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IsoSpec
2.1.2
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The Iso class for the calculation of the isotopic distribution. More...
#include <isoSpec++.h>
Public Member Functions | |
Iso (int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *_isotopeMasses, const double *_isotopeProbabilities) | |
General constructror. More... | |
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. More... | |
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. More... | |
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 |
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.
IsoSpec::Iso::Iso | ( | int | _dimNumber, |
const int * | _isotopeNumbers, | ||
const int * | _atomCounts, | ||
const double * | _isotopeMasses, | ||
const double * | _isotopeProbabilities | ||
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General constructror.
_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 | ||
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The copy constructor.
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.
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Constructor (named) from aminoacid FASTA sequence as C string.
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.
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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.
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A table with numbers of isotopes for each element.
Definition at line 65 of file isoSpec++.h.
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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.
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The number of elements in the chemical formula of the molecule.
Definition at line 63 of file isoSpec++.h.
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A table with numbers of isotopes for each element.
Definition at line 64 of file isoSpec++.h.
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The table of pointers to the distributions of individual subisotopologues.
Definition at line 68 of file isoSpec++.h.