The generator of isotopologues. More...

#include <isoSpec++.h>

Inheritance diagram for IsoSpec::IsoGenerator:

Public Member Functions
virtual bool	advanceToNextConfiguration ()=0
	Advance to the next, not yet visited, most probable isotopologue. More...

virtual ISOSPEC_FORCE_INLINE bool	advanceToNextConfigurationWithinLayer ()

virtual ISOSPEC_FORCE_INLINE bool	nextLayer (double)

virtual double	lprob () const
	Get the log-probability of the current isotopologue. More...

virtual double	mass () const
	Get the mass of the current isotopologue. More...

virtual double	prob () const
	Get the probability of the current isotopologue. More...

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 const _isotopeMasses, const double const _isotopeProbabilities)
	General constructror. More...

	Iso (const char *formula)
	Constructor from the formula object.

	Iso (const std::string &formula)
	Constructor from C++ std::string chemical formula.

	Iso (Iso &&other)
	The move constructor.

	Iso (const Iso &other, bool fullcopy)
	The copy constructor. More...

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.

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.

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

double	modeLProb

Detailed Description

The generator of isotopologues.

This class provides the common interface for all isotopic generators.

Definition at line 154 of file isoSpec++.h.

Member Function Documentation

◆ advanceToNextConfiguration()

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::IsoLayeredGenerator, IsoSpec::IsoThresholdGenerator, and IsoSpec::IsoOrderedGenerator.

◆ lprob()

virtual double IsoSpec::IsoGenerator::lprob ( ) const

inlinevirtual

Get the log-probability of the current isotopologue.

Returns: The log-probability of the current isotopologue.

Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.

Definition at line 175 of file isoSpec++.h.

◆ mass()

virtual double IsoSpec::IsoGenerator::mass ( ) const

inlinevirtual

Get the mass of the current isotopologue.

Returns: The mass of the current isotopologue.

Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.

Definition at line 181 of file isoSpec++.h.

◆ prob()

virtual double IsoSpec::IsoGenerator::prob ( ) const

inlinevirtual

Get the probability of the current isotopologue.

Returns: The probability of the current isotopologue.

Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.

Definition at line 187 of file isoSpec++.h.

Member Data Documentation

◆ partialLProbs

double* IsoSpec::IsoGenerator::partialLProbs

protected

The prefix sum of the log-probabilities of the current isotopologue.

Definition at line 157 of file isoSpec++.h.

◆ partialMasses

double* IsoSpec::IsoGenerator::partialMasses

protected

The prefix sum of the masses of the current isotopologue.

Definition at line 158 of file isoSpec++.h.

◆ partialProbs

double* IsoSpec::IsoGenerator::partialProbs

protected

The prefix product of the probabilities of the current isotopologue.

Definition at line 159 of file isoSpec++.h.

The documentation for this class was generated from the following files:

IsoSpec++/isoSpec++.h
IsoSpec++/isoSpec++.cpp

Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ advanceToNextConfiguration()

◆ lprob()

◆ mass()

◆ prob()

Member Data Documentation

◆ partialLProbs

◆ partialMasses

◆ partialProbs