RDNumeric Namespace Reference

Namespaces
namespace	Alignments
namespace	EigenSolvers

Classes
class	Matrix
	A matrix class for general, non-square matrices. More...
class	SquareMatrix
class	SymmMatrix
	A symmetric matrix class. More...
class	Vector
	A class to represent vectors of numbers. More...

Typedefs
typedef Matrix< double >	DoubleMatrix
typedef SquareMatrix< double >	DoubleSquareMatrix
typedef SymmMatrix< double >	DoubleSymmMatrix
typedef SymmMatrix< int >	IntSymmMatrix
typedef SymmMatrix< unsigned int >	UintSymmMatrix
typedef Vector< double >	DoubleVector

Functions
template<class TYPE >
Matrix< TYPE > &	multiply (const Matrix< TYPE > &A, const Matrix< TYPE > &B, Matrix< TYPE > &C)
	Matrix multiplication.
template<class TYPE >
Vector< TYPE > &	multiply (const Matrix< TYPE > &A, const Vector< TYPE > &x, Vector< TYPE > &y)
	Matrix-Vector multiplication.
template<class TYPE >
SymmMatrix< TYPE > &	multiply (const SymmMatrix< TYPE > &A, const SymmMatrix< TYPE > &B, SymmMatrix< TYPE > &C)
	SymmMatrix-SymmMatrix multiplication.
template<class TYPE >
Vector< TYPE > &	multiply (const SymmMatrix< TYPE > &A, const Vector< TYPE > &x, Vector< TYPE > &y)
	SymmMatrix-Vector multiplication.
template<typename T >
double	TanimotoSimilarity (const Vector< T > &v1, const Vector< T > &v2)
	returns the algebraic tanimoto similarity [defn' from JCIM 46:587-96 (2006)]

Typedef Documentation

DoubleMatrix

typedef Matrix<double> RDNumeric::DoubleMatrix

Definition at line 326 of file Matrix.h.

DoubleSquareMatrix

typedef SquareMatrix<double> RDNumeric::DoubleSquareMatrix

Definition at line 86 of file SquareMatrix.h.

DoubleSymmMatrix

typedef SymmMatrix<double> RDNumeric::DoubleSymmMatrix

Definition at line 339 of file SymmMatrix.h.

DoubleVector

typedef Vector<double> RDNumeric::DoubleVector

Definition at line 296 of file Vector.h.

IntSymmMatrix

typedef SymmMatrix<int> RDNumeric::IntSymmMatrix

Definition at line 340 of file SymmMatrix.h.

UintSymmMatrix

typedef SymmMatrix<unsigned int> RDNumeric::UintSymmMatrix

Definition at line 341 of file SymmMatrix.h.

Function Documentation

multiply() [1/4]

template<class TYPE >

Matrix< TYPE > & RDNumeric::multiply	(	const Matrix< TYPE > &	A,
		const Matrix< TYPE > &	B,
		Matrix< TYPE > &	C
	)

Matrix multiplication.

Multiply a Matrix A with a second Matrix B so the result is C = A*B

Parameters

A	the first Matrix used in the multiplication
B	the Matrix by which to multiply
C	Matrix to use for the results

Returns

the results of multiplying A by B. This is just a reference to C.

Definition at line 255 of file Matrix.h.

References CHECK_INVARIANT, RDNumeric::Matrix< TYPE >::getData(), RDNumeric::Matrix< TYPE >::numCols(), and RDNumeric::Matrix< TYPE >::numRows().

multiply() [2/4]

template<class TYPE >

Vector< TYPE > & RDNumeric::multiply	(	const Matrix< TYPE > &	A,
		const Vector< TYPE > &	x,
		Vector< TYPE > &	y
	)

Matrix-Vector multiplication.

Multiply a Matrix A with a Vector x so the result is y = A*x

Parameters

A	the matrix used in the multiplication
x	the Vector by which to multiply
y	Vector to use for the results

Returns

the results of multiplying x by this This is just a reference to y.

Definition at line 302 of file Matrix.h.

References CHECK_INVARIANT, RDNumeric::Matrix< TYPE >::getData(), RDNumeric::Vector< TYPE >::getData(), RDNumeric::Matrix< TYPE >::numCols(), RDNumeric::Matrix< TYPE >::numRows(), and RDNumeric::Vector< TYPE >::size().

multiply() [3/4]

template<class TYPE >

SymmMatrix< TYPE > & RDNumeric::multiply	(	const SymmMatrix< TYPE > &	A,
		const SymmMatrix< TYPE > &	B,
		SymmMatrix< TYPE > &	C
	)

SymmMatrix-SymmMatrix multiplication.

Multiply SymmMatrix A with a second SymmMatrix B and write the result to C = A*B

Parameters

A	the first SymmMatrix
B	the second SymmMatrix to multiply
C	SymmMatrix to use for the results

Returns

the results of multiplying A by B. This is just a reference to C.

This method is reimplemented here for efficiency reasons (we basically don't want to use getter and setter functions)

Definition at line 262 of file SymmMatrix.h.

References CHECK_INVARIANT, RDNumeric::SymmMatrix< TYPE >::getData(), and RDNumeric::SymmMatrix< TYPE >::numRows().

multiply() [4/4]

template<class TYPE >

Vector< TYPE > & RDNumeric::multiply	(	const SymmMatrix< TYPE > &	A,
		const Vector< TYPE > &	x,
		Vector< TYPE > &	y
	)

SymmMatrix-Vector multiplication.

Multiply a SymmMatrix A with a Vector x so the result is y = A*x

Parameters

A	the SymmMatrix for multiplication
x	the Vector by which to multiply
y	Vector to use for the results

Returns

the results of multiplying x by A This is just a reference to y.

This method is reimplemented here for efficiency reasons (we basically don't want to use getter and setter functions)

Definition at line 313 of file SymmMatrix.h.

References CHECK_INVARIANT, RDNumeric::SymmMatrix< TYPE >::getData(), RDNumeric::Vector< TYPE >::getData(), RDNumeric::SymmMatrix< TYPE >::numRows(), and RDNumeric::Vector< TYPE >::size().

TanimotoSimilarity()

template<typename T >

double RDNumeric::TanimotoSimilarity	(	const Vector< T > &	v1,
		const Vector< T > &	v2
	)

returns the algebraic tanimoto similarity [defn' from JCIM 46:587-96 (2006)]

Definition at line 300 of file Vector.h.

References RDNumeric::Vector< TYPE >::dotProduct(), and RDNumeric::Vector< TYPE >::normL2Sq().