IsoelectricPoint.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: Timo Sachsenberg $
// $Authors: OpenMS Team $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CONCEPT/Types.h>
#include <unordered_map>
 
namespace OpenMS
{
  enum class ProteomicsPkaScale
  {
    LEHNINGER = 0,  
    EMBOSS = 1,     
    SILLERO = 2,    
    BJELLQVIST = 3, 
    SIZE_OF_PROTEOMICS_PKA_SCALES
  };
 
  class OPENMS_DLLAPI IsoelectricPoint
  {
 
  public:
 
    static double computeCharge(
      const AASequence& seq,
      double pH,
      ProteomicsPkaScale scale = ProteomicsPkaScale::LEHNINGER);
 
    static double computePI(
      const AASequence& seq,
      ProteomicsPkaScale scale = ProteomicsPkaScale::LEHNINGER,
      double tolerance = 1e-4);
 
  private:
    struct PkaValues
    {
      double nterm;  
      double cterm;  
      double D;      
      double E;      
      double C;      
      double Y;      
      double H;      
      double K;      
      double R;      
      std::unordered_map<char, double> nterm_by_residue;
      std::unordered_map<char, double> cterm_by_residue;
    };
 
    static const PkaValues& getPkaValues_(ProteomicsPkaScale scale);
 
    static double chargeAcidic_(double pH, double pKa);
 
    static double chargeBasic_(double pH, double pKa);
  };
 
} // namespace OpenMS