bpp::GranthamAAPolarityIndex Class Reference

Polarity index used in Grantham (1974). More...

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

Inheritance diagram for bpp::GranthamAAPolarityIndex:

Collaboration diagram for bpp::GranthamAAPolarityIndex:

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

Detailed Description

Polarity index used in Grantham (1974).

Database: AAindex1
Entry: GRAR740102
 
H GRAR740102
D Polarity (Grantham, 1974)
R LIT:2004143b PMID:4843792
A Grantham, R.
T Amino acid difference formula to help explain protein evolution
J Science 185, 862-864 (1974)
I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
     8.1    10.5    11.6    13.0     5.5    10.5    12.3     9.0    10.4     5.2
     4.9    11.3     5.7     5.2     8.0     9.2     8.6     5.4     6.2     5.9
//

Definition at line 32 of file GranthamAAPolarityIndex.h.

Constructor & Destructor Documentation

GranthamAAPolarityIndex()

bpp::GranthamAAPolarityIndex::GranthamAAPolarityIndex ( )

inline

Definition at line 39 of file GranthamAAPolarityIndex.h.

References polarity_.

Referenced by clone().

~GranthamAAPolarityIndex()

virtual bpp::GranthamAAPolarityIndex::~GranthamAAPolarityIndex ( )

inlinevirtual

Definition at line 66 of file GranthamAAPolarityIndex.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()

GranthamAAPolarityIndex* bpp::GranthamAAPolarityIndex::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex1.

Definition at line 68 of file GranthamAAPolarityIndex.h.

References GranthamAAPolarityIndex().

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(), getIndex(), bpp::GranthamAAVolumeIndex::getIndex(), bpp::KD_AAHydropathyIndex::getIndex(), and bpp::KleinAANetChargeIndex::getIndex().

getIndex() [1/2]

double bpp::GranthamAAPolarityIndex::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 76 of file GranthamAAPolarityIndex.h.

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

getIndex() [2/2]

double bpp::GranthamAAPolarityIndex::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 71 of file GranthamAAPolarityIndex.h.

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

indexVector()

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

inlineoverridevirtual

Returns

A vector object with all indices.

Implements bpp::AlphabetIndex1.

Definition at line 81 of file GranthamAAPolarityIndex.h.

References polarity_.

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=().

polarity_

std::vector<double> bpp::GranthamAAPolarityIndex::polarity_

private

Definition at line 36 of file GranthamAAPolarityIndex.h.

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

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

• Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h