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IsoSpec
1.95
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The generator of isotopologues. More...
#include <isoSpec++.h>
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. | |
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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 |
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int | dimNumber |
int * | isotopeNumbers |
int * | atomCounts |
unsigned int | confSize |
int | allDim |
Marginal ** | marginals |
double | modeLProb |
The generator of isotopologues.
This class provides the common interface for all isotopic generators.
Definition at line 154 of file isoSpec++.h.
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pure virtual |
Advance to the next, not yet visited, most probable isotopologue.
Implemented in IsoSpec::IsoLayeredGenerator, IsoSpec::IsoThresholdGenerator, and IsoSpec::IsoOrderedGenerator.
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inlinevirtual |
Get the log-probability of the current isotopologue.
Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.
Definition at line 175 of file isoSpec++.h.
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inlinevirtual |
Get the mass of the current isotopologue.
Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.
Definition at line 181 of file isoSpec++.h.
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inlinevirtual |
Get the probability of the current isotopologue.
Reimplemented in IsoSpec::IsoLayeredGenerator, and IsoSpec::IsoThresholdGenerator.
Definition at line 187 of file isoSpec++.h.
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protected |
The prefix sum of the log-probabilities of the current isotopologue.
Definition at line 157 of file isoSpec++.h.
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protected |
The prefix sum of the masses of the current isotopologue.
Definition at line 158 of file isoSpec++.h.
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protected |
The prefix product of the probabilities of the current isotopologue.
Definition at line 159 of file isoSpec++.h.