Open Babel  3.0
Public Types | Public Member Functions | Protected Attributes | List of all members
OBGridData Class Reference

#include <openbabel/griddata.h>

Inheritance diagram for OBGridData:
OBGenericData

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

◆ Unit

enum Unit

Unit of measure for grid spacings.

Enumerator
BOHR 
ANGSTROM 
OTHER 

Constructor & Destructor Documentation

◆ OBGridData()

OBGridData ( )

Constructor.

◆ ~OBGridData()

~OBGridData ( )

Destructor.

Member Function Documentation

◆ GetAxes() [1/2]

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.

◆ GetXAxis()

vector3 GetXAxis ( ) const
Returns
X axis direction.

◆ GetYAxis()

vector3 GetYAxis ( ) const
Returns
Y axis direction.

◆ GetZAxis()

vector3 GetZAxis ( ) const
Returns
Z axis direction.

◆ GetAxes() [2/2]

void GetAxes ( vector3 &  v1,
vector3 &  v2,
vector3 &  v3 
) const
Returns
the three axes parallel to the grid edges

◆ GetNumberOfPoints() [1/2]

void GetNumberOfPoints ( int &  nx,
int &  ny,
int &  nz 
) const
Returns
number of points along the three axes parallel to the grid edges.

◆ GetNumberOfPoints() [2/2]

int GetNumberOfPoints ( ) const
Returns
total number of points in the grid.

◆ GetNumberOfSteps()

void GetNumberOfSteps ( int  steps[3]) const
Returns
number of points along the three axes parallel to the grid edges.

◆ GetValues()

std::vector< double > GetValues ( ) const
Returns
grid values as a vector of doubles.

◆ GetValue() [1/3]

double GetValue ( int  i,
int  j,
int  k 
) const
Returns
the value at position i, j, k in the grid.

Referenced by OBForceField::GetGrid().

◆ GetValue() [2/3]

double GetValue ( vector3  pos) const
Returns
the value at a position in the grid (by interpolation)

◆ GetUnit()

OBGridData::Unit GetUnit ( ) const
Returns
the unit of measure for grid spacings.

◆ GetMinValue()

double GetMinValue ( ) const
Returns
the minimum value of all points in the grid.

◆ GetMaxValue()

double GetMaxValue ( ) const
Returns
the maximum value of all points in the grid.

◆ GetOriginVector() [1/2]

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

◆ GetOriginVector() [2/2]

void GetOriginVector ( double  o[3]) const
Parameters
oset to the origin (i.e., the minimum x, y, and z coords of the grid).
Deprecated:
Will be removed.
See also
GetOriginVector()

◆ GetMaxVector()

vector3 GetMaxVector ( ) const
Returns
The maximum point in the grid.

◆ GetUnrestricted()

bool GetUnrestricted ( ) const
Returns
the unrestricted flag.

◆ GetNumSymmetries()

int GetNumSymmetries ( ) const
Returns
the number of symmetries.

◆ SetNumberOfPoints()

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

Set number of points along the three axes.

Referenced by OBForceField::GetGrid().

◆ SetLimits() [1/2]

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().

◆ SetLimits() [2/2]

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)

◆ SetValue()

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

Set an individual value, grid must have been initialised.

Referenced by OBForceField::GetGrid().

◆ SetValues()

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

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

◆ SetUnit()

void SetUnit ( OBGridData::Unit  u)

Set the unit of measure.

◆ SetUnrestricted()

void SetUnrestricted ( bool  u)

Set the unrestricted flag.

◆ SetNumSymmetries()

void SetNumSymmetries ( int  s)

Set the number of symmetries.

◆ Clone()

virtual OBGenericData* Clone ( OBBase *  ) const
inlinevirtualinherited

Reimplemented in OBMatrixData, OBVectorData, OBRotationData, OBElectronicTransitionData, OBOrbitalData, OBDOSData, OBVibrationData, OBSerialNums, OBAngleData, OBTorsionData, OBSymmetryData, OBConformerData, OBUnitCell, OBCisTransStereo, OBRingData, OBVirtualBond, OBTetrahedralStereo, OBSquarePlanarStereo, OBSetData, OBNasaThermoData, OBPairTemplate< ValueT >, OBPairData, OBExternalBondData, AliasData, OBRotamerList, OBCommentData, and OBRateData.

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

◆ SetAttribute()

void SetAttribute ( const std::string &  v)
inlineinherited

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

Referenced by OBGastChrg::AssignPartialCharges(), OpenBabel::ComparePairSecond(), OBMol::DoTransformations(), OBMol::FindLSSR(), OBMol::FindSSSR(), OBForceField::GetAtomTypes(), OBMol::GetFormula(), OBMol::GetLSSR(), OBForceField::GetPartialCharges(), OBMol::GetSSSR(), OBDescriptor::PredictAndSave(), and OBMol::SetFormula().

◆ SetOrigin()

void SetOrigin ( const DataOrigin  s)
inlineinherited

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

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

◆ GetAttribute()

virtual const std::string& GetAttribute ( ) const
inlinevirtualinherited
Returns
The attribute (key), which can be used to retrieve this data

Referenced by OpenBabel::extract_thermochemistry(), and OBMoleculeFormat::MakeCombinedMolecule().

◆ GetDataType()

unsigned int GetDataType ( ) const
inlineinherited
Returns
the data type for this object as defined in OBGenericDataType

◆ GetValue() [3/3]

virtual const std::string& GetValue ( ) const
inlinevirtualinherited

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

Reimplemented in OBPairData, and OBCommentData.

Referenced by OBDepict::AddAtomLabels(), OBDepict::DrawMolecule(), OBDescriptor::FilterCompare(), and OBDescriptor::GetValues().

◆ GetOrigin()

virtual DataOrigin GetOrigin ( ) const
inlinevirtualinherited

Member Data Documentation

◆ _attr

std::string _attr
protectedinherited

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

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

◆ _type

unsigned int _type
protectedinherited

attribute type – declared for each subclass

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

◆ _source

DataOrigin _source
protectedinherited

source of data for accounting

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

The documentation for this class was generated from the following files:
Generated on Tue Oct 15 2019 21:28:05 for Open Babel by   doxygen 1.8.13