ISOSPEC_ISOSTOCHASTICGENERATORTEMPLATE(3)

📦 version 2.3.2, in ubuntu resolute, ubuntu stonking

💖 NAME 💖

IsoSpec::IsoStochasticGeneratorTemplate< IsoType > — bestie, this is a template class in the IsoSpec library, and this page is from the Library Functions Manual. (Yes the page header up top is a little truncated and looks like a glitch, it's giving "IsoSpec::I... IsoType >(3)", we move.) 🎀

✨ SYNOPSIS ✨

It inherits from IsoSpec::IsoGenerator. Family tree moment. 🌸

🫶 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) — the constructor, obvs
  • ISOSPEC_FORCE_INLINE size_t count () const — counts things, no notes given
  • 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 the 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) — no description given, it simply exists 💅

🧚 Public Member Functions inherited from IsoSpec::IsoGenerator

  • IsoGenerator (Iso &&iso, bool alloc_partials=true) — move constructor 🏃‍♀️
  • virtual ~IsoGenerator () — destructor, 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 (their spelling, not mine, keeping it 100)
  • Iso (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) — another overload, no notes attached
  • 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, do not come for her 🚫
  • 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 — no description, just vibes
  • 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 (their spacing, keeping it verbatim, iykyk)
  • 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. Timing is everything, bestie ⏰
  • 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.

🦋 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 an 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 an aminoacid FASTA sequence as a C++ std::string. See above for details 👆

🎀 Public Attributes inherited from IsoSpec::IsoGenerator

  • const double mode_lprob — she's const, she's not changing for anybody

💜 Protected Member Functions inherited from IsoSpec::Iso

  • bool doMarginalsNeedSorting () const — no description, mysterious queen

🍓 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 👑

template<typename IsoType>
class IsoSpec::IsoStochasticGeneratorTemplate< IsoType >"
Yeah there's a stray " at the end of that line in the original. Not me fixing it. It's canon now. 💀

Definition at line 586 of file isoSpec++.h.

🔥 Constructor & Destructor Documentation 🔥

template<typename IsoType> 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.

💅 Member Function Documentation 💅

advanceToNextConfiguration

template<typename IsoType> ISOSPEC_FORCE_INLINE bool IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::advanceToNextConfiguration () [inline],  [final],  [override],  [virtual]

Advance to the next, not yet visited, most probable isotopologue. Main character energy, always moving forward 🚶‍♀️✨

Returns

Return false if it is not possible to advance. (Sad moment, but she's honest about it.)

Implements IsoSpec::IsoGenerator.

Definition at line 610 of file isoSpec++.h.

count

template<typename IsoType> ISOSPEC_FORCE_INLINE size_t IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::count () const [inline]

Definition at line 600 of file isoSpec++.h.

get_conf_signature

template<typename IsoType> ISOSPEC_FORCE_INLINE void IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::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. 🫶 Don't skimp on the buffer, bestie.

Implements IsoSpec::IsoGenerator.

Definition at line 608 of file isoSpec++.h.

get_indexes

template<typename IsoType> ISOSPEC_FORCE_INLINE void IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::get_indexes (int * space) [inline]

Definition at line 685 of file isoSpec++.h.

lprob

template<typename IsoType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::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 606 of file isoSpec++.h.

mass

template<typename IsoType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::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 602 of file isoSpec++.h.

prob

template<typename IsoType> ISOSPEC_FORCE_INLINE double IsoSpec::IsoStochasticGeneratorTemplate< IsoType >::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 604 of file isoSpec++.h.

💖 Author 💖

Generated automatically by Doxygen for IsoSpec from the source code. (Not a human author, just a lil robot doing its thing 🤖✨)

And that's the whole page, bestie! 🎀 This one's from the IsoSpec library, and that footer down at the bottom — the truncated IsoSpec::I... IsoType >(3) one — is just the running footer with the source name IsoSpec and the page name, no date info given. Slay, go generate some isotopologues. 💅🦋

📦 where this page comes from