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:
OBGrid OBBase

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 OBBaseDoTransformations (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
OBGenericDataGetData (const unsigned int type)
OBGenericDataGetData (const std::string &)
OBGenericDataGetData (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 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]
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 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 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=().


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]
double _xmax [protected, inherited]
double _ymin [protected, inherited]
double _ymax [protected, inherited]
double _zmin [protected, inherited]
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().


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