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Manual

IsoSpec

NAME
SYNOPSIS
Classes
Typedefs
Functions
Variables
Detailed Description
Typedef Documentation
typedef int* IsoSpec::Conf
typedef int64_t IsoSpec::IntType
typedef double IsoSpec::RealType
Function Documentation
double * IsoSpec::alloc_lfact_table ()
IntType IsoSpec::boost_binomial_distribution_variate (IntType t_arg,RealType p_arg, std::mt19937 & urng = random_gen)
IntType IsoSpec::btrd (IntType _t, RealType p, IntType m, std::mt19937 &urng = random_gen)
double IsoSpec::calc_mass (const int * conf, const double * masses, intdim) [inline]
double IsoSpec::combinedSum (const int * conf, const pod_vector< double >** valuesContainer, int dimNumber) [inline]
double IsoSpec::combinedSum (const int * conf, const std::vector< double >** valuesContainer, int dimNumber) [inline]
template<typename T > void IsoSpec::copyConf (const T * source, T *destination, int dim) [inline]
template<typename T > void IsoSpec::dealloc_table (T * tbl, int dim)
template<typename T > size_t * IsoSpec::get_inverse_order (T * order_array,size_t N)
double IsoSpec::get_loggamma_nominator (int x)
template<typename T > size_t * IsoSpec::get_order (T * order_array, size_tN)
int * IsoSpec::getConf (void * conf) [inline]
double IsoSpec::getLProb (void * conf) [inline]
double * IsoSpec::getMLogProbs (const double * probs, int isoNo)
template<typename TA , typename TB > void IsoSpec::impose_order (size_t *O, size_t N, TA * A, TB * B)
double IsoSpec::InverseChiSquareCDF2 (int k, double x) [inline]
double IsoSpec::InverseLowerIncompleteGamma2 (int a, double x)
IntType IsoSpec::invert (IntType t, RealType p, std::mt19937 & urng =random_gen)
double IsoSpec::LowerIncompleteGamma2 (int a, double x)
double IsoSpec::NormalCDF (double x, double mean, double stdev)
double IsoSpec::NormalCDFInverse (double p)
double IsoSpec::NormalCDFInverse (double p, double mean, double stdev)
double IsoSpec::NormalPDF (double x, double mean, double stdev)
void IsoSpec::parse_fasta (const char * fasta, int atomCounts[6]) [inline]
unsigned int IsoSpec::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)
template<typename T > void IsoSpec::printArray (const T * array, int size,const char * prefix = ’’)
template<typename T > void IsoSpec::printNestedArray (const T ** array,const int * shape, int size)
template<typename T > void IsoSpec::printOffsets (const T ** array, intsize, const T * offset, const char * prefix = ’’)
template<typename T > void IsoSpec::printVector (const std::vector< T > &vec)
void * IsoSpec::quickselect (void ** array, int n, int start, int end)
double IsoSpec::RationalApproximation (double t)
double IsoSpec::rdvariate_beta_1_b (double b, std::mt19937 & rgen =random_gen) [inline]
size_t IsoSpec::rdvariate_binom (size_t tries, double succ_prob,std::mt19937 & rgen)
template<typename T > void IsoSpec::realloc_append (T ** array, T what,size_t old_array_size)
void IsoSpec::release_g_lfact_table ()
template<typename T > void IsoSpec::reorder_array (T * arr, size_t * order,size_t size, bool can_destroy = false)
double IsoSpec::unnormalized_logProb (const int * conf, const double *logProbs, int dim) [inline]
int IsoSpec::verify_atom_cnt (int atomCnt)
void IsoSpec::writeInitialConfiguration (const int atomCnt, const intisotopeNo, const double * lprobs, int * res)
Variable Documentation
const double IsoSpec::aa_elem_masses
const double IsoSpec::aa_elem_nominal_masses
const double IsoSpec::aa_elem_probabilities
const int IsoSpec::aa_isotope_numbers = {2, 2, 2, 3, 4, 6}
const int IsoSpec::aa_symbol_to_elem_counts
ISOSPEC_C_API const int IsoSpec::elem_table_atomicNo
ISOSPEC_C_API const char * IsoSpec::elem_table_element
ISOSPEC_C_API const int IsoSpec::elem_table_extraNeutrons
ISOSPEC_C_API const int IsoSpec::elem_table_ID
ISOSPEC_C_API const double IsoSpec::elem_table_log_probability
ISOSPEC_C_API const double IsoSpec::elem_table_mass
ISOSPEC_C_API const double IsoSpec::elem_table_massNo
ISOSPEC_C_API const double IsoSpec::elem_table_probability
ISOSPEC_C_API const bool IsoSpec::elem_table_Radioactive
ISOSPEC_C_API const char * IsoSpec::elem_table_symbol
double * IsoSpec::g_lfact_table = alloc_lfact_table()
ISOSPEC_C_API const size_t IsoSpec::isospec_number_of_isotopic_entries =ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES
const double IsoSpec::logpi =1.144729885849400174143427351353058711647294812915311571513623071472137769884826079783623270275489708
const double IsoSpec::pi = 3.14159265358979323846264338328
std::random_device IsoSpec::random_dev
const double IsoSpec::sqrt_pi = 1.772453850905516027298167483341145182798
Author

NAME

IsoSpec

SYNOPSIS

Classes

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

Typedef Documentation

typedef int* IsoSpec::Conf

Definition at line 22 of file conf.h .

typedef int64_t IsoSpec::IntType

Definition at line 28 of file btrd.h .

typedef double IsoSpec::RealType

Definition at line 27 of file btrd.h .

Function Documentation

double * IsoSpec::alloc_lfact_table ()

Definition at line 32 of file isoMath.cpp .

IntType IsoSpec::boost_binomial_distribution_variate (IntType t_arg,RealType p_arg, std::mt19937 & urng = random_gen)

Definition at line 189 of file btrd.h .

IntType IsoSpec::btrd (IntType _t, RealType p, IntType m, std::mt19937 &urng = random_gen)

Definition at line 77 of file btrd.h .

double IsoSpec::calc_mass (const int * conf, const double * masses, intdim) [inline]

Definition at line 71 of file misc.h .

double IsoSpec::combinedSum (const int * conf, const pod_vector< double >** valuesContainer, int dimNumber) [inline]

Definition at line 38 of file misc.h .

double IsoSpec::combinedSum (const int * conf, const std::vector< double >** valuesContainer, int dimNumber) [inline]

Definition at line 29 of file misc.h .

template<typename T > void IsoSpec::copyConf (const T * source, T *destination, int dim) [inline]

Definition at line 26 of file allocator.h .

template<typename T > void IsoSpec::dealloc_table (T * tbl, int dim)

Definition at line 133 of file misc.h .

template<typename T > size_t * IsoSpec::get_inverse_order (T * order_array,size_t N)

Definition at line 162 of file misc.h .

double IsoSpec::get_loggamma_nominator (int x)

Definition at line 149 of file marginalTrek++.cpp .

template<typename T > size_t * IsoSpec::get_order (T * order_array, size_tN)

Definition at line 151 of file misc.h .

int * IsoSpec::getConf (void * conf) [inline]

Definition at line 47 of file misc.h .

double IsoSpec::getLProb (void * conf) [inline]

Definition at line 54 of file misc.h .

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 .

template<typename TA , typename TB > void IsoSpec::impose_order (size_t *O, size_t N, TA * A, TB * B)

Definition at line 173 of file misc.h .

double IsoSpec::InverseChiSquareCDF2 (int k, double x) [inline]

Definition at line 68 of file isoMath.h .

double IsoSpec::InverseLowerIncompleteGamma2 (int a, double x)

Definition at line 131 of file isoMath.cpp .

IntType IsoSpec::invert (IntType t, RealType p, std::mt19937 & urng =random_gen)

Definition at line 160 of file btrd.h .

double IsoSpec::LowerIncompleteGamma2 (int a, double x)

Definition at line 104 of file isoMath.cpp .

double IsoSpec::NormalCDF (double x, double mean, double stdev)

Definition at line 70 of file isoMath.cpp .

double IsoSpec::NormalCDFInverse (double p)

Definition at line 57 of file isoMath.cpp .

double IsoSpec::NormalCDFInverse (double p, double mean, double stdev)

Definition at line 65 of file isoMath.cpp .

double IsoSpec::NormalPDF (double x, double mean, double stdev)

Definition at line 95 of file isoMath.cpp .

void IsoSpec::parse_fasta (const char * fasta, int atomCounts[6]) [inline]

Definition at line 33 of file fasta.h .

unsigned int IsoSpec::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)

Definition at line 355 of file isoSpec++.cpp .

template<typename T > void IsoSpec::printArray (const T * array, int size,const char * prefix = ’’)

Definition at line 85 of file misc.h .

template<typename T > void IsoSpec::printNestedArray (const T ** array,const int * shape, int size)

Definition at line 108 of file misc.h .

template<typename T > void IsoSpec::printOffsets (const T ** array, intsize, const T * offset, const char * prefix = ’’)

Definition at line 99 of file misc.h .

template<typename T > void IsoSpec::printVector (const std::vector< T > &vec)

Definition at line 94 of file misc.h .

void * IsoSpec::quickselect (void ** array, int n, int start, int end)

Definition at line 28 of file misc.cpp .

double IsoSpec::RationalApproximation (double t)

Definition at line 47 of file isoMath.cpp .

double IsoSpec::rdvariate_beta_1_b (double b, std::mt19937 & rgen =random_gen) [inline]

Definition at line 76 of file isoMath.h .

size_t IsoSpec::rdvariate_binom (size_t tries, double succ_prob,std::mt19937 & rgen)

Definition at line 153 of file isoMath.cpp .

template<typename T > void IsoSpec::realloc_append (T ** array, T what,size_t old_array_size)

Definition at line 142 of file misc.h .

void IsoSpec::release_g_lfact_table ()

Definition at line 23 of file isoMath.cpp .

template<typename T > void IsoSpec::reorder_array (T * arr, size_t * order,size_t size, bool can_destroy = false)

Definition at line 134 of file fixedEnvelopes.cpp .

double IsoSpec::unnormalized_logProb (const int * conf, const double *logProbs, int dim) [inline]

Definition at line 61 of file misc.h .

int IsoSpec::verify_atom_cnt (int atomCnt)

Definition at line 156 of file marginalTrek++.cpp .

void IsoSpec::writeInitialConfiguration (const int atomCnt, const intisotopeNo, 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: .PP
= {
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: .PP
= {
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: .PP
= {
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 .

const int IsoSpec::aa_isotope_numbers = {2, 2, 2, 3, 4, 6}

Definition at line 25 of file fasta.cpp .

const int IsoSpec::aa_symbol_to_elem_counts

Definition at line 57 of file fasta.cpp .

ISOSPEC_C_API const int IsoSpec::elem_table_atomicNo

Definition at line 325 of file element_tables.cpp .

ISOSPEC_C_API const char * IsoSpec::elem_table_element

Definition at line 1509 of file element_tables.cpp .

ISOSPEC_C_API const int IsoSpec::elem_table_extraNeutrons

Definition at line 1213 of file element_tables.cpp .

ISOSPEC_C_API const int IsoSpec::elem_table_ID

Definition at line 28 of file element_tables.cpp .

ISOSPEC_C_API const double IsoSpec::elem_table_log_probability

Definition at line 2693 of file element_tables.cpp .

ISOSPEC_C_API const double IsoSpec::elem_table_mass

Definition at line 621 of file element_tables.cpp .

ISOSPEC_C_API const double IsoSpec::elem_table_massNo

Definition at line 917 of file element_tables.cpp .

ISOSPEC_C_API const double IsoSpec::elem_table_probability

Definition at line 2397 of file element_tables.cpp .

ISOSPEC_C_API const bool IsoSpec::elem_table_Radioactive

Definition at line 2101 of file element_tables.cpp .

ISOSPEC_C_API const char * IsoSpec::elem_table_symbol

Definition at line 1805 of file element_tables.cpp .

double * IsoSpec::g_lfact_table = alloc_lfact_table()

Definition at line 44 of file isoMath.cpp .

ISOSPEC_C_API const size_t IsoSpec::isospec_number_of_isotopic_entries =ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES

Definition at line 26 of file element_tables.cpp .

const double IsoSpec::logpi =1.144729885849400174143427351353058711647294812915311571513623071472137769884826079783623270275489708

Definition at line 54 of file isoMath.h .

const double IsoSpec::pi = 3.14159265358979323846264338328

Definition at line 53 of file isoMath.h .

std::random_device IsoSpec::random_dev

Definition at line 149 of file isoMath.cpp .

const double IsoSpec::sqrt_pi = 1.772453850905516027298167483341145182798

Definition at line 102 of file isoMath.cpp .

Author

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