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 override
double	getIndex (int state) const override
	Get the index associated to a state. More...
double	getIndex (const std::string &state) const override
	Get the index associated to a state. More...
const std::vector< double > &	indexVector () const override
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to this index. More...
const Alphabet &	alphabet () const override
	Get the alphabet associated to this index. More...

Private Attributes
std::vector< double >	hydrophobicity_
std::shared_ptr< const ProteicAlphabet >	alpha_

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 30 of file AAChenGuHuangHydrophobicityIndex.h.

Constructor & Destructor Documentation

AAChenGuHuangHydrophobicityIndex()

bpp::AAChenGuHuangHydrophobicityIndex::AAChenGuHuangHydrophobicityIndex ( )

inline

Definition at line 37 of file AAChenGuHuangHydrophobicityIndex.h.

References hydrophobicity_.

Referenced by clone().

~AAChenGuHuangHydrophobicityIndex()

virtual bpp::AAChenGuHuangHydrophobicityIndex::~AAChenGuHuangHydrophobicityIndex ( )

inlinevirtual

Definition at line 64 of file AAChenGuHuangHydrophobicityIndex.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::ProteicAlphabetIndex1::alphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 99 of file AlphabetIndex1.h.

References bpp::ProteicAlphabetIndex1::alpha_.

clone()

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

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 66 of file AAChenGuHuangHydrophobicityIndex.h.

References AAChenGuHuangHydrophobicityIndex().

getAlphabet()

std::shared_ptr<const Alphabet> bpp::ProteicAlphabetIndex1::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 97 of file AlphabetIndex1.h.

References bpp::ProteicAlphabetIndex1::alpha_.

Referenced by bpp::AAChargeIndex::getIndex(), getIndex(), bpp::AAChouFasmanAHelixIndex::getIndex(), bpp::AAChouFasmanBSheetIndex::getIndex(), bpp::AAChouFasmanTurnIndex::getIndex(), bpp::AAIndex1Entry::getIndex(), bpp::AAMassIndex::getIndex(), bpp::AASEA1030Index::getIndex(), bpp::AASEAInf10Index::getIndex(), bpp::AASEASup30Index::getIndex(), bpp::AASurfaceIndex::getIndex(), bpp::AAVolumeIndex::getIndex(), bpp::GranthamAAPolarityIndex::getIndex(), bpp::GranthamAAVolumeIndex::getIndex(), bpp::KD_AAHydropathyIndex::getIndex(), and bpp::KleinAANetChargeIndex::getIndex().

getIndex() [1/2]

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

inlineoverridevirtual

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 77 of file AAChenGuHuangHydrophobicityIndex.h.

References bpp::ProteicAlphabetIndex1::getAlphabet(), and hydrophobicity_.

getIndex() [2/2]

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

inlineoverridevirtual

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 72 of file AAChenGuHuangHydrophobicityIndex.h.

References bpp::ProteicAlphabetIndex1::getAlphabet(), and hydrophobicity_.

indexVector()

const std::vector<double>& bpp::AAChenGuHuangHydrophobicityIndex::indexVector ( ) const

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 82 of file AAChenGuHuangHydrophobicityIndex.h.

References hydrophobicity_.

Member Data Documentation

alpha_

std::shared_ptr<const ProteicAlphabet> bpp::ProteicAlphabetIndex1::alpha_

privateinherited

Definition at line 79 of file AlphabetIndex1.h.

Referenced by bpp::ProteicAlphabetIndex1::alphabet(), bpp::ProteicAlphabetIndex1::getAlphabet(), and bpp::ProteicAlphabetIndex1::operator=().

hydrophobicity_

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

private

Definition at line 34 of file AAChenGuHuangHydrophobicityIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h