Provided by: libisospec++-dev_2.2.1-1build1_amd64 bug

NAME

       IsoSpec

SYNOPSIS

   Classes
       class Allocator
       struct ProbAndConfPtr
       class DirtyAllocator
       class FixedEnvelope
       class Iso
           The Iso class for the calculation of the isotopic distribution.
       class IsoGenerator
           The generator of isotopologues.
       class IsoOrderedGenerator
           The generator of isotopologues sorted by their probability of occurrence.
       class IsoThresholdGenerator
           The generator of isotopologues above a given threshold value.
       class IsoLayeredGenerator
       class IsoStochasticGenerator
       class Marginal
           The marginal distribution class (a subisotopologue).
       class MarginalTrek
           The marginal distribution class (a subisotopologue).
       class PrecalculatedMarginal
           Precalculated Marginal class.
       class LayeredMarginal
           LayeredMarginal class.
       class KeyHasher
       class ConfEqual
       class ConfOrder
       class ConfOrderMarginal
       class ConfOrderMarginalDescending
       class ReverseOrder
       class TableOrder
       class OrderMarginalsBySizeDecresing
       class SSummator
       class Summator
       class TSummator

   Typedefs
       typedef double RealType
       typedef int64_t IntType
       typedef int * Conf

   Functions
       template<typename T > void copyConf (const T *source, T *destination, int dim)
       IntType btrd (IntType _t, RealType p, IntType m, std::mt19937 &urng=random_gen)
       IntType invert (IntType t, RealType p, std::mt19937 &urng=random_gen)
       IntType boost_binomial_distribution_variate (IntType t_arg, RealType p_arg, std::mt19937
           &urng=random_gen)
       void parse_fasta (const char *fasta, int atomCounts[6])
       template<typename T > void reorder_array (T *arr, size_t *order, size_t size, bool
           can_destroy=false)
       double AbyssalWassersteinDistanceGrad (FixedEnvelope *const *envelopes, const double
           *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double
           abyss_depth_the)
       void release_g_lfact_table ()
       double * alloc_lfact_table ()
       double RationalApproximation (double t)
       double NormalCDFInverse (double p)
       double NormalCDFInverse (double p, double mean, double stdev)
       double NormalCDF (double x, double mean, double stdev)
       double NormalPDF (double x, double mean, double stdev)
       double LowerIncompleteGamma2 (int a, double x)
       double InverseLowerIncompleteGamma2 (int a, double x)
       std::mt19937 random_gen (random_dev())
       std::uniform_real_distribution< double > stdunif (0.0, 1.0)
       size_t rdvariate_binom (size_t tries, double succ_prob, std::mt19937 &rgen)
       double InverseChiSquareCDF2 (int k, double x)
       double rdvariate_beta_1_b (double b, std::mt19937 &rgen=random_gen)
       unsigned int parse_formula (const char *formula, std::vector< double > &isotope_masses,
           std::vector< double > &isotope_probabilities, int **isotopeNumbers, int **atomCounts,
           unsigned int *confSize, bool use_nominal_masses)
       void writeInitialConfiguration (const int atomCnt, const int isotopeNo, const double
           *lprobs, int *res)
           Find one of the most probable subisotopologues.
       double * getMLogProbs (const double *probs, int isoNo)
       double get_loggamma_nominator (int x)
       int verify_atom_cnt (int atomCnt)
       void * quickselect (void **array, int n, int start, int end)
       double combinedSum (const int *conf, const std::vector< double > **valuesContainer, int
           dimNumber)
       double combinedSum (const int *conf, const pod_vector< double > **valuesContainer, int
           dimNumber)
       int * getConf (void *conf)
       double getLProb (void *conf)
       double unnormalized_logProb (const int *conf, const double *logProbs, int dim)
       double calc_mass (const int *conf, const double *masses, int dim)
       template<typename T > void printArray (const T *array, int size, const char *prefix='')
       template<typename T > void printVector (const std::vector< T > &vec)
       template<typename T > void printOffsets (const T **array, int size, const T *offset, const
           char *prefix='')
       template<typename T > void printNestedArray (const T **array, const int *shape, int size)
       void * quickselect (const void **array, int n, int start, int end)
           Quickly select the n'th positional statistic, including the weights.
       template<typename T > void dealloc_table (T *tbl, int dim)
       template<typename T > void realloc_append (T **array, T what, size_t old_array_size)
       template<typename T > size_t * get_order (T *order_array, size_t N)
       template<typename T > size_t * get_inverse_order (T *order_array, size_t N)
       template<typename TA , typename TB > void impose_order (size_t *O, size_t N, TA *A, TB *B)

   Variables
       const size_t isospec_number_of_isotopic_entries = ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES
       const int elem_table_ID [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const int elem_table_atomicNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const double elem_table_mass [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const double elem_table_massNo [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const int elem_table_extraNeutrons [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const char * elem_table_element [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const char * elem_table_symbol [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const bool elem_table_Radioactive [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const double elem_table_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const double elem_table_log_probability [ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES]
       const int aa_isotope_numbers [6] = {2, 2, 2, 3, 4, 6}
       const double aa_elem_masses [19]
       const double aa_elem_nominal_masses [19]
       const double aa_elem_probabilities [19]
       const int aa_symbol_to_elem_counts [256 *6]
       double * g_lfact_table = alloc_lfact_table()
       const double sqrt_pi = 1.772453850905516027298167483341145182798
       std::random_device random_dev
       const double pi = 3.14159265358979323846264338328
       const double logpi =
           1.144729885849400174143427351353058711647294812915311571513623071472137769884826079783623270275489708
       std::mt19937 random_gen
       std::uniform_real_distribution< double > stdunif

Detailed Description

       Copyright (C) 2015-2020 Mateusz Łącki and Michał Startek.

       This file is part of IsoSpec.

       IsoSpec is free software: you can redistribute it and/or modify it under the terms of the
       Simplified ('2-clause') BSD licence.

       IsoSpec is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
       without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

       You should have received a copy of the Simplified BSD Licence along with IsoSpec. If not,
       see https://opensource.org/licenses/BSD-2-Clause.

Function Documentation

   double* IsoSpec::getMLogProbs (const double * probs, int isoNo)
       Here we order the processor to round the numbers up rather than down. Rounding down could
       result in the algorithm falling in an infinite loop because of the numerical instability
       of summing.

       Definition at line 122 of file marginalTrek++.cpp.

   void IsoSpec::writeInitialConfiguration (const int atomCnt, const int isotopeNo, const double
       * lprobs, int * res)
       Find one of the most probable subisotopologues. The algorithm uses the hill-climbing
       algorithm. It starts from a subisotopologue close to the mean of the underlying
       multinomial distribution. There might be more than one modes, in case of which this
       function will return only one of them, close to the mean.

       Parameters
           atomCnt

       Here we perform hill climbing to the mode of the marginal distribution (the
       subisotopologue distribution). We start from the point close to the mean of the underlying
       multinomial distribution.

       Definition at line 50 of file marginalTrek++.cpp.

Variable Documentation

   const double IsoSpec::aa_elem_masses
       Initial value:

       = {
           elem_table_mass[9], elem_table_mass[10],
           elem_table_mass[0], elem_table_mass[1],
           elem_table_mass[11], elem_table_mass[12],
           elem_table_mass[13], elem_table_mass[14], elem_table_mass[15],
           elem_table_mass[29], elem_table_mass[30], elem_table_mass[31], elem_table_mass[32],
           elem_table_mass[85], elem_table_mass[86], elem_table_mass[87], elem_table_mass[88], elem_table_mass[89], elem_table_mass[90]
       }

       Definition at line 27 of file fasta.cpp.

   const double IsoSpec::aa_elem_nominal_masses
       Initial value:

       = {
           elem_table_massNo[9], elem_table_massNo[10],
           elem_table_massNo[0], elem_table_massNo[1],
           elem_table_massNo[11], elem_table_massNo[12],
           elem_table_massNo[13], elem_table_massNo[14], elem_table_massNo[15],
           elem_table_massNo[29], elem_table_massNo[30], elem_table_massNo[31], elem_table_massNo[32],
           elem_table_massNo[85], elem_table_massNo[86], elem_table_massNo[87], elem_table_massNo[88], elem_table_massNo[89], elem_table_massNo[90]
       }

       Definition at line 37 of file fasta.cpp.

   const double IsoSpec::aa_elem_probabilities
       Initial value:

       = {
           elem_table_probability[9], elem_table_probability[10],
           elem_table_probability[0], elem_table_probability[1],
           elem_table_probability[11], elem_table_probability[12],
           elem_table_probability[13], elem_table_probability[14], elem_table_probability[15],
           elem_table_probability[29], elem_table_probability[30], elem_table_probability[31], elem_table_probability[32],
           elem_table_probability[85], elem_table_probability[86], elem_table_probability[87], elem_table_probability[88], elem_table_probability[89], elem_table_probability[90]
       }

       Definition at line 47 of file fasta.cpp.

Author

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