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IsoSpec
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IsoSpec
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Public Member Functions | |
| IsoStochasticGeneratorTemplate (Iso &&iso, size_t no_molecules, double precision=0.9999, double beta_bias=5.0, std::mt19937 &rdvariate_gen=random_gen) | |
| ISOSPEC_FORCE_INLINE size_t | count () const |
| ISOSPEC_FORCE_INLINE double | mass () const override final |
| Get the mass of the current isotopologue. | |
| ISOSPEC_FORCE_INLINE double | prob () const override final |
| Get the probability of the current isotopologue. | |
| ISOSPEC_FORCE_INLINE double | lprob () const override final |
| Get the log-probability of the current isotopologue. | |
| ISOSPEC_FORCE_INLINE void | get_conf_signature (int *space) const override final |
| Write the signature of configuration into target memory location. It must be large enough to accomodate it. | |
| ISOSPEC_FORCE_INLINE bool | advanceToNextConfiguration () override final |
| Advance to the next, not yet visited, most probable isotopologue. | |
| ISOSPEC_FORCE_INLINE void | get_indexes (int *space) |
| Public Member Functions inherited from IsoSpec::IsoGenerator | |
| 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. | |
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. | |
| Public Attributes inherited from IsoSpec::IsoGenerator | |
| const double | mode_lprob |
| Protected Member Functions inherited from IsoSpec::Iso | |
| bool | doMarginalsNeedSorting () const |
| Protected Attributes inherited from IsoSpec::IsoGenerator | |
| 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 |
Definition at line 586 of file isoSpec++.h.
| IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::IsoStochasticGeneratorTemplate | ( | Iso && | iso, |
| size_t | no_molecules, | ||
| double | precision = 0.9999, | ||
| double | beta_bias = 5.0, | ||
| std::mt19937 & | rdvariate_gen = random_gen ) |
Definition at line 930 of file isoSpec++.cpp.
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inlinefinaloverridevirtual |
Advance to the next, not yet visited, most probable isotopologue.
Implements IsoSpec::IsoGenerator.
Definition at line 610 of file isoSpec++.h.
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inline |
Definition at line 600 of file isoSpec++.h.
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inlinefinaloverridevirtual |
Write the signature of configuration into target memory location. It must be large enough to accomodate it.
Implements IsoSpec::IsoGenerator.
Definition at line 608 of file isoSpec++.h.
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inline |
Definition at line 685 of file isoSpec++.h.
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inlinefinaloverridevirtual |
Get the log-probability of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator.
Definition at line 606 of file isoSpec++.h.
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inlinefinaloverridevirtual |
Get the mass of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator.
Definition at line 602 of file isoSpec++.h.
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inlinefinaloverridevirtual |
Get the probability of the current isotopologue.
Reimplemented from IsoSpec::IsoGenerator.
Definition at line 604 of file isoSpec++.h.
1.15.0