#include <openbabel/grid.h>

Inheritance diagram for OBFloatGrid:

Public Member Functions
	OBFloatGrid ()

	~OBFloatGrid ()

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

vector3	GetMin ()

void	GetMin (double *a)

vector3	GetMax ()

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 ()

vector3	GetXAxis () const

vector3	GetYAxis () const

vector3	GetZAxis () const

void	SetNumberOfPoints (int nx, int ny, int nz)

void	SetXAxis (vector3)

void	SetYAxis (vector3)

void	SetZAxis (vector3)

void	SetLimits (const vector3 &origin, const vector3 &x, const vector3 &y, const vector3 &z)

void	SetLimits (const double origin[3], const double x[3], const double y[3], const double z[3])

std::vector< double >	GetDataVector ()

void	SetVals (const std::vector< double > &vals)

double *	GetVals ()

double	GetValue (int i, int j, int k)

void	SetVals (double *ptr)

bool	SetValue (int i, int j, int k, double val)

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)

bool	PointIsInBox (vector3 v)

virtual bool	Clear ()

virtual OBBase *	DoTransformations (const std::map< std::string, std::string > , OBConversion )

template<class T >
T *	CastAndClear (bool clear=true)

virtual const char *	GetTitle (bool replaceNewlines=true) const

virtual void	SetTitle (const char *)

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 *> &)

bool	DeleteData (const std::string &s)

void	SetData (OBGenericData *d)

void	CloneData (OBGenericData *d)

size_t	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)

std::vector< OBGenericData * >	GetAllData (const unsigned int type)

OBDataIterator	BeginData ()

OBDataIterator	EndData ()

Static Public Member Functions
static const char *	ClassDescription ()

Protected Attributes
std::vector< double >	_values

int *	_ival

double	_midz

double	_midx

double	_midy

int	_ydim

int	_xdim

int	_zdim

double	_spacing

double	_inv_spa

double	_halfSpace

vector3	_xAxis

vector3	_yAxis

vector3	_zAxis

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 double precision 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. Typically you will want to use OBGridData which uses OBFloatGrid to store its data.

See also: OBGridData

Constructor & Destructor Documentation

◆ OBFloatGrid()

OBFloatGrid ( )

inline

◆ ~OBFloatGrid()

~OBFloatGrid ( )

inline

Member Function Documentation

◆ Init() [1/2]

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.

Referenced by OBForceField::GetGrid().

◆ GetMin() [1/2]

vector3 GetMin ( )

inline

Returns: the minimum point in the grid.

Referenced by OBForceField::GetGrid().

◆ GetMin() [2/2]

void GetMin ( double * a )

inline

Get the minimum point in the grid.

Deprecated:: Will be removed. Use

See also: GetMin()

◆ GetMax() [1/2]

vector3 GetMax ( )

inline

Returns: the minimum point in the grid.

◆ GetMax() [2/2]

void GetMax ( double * a )

inline

Get the maximum point in the grid.

Deprecated:: Will be removed.

See also: GetMax()

◆ GetSpacing() [1/2]

double GetSpacing ( ) const

inline

Returns: The grid spacing.

◆ GetSpacing() [2/2]

void GetSpacing ( double & s )

inline

Get the grid spacing.

Deprecated:: Will be removed.

See also: GetSpacing()

◆ GetScale()

double GetScale ( ) const

inline

Returns: Inverse of the grid spacing.

◆ GetHalfSpace()

double GetHalfSpace ( ) const

inline

Returns: Half of the spacing between grid points.

◆ GetXdim()

int GetXdim ( ) const

inline

Returns: Size of the grid in the x dimension.

Referenced by OBForceField::GetGrid().

◆ GetYdim()

int GetYdim ( ) const

inline

Returns: Size of the grid in the y dimension.

Referenced by OBForceField::GetGrid().

◆ GetZdim()

int GetZdim ( ) const

inline

Returns: Size of the grid in the z dimension.

Referenced by OBForceField::GetGrid().

◆ GetDim()

void GetDim ( int * a )

inline

Get the x, y and z dimensions (must pass an double[3] at least).

Deprecated:: May be removed in future.

See also: GetXdim(); GetYdim(); GetZdim()

◆ GetMidpointVector()

vector3 GetMidpointVector ( )

inline

Returns: Position of the center of the grid.

◆ GetXAxis()

vector3 GetXAxis ( ) const

inline

Returns: X axis direction.

◆ GetYAxis()

vector3 GetYAxis ( ) const

inline

Returns: Y axis direction.

◆ GetZAxis()

vector3 GetZAxis ( ) const

inline

Returns: Z axis direction.

◆ SetNumberOfPoints()

void SetNumberOfPoints	(	int	nx,
		int	ny,
		int	nz
	)

Sets the number of points in the x, y and z directions.

◆ SetXAxis()

void SetXAxis ( vector3 v )

Set the direction of the x axis.

◆ SetYAxis()

void SetYAxis ( vector3 v )

Set the direction of the y axis.

◆ SetZAxis()

void SetZAxis ( vector3 v )

Set the direction of the z axis.

◆ SetLimits() [1/2]

void SetLimits	(	const vector3 &	origin,
		const vector3 &	x,
		const vector3 &	y,
		const vector3 &	z
	)

Set the limits (i.e., the origin point and the axes) NOTE: You must set the number of points first, with SetNumberOfPoints so the grid spacing can be calculated

◆ SetLimits() [2/2]

void SetLimits	(	const double	origin[3],
		const double	x[3],
		const double	y[3],
		const double	z[3]
	)

Deprecated:: Will be removed.

See also: SetLimits(const vector3& origin, const vector3& x, const vector3& y, const vector3& z)

◆ GetDataVector()

std::vector< double > GetDataVector ( )

Get a copy of the vector that stores the points in the grid.

◆ SetVals() [1/2]

void SetVals ( const std::vector< double > & vals )

Set the values in the grid to those in the vector passed. Note that the vector must be of the same dimensions as the grid based on the values given in SetNumberOfPoints(int nx, int ny, int nz).

◆ GetVals()

double* GetVals ( )

inline

Returns: Pointer to the first element of the grid point data stored as a one dimensional array.

Deprecated:: Will be removed.

See also: GetDataVector()

◆ GetValue()

double GetValue	(	int	i,
		int	j,
		int	k
	)

inline

Returns: Value at the point in the grid specified by i, j and k.

◆ SetVals() [2/2]

void SetVals ( double * ptr )

inline

Deprecated:: Will be removed.

See also: SetVals(const std::vector<double> & vals)

◆ SetValue()

bool SetValue	(	int	i,
		int	j,
		int	k,
		double	val
	)

inline

Set the value at the grid point specified by i, j and k to val.

◆ Center()

vector3 Center ( )

inline

Returns: Position of the center of the grid.

◆ Inject()

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

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

◆ IndexToCoords()

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

◆ CoordsToIndex() [1/2]

void CoordsToIndex	(	int *	idx,
		double *	c
	)

◆ CoordsToIndex() [2/2]

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

◆ Interpolate()

double Interpolate	(	double	x,
		double	y,
		double	z
	)

Returns: the interpolated value for the given point

◆ InterpolateDerivatives()

double InterpolateDerivatives	(	double	x,
		double	y,
		double	z,
		double *	derivatives
	)

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

◆ Init() [2/2]

void Init ( OBMol & box )

virtualinherited

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.

◆ GetXmin()

double GetXmin ( ) const

inlineinherited

Returns: the minimum x point of the grid

◆ GetYmin()

double GetYmin ( ) const

inlineinherited

Returns: the minimum y point of the grid

◆ GetZmin()

double GetZmin ( ) const

inlineinherited

Returns: the minimum z point of the grid

◆ GetXmax()

double GetXmax ( ) const

inlineinherited

Returns: the maximum x point of the grid

◆ GetYmax()

double GetYmax ( ) const

inlineinherited

Returns: the maximum y point of the grid

◆ GetZmax()

double GetZmax ( ) const

inlineinherited

Returns: the maximum z point of the grid

◆ PointIsInBox() [1/3]

bool PointIsInBox	(	double	x,
		double	y,
		double	z
	)

inlineinherited

Returns: whether the supplied XYZ coordinates fall within the box

◆ PointIsInBox() [2/3]

bool PointIsInBox ( double * c )

inlineinherited

Returns: true if the point falls within the box

◆ PointIsInBox() [3/3]

bool PointIsInBox ( vector3 v )

inlineinherited

Returns: true if the point falls within the box

◆ Clear()

bool Clear ( void )

virtualinherited

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 OBMol, OBAtom, OBReaction, and OBResidue.

Referenced by OBResidue::Clear().

◆ DoTransformations()

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)

inlinevirtualinherited

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() Base type does nothing

Reimplemented in OBMol.

◆ ClassDescription()

static const char* ClassDescription ( )

inlinestaticinherited

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

◆ CastAndClear()

T* CastAndClear ( bool clear = true )

inlineinherited

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

◆ GetTitle()

virtual const char* GetTitle ( bool replaceNewlines = true ) const

inlinevirtualinherited

Base type does nothing Made virtual around r3535 to simplify code which passes around OBBase*.

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ SetTitle()

virtual void SetTitle ( const char * )

inlinevirtualinherited

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

◆ HasData() [1/3]

bool HasData ( const std::string & s )

inherited

Returns: whether the generic attribute/value pair exists

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

◆ HasData() [2/3]

bool HasData ( const char * s )

inherited

Returns: whether the generic attribute/value pair exists

◆ HasData() [3/3]

bool HasData ( const unsigned int type )

inherited

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

◆ DeleteData() [1/4]

void DeleteData ( unsigned int type )

inherited

Delete any data matching the given OBGenericDataType.

Referenced by OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OpenBabel::DeleteStereoOnAtom(), and OBMol::RenumberAtoms().

◆ DeleteData() [2/4]

void DeleteData ( OBGenericData * gd )

inherited

Delete the given generic data from this object.

◆ DeleteData() [3/4]

void DeleteData ( std::vector< OBGenericData *> & vg )

inherited

Delete all of the given generic data from this object.

◆ DeleteData() [4/4]

bool DeleteData ( const std::string & s )

inherited

Deletes the generic data with the specified attribute, returning false if not found.

◆ SetData()

void SetData ( OBGenericData * d )

inlineinherited

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

Referenced by OBGastChrg::AssignPartialCharges(), OBMol::CopySubstructure(), AliasData::Expand(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), AliasData::RevertToAliasForm(), and OBMol::SetEnergies().

◆ CloneData()

void CloneData ( OBGenericData * d )

inherited

Adds a copy of a data object; does nothing if d == NULL

Since: version 2.2

Referenced by AliasData::Expand().

◆ DataSize()

size_t DataSize ( ) const

inlineinherited

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

◆ GetData() [1/5]

OBGenericData * GetData ( const unsigned int type )

inherited

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

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OpenBabel::extract_thermochemistry(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OpenBabel::IsSuppressibleHydrogen(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), and OBDescriptor::PredictAndSave().

◆ GetData() [2/5]

OBGenericData * GetData ( const std::string & s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [3/5]

OBGenericData * GetData ( const char * s )

inherited

Returns: any data matching the given attribute name or NULL if nothing matches; the value given an attribute name

◆ GetData() [4/5]

std::vector<OBGenericData*>& GetData ( )

inlineinherited

Returns: all data, suitable for iterating

Referenced by OBMol::GetEnergies(), OBMol::GetEnergy(), and OBMol::SetEnergies().

◆ GetData() [5/5]

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

inherited

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

◆ GetAllData()

std::vector< OBGenericData * > GetAllData ( const unsigned int type )

inherited

Returns: the all matching data for a given type from OBGenericDataType or an empty vector if nothing matches

Since: version 2.2

Referenced by OpenBabel::CanonicalLabels(), OBMol::CopySubstructure(), OBBuilder::CorrectStereoAtoms(), OBBuilder::CorrectStereoBonds(), OpenBabel::DeleteStereoOnAtom(), and OBMol::operator+=().

◆ BeginData()

OBDataIterator BeginData ( )

inlineinherited

Returns: An iterator pointing to the beginning of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

◆ EndData()

OBDataIterator EndData ( )

inlineinherited

Returns: An iterator pointing to the end of the data

Referenced by OBMol::AddBond(), OBAtom::Duplicate(), OBMoleculeFormat::MakeCombinedMolecule(), and OBMol::operator=().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const OBFloatGrid &	fg
	)

friend

◆ operator>>

std::istream& operator>>	(	std::istream &	is,
		OBFloatGrid &	fg
	)

friend

Member Data Documentation

◆ _values

std::vector<double> _values

protected

floating point values

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _ival

int* _ival

protected

for integer values (deprecated)

◆ _midz

double _midz

protected

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _midx

double _midx

protected

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _midy

double _midy

protected

center of grid in world coordinates

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _ydim

int _ydim

protected

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _xdim

int _xdim

protected

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _zdim

int _zdim

protected

grid dimensions

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _spacing

double _spacing

protected

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _inv_spa

double _inv_spa

protected

spacing between grid points and its inverse

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _halfSpace

double _halfSpace

protected

half of the grid spacing

Referenced by OpenBabel::operator>>().

◆ _xAxis

vector3 _xAxis

protected

Three axes (i.e., translation vectors like a unit cell)

◆ _yAxis

vector3 _yAxis

protected

◆ _zAxis

vector3 _zAxis

protected

◆ _xmin

double _xmin

protectedinherited

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _xmax

double _xmax

protectedinherited

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _ymin

double _ymin

protectedinherited

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _ymax

double _ymax

protectedinherited

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _zmin

double _zmin

protectedinherited

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _zmax

double _zmax

protectedinherited

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

Referenced by OpenBabel::operator<<(), and OpenBabel::operator>>().

◆ _vdata

std::vector<OBGenericData*> _vdata

protectedinherited

Custom data.

Referenced by OBMol::OBMol().

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ OBFloatGrid()

◆ ~OBFloatGrid()

Member Function Documentation

◆ Init() [1/2]

◆ GetMin() [1/2]

◆ GetMin() [2/2]

◆ GetMax() [1/2]

◆ GetMax() [2/2]

◆ GetSpacing() [1/2]

◆ GetSpacing() [2/2]

◆ GetScale()

◆ GetHalfSpace()

◆ GetXdim()

◆ GetYdim()

◆ GetZdim()

◆ GetDim()

◆ GetMidpointVector()

◆ GetXAxis()

◆ GetYAxis()

◆ GetZAxis()

◆ SetNumberOfPoints()

◆ SetXAxis()

◆ SetYAxis()

◆ SetZAxis()

◆ SetLimits() [1/2]

◆ SetLimits() [2/2]

◆ GetDataVector()

◆ SetVals() [1/2]

◆ GetVals()

◆ GetValue()

◆ SetVals() [2/2]

◆ SetValue()

◆ Center()

◆ Inject()

◆ IndexToCoords()

◆ CoordsToIndex() [1/2]

◆ CoordsToIndex() [2/2]

◆ Interpolate()

◆ InterpolateDerivatives()

◆ Init() [2/2]

◆ GetXmin()

◆ GetYmin()

◆ GetZmin()

◆ GetXmax()

◆ GetYmax()

◆ GetZmax()

◆ PointIsInBox() [1/3]

◆ PointIsInBox() [2/3]

◆ PointIsInBox() [3/3]

◆ Clear()

◆ DoTransformations()

◆ ClassDescription()

◆ CastAndClear()

◆ GetTitle()

◆ SetTitle()

◆ HasData() [1/3]

◆ HasData() [2/3]

◆ HasData() [3/3]

◆ DeleteData() [1/4]

◆ DeleteData() [2/4]

◆ DeleteData() [3/4]

◆ DeleteData() [4/4]

◆ SetData()

◆ CloneData()

◆ DataSize()

◆ GetData() [1/5]

◆ GetData() [2/5]

◆ GetData() [3/5]

◆ GetData() [4/5]

◆ GetData() [5/5]

◆ GetAllData()

◆ BeginData()

◆ EndData()

Friends And Related Function Documentation