OBFloatGrid Class Reference

Handle floating-point 3D grids (e.g., charge density around an OBMol). More...

#include <openbabel/grid.h>

Inheritance diagram for OBFloatGrid:


Public Member Functions
	OBFloatGrid ()
	~OBFloatGrid ()
void	Init (OBMol &box, double spacing, double pad=0.0)
void	GetMin (double *a)
void	GetMax (double *a)
double	GetSpacing () const
void	GetSpacing (double &s)
double	GetScale () const
double	GetHalfSpace () const
int	GetXdim () const
int	GetYdim () const
int	GetZdim () const
void	GetDim (int *a)
vector3	GetMidpointVector ()
double *	GetVals ()
void	SetVals (double *ptr)
vector3	Center ()
double	Inject (double x, double y, double z)
void	IndexToCoords (int idx, double &x, double &y, double &z)
void	CoordsToIndex (int , double )
int	CoordsToIndex (double &x, double &y, double &z)
double	Interpolate (double, double, double)
double	InterpolateDerivatives (double, double, double, double *derivatives)
virtual void	Init (OBMol &box)
double	GetXmin () const
double	GetYmin () const
double	GetZmin () const
double	GetXmax () const
double	GetYmax () const
double	GetZmax () const
bool	PointIsInBox (double x, double y, double z)
bool	PointIsInBox (double *c)
virtual bool	Clear ()
virtual OBBase *	DoTransformations (const std::map< std::string, std::string > *)
template<class T>
T *	CastAndClear (bool clear=true)
Generic data handling methods (via OBGenericData)
bool	HasData (const std::string &)
bool	HasData (const char *)
bool	HasData (const unsigned int type)
void	DeleteData (unsigned int type)
void	DeleteData (OBGenericData *)
void	DeleteData (std::vector< OBGenericData * > &)
void	SetData (OBGenericData *d)
unsigned int	DataSize () const
OBGenericData *	GetData (const unsigned int type)
OBGenericData *	GetData (const std::string &)
OBGenericData *	GetData (const char *)
std::vector< OBGenericData * > &	GetData ()
std::vector< OBGenericData * >	GetData (DataOrigin source)
OBDataIterator	BeginData ()
OBDataIterator	EndData ()
Static Public Member Functions
static const char *	ClassDescription ()
Protected Attributes
double *	_val
int *	_ival
double	_midz
double	_midx
double	_midy
int	_ydim
int	_xdim
int	_zdim
double	_spacing
double	_inv_spa
double	_halfSpace
double	_xmin
double	_xmax
double	_ymin
double	_ymax
double	_zmin
double	_zmax
std::vector< OBGenericData * >	_vdata
Friends
std::ostream &	operator<< (std::ostream &, const OBFloatGrid &)
std::istream &	operator>> (std::istream &, OBFloatGrid &)

Detailed Description

Handle floating-point 3D grids (e.g., charge density around an OBMol).

Supports input/output and base functionality for simple 3D discrete grids of some function -- typically around a molecule

Constructor & Destructor Documentation

OBFloatGrid ( ) [inline]

~OBFloatGrid ( ) [inline]

Member Function Documentation

void Init	(	OBMol &	box,
		double	spacing,
		double	pad = `0.0`
	)

Initialize the grid using this molecule as a box (plus a padding) with the supplied spacing between points

void GetMin ( double * a ) [inline]

void GetMax ( double * a ) [inline]

double GetSpacing ( ) const [inline]

void GetSpacing ( double & s ) [inline]

double GetScale ( ) const [inline]

double GetHalfSpace ( ) const [inline]

int GetXdim ( ) const [inline]

int GetYdim ( ) const [inline]

int GetZdim ( ) const [inline]

void GetDim ( int * a ) [inline]

vector3 GetMidpointVector ( ) [inline]

double* GetVals ( ) [inline]

void SetVals ( double * ptr ) [inline]

vector3 Center ( ) [inline]

double Inject	(	double	x,
		double	y,
		double	z
	)

Returns:: the value at the given point (rounding as needed)

void IndexToCoords	(	int	idx,
		double &	x,
		double &	y,
		double &	z
	)

void CoordsToIndex	(	int *	,
		double *
	)

int CoordsToIndex	(	double &	x,
		double &	y,
		double &	z
	)

double Interpolate	(	double	,
		double	,
		double
	)

Returns:: the interpolated value for the given point

double InterpolateDerivatives	(	double	,
		double	,
		double	,
		double *	derivatives
	)

Returns:: the interpolated value for the given point and set the dx, dy, dz derivatives

void Init ( OBMol & box ) [virtual, inherited]

Initialize the grid based on a box around the molecule box Subclasses should overload this method -- this only tracks the dimension of the box itself.

double GetXmin ( ) const [inline, inherited]

Returns:: the minimum x value of the grid

double GetYmin ( ) const [inline, inherited]

Returns:: the minimum y value of the grid

double GetZmin ( ) const [inline, inherited]

Returns:: the minimum z value of the grid

double GetXmax ( ) const [inline, inherited]

Returns:: the maximum x value of the grid

double GetYmax ( ) const [inline, inherited]

Returns:: the maximum y value of the grid

double GetZmax ( ) const [inline, inherited]

Returns:: the maximum z value of the grid

bool PointIsInBox	(	double	x,
		double	y,
		double	z
	)			`[inline, inherited]`

Returns:: whether the supplied XYZ coordinates fall within the box

bool PointIsInBox ( double * c ) [inline, inherited]

Returns:: true if the point falls within the box

bool Clear ( void ) [virtual, inherited]

Clear any and all data associated with this object.

This method can be called by OBConversion::Read() before reading data. Derived classes should be sure to call OBBase::Clear() to remove inherited generic data.

Returns:: Whether the call was successful.

Since:: version 2.1.

Reimplemented in OBAtom, OBMol, and OBResidue.

virtual OBBase* DoTransformations ( const std::map< std::string, std::string > * ) [inline, virtual, inherited]

Perform a set of transformations specified by the user

Typically these are program options to filter or modify an object For example, see OBMol::DoTransformations() and OBMol::ClassDescription()

Reimplemented in OBMol.

static const char* ClassDescription ( ) [inline, static, inherited]

Returns:: A list of descriptions of command-line options for DoTransformations()

Reimplemented in OBMol.

T* CastAndClear ( bool clear = true ) [inline, inherited]

By default clears the object. Called from ReadMolecule of most format classes.

bool HasData ( const std::string & ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const char * ) [inherited]

Returns:: whether the generic attribute/value pair exists

bool HasData ( const unsigned int type ) [inherited]

Returns:: whether the generic attribute/value pair exists, for a given OBGenericDataType

void DeleteData ( unsigned int type ) [inherited]

Delete any data matching the given OBGenericDataType.

void DeleteData ( OBGenericData * ) [inherited]

Delete the given generic data from this object.

void DeleteData ( std::vector< OBGenericData * > & ) [inherited]

Delete all of the given generic data from this object.

void SetData ( OBGenericData * d ) [inline, inherited]

Adds a data object; does nothing if d==NULL.

unsigned int DataSize ( ) const [inline, inherited]

Returns:: the number of OBGenericData items attached to this molecule.

OBGenericData * GetData ( const unsigned int type ) [inherited]

Returns:: the first matching data for a given type from OBGenericDataType or NULL if nothing matches

OBGenericData * GetData ( const std::string & ) [inherited]

Returns:: the value given an attribute name

OBGenericData * GetData ( const char * ) [inherited]

Returns:: the value given an attribute name

std::vector<OBGenericData*>& GetData ( ) [inline, inherited]

Returns:: all data, suitable for iterating

std::vector< OBGenericData * > GetData ( DataOrigin source ) [inherited]

Returns:: all data with a specific origin, suitable for iterating

OBDataIterator BeginData ( ) [inline, inherited]

Returns:: An iterator pointing to the beginning of the data

OBDataIterator EndData ( ) [inline, inherited]

Returns:: An iterator pointing to the end of the data

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const OBFloatGrid &	fg
	)			`[friend]`

std::istream& operator>>	(	std::istream &	is,
		OBFloatGrid &	fg
	)			`[friend]`

Member Data Documentation

double* _val [protected]

floating point values

int* _ival [protected]

for integer values (deprecated)

double _midz [protected]

double _midx [protected]

double _midy [protected]

center of grid in world coordinates

int _ydim [protected]

int _xdim [protected]

int _zdim [protected]

grid dimensions

double _spacing [protected]

double _inv_spa [protected]

spacing between grid points and its inverse

double _halfSpace [protected]

half of the grid spacing */

double _xmin [protected, inherited]

double _xmax [protected, inherited]

double _ymin [protected, inherited]

double _ymax [protected, inherited]

double _zmin [protected, inherited]

double _zmax [protected, inherited]

the min/max values in XYZ axes (i.e., the box)

std::vector<OBGenericData*> _vdata [protected, inherited]

Custom data.

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

OBFloatGrid Class Reference

Public Member Functions

Static Public Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation