GranthamAAPolarityIndex.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_ALPHABETINDEX_GRANTHAMAAPOLARITYINDEX_H
#define BPP_SEQ_ALPHABETINDEX_GRANTHAMAAPOLARITYINDEX_H
 
 
#include "AlphabetIndex1.h"
 
namespace bpp
{
class GranthamAAPolarityIndex :
  public virtual ProteicAlphabetIndex1
{
private:
  std::vector<double> polarity_;
 
public:
  GranthamAAPolarityIndex() :
    ProteicAlphabetIndex1(),
    polarity_()
  {
    polarity_.resize(20);
    polarity_[ 0] =  8.1; // A
    polarity_[ 1] = 10.5; // R
    polarity_[ 2] = 11.6; // N
    polarity_[ 3] = 13.0; // D
    polarity_[ 4] =  5.5; // C
    polarity_[ 5] = 10.5; // Q
    polarity_[ 6] = 12.3; // E
    polarity_[ 7] =  9.0; // G
    polarity_[ 8] = 10.4; // H
    polarity_[ 9] =  5.2; // I
    polarity_[10] =  4.9; // L
    polarity_[11] = 11.3; // K
    polarity_[12] =  5.7; // M
    polarity_[13] =  5.2; // F
    polarity_[14] =  8.0; // P
    polarity_[15] =  9.2; // S
    polarity_[16] =  8.6; // T
    polarity_[17] =  5.4; // W
    polarity_[18] =  6.2; // Y
    polarity_[19] =  5.9; // V
  }
 
  virtual ~GranthamAAPolarityIndex() {}
 
  GranthamAAPolarityIndex* clone() const override { return new GranthamAAPolarityIndex(); }
 
public:
  double getIndex(int state) const override
  {
    return polarity_[getAlphabet()->getStateIndex(state) - 1];
  }
 
  double getIndex(const std::string& state) const override
  {
    return polarity_[getAlphabet()->getStateIndex(state) - 1];
  }
 
  const std::vector<double>& indexVector() const override { return polarity_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_ALPHABETINDEX_GRANTHAMAAPOLARITYINDEX_H