#include <openbabel/grid.h>

Inheritance diagram for OBProxGrid:

Public Member Functions
	OBProxGrid (int gridtype=0)

	~OBProxGrid ()

void	Setup (OBMol &mol, OBMol &box, double cutoff, double resolution=0.5)

void	Setup (OBMol &mol, OBMol &box, double cutoff, std::vector< bool > &use, double resolution=0.5)

std::vector< int > *	GetProxVector (double, double, double)

std::vector< int > *	GetProxVector (double *)

bool	LipoGrid ()

bool	PolarGrid ()

void	SetGridType (int gridtype)

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
int	_gridtype

int	_nxinc

int	_nyinc

int	_nzinc

int	_maxinc

double	_inc

std::vector< std::vector< int > >	cell

double	_xmin

double	_xmax

double	_ymin

double	_ymax

double	_zmin

double	_zmax

std::vector< OBGenericData * >	_vdata

Detailed Description

A grid for determining the proximity of a given point to atoms in an OBMol.

Deprecated:: May be removed in the future, since docking is not a key feature

Constructor & Destructor Documentation

◆ OBProxGrid()

OBProxGrid ( int gridtype = 0 )

inline

◆ ~OBProxGrid()

~OBProxGrid ( )

inline

Member Function Documentation

◆ Setup() [1/2]

void Setup	(	OBMol &	mol,
		OBMol &	box,
		double	cutoff,
		double	resolution = `0.5`
	)

◆ Setup() [2/2]

void Setup	(	OBMol &	mol,
		OBMol &	box,
		double	cutoff,
		std::vector< bool > &	use,
		double	resolution = `0.5`
	)

◆ GetProxVector() [1/2]

vector< int > * GetProxVector	(	double	x,
		double	y,
		double	z
	)

◆ GetProxVector() [2/2]

vector< int > * GetProxVector ( double * c )

◆ LipoGrid()

bool LipoGrid ( )

inline

◆ PolarGrid()

bool PolarGrid ( )

inline

◆ SetGridType()

void SetGridType ( int gridtype )

inline

◆ Init()

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=().

Member Data Documentation

◆ _gridtype

int _gridtype

protected

◆ _nxinc

int _nxinc

protected

◆ _nyinc

int _nyinc

protected

◆ _nzinc

int _nzinc

protected

◆ _maxinc

int _maxinc

protected

◆ _inc

double _inc

protected

◆ cell

std::vector<std::vector<int> > cell

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

Detailed Description

Constructor & Destructor Documentation

◆ OBProxGrid()

◆ ~OBProxGrid()

Member Function Documentation

◆ Setup() [1/2]

◆ Setup() [2/2]

◆ GetProxVector() [1/2]

◆ GetProxVector() [2/2]

◆ LipoGrid()

◆ PolarGrid()

◆ SetGridType()

◆ Init()

◆ 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()

Member Data Documentation

◆ _gridtype

◆ _nxinc

◆ _nyinc

◆ _nzinc

◆ _maxinc

◆ _inc

◆ cell

◆ _xmin

◆ _xmax

◆ _ymin

◆ _ymax

◆ _zmin

◆ _zmax

◆ _vdata