bpp::KleinAANetChargeIndex Class Reference

Charge of each amino acid. More...

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

Inheritance diagram for bpp::KleinAANetChargeIndex:

Collaboration diagram for bpp::KleinAANetChargeIndex:

Public Member Functions
	KleinAANetChargeIndex ()
virtual	~KleinAANetChargeIndex ()
KleinAANetChargeIndex *	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 >	charge_
std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Charge of each amino acid.

Database: AAindex
Entry: KLEP840101
 
H KLEP840101
D Net charge (Klein et al., 1984)
R LIT:1008055 PMID:6547351
A Klein, P., Kanehisa, M. and DeLisi, C.
T Prediction of protein function from sequence properties: Discriminant
analysis of a data base
J Biochim. Biophys. Acta 787, 221-226 (1984)
C ZIMJ680104    0.941
I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
      0.      1.      0.     -1.      0.      0.     -1.      0.      0.      0.
      0.      1.      0.      0.      0.      0.      0.      0.      0.      0.
//

Definition at line 34 of file KleinAANetChargeIndex.h.

Constructor & Destructor Documentation

KleinAANetChargeIndex()

bpp::KleinAANetChargeIndex::KleinAANetChargeIndex ( )

inline

Definition at line 41 of file KleinAANetChargeIndex.h.

References charge_.

Referenced by clone().

~KleinAANetChargeIndex()

virtual bpp::KleinAANetChargeIndex::~KleinAANetChargeIndex ( )

inlinevirtual

Definition at line 68 of file KleinAANetChargeIndex.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()

KleinAANetChargeIndex* bpp::KleinAANetChargeIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 70 of file KleinAANetChargeIndex.h.

References KleinAANetChargeIndex().

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(), bpp::AAChenGuHuangHydrophobicityIndex::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 getIndex().

getIndex() [1/2]

double bpp::KleinAANetChargeIndex::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 78 of file KleinAANetChargeIndex.h.

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

getIndex() [2/2]

double bpp::KleinAANetChargeIndex::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 73 of file KleinAANetChargeIndex.h.

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

indexVector()

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

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 83 of file KleinAANetChargeIndex.h.

References charge_.

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=().

charge_

std::vector<double> bpp::KleinAANetChargeIndex::charge_

private

Definition at line 38 of file KleinAANetChargeIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h