Grantham (1974) Amino-Acid chemical distance. More...

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

Inheritance diagram for bpp::GranthamAAChemicalDistance:

Collaboration diagram for bpp::GranthamAAChemicalDistance:

Public Member Functions
	GranthamAAChemicalDistance ()

	GranthamAAChemicalDistance (const GranthamAAChemicalDistance &gd)

GranthamAAChemicalDistance &	operator= (const GranthamAAChemicalDistance &gd)

GranthamAAChemicalDistance *	clone () const override

virtual	~GranthamAAChemicalDistance ()

void	setSymmetric (bool yn)

bool	isSymmetric () const override

void	setPC1Sign (bool yn)
	The sign of the distance is computed using the coordinate on the first axis of a principal component analysis with the 3 elementary properties (Volume, Polarity, Composition). Otherwise, use the default arbitrary sign. Using this option will lead isSymmetric to return false. More...

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...

Methods from the AlphabetIndex2 interface.
double	getIndex (int state1, int state2) const override
	Get the index associated to a pair of states. More...

double	getIndex (const std::string &state1, const std::string &state2) const override
	Get the index associated to a pair of states. More...

const Matrix< double > &	getIndexMatrix () const override

Static Public Attributes
static short int	SIGN_ARBITRARY = 1

static short int	SIGN_PC1 = 2

static short int	SIGN_NONE = 0

Protected Member Functions
void	computeIndexMatrix_ ()

Private Attributes
LinearMatrix< double >	distanceMatrix_

LinearMatrix< double >	signMatrix_

LinearMatrix< double >	indexMatrix_

short int	sign_

std::shared_ptr< const ProteicAlphabet >	alpha_

Detailed Description

Grantham (1974) Amino-Acid chemical distance.

Two kinds of matrix can be built:

a symmetric one, with $I_{i,j} = I_{i,j}$ ,
or a non-symmetric one, with $I_{i,j} = -I_{i,j}$ . In the second case, which one of the two entries between $I_{i,j}$ and $I_{i,j}$ is positive is arbitrary by default. It is also possible to use the coordinate on a principal component analysis between the elementary properties of the distance instead (setPC1Sign(true)). The following R code was use in order to get those signs:
library(seqinr)

data(aaindex)

data<-data.frame(composition=aaindex[["GRAR740101"]]$I,

polarity=aaindex[["GRAR740102"]]$I,

volume=aaindex[["GRAR740103"]]$I)

library(ade4)

pca<-dudi.pca(data)

plot(pca$li[, 1:2], type="n")

text(pca$li[, 1:2], rownames(data))

s.corcircle(pca$co)

layout(matrix(1:3,nrow=1))

a1<-pca$li[,1]; names(a1)<-rownames(data); dotchart(sort(a1))

a2<-pca$li[,2]; names(a2)<-rownames(data); dotchart(sort(a2))

a3<-pca$li[,3]; names(a3)<-rownames(data); dotchart(sort(a3))

x<-pca$li[,1] #Contains the coordinates on the first axis.

m<-matrix(nrow=20, ncol=20)

for(i in 1:length(x))

for(j in 1:length(x))

m[i,j]<-sign(x[j] - x[i])

Reference: Grantham, R. Amino acid difference formula to help explain protein evolution Science 185, 862-864 (1974)

Data from AAIndex2 database, Accession Number GRAR740104.

Definition at line 61 of file GranthamAAChemicalDistance.h.

Constructor & Destructor Documentation

◆ GranthamAAChemicalDistance() [1/2]

GranthamAAChemicalDistance::GranthamAAChemicalDistance ( )

Definition at line 19 of file GranthamAAChemicalDistance.cpp.

References computeIndexMatrix_().

Referenced by clone().

◆ GranthamAAChemicalDistance() [2/2]

bpp::GranthamAAChemicalDistance::GranthamAAChemicalDistance ( const GranthamAAChemicalDistance & gd )

inline

Definition at line 73 of file GranthamAAChemicalDistance.h.

◆ ~GranthamAAChemicalDistance()

virtual bpp::GranthamAAChemicalDistance::~GranthamAAChemicalDistance ( )

inlinevirtual

Definition at line 94 of file GranthamAAChemicalDistance.h.

Member Function Documentation

◆ alphabet()

const Alphabet& bpp::ProteicAlphabetIndex2::alphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns: Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 104 of file AlphabetIndex2.h.

References bpp::ProteicAlphabetIndex2::alpha_.

◆ clone()

GranthamAAChemicalDistance* bpp::GranthamAAChemicalDistance::clone ( ) const

inlineoverridevirtual

Implements bpp::ProteicAlphabetIndex2.

Definition at line 92 of file GranthamAAChemicalDistance.h.

References GranthamAAChemicalDistance().

◆ computeIndexMatrix_()

void GranthamAAChemicalDistance::computeIndexMatrix_ ( )

protected

Definition at line 47 of file GranthamAAChemicalDistance.cpp.

References distanceMatrix_, indexMatrix_, sign_, SIGN_NONE, SIGN_PC1, and signMatrix_.

Referenced by GranthamAAChemicalDistance(), setPC1Sign(), and setSymmetric().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::ProteicAlphabetIndex2::getAlphabet ( ) const

inlineoverridevirtualinherited

Get the alphabet associated to this index.

Returns: Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 102 of file AlphabetIndex2.h.

References bpp::ProteicAlphabetIndex2::alpha_.

Referenced by bpp::AAIndex2Entry::getIndex(), bpp::BLOSUM50::getIndex(), getIndex(), and bpp::MiyataAAChemicalDistance::getIndex().

◆ getIndex() [1/2]

double GranthamAAChemicalDistance::getIndex	(	const std::string &	state1,
		const std::string &	state2
	)		const

overridevirtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a string value.
state2	Second state to consider, as a string value.

Returns: The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 42 of file GranthamAAChemicalDistance.cpp.

References bpp::ProteicAlphabetIndex2::getAlphabet(), and getIndex().

◆ getIndex() [2/2]

double GranthamAAChemicalDistance::getIndex	(	int	state1,
		int	state2
	)		const

overridevirtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a int value in the Alphabet
state2	Second state to consider, as a int value in the Alphabet

Returns: The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 31 of file GranthamAAChemicalDistance.cpp.

References distanceMatrix_, bpp::ProteicAlphabetIndex2::getAlphabet(), sign_, SIGN_NONE, SIGN_PC1, and signMatrix_.

Referenced by getIndex().

◆ getIndexMatrix()

const Matrix<double>& bpp::GranthamAAChemicalDistance::getIndexMatrix ( ) const

inlineoverridevirtual

Returns: A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 104 of file GranthamAAChemicalDistance.h.

References indexMatrix_.

◆ isSymmetric()

bool bpp::GranthamAAChemicalDistance::isSymmetric ( ) const

inlineoverridevirtual

Returns: True if the index is symetric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 116 of file GranthamAAChemicalDistance.h.

References sign_, and SIGN_NONE.

◆ operator=()

GranthamAAChemicalDistance& bpp::GranthamAAChemicalDistance::operator= ( const GranthamAAChemicalDistance & gd )

inline

Definition at line 81 of file GranthamAAChemicalDistance.h.

References distanceMatrix_, indexMatrix_, bpp::ProteicAlphabetIndex2::operator=(), sign_, and signMatrix_.

◆ setPC1Sign()

void bpp::GranthamAAChemicalDistance::setPC1Sign ( bool yn )

inline

The sign of the distance is computed using the coordinate on the first axis of a principal component analysis with the 3 elementary properties (Volume, Polarity, Composition). Otherwise, use the default arbitrary sign. Using this option will lead isSymmetric to return false.

Parameters