OBGridData Class Reference

Store values for numeric grids such as orbitals or electrostatic potential. More...

#include <openbabel/griddata.h>

Inheritance diagram for OBGridData:

Inheritance graph
[legend]

List of all members.

Public Types

enum  Unit { BOHR, ANGSTROM, OTHER }

Public Member Functions

 OBGridData ()
 ~OBGridData ()
virtual OBGenericData * Clone (OBBase *) const
void SetAttribute (const std::string &v)
void SetOrigin (const DataOrigin s)
virtual const std::string & GetAttribute () const
unsigned int GetDataType () const
virtual const std::string & GetValue () const
virtual DataOrigin GetOrigin () const
Property Methods
void GetAxes (double x[3], double y[3], double z[3]) const
vector3 GetXAxis () const
vector3 GetYAxis () const
vector3 GetZAxis () const
void GetAxes (vector3 &v1, vector3 &v2, vector3 &v3) const
void GetNumberOfPoints (int &nx, int &ny, int &nz) const
int GetNumberOfPoints () const
void GetNumberOfSteps (int steps[3]) const
std::vector< double > GetValues () const
double GetValue (int i, int j, int k) const
double GetValue (vector3 pos) const
Unit GetUnit () const
double GetMinValue () const
double GetMaxValue () const
vector3 GetOriginVector () const
void GetOriginVector (double o[3]) const
vector3 GetMaxVector () const
bool GetUnrestricted () const
int GetNumSymmetries () const
Modification Methods
void SetNumberOfPoints (int nx, int ny, int nz)
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])
bool SetValue (int i, int j, int k, double val)
void SetValues (const std::vector< double > &v)
void SetUnit (Unit u)
void SetUnrestricted (bool u)
void SetNumSymmetries (int s)

Protected Attributes

std::string _attr
unsigned int _type
DataOrigin _source

Detailed Description

Store values for numeric grids such as orbitals or electrostatic potential.

Since:
version 2.2
See also:
OBFloatGrid
OBGridData facilitates attaching grids and cubes to molecular data. A "grid" is data representing some function f(x,y,z), such as a molecule's electrostatic potential or molecular orbitals. This need not be a "cube" even though this file format from Gaussian is frequently used. Axes need not be identical, and indeed do not need to be orthogonal.

Open Babel supports reading several types of grid file formats, including Gaussian cube, and OpenDX. The latter is notably used by the APBS program for numeric evaluation of molecular and protein electrostatic potential.

    OBGridData *gd = new OBGridData;
    gd->SetAttribute("Example Grid"); // the title of the grid -- e.g., for user display
    vector<int> voxels(3); // the number of voxels in each direction
    vector3 origin; // the beginning x, y, z coordinate of the grid
    vector<vector3> axes; // the xyz displacements for each of the grid axes
    ...
    gd->SetNumberOfPoints(voxels[0], voxels[1], voxels[2]);
    gd->SetLimits(origin, axes[0], axes[1], axes[2]);
    gd->SetUnit(OBGridData::ANGSTROM);
    gd->SetOrigin(fileformatInput); // i.e., is this data from a file or determined by Open Babel
    
    for (int k = 0; k < voxels[2]; ++k)
      for (int j = 0; j < voxels[1]; ++j)
        for (int i = 0; i < voxels[0]; ++i)
          {
            gd->SetValue(i, j, k, 
                         grid[k*voxels[0]*voxels[1] + j*voxels[0] + i]);
          }
    
    mol->SetData(gd);


    if (mol->HasData(OBGenericDataType::GridData)) {
      vector<OBGenericData*> grids = mol->GetAllData(OBGenericDataType::GridData)
      // Output the name of the grid
      if (grids[0] != NULL)
        cout << grids[0]->GetAttribute();
    }

Member Enumeration Documentation

enum Unit

Unit of measure for grid spacings.

Enumerator:
BOHR 
ANGSTROM 
OTHER 

Constructor & Destructor Documentation

OBGridData (  ) 

Constructor.

~OBGridData (  ) 

Destructor.

Member Function Documentation

void GetAxes ( double  x[3],
double  y[3],
double  z[3] 
) const

Returns:
the three axes parallel to the grid edges. The length of the returned vector is the step along that direction.

vector3 GetXAxis (  )  const

Returns:
X axis direction.

vector3 GetYAxis (  )  const

Returns:
Y axis direction.

vector3 GetZAxis (  )  const

Returns:
Z axis direction.

void GetAxes ( vector3 &  v1,
vector3 &  v2,
vector3 &  v3 
) const

Returns:
the three axes parallel to the grid edges

void GetNumberOfPoints ( int &  nx,
int &  ny,
int &  nz 
) const

Returns:
number of points along the three axes parallel to the grid edges.

int GetNumberOfPoints (  )  const

Returns:
total number of points in the grid.

void GetNumberOfSteps ( int  steps[3]  )  const

Returns:
number of points along the three axes parallel to the grid edges.

std::vector< double > GetValues (  )  const

Returns:
grid values as a vector of doubles.

double GetValue ( int  i,
int  j,
int  k 
) const

Returns:
the value at position i, j, k in the grid.

Referenced by OBForceField::GetGrid().

double GetValue ( vector3  pos  )  const

Returns:
the value at a position in the grid (by interpolation)

OBGridData::Unit GetUnit (  )  const

Returns:
the unit of measure for grid spacings.

double GetMinValue (  )  const

Returns:
the minimum value of all points in the grid.

double GetMaxValue (  )  const

Returns:
the maximum value of all points in the grid.

vector3 GetOriginVector (  )  const

Returns:
vector3 of the origin (i.e., the minimum x, y, and z coords of the grid).

void GetOriginVector ( double  o[3]  )  const

Parameters:
o set to the origin (i.e., the minimum x, y, and z coords of the grid).
Deprecated:
Will be removed.
See also:
GetOriginVector()

vector3 GetMaxVector (  )  const

Returns:
The maximum point in the grid.

bool GetUnrestricted (  )  const

Returns:
the unrestricted flag.

int GetNumSymmetries (  )  const

Returns:
the number of symmetries.

void SetNumberOfPoints ( int  nx,
int  ny,
int  nz 
)

Set number of points along the three axes.

Referenced by OBForceField::GetGrid().

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 OBForceField::GetGrid().

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)

bool SetValue ( int  i,
int  j,
int  k,
double  val 
)

Set an individual value, grid must have been initialised.

Referenced by OBForceField::GetGrid().

void SetValues ( const std::vector< double > &  v  ) 

Set the values, this vector must match the dimensions of the grid.

void SetUnit ( OBGridData::Unit  u  ) 

Set the unit of measure.

void SetUnrestricted ( bool  u  ) 

Set the unrestricted flag.

void SetNumSymmetries ( int  s  ) 

Set the number of symmetries.

virtual OBGenericData* Clone ( OBBase *   )  const [inline, virtual, inherited]

Reimplemented in AliasData, OBAtomClassData, OBCommentData, OBExternalBondData, OBPairData, OBSetData, OBVirtualBond, OBRingData, OBUnitCell, OBConformerData, OBSymmetryData, OBTorsionData, OBAngleData, OBChiralData, OBSerialNums, OBVibrationData, OBRotationData, OBVectorData, OBMatrixData, OBRateData, OBNasaThermoData, and OBRotamerList.

Referenced by OBBase::CloneData(), and OBMoleculeFormat::MakeCombinedMolecule().

void SetAttribute ( const std::string &  v  )  [inline, inherited]

Set the attribute (key), which can be used to retrieve this data.

Referenced by OBGastChrg::AssignPartialCharges(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBForceField::GetPartialCharges(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

void SetOrigin ( const DataOrigin  s  )  [inline, inherited]

Set the origin of this data, which can be used to filter the data.

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::CalcSignedVolume(), OBMol::FindAngles(), OBMol::FindSSSR(), OBMol::FindTorsions(), OBMol::GetFormula(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

virtual const std::string& GetAttribute (  )  const [inline, virtual, inherited]

Returns:
The attribute (key), which can be used to retrieve this data

Referenced by OBMoleculeFormat::MakeCombinedMolecule().

unsigned int GetDataType (  )  const [inline, inherited]

Returns:
the data type for this object as defined in OBGenericDataType

virtual const std::string& GetValue (  )  const [inline, virtual, inherited]

Base class returns a default value (the attribute type) but should never be called.

Reimplemented in OBCommentData, and OBPairData.

Referenced by OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

virtual DataOrigin GetOrigin (  )  const [inline, virtual, inherited]

Member Data Documentation

std::string _attr [protected, inherited]

attribute tag (e.g., "UnitCell", "Comment" or "Author")

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

unsigned int _type [protected, inherited]

attribute type -- declared for each subclass

Referenced by OBRotamerList::Clone(), and OBNasaThermoData::OBNasaThermoData().

DataOrigin _source [protected, inherited]

source of data for accounting

Referenced by OBChiralData::operator=(), OBTorsionData::operator=(), OBAngleData::operator=(), OBConformerData::operator=(), and OBSymmetryData::operator=().

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