HydrophobicityProfile.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: $
// $Authors: Markus Apel, Nora Heese $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/CONCEPT/Types.h>
#include <functional>
#include <sstream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI HydrophobicityProfile 
  {
 
public:
 
    double computeGRAVY(const AASequence& seq) const;
    
    std::vector<double> computeProfile(
      const AASequence& seq, 
      const HydrophobicityScaleMethod scale = HydrophobicityScaleMethod::KYTE_DOOLITTLE
    ) const;
    
    std::vector<double> computeWindowedProfile(
      const AASequence& seq,
      const Size window_size = 7,
      const HydrophobicityScaleMethod scale = HydrophobicityScaleMethod::KYTE_DOOLITTLE
    ) const;
      
    std::vector<double> computeHydrophobicMoment(
      const AASequence& seq,
      const Size window_size = 11,
      const double angle = 100.0  // degrees; 100 = alpha-helix, 160 = beta-sheet
    ) const;  
  }; 
} // namespace OpenMS