const` [inline]`, ` [virtual]` Get the log-probability of the current isotopologue. **Returns** The log-probability of the current isotopologue. Reimplemented in **IsoSpec::IsoThresholdGenerator**, **IsoSpec::IsoLayeredGenerator**, and **IsoSpec::IsoStochasticGenerator**. Definition at line **204** of file **isoSpec++.h**. ### virtual double IsoSpec::IsoGenerator::mass () const` [inline]`, ` [virtual]` Get the mass of the current isotopologue. **Returns** The mass of the current isotopologue. Reimplemented in **IsoSpec::IsoThresholdGenerator**, **IsoSpec::IsoLayeredGenerator**, and **IsoSpec::IsoStochasticGenerator**. Definition at line **210** of file **isoSpec++.h**. ### virtual double IsoSpec::IsoGenerator::prob () const` [inline]`, ` [virtual]` Get the probability of the current isotopologue. **Returns** The probability of the current isotopologue. Reimplemented in **IsoSpec::IsoThresholdGenerator**, **IsoSpec::IsoLayeredGenerator**, and **IsoSpec::IsoStochasticGenerator**. Definition at line **216** of file **isoSpec++.h**. ## Member Data Documentation ### const double IsoSpec::IsoGenerator::mode\_lprob Definition at line **186** of file **isoSpec++.h**. ### double\* IsoSpec::IsoGenerator::partialLProbs` [protected]` The prefix sum of the log-probabilities of the current isotopologue. Definition at line **189** of file **isoSpec++.h**. ### double\* IsoSpec::IsoGenerator::partialMasses` [protected]` The prefix sum of the masses of the current isotopologue. Definition at line **190** of file **isoSpec++.h**. ### double\* IsoSpec::IsoGenerator::partialProbs` [protected]` The prefix product of the probabilities of the current isotopologue. Definition at line **191** of file **isoSpec++.h**. ## Author Generated automatically by Doxygen for IsoSpec from the source code.