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:

Inheritance graph
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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 > *)
template<class T>
T * CastAndClear (bool clear=true)
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)
unsigned int 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 
)

Referenced by OBProxGrid::GetProxVector().

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.

Referenced by OBFloatGrid::Init(), and 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, and OBResidue.

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

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

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.

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

Returns:
whether the generic attribute/value pair exists

Referenced by OBMol::AddAtom(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetSSSR(), OBBase::HasData(), OBDescriptor::MatchPairData(), OBMol::NewAtom(), 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 OBMol::AddAtom(), OBMol::BeginModify(), OBBuilder::CorrectStereoBonds(), OBDescriptor::DeleteProperties(), OBMol::FindSSSR(), OBMol::NewAtom(), 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]

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

Referenced by OBMol::AddBond(), OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::DoTransformations(), OBAtom::Duplicate(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), OBMol::GetNextFragment(), OBMol::GetSSSR(), OBMoleculeFormat::MakeCombinedMolecule(), OBMol::operator=(), OBDescriptor::PredictAndSave(), OBMol::SetEnergies(), and OBMol::SetFormula().

void CloneData ( OBGenericData *  d  )  [inherited]

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

Since:
version 2.2

unsigned int 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(), OBDescriptor::FilterCompare(), OBForceField::GetConformers(), OBForceField::GetCoordinates(), OBMol::GetNextFragment(), 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(), OBMol::FindSSSR(), OBBase::GetData(), OBMol::GetEnergies(), OBMol::GetEnergy(), OBMol::GetFormula(), 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

OBDataIterator BeginData (  )  [inline, inherited]

Returns:
An iterator pointing to the beginning of the data

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

Member Data Documentation

int _gridtype [protected]

int _nxinc [protected]

Referenced by OBProxGrid::Setup().

int _nyinc [protected]

Referenced by OBProxGrid::GetProxVector(), and OBProxGrid::Setup().

int _nzinc [protected]

Referenced by OBProxGrid::GetProxVector(), and OBProxGrid::Setup().

int _maxinc [protected]

Referenced by OBProxGrid::GetProxVector(), and OBProxGrid::Setup().

double _inc [protected]

Referenced by OBProxGrid::GetProxVector(), and OBProxGrid::Setup().

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

Referenced by OBProxGrid::GetProxVector(), and OBProxGrid::Setup().

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: