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// File: AAChenGuHuangHydrophobicityIndex.h
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// Created by: Bastien Boussau
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// Created on: Fri Jan 14 10:31 2011
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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 _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
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#define _AACHENGUHUANGHYDROPHOBICITYINDEX_H_
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#include "AlphabetIndex1.h"
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#include "../Alphabet/ProteicAlphabet.h"
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* @brief Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006.
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* Database: AAChenGuHuangHydrophobicity
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* D Hydrophobicity (Chen et al., 2006)
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* R PMCID:PMC1780123 PMID:17217506
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* A Hang Chen, Fei Gu, and Zhengge Huang.
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* T Improved Chou-Fasman method for protein secondary structure prediction
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* J BMC Bioinformatics. 2006; 7(Suppl 4): S14. (2006)
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class AAChenGuHuangHydrophobicityIndex:
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public AlphabetIndex1<double>
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std::vector<double> hydrophobicity_;
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AAChenGuHuangHydrophobicityIndex() :
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hydrophobicity_.resize(20);
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hydrophobicity_[ 0] = 0.87; //A
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hydrophobicity_[ 1] = 0.85; //R
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hydrophobicity_[ 2] = 0.09; //N
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hydrophobicity_[ 3] = 0.66; //D
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hydrophobicity_[ 4] = 1.52; //C
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hydrophobicity_[ 5] = 0.00; //Q
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hydrophobicity_[ 6] = 0.67; //E
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hydrophobicity_[ 7] = 0.00; //G
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hydrophobicity_[ 8] = 0.87; //H
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hydrophobicity_[ 9] = 3.15; //I
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hydrophobicity_[10] = 2.17; //L
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hydrophobicity_[11] = 1.64; //K
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hydrophobicity_[12] = 1.67; //M
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hydrophobicity_[13] = 2.87; //F
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hydrophobicity_[14] = 2.77; //P
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hydrophobicity_[15] = 0.07; //S
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hydrophobicity_[16] = 0.07; //T
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hydrophobicity_[17] = 3.77; //W
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hydrophobicity_[18] = 2.76; //Y
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hydrophobicity_[19] = 1.87; //V
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virtual ~AAChenGuHuangHydrophobicityIndex() {}
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AAChenGuHuangHydrophobicityIndex* clone() const { return new AAChenGuHuangHydrophobicityIndex(); }
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double getIndex(int state) const throw (BadIntException)
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if (state < 0 || state > 19) throw BadIntException(state, "AAChenGuHuangHydrophobicityIndex::getIndex(). Invalid state.", &AlphabetTools::PROTEIN_ALPHABET);
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return hydrophobicity_[state];
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double getIndex(const std::string& state) const throw (BadCharException)
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return hydrophobicity_[AlphabetTools::PROTEIN_ALPHABET.charToInt(state)];
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std::vector<double>* getIndexVector() const { return new std::vector<double>(hydrophobicity_); }
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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 //_AACHENGUHUANGHYDROPHOBICITYINDEX_H_
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src/Bpp/Seq/StateProperties/AAChenGuHuangHydrophobicityIndex.h
