Handle double precision 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)
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 ( ) [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.

Referenced by OBForceField::GetGrid().

vector3 GetMin ( ) [inline]

Returns:: the minimum point in the grid.

Referenced by OBForceField::GetGrid().

void GetMin ( double * a ) [inline]

Get the minimum point in the grid.

Deprecated:: Will be removed. Use

See also:: GetMin()

vector3 GetMax ( ) [inline]

Returns:: the minimum point in the grid.

void GetMax ( double * a ) [inline]

Get the maximum point in the grid.

Deprecated:: Will be removed.

See also:: GetMax()

double GetSpacing ( ) const [inline]

Returns:: The grid spacing.

void GetSpacing ( double & s ) [inline]

Get the grid spacing.

Deprecated:: Will be removed.

See also:: GetSpacing()

double GetScale ( ) const [inline]

Returns:: Inverse of the grid spacing.

double GetHalfSpace ( ) const [inline]

Returns:: Half of the spacing between grid points.

int GetXdim ( ) const [inline]

Returns:: Size of the grid in the x dimension.

Referenced by OBForceField::GetGrid().

int GetYdim ( ) const [inline]

Returns:: Size of the grid in the y dimension.

Referenced by OBForceField::GetGrid().

int GetZdim ( ) const [inline]

Returns:: Size of the grid in the z dimension.

Referenced by OBForceField::GetGrid().

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()

vector3 GetMidpointVector ( ) [inline]

Returns:: Position of the center of the grid.

vector3 GetXAxis ( ) const [inline]

Returns:: X axis direction.

vector3 GetYAxis ( ) const [inline]

Returns:: Y axis direction.

vector3 GetZAxis ( ) const [inline]

Returns:: Z axis direction.

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

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

void SetXAxis ( vector3 v )

Set the direction of the x axis.

Referenced by OBFloatGrid::SetLimits().

void SetYAxis ( vector3 v )

Set the direction of the y axis.

Referenced by OBFloatGrid::SetLimits().

void SetZAxis ( vector3 v )

Set the direction of the z axis.

Referenced by OBFloatGrid::SetLimits().

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

Referenced by OBFloatGrid::SetLimits().

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)

std::vector< double > GetDataVector ( )

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

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).

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()

double GetValue	(	int	i,
		int	j,
		int	k
	)			`[inline]`

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

void SetVals ( double * ptr ) [inline]

Deprecated:: Will be removed.

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

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.

vector3 Center ( ) [inline]

Returns:: Position of the center of the grid.

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 *	idx,
		double *	c
	)

Referenced by OBFloatGrid::Inject().

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

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

Returns:: the interpolated value for the given point

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

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.

Referenced by OBProxGrid::Setup().

double GetXmin ( ) const [inline, inherited]

Returns:: the minimum x point of the grid

double GetYmin ( ) const [inline, inherited]

Returns:: the minimum y point of the grid

double GetZmin ( ) const [inline, inherited]

Returns:: the minimum z point of the grid

double GetXmax ( ) const [inline, inherited]

Returns:: the maximum x point of the grid

double GetYmax ( ) const [inline, inherited]

Returns:: the maximum y point of the grid

double GetZmax ( ) const [inline, inherited]

Returns:: the maximum z point of the grid

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

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

Referenced by OBProxGrid::Setup().

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

Returns:: true if the point falls within the box

bool PointIsInBox ( vector3 v ) [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, OBReaction, and OBResidue.

Referenced by OBResidue::Clear(), OBMol::Clear(), and OBAtom::Clear().

virtual OBBase* DoTransformations	(	const std::map< std::string, std::string > *	,
		OBConversion *
	)			`[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() Base type does nothing

Reimplemented in OBMol.

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

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

Reimplemented in OBMol, and OBReaction.

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

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

virtual const char* GetTitle ( bool replaceNewlines = true ) const [inline, virtual, inherited]

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

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

virtual void SetTitle ( const char * ) [inline, virtual, inherited]

Reimplemented in OBMol.

Referenced by OBMoleculeFormat::DoOutputOptions().

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

Returns:: whether the generic attribute/value pair exists

Referenced by OBMol::AddAtom(), OBDepict::DrawMolecule(), OBMol::FindAngles(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), OBMol::operator=(), OBMoleculeFormat::ReadChemObjectImpl(), and OBMol::SetEnergies().

bool HasData ( const char * s ) [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.

Referenced by OBMol::AddAtom(), OBMol::BeginModify(), OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), OBMol::EndModify(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBMol::NewAtom(), OBMol::RenumberAtoms(), and OBForceField::Setup().

void DeleteData ( OBGenericData * gd ) [inherited]

Delete the given generic data from this object.

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

Delete all of the given generic data from this object.

bool DeleteData ( const std::string & s ) [inherited]

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

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

void CloneData ( OBGenericData * d ) [inherited]

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

Since:: version 2.2

Referenced by OBMol::AddBond().

size_t 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

Referenced by OpenBabel::CalcSignedVolume(), OpenBabel::CorrectChirality(), OBDepict::DrawMolecule(), AliasData::Expand(), OBDescriptor::FilterCompare(), OpenBabel::GetAtomSymClass(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBDescriptor::GetValues(), OBMoleculeFormat::MakeCombinedMolecule(), OBMolAngleIter::OBMolAngleIter(), OBMolRingIter::OBMolRingIter(), OBMolTorsionIter::OBMolTorsionIter(), OBMol::operator=(), and OBDescriptor::PredictAndSave().

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

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

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

Returns:: all data, suitable for iterating

Referenced by OBMol::BeginModify(), OBMol::DoTransformations(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetLSSR(), OBMol::GetSSSR(), OBMol::SetEnergies(), and OBMol::SetFormula().

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

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

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(), OBBuilder::CorrectStereoAtoms(), and OBBuilder::CorrectStereoBonds().

OBDataIterator BeginData ( ) [inline, inherited]

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

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

OBDataIterator EndData ( ) [inline, inherited]

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

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

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

std::vector<double> _values [protected]

floating point values

Referenced by OBFloatGrid::GetDataVector(), OBFloatGrid::Init(), OBFloatGrid::Inject(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetNumberOfPoints(), and OBFloatGrid::SetVals().

int* _ival [protected]

for integer values (deprecated)

Referenced by OBFloatGrid::Init().

double _midz [protected]

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

double _midx [protected]

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

double _midy [protected]

center of grid in world coordinates

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

int _ydim [protected]

Referenced by OBFloatGrid::CoordsToIndex(), OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), OBFloatGrid::SetNumberOfPoints(), and OBFloatGrid::SetVals().

int _xdim [protected]

Referenced by OBFloatGrid::Init(), OBFloatGrid::Interpolate(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), OBFloatGrid::SetNumberOfPoints(), and OBFloatGrid::SetVals().

int _zdim [protected]

grid dimensions

Referenced by OBFloatGrid::CoordsToIndex(), OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), OBFloatGrid::SetNumberOfPoints(), and OBFloatGrid::SetVals().

double _spacing [protected]

Referenced by OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OpenBabel::operator<<(), OpenBabel::operator>>(), and OBFloatGrid::SetLimits().

double _inv_spa [protected]

spacing between grid points and its inverse

Referenced by OBFloatGrid::CoordsToIndex(), OBFloatGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), and OBFloatGrid::SetLimits().

double _halfSpace [protected]

half of the grid spacing

Referenced by OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator>>(), and OBFloatGrid::SetLimits().

vector3 _xAxis [protected]

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

Referenced by OBFloatGrid::SetXAxis().

vector3 _yAxis [protected]

Referenced by OBFloatGrid::SetYAxis().

vector3 _zAxis [protected]

Referenced by OBFloatGrid::SetZAxis().

double _xmin [protected, inherited]

Referenced by OBFloatGrid::CoordsToIndex(), OBProxGrid::GetProxVector(), OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

double _xmax [protected, inherited]

Referenced by OBProxGrid::GetProxVector(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Inject(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

double _ymin [protected, inherited]

Referenced by OBFloatGrid::CoordsToIndex(), OBProxGrid::GetProxVector(), OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

double _ymax [protected, inherited]

Referenced by OBProxGrid::GetProxVector(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Inject(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

double _zmin [protected, inherited]

Referenced by OBFloatGrid::CoordsToIndex(), OBProxGrid::GetProxVector(), OBFloatGrid::IndexToCoords(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

double _zmax [protected, inherited]

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

Referenced by OBProxGrid::GetProxVector(), OBFloatGrid::Init(), OBGrid::Init(), OBFloatGrid::Inject(), OBFloatGrid::Interpolate(), OBFloatGrid::InterpolateDerivatives(), OpenBabel::operator<<(), OpenBabel::operator>>(), OBFloatGrid::SetLimits(), and OBProxGrid::Setup().

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

Custom data.

Referenced by OBBase::Clear(), OBBase::CloneData(), OBBase::DeleteData(), OBAtom::Duplicate(), OBBase::GetAllData(), OBBase::GetData(), OBBase::HasData(), OBBond::OBBond(), OBMol::OBMol(), and OBResidue::OBResidue().

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

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