Provide a data structure for regularly spaced 3D grids. More...

#include <avogadro/core/cube.h>

Public Types
enum	Type { VdW , SolventAccessible , SolventExcluded , ESP , ElectronDensity , SpinDensity , MO , FromFile , None }

Public Member Functions
Vector3	min () const
Vector3	max () const
Vector3	spacing () const
Vector3i	dimensions () const
bool	setLimits (const Vector3 &min, const Vector3 &max, const Vector3i &points)
bool	setLimits (const Vector3 &min, const Vector3 &max, float spacing)
bool	setLimits (const Vector3 &min, const Vector3i &dim, float spacing)
bool	setLimits (const Vector3 &min, const Vector3i &dim, const Vector3 &spacing)
bool	setLimits (const Cube &cube)
bool	setLimits (const Molecule &mol, float spacing, float padding)
std::vector< float > *	data ()
const std::vector< float > *	data () const
bool	setData (const std::vector< float > &values)
bool	addData (const std::vector< float > &values)
std::vector< float >::const_iterator	getRowIter (int j, int k) const
unsigned int	closestIndex (const Vector3 &pos) const
Vector3i	indexVector (const Vector3 &pos) const
Vector3	position (unsigned int index) const
float	value (int i, int j, int k) const
float	value (const Vector3i &pos) const
float	valuef (const Vector3f &pos) const
float	value (const Vector3 &pos) const
bool	setValue (unsigned int i, unsigned int j, unsigned int k, float value)
bool	setValue (unsigned int i, float value)
void	fill (float value)
bool	fillStripe (unsigned int i, unsigned int j, unsigned int kfirst, unsigned int klast, float value)
float	minValue () const
float	maxValue () const
void	setName (const std::string &name_)
std::string	name () const
void	setCubeType (Type type)
Type	cubeType () const
Mutex *	lock () const
std::array< float, 3 >	computeGradient (int i, int j, int k) const
std::array< float, 8 >	getValsCube (int i, int j, int k) const
std::array< std::array< float, 3 >, 8 >	getGradCube (int i, int j, int k) const
float	getData (int i, int j, int k) const
std::array< std::array< float, 3 >, 8 >	getPosCube (int i, int j, int k) const

Protected Attributes
std::vector< float >	m_data
Vector3	m_min
Vector3	m_max
Vector3	m_spacing
Vector3i	m_points
float	m_minValue
float	m_maxValue
std::string	m_name
Type	m_cubeType
Mutex *	m_lock

Detailed Description

Author: Marcus D. Hanwell; Perminder Singh

Member Enumeration Documentation

◆ Type

enum Type

Different Cube types relating to the data

Member Function Documentation

◆ min()

Vector3 min ( ) const

Returns: The minimum point in the cube.

◆ max()

Vector3 max ( ) const

Returns: The maximum point in the cube.

◆ spacing()

Vector3 spacing ( ) const

Returns: The spacing of the grid.

◆ dimensions()

Vector3i dimensions ( ) const

Returns: The x, y and z dimensions of the cube.

◆ setLimits() [1/6]

bool setLimits	(	const Vector3 &	min,
		const Vector3 &	max,
		const Vector3i &	points )

Set the limits of the cube.

Parameters

min	The minimum point in the cube.
max	The maximum point in the cube.
points	The number of (integer) points in the cube.

◆ setLimits() [2/6]

bool setLimits	(	const Vector3 &	min,
		const Vector3 &	max,
		float	spacing )

Set the limits of the cube.

Parameters

min	The minimum point in the cube.
max	The maximum point in the cube.
spacing	The interval between points in the cube.

◆ setLimits() [3/6]

bool setLimits	(	const Vector3 &	min,
		const Vector3i &	dim,
		float	spacing )

Set the limits of the cube.

Parameters

min	The minimum point in the cube.
dim	The integer dimensions of the cube in x, y and z.
spacing	The interval between points in the cube.

◆ setLimits() [4/6]

bool setLimits	(	const Vector3 &	min,
		const Vector3i &	dim,
		const Vector3 &	spacing )

Set the limits of the cube.

Parameters

min	The minimum point in the cube.
dim	The integer dimensions of the cube in x, y and z.
spacing	The interval between points in the cube.

◆ setLimits() [5/6]

bool setLimits ( const Cube & cube )

Set the limits of the cube - copy the limits of an existing Cube.

Parameters

cube	Existing Cube to copy the limits from.

◆ setLimits() [6/6]

bool setLimits	(	const Molecule &	mol,
		float	spacing,
		float	padding )

Set the limits of the cube.

Parameters

mol	Molecule to take limits from
spacing	The spacing of the regular grid
padding	Padding around the molecule

◆ data()

std::vector< float > * data ( )

Returns: Pointer to the vector containing all the data in a one-dimensional array.

◆ setData()

bool setData ( const std::vector< float > & values )

Set the values in the cube to those passed in the vector.

◆ addData()

bool addData ( const std::vector< float > & values )

Adds the values in the cube to those passed in the vector.

◆ getRowIter()

std::vector< float >::const_iterator getRowIter	(	int	j,
		int	k ) const

Returns: Const iterator to the beginning of a specific row in the cube data.

◆ closestIndex()

unsigned int closestIndex ( const Vector3 & pos ) const

Returns: Index of the point closest to the position supplied.

Parameters

pos	Position to get closest index for.

◆ indexVector()

Vector3i indexVector ( const Vector3 & pos ) const

Parameters

pos	Position to get closest index for.

Returns: The i, j, k index closest to the position supplied.

◆ position()

Vector3 position ( unsigned int index ) const

Parameters

index Index to be translated to a position.

Returns: Position of the given index.

◆ value() [1/3]

float value	(	int	i,
		int	j,
		int	k ) const

This function is very quick as it just returns the value at the point.

Returns: Cube value at the integer point i, j, k.

◆ value() [2/3]

float value ( const Vector3i & pos ) const

This function is very quick as it just returns the value at the point.

Returns: Cube value at the integer point pos.

◆ valuef()

float valuef ( const Vector3f & pos ) const

This function uses trilinear interpolation to find the value at points between those specified in the cube.

Returns: Cube value at the specified position.

Warning: This function is quite computationally expensive and should be avoided where possible.

◆ value() [3/3]

float value ( const Vector3 & pos ) const

This function uses trilinear interpolation to find the value at points between those specified in the cube.

Returns: Cube value at the specified position.

Warning: This function is quite computationally expensive and should be avoided where possible.

◆ setValue() [1/2]

bool setValue	(	unsigned int	i,
		unsigned int	j,
		unsigned int	k,
		float	value )

Sets the value at the specified point in the cube.

Parameters

i	x component of the position.
j	y component of the position.
k	z component of the position.
value	Value at the specified position.

◆ setValue() [2/2]

bool setValue	(	unsigned int	i,
		float	value )

Sets the value at the specified index in the cube.

Parameters

i	1-dimensional index of the point to set in the cube.

◆ fill()

void fill ( float value )

Sets all indices in the cube to the specified value.

Parameters

value Value to fill the cube with.

◆ fillStripe()

bool fillStripe	(	unsigned int	i,
		unsigned int	j,
		unsigned int	kfirst,
		unsigned int	klast,
		float	value )

Sets all indices in a Z stripe of the cube to the specified value.

Parameters

i	x component of the position.
j	y component of the position.
kfirst	first z position to fill.
klast	last z position to fill.
value	Value to fill the stripe with.

◆ minValue()

float minValue ( ) const

Returns: The minimum value at any point in the Cube.

◆ maxValue()

float maxValue ( ) const

Returns: The maximum value at any point in the Cube.

◆ lock()

Mutex * lock ( ) const

Provides locking.

◆ computeGradient()

std::array< float, 3 > computeGradient	(	int	i,
		int	j,
		int	k ) const

Compute the gradient at a specific point in the cube.

Parameters

i	x index
j	y index
k	z index

Returns: Gradient vector at the specified point.

◆ getValsCube()

std::array< float, 8 > getValsCube	(	int	i,
		int	j,
		int	k ) const

Get the values of the eight corners of a cube defined by the indices (i, j, k).

Parameters

i	x index
j	y index
k	z index

Returns: Array of values at the eight corners.

◆ getGradCube()

std::array< std::array< float, 3 >, 8 > getGradCube	(	int	i,
		int	j,
		int	k ) const

Get the gradients at the eight corners of the cube defined by the indices (i, j, k).

Parameters

i	x index
j	y index
k	z index

Returns: Array of gradients at the eight corners. Each gradient is a 3D vector.

◆ getData()

float getData	(	int	i,
		int	j,
		int	k ) const

Get the data value at the specified indices.

Parameters

i	x index
j	y index
k	z index

Returns: Value at the specified indices.

◆ getPosCube()

std::array< std::array< float, 3 >, 8 > getPosCube	(	int	i,
		int	j,
		int	k ) const

Retrieves the positions of the eight corners of a cube at grid indices (i, j, k).

The indices (i, j, k) are converted to real-space positions (xpos, ypos, zpos), mapping grid indices to physical coordinates. The method returns a cube that spans one step in each of the x, y, and z directions, with step sizes defined by m_spacing.

Parameters

i	X-index.
j	Y-index.
k	Z-index.

Returns: A std::array of eight (x, y, z) coordinates representing the cube's corners.

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

cube.h

Public Types

Public Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ Type

Member Function Documentation

◆ min()

◆ max()

◆ spacing()

◆ dimensions()

◆ setLimits() [1/6]

◆ setLimits() [2/6]

◆ setLimits() [3/6]

◆ setLimits() [4/6]

◆ setLimits() [5/6]

◆ setLimits() [6/6]

◆ data()

◆ setData()

◆ addData()

◆ getRowIter()

◆ closestIndex()

◆ indexVector()

◆ position()

◆ value() [1/3]

◆ value() [2/3]

◆ valuef()

◆ value() [3/3]

◆ setValue() [1/2]

◆ setValue() [2/2]

◆ fill()

◆ fillStripe()

◆ minValue()

◆ maxValue()

◆ lock()

◆ computeGradient()

◆ getValsCube()

◆ getGradCube()

◆ getData()

◆ getPosCube()