OBProxGrid Class Reference

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

#include <openbabel/grid.h>

Inheritance diagram for OBProxGrid:

List of all members.

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

(

int

gridtype = 0 )

[inline]

~OBProxGrid

(

)

[inline]

---

Member Function Documentation

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
	)

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

vector< int > * GetProxVector

(

double *

c )

bool LipoGrid

(

)

[inline]

bool PolarGrid

(

)

[inline]

void SetGridType

(

int

gridtype )

[inline]

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 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

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().

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 OBDepict::DrawMolecule(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBForceField::GetPartialCharges(), OBDescriptor::MatchPairData(), OBMol::operator=(), 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 OpenBabel::CanonicalLabels(), OBDescriptor::DeleteProperties(), and OBMol::RenumberAtoms().

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]

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

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBForceField::GetAtomTypes(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetNextFragment(), OBForceField::GetPartialCharges(), OBMoleculeFormat::MakeCombinedMolecule(), OBDescriptor::PredictAndSave(), and OBMol::SetEnergies().

void CloneData

(

OBGenericData *

d )

[inherited]

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

Since:

version 2.2

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

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

OBDataIterator EndData

(

)

[inline, inherited]

Returns:

An iterator pointing to the end of the data

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

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Member Data Documentation

int _gridtype [protected]

int _nxinc [protected]

int _nyinc [protected]

int _nzinc [protected]

int _maxinc [protected]

double _inc [protected]

std::vector<std::vector<int> > cell [protected]

double _xmin [protected, inherited]

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

double _xmax [protected, inherited]

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

double _ymin [protected, inherited]

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

double _ymax [protected, inherited]

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

double _zmin [protected, inherited]

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

double _zmax [protected, inherited]

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

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

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

Custom data.

Referenced by OBMol::OBMol().

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

• grid.h
• grid.cpp