bpp::AAChargeIndex Class Reference

Charge of each amino acid. More...

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

Inheritance diagram for bpp::AAChargeIndex:

Collaboration diagram for bpp::AAChargeIndex:

Public Member Functions
	AAChargeIndex ()
virtual	~AAChargeIndex ()
AAChargeIndex *	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: AAindex1
Entry: FAUJ880111
 
H FAUJ880111
D Positive charge (Fauchere et al., 1988)
R LIT:1414114 PMID:3209351
A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
T Amino acid side chain parameters for correlation studies in biology and
  pharmacology
J Int. J. Peptide Protein Res. 32, 269-278 (1988)
C ZIMJ680104    0.813
I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
     0.      1.      0.      0.      0.      0.      0.      0.      1.      0.
     0.      1.      0.      0.      0.      0.      0.      0.      0.      0.
//

Database: AAindex1
Entry: FAUJ880111
 
H FAUJ880112
D Negative charge (Fauchere et al., 1988)
R LIT:1414114 PMID:3209351
A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
T Amino acid side chain parameters for correlation studies in biology and
  pharmacology
J Int. J. Peptide Protein Res. 32, 269-278 (1988)
C RICJ880106    0.849
I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
      0.      0.      0.      1.      0.      0.      1.      0.      0.      0.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.
//

Hence, combining the two:

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.      1.      0.
      0.      1.      0.      0.      0.      0.      0.      0.      0.      0.

Definition at line 59 of file AAChargeIndex.h.

Constructor & Destructor Documentation

AAChargeIndex()

bpp::AAChargeIndex::AAChargeIndex ( )

inline

Definition at line 66 of file AAChargeIndex.h.

References charge_.

Referenced by clone().

~AAChargeIndex()

virtual bpp::AAChargeIndex::~AAChargeIndex ( )

inlinevirtual

Definition at line 93 of file AAChargeIndex.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()

AAChargeIndex* bpp::AAChargeIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 95 of file AAChargeIndex.h.

References AAChargeIndex().

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 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 bpp::KleinAANetChargeIndex::getIndex().

getIndex() [1/2]

double bpp::AAChargeIndex::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 103 of file AAChargeIndex.h.

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

getIndex() [2/2]

double bpp::AAChargeIndex::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 98 of file AAChargeIndex.h.

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

indexVector()

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

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 108 of file AAChargeIndex.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::AAChargeIndex::charge_

private

Definition at line 63 of file AAChargeIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/AAChargeIndex.h