ISOSPEC_ISOSTOCHASTICGENERATOR(3)

📦
version 2.2.1 · 3 versions
, in debian trixie, ubuntu noble, ubuntu questing

💖 IsoSpec::IsoStochasticGenerator — Library Functions Manual 💖

okay bestie, welcome to the IsoSpec::IsoStochasticGenerator(3) page, from the Library Functions Manual. this is the stochastic generator class in IsoSpec and she is serving. let's get into it ✨

🌸 NAME 🌸

IsoSpec::IsoStochasticGenerator — the iconic class itself. periodt.

🦋 SYNOPSIS 🦋

she inherits from IsoSpec::IsoGenerator. family tree matters, ok?

✨ Public Member Functions ✨

  • IsoStochasticGenerator (Iso &&iso, size_t no_molecules, double precision=0.9999, double beta_bias=5.0) — the glow-up constructor, takes an rvalue Iso, a molecule count, a precision (defaults to 0.9999) and a beta bias (defaults to 5.0).
  • ISOSPEC_FORCE_INLINE size_t count () const — counts things. she's giving efficiency.
  • 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. no cap.
  • ISOSPEC_FORCE_INLINE double lprob () const override final — get the log-probability of the current isotopologue. math girlie behavior.
  • 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. (yes, we said accomodate, that's literally how the original spells it, don't @ me 😭)
  • ISOSPEC_FORCE_INLINE bool advanceToNextConfiguration () override final — advance to the next, not yet visited, most probable isotopologue. moving forward, always. 🧚

💜 Public Member Functions inherited from IsoSpec::IsoGenerator

  • IsoGenerator (Iso &&iso, bool alloc_partials=true) — the move constructor. she moves, she grooves.
  • virtual ~IsoGenerator () — the destructor. say bye bestie 🫶

🎀 Public Member Functions inherited from IsoSpec::Iso

  • Iso (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities) — the general constructror. (again, original spelling, i don't make the rules ✋)
  • Iso (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) — another constructor, this time with const pointers to pointers. extra spice.
  • 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 a C++ std::string chemical formula.
  • Iso (Iso &&other) — the move constructor.
  • Iso & operator= (const Iso &other)=delete — deleted. not allowed. she said no thank u 💀
  • Iso (const Iso &other, bool fullcopy) — the copy constructor.
  • virtual ~Iso () — the destructor.
  • double getLightestPeakMass () const — get the mass of the lightest peak in the isotopic distribution. tiny queen 👑
  • double getHeaviestPeakMass () const — get the mass of the heaviest peak in the isotopic distribution.
  • double getMonoisotopicPeakMass () const — the monoisotopic peak mass. that's it, that's the function.
  • double getModeLProb () const — get the log-probability of the mode-configuration. if there are many modes, they share this value. sharing is caring.
  • double getUnlikeliestPeakLProb () const — get the logprobability of the least probable subisotopologue. (one word, logprobability, we keep it as is 💅)
  • double getModeMass () const — get the mass of the mode-configuration. if there are many modes, it is undefined which one will be selected. lowkey chaotic but okay.
  • 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 bestie: this method can only be used BEFORE Iso is used to construct an IsoGenerator instance. like, before. do not try her afterwards. she will not play.
  • void saveMarginalLogSizeEstimates (double *priorities, double target_total_prob) const — save estimates of logarithms of target sizes of marginals using Gaussian approximation into the argument array. the array priorities must have length equal to dimNumber. no short arrays allowed 🙈

🌈 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 a 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 a C++ std::string. see above for details. iykyk.

💖 Public Attributes inherited from IsoSpec::IsoGenerator

  • const double mode_lprob — a whole public attribute, and she is const. respect.

🌸 Protected Member Functions inherited from IsoSpec::Iso

  • bool doMarginalsNeedSorting () const — asks the question we all ask ourselves sometimes.

🎀 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

👑 Detailed Description 👑

definition at line 542 of file isoSpec++.h. that's the whole description, she's mysterious like that. main character energy ✨

💅 Constructor & Destructor Documentation 💅

IsoSpec::IsoStochasticGenerator::IsoStochasticGenerator (Iso && iso, size_t no_molecules, double precision = 0.9999, double beta_bias = 5.0)

definition at line 923 of file isoSpec++.cpp. that's where she lives. 🏠

🔥 Member Function Documentation 🔥

ISOSPEC_FORCE_INLINE bool IsoSpec::IsoStochasticGenerator::advanceToNextConfiguration () [inline], [final], [override], [virtual]

advance to the next, not yet visited, most probable isotopologue. 💫

Returns

return false if it is not possible to advance. (sad but true.)

implements IsoSpec::IsoGenerator.

definition at line 565 of file isoSpec++.h.

ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGenerator::count () const [inline]

definition at line 555 of file isoSpec++.h. no description, just vibes. 🫶

ISOSPEC_FORCE_INLINE void IsoSpec::IsoStochasticGenerator::get_conf_signature (int * space) const [inline], [final], [override], [virtual]

write the signature of configuration into target memory location. it must be large enough to accomodate it. (yes, still spelled that way, love that for us 💖)

implements IsoSpec::IsoGenerator.

definition at line 563 of file isoSpec++.h.

ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::lprob () const [inline], [final], [override], [virtual]

get the log-probability of the current isotopologue.

Returns

the log-probability of the current isotopologue.

reimplemented from IsoSpec::IsoGenerator.

definition at line 561 of file isoSpec++.h.

ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::mass () const [inline], [final], [override], [virtual]

get the mass of the current isotopologue. ⚖️

Returns

the mass of the current isotopologue.

reimplemented from IsoSpec::IsoGenerator.

definition at line 557 of file isoSpec++.h.

ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGenerator::prob () const [inline], [final], [override], [virtual]

get the probability of the current isotopologue.

Returns

the probability of the current isotopologue.

reimplemented from IsoSpec::IsoGenerator.

definition at line 559 of file isoSpec++.h.

🎀 Author 🎀

generated automatically by Doxygen for IsoSpec from the source code. so technically the author is a robot but we love her anyway 🤖💖

and that's the whole page bestie!! this was IsoSpec, version 2.2.1, and you were reading IsoSpec::I...icGenerator(3). slay, go generate some isotopologues, and remember: keep every flag, every default, every number. periodt. 💅✨🦋

📦 where this page comes from