.TH "IsoSpec::Iso" 3 "Version 2.2.1" "IsoSpec" \" -*- nroff -*- .ad l .nh .SH NAME IsoSpec::Iso \- The \fBIso\fP class for the calculation of the isotopic distribution\&. .SH SYNOPSIS .br .PP .PP \fC#include \fP .PP Inherited by \fBIsoSpec::IsoGenerator\fP\&. .SS "Public Member Functions" .in +1c .ti -1c .RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities)" .br .RI "General constructror\&. " .ti -1c .RI "\fBIso\fP (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities)" .br .ti -1c .RI "\fBIso\fP (const char *formula, bool use_nominal_masses=false)" .br .RI "Constructor from the formula object\&. " .ti -1c .RI "\fBIso\fP (const std::string &formula, bool use_nominal_masses=false)" .br .RI "Constructor from C++ std::string chemical formula\&. " .ti -1c .RI "\fBIso\fP (\fBIso\fP &&other)" .br .RI "The move constructor\&. " .ti -1c .RI "\fBIso\fP & \fBoperator=\fP (const \fBIso\fP &other)=delete" .br .ti -1c .RI "\fBIso\fP (const \fBIso\fP &other, bool fullcopy)" .br .RI "The copy constructor\&. " .ti -1c .RI "virtual \fB~Iso\fP ()" .br .RI "Destructor\&. " .ti -1c .RI "double \fBgetLightestPeakMass\fP () const" .br .RI "Get the mass of the lightest peak in the isotopic distribution\&. " .ti -1c .RI "double \fBgetHeaviestPeakMass\fP () const" .br .RI "Get the mass of the heaviest peak in the isotopic distribution\&. " .ti -1c .RI "double \fBgetMonoisotopicPeakMass\fP () const" .br .ti -1c .RI "double \fBgetModeLProb\fP () const" .br .RI "Get the log-probability of the mode-configuration (if there are many modes, they share this value)\&. " .ti -1c .RI "double \fBgetUnlikeliestPeakLProb\fP () const" .br .RI "Get the logprobability of the least probable subisotopologue\&. " .ti -1c .RI "double \fBgetModeMass\fP () const" .br .RI "Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected)\&. " .ti -1c .RI "double \fBgetTheoreticalAverageMass\fP () const" .br .RI "Get the theoretical average mass of the molecule\&. " .ti -1c .RI "double \fBvariance\fP () const" .br .RI "Get the theoretical variance of the distribution\&. " .ti -1c .RI "double \fBstddev\fP () const" .br .RI "Get the standard deviation of the theoretical distribution\&. " .ti -1c .RI "int \fBgetDimNumber\fP () const" .br .RI "Get the number of elements in the chemical formula of the molecule\&. " .ti -1c .RI "int \fBgetAllDim\fP () const" .br .RI "Get the total number of isotopes of elements present in a chemical formula\&. " .ti -1c .RI "void \fBaddElement\fP (int atomCount, int noIsotopes, const double *isotopeMasses, const double *isotopeProbabilities)" .br .RI "Add an element to the molecule\&. Note: this method can only be used BEFORE \fBIso\fP is used to construct an \fBIsoGenerator\fP instance\&. " .ti -1c .RI "void \fBsaveMarginalLogSizeEstimates\fP (double *priorities, double target_total_prob) const" .br .RI "Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array\&. Array priorities must have length equal to dimNumber\&. " .in -1c .SS "Static Public Member Functions" .in +1c .ti -1c .RI "static \fBIso\fP \fBFromFASTA\fP (const char *fasta, bool use_nominal_masses=false, bool add_water=true)" .br .RI "Constructor (named) from aminoacid FASTA sequence as C string\&. " .ti -1c .RI "static \fBIso\fP \fBFromFASTA\fP (const std::string &fasta, bool use_nominal_masses=false, bool add_water=true)" .br .RI "Constructor (named) from aminoacid FASTA sequence as C++ std::string\&. See above for details\&. " .in -1c .SS "Protected Member Functions" .in +1c .ti -1c .RI "bool \fBdoMarginalsNeedSorting\fP () const" .br .in -1c .SS "Protected Attributes" .in +1c .ti -1c .RI "int \fBdimNumber\fP" .br .ti -1c .RI "int * \fBisotopeNumbers\fP" .br .ti -1c .RI "int * \fBatomCounts\fP" .br .ti -1c .RI "unsigned int \fBconfSize\fP" .br .ti -1c .RI "int \fBallDim\fP" .br .ti -1c .RI "\fBMarginal\fP ** \fBmarginals\fP" .br .in -1c .SH "Detailed Description" .PP The \fBIso\fP 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\&. .PP Definition at line \fB49\fP of file \fBisoSpec++\&.h\fP\&. .SH "Constructor & Destructor Documentation" .PP .SS "IsoSpec::Iso::Iso ()" .PP Definition at line \fB50\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::Iso (int _dimNumber, const int * _isotopeNumbers, const int * _atomCounts, const double * _isotopeMasses, const double * _isotopeProbabilities)" .PP General constructror\&. .PP \fBParameters\fP .RS 4 \fI_dimNumber\fP The number of elements in the formula, e\&.g\&. for C100H202 it would be 2, as there are only carbon and hydrogen atoms\&. .br \fI_isotopeNumbers\fP 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\&. .br \fI_atomCounts\fP Number of atoms of each element in the formula, e\&.g\&. for C100H202 corresponds to {100, 202}\&. .br \fI_isotopeMasses\fP 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\&. .br \fI_isotopeProbabilities\fP A table of tables of isotope frequencies of the elements in the chemical formula, e\&.g\&. {{\&.989212, \&.010788}, {\&.999885, \&.000115}} for C100H202\&. .RE .PP .PP Definition at line \fB109\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::Iso (int _dimNumber, const int * _isotopeNumbers, const int * _atomCounts, const double *const * _isotopeMasses, const double *const * _isotopeProbabilities)" .PP Definition at line \fB61\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::Iso (const char * formula, bool use_nominal_masses = \fCfalse\fP)" .PP Constructor from the formula object\&. .PP Definition at line \fB310\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::Iso (const std::string & formula, bool use_nominal_masses = \fCfalse\fP)\fC [inline]\fP" .PP Constructor from C++ std::string chemical formula\&. .PP Definition at line \fB102\fP of file \fBisoSpec++\&.h\fP\&. .SS "IsoSpec::Iso::Iso (\fBIso\fP && other)" .PP The move constructor\&. .PP Definition at line \fB140\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::Iso (const \fBIso\fP & other, bool fullcopy)" .PP The copy constructor\&. .PP \fBParameters\fP .RS 4 \fIother\fP The other instance of the \fBIso\fP class\&. .br \fIfullcopy\fP 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\&. .RE .PP .PP Definition at line \fB153\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "IsoSpec::Iso::~Iso ()\fC [virtual]\fP" .PP Destructor\&. .PP Definition at line \fB221\fP of file \fBisoSpec++\&.cpp\fP\&. .SH "Member Function Documentation" .PP .SS "void IsoSpec::Iso::addElement (int atomCount, int noIsotopes, const double * isotopeMasses, const double * isotopeProbabilities)" .PP Add an element to the molecule\&. Note: this method can only be used BEFORE \fBIso\fP is used to construct an \fBIsoGenerator\fP instance\&. .PP Definition at line \fB324\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "bool IsoSpec::Iso::doMarginalsNeedSorting () const\fC [protected]\fP" .PP Definition at line \fB232\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "\fBIso\fP IsoSpec::Iso::FromFASTA (const char * fasta, bool use_nominal_masses = \fCfalse\fP, bool add_water = \fCtrue\fP)\fC [static]\fP" .PP Constructor (named) from aminoacid FASTA sequence as C string\&. .PP \fBParameters\fP .RS 4 \fIfasta\fP 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\&. .RE .PP .PP Definition at line \fB169\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "static \fBIso\fP IsoSpec::Iso::FromFASTA (const std::string & fasta, bool use_nominal_masses = \fCfalse\fP, bool add_water = \fCtrue\fP)\fC [inline]\fP, \fC [static]\fP" .PP Constructor (named) from aminoacid FASTA sequence as C++ std::string\&. See above for details\&. .PP Definition at line \fB116\fP of file \fBisoSpec++\&.h\fP\&. .SS "int IsoSpec::Iso::getAllDim () const\fC [inline]\fP" .PP Get the total number of isotopes of elements present in a chemical formula\&. .PP Definition at line \fB169\fP of file \fBisoSpec++\&.h\fP\&. .SS "int IsoSpec::Iso::getDimNumber () const\fC [inline]\fP" .PP Get the number of elements in the chemical formula of the molecule\&. .PP Definition at line \fB166\fP of file \fBisoSpec++\&.h\fP\&. .SS "double IsoSpec::Iso::getHeaviestPeakMass () const" .PP Get the mass of the heaviest peak in the isotopic distribution\&. .PP Definition at line \fB253\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::getLightestPeakMass () const" .PP Get the mass of the lightest peak in the isotopic distribution\&. .PP Definition at line \fB245\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::getModeLProb () const" .PP Get the log-probability of the mode-configuration (if there are many modes, they share this value)\&. .PP Definition at line \fB285\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::getModeMass () const" .PP Get the mass of the mode-configuration (if there are many modes, it is undefined which one will be selected)\&. .PP Definition at line \fB277\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "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 \fBgetLightestPeakMass()\fP .PP Definition at line \fB261\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::getTheoreticalAverageMass () const" .PP Get the theoretical average mass of the molecule\&. .PP Definition at line \fB293\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::getUnlikeliestPeakLProb () const" .PP Get the logprobability of the least probable subisotopologue\&. .PP Definition at line \fB269\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "void IsoSpec::Iso::saveMarginalLogSizeEstimates (double * priorities, double target_total_prob) const" .PP Save estimates of logarithms of target sizes of marginals using Gaussian approximation into argument array\&. Array priorities must have length equal to dimNumber\&. .PP Definition at line \fB335\fP of file \fBisoSpec++\&.cpp\fP\&. .SS "double IsoSpec::Iso::stddev () const\fC [inline]\fP" .PP Get the standard deviation of the theoretical distribution\&. .PP Definition at line \fB163\fP of file \fBisoSpec++\&.h\fP\&. .SS "double IsoSpec::Iso::variance () const" .PP Get the theoretical variance of the distribution\&. .PP Definition at line \fB301\fP of file \fBisoSpec++\&.cpp\fP\&. .SH "Member Data Documentation" .PP .SS "int IsoSpec::Iso::allDim\fC [protected]\fP" The total number of isotopes of elements present in a chemical formula, e\&.g\&. for H20 it is 2+3=5\&. .PP Definition at line \fB67\fP of file \fBisoSpec++\&.h\fP\&. .SS "int* IsoSpec::Iso::atomCounts\fC [protected]\fP" A table with numbers of isotopes for each element\&. .PP Definition at line \fB65\fP of file \fBisoSpec++\&.h\fP\&. .SS "unsigned int IsoSpec::Iso::confSize\fC [protected]\fP" The number of bytes needed to represent the counts of isotopes present in the extended chemical formula\&. .PP Definition at line \fB66\fP of file \fBisoSpec++\&.h\fP\&. .SS "int IsoSpec::Iso::dimNumber\fC [protected]\fP" The number of elements in the chemical formula of the molecule\&. .PP Definition at line \fB63\fP of file \fBisoSpec++\&.h\fP\&. .SS "int* IsoSpec::Iso::isotopeNumbers\fC [protected]\fP" A table with numbers of isotopes for each element\&. .PP Definition at line \fB64\fP of file \fBisoSpec++\&.h\fP\&. .SS "\fBMarginal\fP** IsoSpec::Iso::marginals\fC [protected]\fP" The table of pointers to the distributions of individual subisotopologues\&. .PP Definition at line \fB68\fP of file \fBisoSpec++\&.h\fP\&. .SH "Author" .PP Generated automatically by Doxygen for IsoSpec from the source code\&.