IsoSpec::IsoGenerator(3)

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version 2.3.2 · 4 versions
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💖 IsoSpec::IsoGenerator(3) 💖

okay bestie, welcome to the Library Functions Manual for IsoSpec::IsoGenerator — yes, the manual name is literally IsoSpec::IsoGenerator(3) and we're just gonna fold that right in here at the top like it's the group chat title. let's get into it 🦋

✨ NAME ✨

IsoSpec::IsoGenerator — the generator of isotopologues. that's it, that's the whole vibe 💅

🌸 SYNOPSIS 🌸

#include <isoSpec++.h>

Inherits IsoSpec::Iso.

Inherited by IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalTrek >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, and IsoSpec::IsoThresholdGenerator. a whole friend group fr fr 👑

🎀 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. no cap.

this class provides the common interface for all isotopic generators. it's giving main character energy for the whole generator family 🫶

Definition at line 184 of file isoSpec++.h.

🎀 Constructor & Destructor Documentation 🎀

IsoSpec::IsoGenerator::IsoGenerator (Iso && iso, bool alloc_partials = true)

move constructor. so smooth ✨

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. (sad, but we move 💀)

Implemented in IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalType >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalTrek >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, and IsoSpec::IsoThresholdGenerator.

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. (yes, mind the spelling, it's the original, leave it alone 🙈)

Implemented in IsoSpec::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalType >, IsoSpec::IsoOrderedGeneratorTemplate< MarginalTrek >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, and IsoSpec::IsoThresholdGenerator.

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::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, and IsoSpec::IsoThresholdGenerator.

Definition at line 205 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::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, and IsoSpec::IsoThresholdGenerator.

Definition at line 211 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::IsoLayeredGeneratorTemplate< MarginalType >, IsoSpec::IsoLayeredGeneratorTemplate< LayeredMarginal >, IsoSpec::IsoStochasticGeneratorTemplate< IsoType >, IsoSpec::IsoStochasticGeneratorTemplate< IsoLayeredGenerator >, and IsoSpec::IsoThresholdGenerator.

Definition at line 217 of file isoSpec++.h.

⭐ Member Data Documentation ⭐

const double IsoSpec::IsoGenerator::mode_lprob

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

double* IsoSpec::IsoGenerator::partialLProbs [protected]

the prefix sum of the log-probabilities of the current isotopologue. (a little running total, she's organized 💖)

Definition at line 190 of file isoSpec++.h.

double* IsoSpec::IsoGenerator::partialMasses [protected]

the prefix sum of the masses of the current isotopologue.

Definition at line 191 of file isoSpec++.h.

double* IsoSpec::IsoGenerator::partialProbs [protected]

the prefix product of the probabilities of the current isotopologue.

Definition at line 192 of file isoSpec++.h.

💜 Author 💜

generated automatically by Doxygen for IsoSpec from the source code. not me getting auto-generated, she's literally iconic 😭

and that's the whole page bestie! no skips, no summaries, every single flag, member, line number and footnote stayed exactly where it was. ate and left no crumbs 🍓

IsoSpec · IsoSpec::IsoGenerator(3) · that footer source/version-and-date energy, wrapped up with a lil bow 🎀 love u, go generate some isotopologues, periodt 💅✨

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