| OpenMS 2.5.0

Static Public Member Functions | List of all members
MetaProSIPDecomposition Class Reference

## Static Public Member Functions

static Int | calculateDecompositionWeightsIsotopicPatterns (Size n_bins, const vector< double > &isotopic_intensities, const IsotopePatterns &patterns, MapRateToScoreType &map_rate_to_decomposition_weight, SIPPeptide &sip_peptide)
| > Perform the decomposition More...
static IsotopePatterns | calculateIsotopePatternsFor13CRange (const AASequence &peptide, Size additional_isotopes=5)
static Size | getNumberOfLabelingElements (const String &labeling_element, const AASequence &peptide)
static IsotopePatterns | calculateIsotopePatternsFor15NRange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns | calculateIsotopePatternsFor2HRange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns | calculateIsotopePatternsFor18ORange (const AASequence &peptide, Size additional_isotopes=5)
static IsotopePatterns | calculateIsotopePatternsFor15NRangeOfAveraginePeptide (double mass)
static IsotopePatterns | calculateIsotopePatternsFor13CRangeOfAveraginePeptide (double mass)
static IsotopePatterns | calculateIsotopePatternsFor2HRangeOfAveraginePeptide (double mass)
static IsotopePatterns | calculateIsotopePatternsFor18ORangeOfAveraginePeptide (double mass)

## Member Function Documentation

## ◆ calculateDecompositionWeightsIsotopicPatterns()

static Int calculateDecompositionWeightsIsotopicPatterns | ( | Size | n_bins,
|  | const vector< double > & | isotopic_intensities,
|  | const IsotopePatterns & | patterns,
|  | MapRateToScoreType & | map_rate_to_decomposition_weight,
|  | SIPPeptide & | sip_peptide
| ) |  |

inline static

> Perform the decomposition

References SIPPeptide::charge, SIPPeptide::mass_diff, OpenMS::Math::mean(), SIPPeptide::mz_theo, SIPPeptide::reconstruction, SIPPeptide::reconstruction_monoistopic, SIPPeptide::RR, Peak1D::setIntensity(), Peak1D::setMZ(), and NonNegativeLeastSquaresSolver::solve().

## ◆ calculateIsotopePatternsFor13CRange()

static IsotopePatterns calculateIsotopePatternsFor13CRange | ( | const AASequence & | peptide,
|  | Size | additional_isotopes = `5`
| ) |  |

inline static

> Given a peptide sequence calculate the theoretical isotopic patterns given all incorporations rate (13C Version) > extend isotopic patterns by additional_isotopes to collect other element higher isotopes at 100% incorporation

References IsotopeDistribution::clear(), AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::insert(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

## ◆ calculateIsotopePatternsFor13CRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor13CRangeOfAveraginePeptide | ( | double | mass | ) |

inline static

References IsotopeDistribution::clear(), CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::insert(), and Element::setIsotopeDistribution().

## ◆ calculateIsotopePatternsFor15NRange()

static IsotopePatterns calculateIsotopePatternsFor15NRange | ( | const AASequence & | peptide,
|  | Size | additional_isotopes = `5`
| ) |  |

inline static

> Given a peptide sequence calculate the theoretical isotopic patterns given all incorporations rate (15C Version) > extend isotopic patterns by additional_isotopes to collect other element higher isotopes at 100% incorporation

References IsotopeDistribution::clear(), AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::insert(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

## ◆ calculateIsotopePatternsFor15NRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor15NRangeOfAveraginePeptide | ( | double | mass | ) |

inline static

References IsotopeDistribution::clear(), CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::insert(), and Element::setIsotopeDistribution().

## ◆ calculateIsotopePatternsFor18ORange()

static IsotopePatterns calculateIsotopePatternsFor18ORange | ( | const AASequence & | peptide,
|  | Size | additional_isotopes = `5`
| ) |  |

inline static

References IsotopeDistribution::clear(), AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::insert(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

## ◆ calculateIsotopePatternsFor18ORangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor18ORangeOfAveraginePeptide | ( | double | mass | ) |

inline static

References IsotopeDistribution::clear(), CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::insert(), and Element::setIsotopeDistribution().

## ◆ calculateIsotopePatternsFor2HRange()

static IsotopePatterns calculateIsotopePatternsFor2HRange | ( | const AASequence & | peptide,
|  | Size | additional_isotopes = `5`
| ) |  |

inline static

References IsotopeDistribution::clear(), AASequence::fromString(), IsotopeDistribution::getContainer(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getIsotopeDistribution(), EmpiricalFormula::getNumberOf(), IsotopeDistribution::insert(), IsotopeDistribution::set(), Element::setIsotopeDistribution(), and AASequence::toUnmodifiedString().

## ◆ calculateIsotopePatternsFor2HRangeOfAveraginePeptide()

static IsotopePatterns calculateIsotopePatternsFor2HRangeOfAveraginePeptide | ( | double | mass | ) |

inline static

References IsotopeDistribution::clear(), CoarseIsotopePatternGenerator::estimateFromPeptideWeight(), IsotopeDistribution::getContainer(), ElementDB::getElement(), ElementDB::getInstance(), IsotopeDistribution::insert(), and Element::setIsotopeDistribution().

## ◆ getNumberOfLabelingElements()

static Size getNumberOfLabelingElements | ( | const String & | labeling_element,
|  | const AASequence & | peptide
| ) |  |

inline static

References AASequence::fromString(), ElementDB::getElement(), AASequence::getFormula(), ElementDB::getInstance(), EmpiricalFormula::getNumberOf(), and AASequence::toUnmodifiedString().