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// File: GranthamAAPolarityIndex.h
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// Created by: Julien Dutheil
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// Created on: Tue Apr 21 2005
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Copyright or © or Copr. CNRS, (November 17, 2004)
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This software is a computer program whose purpose is to provide classes
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for sequences analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _GRANTHAMAAPOLARITYINDEX_H_
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#define _GRANTHAMAAPOLARITYINDEX_H_
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#include "AlphabetIndex1.h"
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#include "../Alphabet/ProteicAlphabet.h"
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* @brief Polarity index used in Grantham (1974).
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* D Polarity (Grantham, 1974)
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* R LIT:2004143b PMID:4843792
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* T Amino acid difference formula to help explain protein evolution
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* J Science 185, 862-864 (1974)
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* I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
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* 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2
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* 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9
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class GranthamAAPolarityIndex:
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public AlphabetIndex1<double>
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std::vector<double> polarity_;
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GranthamAAPolarityIndex() :
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polarity_[ 0] = 8.1; //A
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polarity_[ 1] = 10.5; //R
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polarity_[ 2] = 11.6; //N
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polarity_[ 3] = 13.0; //D
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polarity_[ 4] = 5.5; //C
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polarity_[ 5] = 10.5; //Q
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polarity_[ 6] = 12.3; //E
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polarity_[ 7] = 9.0; //G
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polarity_[ 8] = 10.4; //H
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polarity_[ 9] = 5.2; //I
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polarity_[10] = 4.9; //L
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polarity_[11] = 11.3; //K
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polarity_[12] = 5.7; //M
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polarity_[13] = 5.2; //F
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polarity_[14] = 8.0; //P
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polarity_[15] = 9.2; //S
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polarity_[16] = 8.6; //T
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polarity_[17] = 5.4; //W
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polarity_[18] = 6.2; //Y
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polarity_[19] = 5.9; //V
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virtual ~GranthamAAPolarityIndex() {}
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GranthamAAPolarityIndex* clone() const { return new GranthamAAPolarityIndex(); }
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double getIndex(int state) const throw (BadIntException)
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if (state < 0 || state > 19) throw BadIntException(state, "GranthamAAPolarityIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
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return polarity_[state];
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double getIndex(const std::string& state) const throw (BadCharException)
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return polarity_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
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std::vector<double>* getIndexVector() const { return new std::vector<double>(polarity_); }
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const Alphabet* getAlphabet() const { return &AlphabetTools::PROTEIN_ALPHABET; }
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} //end of namespace bpp.
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#endif //_GRANTHAMAAPOLARITYINDEX_H_
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src/Bpp/Seq/StateProperties/GranthamAAPolarityIndex.h
