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
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 >	charge_

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. * Soit:
//

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 95 of file AAChargeIndex.h.

Constructor & Destructor Documentation

AAChargeIndex()

bpp::AAChargeIndex::AAChargeIndex ( )

inline

Definition at line 102 of file AAChargeIndex.h.

References charge_.

Referenced by clone().

~AAChargeIndex()

virtual bpp::AAChargeIndex::~AAChargeIndex ( )

inlinevirtual

Definition at line 128 of file AAChargeIndex.h.

Member Function Documentation

clone()

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

inlinevirtual

Implements bpp::AlphabetIndex1.

Definition at line 130 of file AAChargeIndex.h.

References AAChargeIndex().

getAlphabet()

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

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 146 of file AAChargeIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

getIndex() [1/2]

double bpp::AAChargeIndex::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 133 of file AAChargeIndex.h.

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

getIndex() [2/2]

double bpp::AAChargeIndex::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 139 of file AAChargeIndex.h.

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

getIndexVector()

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

inlinevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 144 of file AAChargeIndex.h.

References charge_.

Member Data Documentation

charge_

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

private

Definition at line 99 of file AAChargeIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/AAChargeIndex.h