bpp::AAChenGuHuangHydrophobicityIndex Class Reference

Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006. More...

#include <Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h>

Inheritance diagram for bpp::AAChenGuHuangHydrophobicityIndex:

Collaboration diagram for bpp::AAChenGuHuangHydrophobicityIndex:

Public Member Functions
	AAChenGuHuangHydrophobicityIndex ()
virtual	~AAChenGuHuangHydrophobicityIndex ()
AAChenGuHuangHydrophobicityIndex *	clone () const
double	getIndex (int state) const throw (BadIntException)
	Get the index associated to a state. More...
double	getIndex (const std::string &state) const throw (BadCharException)
	Get the index associated to a state. More...
std::vector< double > *	getIndexVector () const
const Alphabet *	getAlphabet () const
	Get the alphabet associated to this index. More...

Private Attributes
std::vector< double >	hydrophobicity_

Detailed Description

Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006.

Database: AAChenGuHuangHydrophobicity
Entry: CHENH06

H FAUJ880111
D Hydrophobicity (Chen et al., 2006)
R PMCID:PMC1780123 PMID:17217506
A Hang Chen, Fei Gu, and Zhengge Huang.
T Improved Chou-Fasman method for protein secondary structure prediction
J BMC Bioinformatics. 2006; 7(Suppl 4): S14.  (2006)
//

Definition at line 66 of file AAChenGuHuangHydrophobicityIndex.h.

Constructor & Destructor Documentation

AAChenGuHuangHydrophobicityIndex()

bpp::AAChenGuHuangHydrophobicityIndex::AAChenGuHuangHydrophobicityIndex ( )

inline

Definition at line 73 of file AAChenGuHuangHydrophobicityIndex.h.

References hydrophobicity_.

Referenced by clone().

~AAChenGuHuangHydrophobicityIndex()

virtual bpp::AAChenGuHuangHydrophobicityIndex::~AAChenGuHuangHydrophobicityIndex ( )

inlinevirtual

Definition at line 99 of file AAChenGuHuangHydrophobicityIndex.h.

Member Function Documentation

clone()

AAChenGuHuangHydrophobicityIndex* bpp::AAChenGuHuangHydrophobicityIndex::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 101 of file AAChenGuHuangHydrophobicityIndex.h.

References AAChenGuHuangHydrophobicityIndex().

getAlphabet()

const Alphabet* bpp::AAChenGuHuangHydrophobicityIndex::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 117 of file AAChenGuHuangHydrophobicityIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AAChenGuHuangHydrophobicityIndex::getIndex ( int  state ) const throw ( BadIntException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a int value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 104 of file AAChenGuHuangHydrophobicityIndex.h.

References hydrophobicity_, and bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [2/2]

double bpp::AAChenGuHuangHydrophobicityIndex::getIndex ( const std::string &  state ) const throw ( BadCharException )

inlinevirtual

Get the index associated to a state.

Parameters

state

The state to consider, as a string value.

Returns

The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 110 of file AAChenGuHuangHydrophobicityIndex.h.

References bpp::LetterAlphabet::charToInt(), hydrophobicity_, and bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndexVector()

std::vector<double>* bpp::AAChenGuHuangHydrophobicityIndex::getIndexVector ( ) const

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 115 of file AAChenGuHuangHydrophobicityIndex.h.

References hydrophobicity_.

Member Data Documentation

hydrophobicity_

std::vector<double> bpp::AAChenGuHuangHydrophobicityIndex::hydrophobicity_

private

Definition at line 70 of file AAChenGuHuangHydrophobicityIndex.h.

Referenced by AAChenGuHuangHydrophobicityIndex(), getIndex(), and getIndexVector().

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The documentation for this class was generated from the following file:

• Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h