Avogadro::Core::Cube#

class Cube#

Provide a data structure for regularly spaced 3D grids.

Author: Marcus D. Hanwell
Author: Perminder Singh

Public Types

enum Type#

Different Cube types relating to the data

Values:

enumerator VdW#

enumerator SolventAccessible#

enumerator SolventExcluded#

enumerator ESP#

enumerator ElectronDensity#

enumerator SpinDensity#

enumerator MO#

enumerator FromFile#

enumerator None#

Public Functions

Cube()#

~Cube()#

inline Vector3 min() const#

Returns:: The minimum point in the cube.

inline Vector3 max() const#

Returns:: The maximum point in the cube.

inline Vector3 spacing() const#

Returns:: The spacing of the grid.

inline Vector3i dimensions() const#

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

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.

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.

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.

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.

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.

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

std::vector<float> *data()#

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

const std::vector<float> *data() const#

bool setData(const std::vector<float> &values)#: Set the values in the cube to those passed in the vector.

bool addData(const std::vector<float> &values)#: Adds the values in the cube to those passed in the vector.

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.

unsigned int closestIndex(const Vector3 &pos) const#

Parameters:: pos – Position to get closest index for.
Returns:: Index of the point closest to the position supplied.

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.

Vector3 position(unsigned int index) const#

Parameters:: index – Index to be translated to a position.
Returns:: Position of the given index.

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.

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.

float valuef(const Vector3f &pos) const#

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

Warning

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

Returns:: Cube value at the specified position.

float value(const Vector3 &pos) const#

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

Warning

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

Returns:: Cube value at the specified position.

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.

inline 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.

void fill(float value)#

Sets all indices in the cube to the specified value.

Parameters:: value – Value to fill the cube with.

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.

inline float minValue() const#

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

inline float maxValue() const#

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

inline void setName(const std::string &name_)#

inline std::string name() const#

inline void setCubeType(Type type)#

inline Type cubeType() const#

inline Mutex *lock() const#: Provides locking.

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.

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.

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.

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.

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.

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#