NAME

       IsoSpec::Iso - The Iso class for the calculation of the isotopic distribution.

SYNOPSIS

       #include <isoSpec++.h>

       Inherited by IsoSpec::IsoGenerator.

   Public Member Functions
       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.

   Static Public Member Functions
       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
       bool doMarginalsNeedSorting () const

   Protected Attributes
       int dimNumber
       int * isotopeNumbers
       int * atomCounts
       unsigned int confSize
       int allDim
       Marginal ** marginals

Detailed Description

       The Iso class for the calculation of the isotopic distribution.

       It contains full description of the molecule for which one would like to calculate the
       isotopic distribution.

       Definition at line 49 of file isoSpec++.h.

Constructor & Destructor Documentation

   IsoSpec::Iso::Iso (int _dimNumber, const int * _isotopeNumbers, const int * _atomCounts, const
       double * _isotopeMasses, const double * _isotopeProbabilities)
       General constructror.

       Parameters
           _dimNumber The number of elements in the formula, e.g. for C100H202 it would be 2, as
           there are only carbon and hydrogen atoms.
           _isotopeNumbers A table with numbers of isotopes for each element, e.g. for C100H202
           it would be {2, 2}, because both C and H have two stable isotopes.
           _atomCounts Number of atoms of each element in the formula, e.g. for C100H202
           corresponds to {100, 202}.
           _isotopeMasses A table of tables of masses of isotopes of the elements in the chemical
           formula, e.g. {{12.0, 13.003355}, {1.007825, 2.014102}} for C100H202.
           _isotopeProbabilities A table of tables of isotope frequencies of the elements in the
           chemical formula, e.g. {{.989212, .010788}, {.999885, .000115}} for C100H202.

       Definition at line 109 of file isoSpec++.cpp.

   IsoSpec::Iso::Iso (const Iso & other, bool fullcopy)
       The copy constructor.

       Parameters
           other The other instance of the Iso class.
           fullcopy If false, copy only the number of atoms in the formula, the size of the
           configuration, the total number of isotopes, and the probability of the mode
           isotopologue.

       Definition at line 153 of file isoSpec++.cpp.

Member Function Documentation

   Iso IsoSpec::Iso::FromFASTA (const char * fasta, bool use_nominal_masses = false, bool
       add_water = true) [static]
       Constructor (named) from aminoacid FASTA sequence as C string.

       Parameters
           fasta An aminoacid FASTA sequence. May be upper/lower/mixed case, may contain
           selenocystein (U) or xleucine (J). Other characters, including FASTA codes of
           indeterminate chemical formula (X, *, -, B, ...) are silently ignored. That means
           'AEDA', 'AE-DA', 'EAXXDA', 'AE DA' will all result in the same chemical formula.
           Subisotopologues will be in order: CHNOS, possibly with Se added at an end if present.
           \use_nominal_masses Whether to use nucleon number instead of the real mass of each
           isotope during calculations. \add_water Whether the chain should have the terminating
           -H and -OH groups at the N and C terminus, respectively.

       Definition at line 169 of file isoSpec++.cpp.

   double IsoSpec::Iso::getMonoisotopicPeakMass () const
       Get the mass of the monoisotopic peak in the isotopic distribution. Monoisotopc molecule
       is defined as consisting only of the most frequent isotopes of each element. These are
       often (but not always) the lightest ones, making this often (but again, not always) equal
       to getLightestPeakMass()

       Definition at line 261 of file isoSpec++.cpp.

Member Data Documentation

   int IsoSpec::Iso::allDim [protected]
       The total number of isotopes of elements present in a chemical formula, e.g. for H20 it is
       2+3=5.

       Definition at line 67 of file isoSpec++.h.

   int* IsoSpec::Iso::atomCounts [protected]
       A table with numbers of isotopes for each element.

       Definition at line 65 of file isoSpec++.h.

   unsigned int IsoSpec::Iso::confSize [protected]
       The number of bytes needed to represent the counts of isotopes present in the extended
       chemical formula.

       Definition at line 66 of file isoSpec++.h.

   int IsoSpec::Iso::dimNumber [protected]
       The number of elements in the chemical formula of the molecule.

       Definition at line 63 of file isoSpec++.h.

   int* IsoSpec::Iso::isotopeNumbers [protected]
       A table with numbers of isotopes for each element.

       Definition at line 64 of file isoSpec++.h.

   Marginal** IsoSpec::Iso::marginals [protected]
       The table of pointers to the distributions of individual subisotopologues.

       Definition at line 68 of file isoSpec++.h.

Author

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