#include <openbabel/math/matrix3x3.h>

Inheritance diagram for matrix3x3:

Public Member Functions
	matrix3x3 (void)

	matrix3x3 (double s)

	matrix3x3 (vector3 row1, vector3 row2, vector3 row3)

	matrix3x3 (double d[3][3])

	~matrix3x3 ()

void	GetArray (double *m)

const double &	operator() (int row, int column) const

double &	operator() (int row, int column)

matrix3x3	inverse (void) const

matrix3x3	transpose (void) const

double	determinant () const

bool	isSymmetric (void) const

bool	isOrthogonal (void) const

bool	isDiagonal (void) const

bool	isUnitMatrix (void) const

double	Get (int row, int column) const

void	Set (int row, int column, double v)

void	SetColumn (int column, const vector3 &v)

void	SetRow (int row, const vector3 &v)

vector3	GetColumn (unsigned int col) const

vector3	GetRow (unsigned int row) const

matrix3x3 &	operator*= (const double &c)

matrix3x3 &	operator/= (const double &c)

void	SetupRotMat (double x, double y, double z)

void	PlaneReflection (const vector3 &norm)

void	RotAboutAxisByAngle (const vector3 &axis, const double angle)

void	FillOrth (double alpha, double beta, double gamma, double a, double b, double c)

matrix3x3	findEigenvectorsIfSymmetric (vector3 &eigenvals) const

Static Public Member Functions
static void	jacobi (unsigned int n, double a, double d, double *v)

Friends
vector3	operator* (const matrix3x3 &, const vector3 &)

matrix3x3	operator* (const matrix3x3 &, const matrix3x3 &)

std::ostream &	operator<< (std::ostream &, const matrix3x3 &)

Detailed Description

Represents a real 3x3 matrix.

Rotating points in space can be performed by a vector-matrix multiplication. The matrix3x3 class is designed as a helper to the vector3 class for rotating points in space. The rotation matrix may be initialised by passing in the array of floating point values, by passing euler angles, or a rotation vector and angle of rotation about that vector. Once set, the matrix3x3 class can be used to rotate vectors by the overloaded multiplication operator. The following demonstrates the usage of the matrix3x3 class:

matrix3x3 mat;
mat.SetupRotMat(0.0,180.0,0.0); //rotate theta by 180 degrees
vector3 v = VX;
v *= mat; //apply the rotation

Constructor & Destructor Documentation

◆ matrix3x3() [1/4]

matrix3x3 ( void )

inline

Constructs the zero-matrix.

◆ matrix3x3() [2/4]

matrix3x3 ( double s )

inline

Constructs s times the unit matrix.

◆ matrix3x3() [3/4]

matrix3x3	(	vector3	row1,
		vector3	row2,
		vector3	row3
	)

inline

Constructs a matrix from row vectors.

◆ matrix3x3() [4/4]

matrix3x3 ( double d[3][3] )

inline

Constructs a matrix from a 3x3-array of doubles.

The first index represents the row, the second index the column

◆ ~matrix3x3()

~matrix3x3 ( )

inline

Destructor.

Member Function Documentation

◆ GetArray()

void GetArray ( double * m )

inline

Access function.

Writes the matrix into the 1-dimensional array m, row by row. The array must be able to hold 9 doubles, otherwise your program will segfault.

◆ operator()() [1/2]

const double& operator()	(	int	row,
		int	column
	)		const

inline

Returns: a constant reference to an element of the matrix. row and column must be between 0 and 2. No check is done.

◆ operator()() [2/2]

double& operator()	(	int	row,
		int	column
	)

inline

Returns: a non-constant reference to an element of the matrix. row and column must be between 0 and 2. No check is done.

◆ inverse()

matrix3x3 inverse ( void ) const

Calculates the inverse of a matrix.

This method checks if the absolute value of the determinant is smaller than 1e-6. If so, nothing is done and an exception is thrown. Otherwise, the inverse matrix is calculated and returned. *this is not changed.

Warning: If the determinant is close to zero, but not == 0.0, this method may behave in unexpected ways and return almost random results; details may depend on your particular floating point implementation. The use of this method is therefore highly discouraged, unless you are certain that the determinant is in a reasonable range, away from 0.0 (Stefan Kebekus)

Referenced by OBUnitCell::CartesianToFractional(), OBUnitCell::GetFractionalMatrix(), and OBUnitCell::SetData().

◆ transpose()

matrix3x3 transpose ( void ) const

Calculates the transpose of a matrix.

Referenced by OBUnitCell::GetCellMatrix(), and OBUnitCell::SetData().

◆ determinant()

double determinant ( void ) const

Returns: The determinant of the matrix

◆ isSymmetric()

bool isSymmetric ( void ) const

Checks if a matrix is symmetric.

Returns: False if there are indices i,j such that fabs(*this[i][j]-*this[j][i]) > 1e-6. Otherwise, it returns true.

◆ isOrthogonal()

bool isOrthogonal ( void ) const

inline

Checks if a matrix is orthogonal.

This method checks if a matrix is orthogonal, i.e. if all column vectors are normalized and are mutually orthogonal. A matrix is orthogonal if, and only if the transformation it describes is orthonormal. An orthonormal transformation is a transformation that preserves length and angle.

The check is performed using the method isUnitMatrix() to check if

*this * transpose()

is a unit matrix. The criterion is therefore numerically quite tight.

◆ isDiagonal()

bool isDiagonal ( void ) const

Returns: if a matrix is diagonal

This method returns true if and only if the matrix is (approximately) a diagonal matrix. The precision used by this function is 1e-6.

◆ isUnitMatrix()

bool isUnitMatrix ( void ) const

Returns: if a matrix is the unit matrix

This method returns true if and only if the matrix is (approximately) equal to the identity matrix. The precision used by this function is 1e-6.

◆ Get()

double Get	(	int	row,
		int	column
	)		const

inline

Access function.

Warning: row or column are not in the range 0..2, zero is returned !

Deprecated:: use the constant operator() instead

Referenced by vector3::operator*=().

◆ Set()

void Set	(	int	row,
		int	column,
		double	v
	)

inline

Access function.

Warning: if row or column are not in the range 0..2, nothing will happen !

Deprecated:: use the non-constant operator() instead

◆ SetColumn()

void SetColumn	(	int	column,
		const vector3 &	v
	)

Access function.

Warning: If column is not in the range 0..2, the vector remains unchanged and an exception is thrown.

◆ SetRow()

void SetRow	(	int	row,
		const vector3 &	v
	)

Access function.

Warning: If column is not in the range 0..2, the vector remains unchanged and an exception is thrown.

◆ GetColumn()

vector3 GetColumn ( unsigned int col ) const

Access function.

Warning: If col is not in the range 0..2, an exception is thrown.

Referenced by OBUnitCell::GetA(), OBUnitCell::GetAlpha(), OBUnitCell::GetB(), OBUnitCell::GetBeta(), OBUnitCell::GetC(), and OBUnitCell::GetGamma().

◆ GetRow()

vector3 GetRow ( unsigned int row ) const

Access function.

Warning: If row is not in the range 0..2, an exception is thrown.

Referenced by OBUnitCell::GetCellVectors(), and OBUnitCell::SetData().

◆ operator*=()

matrix3x3& operator*= ( const double & c )

inline

Multiplies all entries of the matrix by a scalar c.

◆ operator/=()

matrix3x3& operator/= ( const double & c )

inline

Divides all entries of the matrix by a scalar c.

◆ SetupRotMat()

void SetupRotMat	(	double	x,
		double	y,
		double	z
	)

Calculate a rotation matrix for rotation about the x, y, and z axes by the angles specified (in degrees)

Referenced by OBBuilder::Connect().

◆ PlaneReflection()

void PlaneReflection ( const vector3 & norm )

Calculates a matrix that represents reflection on a plane.

Replaces *this with a matrix that represents reflection on the plane through 0 which is given by the normal vector norm.

Warning: If the vector norm has length zero, this method will generate the 0-matrix. If the length of the axis is close to zero, but not == 0.0, this method may behave in unexpected ways and return almost random results; details may depend on your particular floating point implementation. The use of this method is therefore highly discouraged, unless you are certain that the length is in a reasonable range, away from 0.0 (Stefan Kebekus)

Deprecated:: This method will probably replaced by a safer algorithm in the future.

Todo:: Replace this method with a more fool-proof version.

Parameters

norm	specifies the normal to the plane

◆ RotAboutAxisByAngle()

void RotAboutAxisByAngle	(	const vector3 &	v,
		const double	angle
	)

Calculates a rotation matrix, rotating around the specified axis by the specified angle (in degrees)

Replaces *this with a matrix that represents rotation about the axis by a an angle.

Warning: If the vector axis has length zero, this method will generate the 0-matrix. If the length of the axis is close to zero, but not == 0.0, this method may behave in unexpected ways and return almost random results; details may depend on your particular floating point implementation. The use of this method is therefore highly discouraged, unless you are certain that the length is in a reasonable range, away from 0.0 (Stefan Kebekus)

Deprecated:: This method will probably replaced by a safer algorithm in the future.

Todo:: Replace this method with a more fool-proof version.

Parameters

v	specifies the axis of the rotation
angle	angle in degrees (0..360)

Referenced by OBMol::Align(), OBBuilder::Build(), OBBuilder::GetNewBondVector(), OBBuilder::IsSpiroAtom(), and OBAtom::SetHybAndGeom().

◆ FillOrth()

void FillOrth	(	double	alpha,
		double	beta,
		double	gamma,
		double	a,
		double	b,
		double	c
	)

Calculate an orthogonalisation matrix for a unit cell specified by the parameters alpha, beta, gamma, a, b, c where alpha, beta, and gamma are the cell angles (in degrees) and a, b, and c are the cell vector lengths Used by OBUnitCell

Referenced by OBUnitCell::SetData().

◆ findEigenvectorsIfSymmetric()

matrix3x3 findEigenvectorsIfSymmetric ( vector3 & eigenvals ) const

Find the eigenvalues and -vectors of a symmetric matrix.

This method employs the static method matrix3x3::jacobi(...) to find the eigenvalues and eigenvectors of a symmetric matrix. On entry it is checked if the matrix really is symmetric: if isSymmetric() returns 'false', an OBError is thrown.

Note: The jacobi algorithm is should work great for all symmetric 3x3 matrices. If you need to find the eigenvectors of a non-symmetric matrix, you might want to resort to the sophisticated routines of LAPACK.

Parameters

eigenvals a reference to a vector3 where the eigenvalues will be stored. The eigenvalues are ordered so that eigenvals[0] <= eigenvals[1] <= eigenvals[2].

Returns: an orthogonal matrix whose ith column is an eigenvector for the eigenvalue eigenvals[i]. Here 'orthogonal' means that all eigenvectors have length one and are mutually orthogonal. The ith eigenvector can thus be conveniently accessed by the GetColumn() method, as in the following example.
// Calculate eigenvectors and -values
vector3 eigenvals;
matrix3x3 eigenmatrix = somematrix.findEigenvectorsIfSymmetric(eigenvals);
// Print the 2nd eigenvector
cout << eigenmatrix.GetColumn(1) << endl;
With these conventions, a matrix is diagonalized in the following way:
// Diagonalize the matrix
matrix3x3 diagonalMatrix = eigenmatrix.inverse() * somematrix * eigenmatrix;

◆ jacobi()

void jacobi	(	unsigned int	n,
		double *	a,
		double *	d,
		double *	v
	)

static

Eigenvalue calculation.

This static function computes the eigenvalues and eigenvectors of a SYMMETRIC nxn matrix. This method is used internally by OpenBabel, but may be useful as a general eigenvalue finder.

The algorithm uses Jacobi transformations. It is described e.g. in Wilkinson, Reinsch "Handbook for automatic computation, Volume II: Linear Algebra", part II, contribution II/1. The implementation is also similar to the implementation in this book. This method is adequate to solve the eigenproblem for small matrices, of size perhaps up to 10x10. For bigger problems, you might want to resort to the sophisticated routines of LAPACK.

Note: If you plan to find the eigenvalues of a symmetric 3x3 matrix, you will probably prefer to use the more convenient method findEigenvectorsIfSymmetric()

Parameters

n	the size of the matrix that should be diagonalized
a	array of size n^2 which holds the symmetric matrix whose eigenvectors are to be computed. The convention is that the entry in row r and column c is addressed as a[n*r+c] where, of course, 0 <= r < n and 0 <= c < n. There is no check that the matrix is actually symmetric. If it is not, the behaviour of this function is undefined. On return, the matrix is overwritten with junk.
d	pointer to a field of at least n doubles which will be overwritten. On return of this function, the entries d[0]..d[n-1] will contain the eigenvalues of the matrix.
v	an array of size n^2 where the eigenvectors will be stored. On return, the columns of this matrix will contain the eigenvectors. The eigenvectors are normalized and mutually orthogonal.

Friends And Related Function Documentation

◆ operator* [1/2]

vector3 operator*	(	const matrix3x3 &	m,
		const vector3 &	v
	)

friend

Matrix-vector multiplication.

Calculates the product m*v of the matrix m and the column vector represented by v

◆ operator* [2/2]

matrix3x3 operator*	(	const matrix3x3 &	A,
		const matrix3x3 &	B
	)

friend

Matrix-matrix multiplication.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	co,
		const matrix3x3 &	m
	)

friend

Output a text representation of a matrix.

Print a text representation of the matrix in the standardized form: [ a, b, c ]
[ d, e, f ]
[ g, h, i ]
where the letters represent the appropriate entries in the matrix. Uses the standard output format for the individual entries, separated by ", " for each column, and [ ] indicating each row.

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

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ matrix3x3() [1/4]

◆ matrix3x3() [2/4]

◆ matrix3x3() [3/4]

◆ matrix3x3() [4/4]

◆ ~matrix3x3()

Member Function Documentation

◆ GetArray()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ inverse()

◆ transpose()

◆ determinant()

◆ isSymmetric()

◆ isOrthogonal()

◆ isDiagonal()

◆ isUnitMatrix()

◆ Get()

◆ Set()

◆ SetColumn()

◆ SetRow()

◆ GetColumn()

◆ GetRow()

◆ operator*=()

◆ operator/=()

◆ SetupRotMat()

◆ PlaneReflection()

◆ RotAboutAxisByAngle()

◆ FillOrth()

◆ findEigenvectorsIfSymmetric()

◆ jacobi()

Friends And Related Function Documentation

◆ operator* [1/2]

◆ operator* [2/2]

◆ operator<<