bpp-seq  2.2.0
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 ()
 
KleinAANetChargeIndexclone () 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 AlphabetgetAlphabet () const
 Get the alphabet associated to this index. More...
 

Private Attributes

std::vector< double > charge_
 

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 69 of file KleinAANetChargeIndex.h.

Constructor & Destructor Documentation

◆ KleinAANetChargeIndex()

bpp::KleinAANetChargeIndex::KleinAANetChargeIndex ( )
inline

Definition at line 76 of file KleinAANetChargeIndex.h.

References charge_.

Referenced by clone().

◆ ~KleinAANetChargeIndex()

virtual bpp::KleinAANetChargeIndex::~KleinAANetChargeIndex ( )
inlinevirtual

Definition at line 101 of file KleinAANetChargeIndex.h.

Member Function Documentation

◆ clone()

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

Implements bpp::AlphabetIndex1.

Definition at line 103 of file KleinAANetChargeIndex.h.

References KleinAANetChargeIndex().

◆ getAlphabet()

const Alphabet* bpp::KleinAANetChargeIndex::getAlphabet ( ) const
inlinevirtual

Get the alphabet associated to this index.

Returns
Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex1.

Definition at line 119 of file KleinAANetChargeIndex.h.

References bpp::AlphabetTools::PROTEIN_ALPHABET.

◆ getIndex() [1/2]

double bpp::KleinAANetChargeIndex::getIndex ( int  state) const
throw (BadIntException
)
inlinevirtual

Get the index associated to a state.

Parameters
stateThe state to consider, as a int value.
Returns
The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 106 of file KleinAANetChargeIndex.h.

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

◆ getIndex() [2/2]

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

Get the index associated to a state.

Parameters
stateThe state to consider, as a string value.
Returns
The index associated to the state

Implements bpp::AlphabetIndex1.

Definition at line 112 of file KleinAANetChargeIndex.h.

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

◆ getIndexVector()

std::vector<double>* bpp::KleinAANetChargeIndex::getIndexVector ( ) const
inlinevirtual
Returns
A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 117 of file KleinAANetChargeIndex.h.

References charge_.

Member Data Documentation

◆ charge_

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

Definition at line 73 of file KleinAANetChargeIndex.h.

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


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