OBFloatGrid Class Reference

Handle double precision floating point 3D grids (e.g., charge density around an OBMol). More...

#include <openbabel/grid.h>

Inheritance diagram for OBFloatGrid:

Inheritance graph
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List of all members.

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 > *)
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

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 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=().

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: