CoarseIsotopePatternGenerator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
 
#include <map>
#include <set>
 
namespace OpenMS
{
  class Element;
  class OPENMS_DLLAPI CoarseIsotopePatternGenerator
    : public IsotopePatternGenerator
  {
 
 public:
    CoarseIsotopePatternGenerator(const Size max_isotope = 0, const bool round_masses = false);
 
    ~CoarseIsotopePatternGenerator() override;
 
 
    void setMaxIsotope(const Size& max_isotope);
 
    void setRoundMasses(const bool round_masses);
 
    Size getMaxIsotope() const;
 
    bool getRoundMasses() const;
 
    void setIsotopeOverride(const Element* element, const IsotopeDistribution& isotopes);
 
    void clearIsotopeOverrides();
 
    const std::map<const Element*, IsotopeDistribution>& getIsotopeOverrides() const;
 
    IsotopeDistribution run(const EmpiricalFormula& ef) const override;
 
    IsotopeDistribution estimateFromPeptideWeight(double average_weight);
 
      IsotopeDistribution estimateFromPeptideMonoWeight(double mono_weight);
 
 
    IsotopeDistribution estimateFromPeptideWeightAndS(double average_weight, UInt S);
 
    static IsotopeDistribution approximateFromPeptideWeight(double mass, UInt num_peaks = 20, UInt charge = 1);
 
    static std::vector<double> approximateIntensities(double mass, UInt num_peaks = 20);
 
    IsotopeDistribution estimateFromRNAWeight(double average_weight);
 
   IsotopeDistribution estimateFromRNAMonoWeight(double mono_weight);
 
 
    IsotopeDistribution estimateFromDNAWeight(double average_weight);
 
    IsotopeDistribution estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);
 
    IsotopeDistribution estimateFromMonoWeightAndComp(double mono_weight, double C, double H, double N, double O, double S, double P);
 
 
    IsotopeDistribution estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);
 
    IsotopeDistribution estimateForFragmentFromPeptideWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
 
    IsotopeDistribution estimateForFragmentFromPeptideWeightAndS(double average_weight_precursor, UInt S_precursor, double average_weight_fragment, UInt S_fragment, const std::set<UInt>& precursor_isotopes) const;
 
    IsotopeDistribution estimateForFragmentFromRNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
 
    IsotopeDistribution estimateForFragmentFromDNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);
 
    IsotopeDistribution estimateForFragmentFromWeightAndComp(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes, double C, double H, double N, double O, double S, double P) const;
 
    IsotopeDistribution calcFragmentIsotopeDist(const IsotopeDistribution& fragment_isotope_dist, const IsotopeDistribution& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes, const double fragment_mono_mass) const;
 
    CoarseIsotopePatternGenerator& operator=(const CoarseIsotopePatternGenerator& iso);
 
    IsotopeDistribution::ContainerType convolve(const IsotopeDistribution::ContainerType& left, const IsotopeDistribution::ContainerType& right) const;
 
  protected:
 
    IsotopeDistribution::ContainerType convolvePow_(const IsotopeDistribution::ContainerType& input, Size factor) const;
 
    IsotopeDistribution::ContainerType convolveSquare_(const IsotopeDistribution::ContainerType& input) const;
 
    IsotopeDistribution::ContainerType correctMass_(const IsotopeDistribution::ContainerType& input, const double mono_weight) const;
 
    IsotopeDistribution calcFragmentIsotopeDist_(const IsotopeDistribution::ContainerType& fragment_isotope_dist, const IsotopeDistribution::ContainerType& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes) const;
 
    IsotopeDistribution::ContainerType fillGaps_(const IsotopeDistribution::ContainerType& id) const;
 
    Size max_isotope_;
    bool round_masses_;
    std::map<const Element*, IsotopeDistribution> isotope_overrides_;
 
  };
 
} // namespace OpenMS