Class Avogadro::Core::Cube

class Cube

Provide a data structure for regularly spaced 3D grids.

Author

Marcus D. Hanwell

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:

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.

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.

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