# OEOverlap¶

class OEOverlap


Note

This deprecated class will not be developed further. It is being replaced by derivatives of OEShapeFunc which provides more control and greater expandability.

OEOverlap calculates the static shape overlap between a reference molecule or grid and a fit molecule or grid. Note that this does not move the fit molecule(grid) nor does it optimize the overlap. It simply calculates the score for the provided orientation.

## Constructors¶

OEOverlap()
OEOverlap(const OEOverlap &rhs)
OEOverlap(const OEChem::OEMolBase &refmol)
OEOverlap(const OESystem::OEScalarGrid &refmol)


Default and copy constructors.

## operator=¶

OEOverlap &operator=(const OEOverlap &rhs)

Assignment operator. The contents of the passed OEOverlap reference are copied into the current OEOverlap instance.

float GetCarbonRadius() const


Return the current value for the carbon radius approximation.

## GetGridSpacing¶

float GetGridSpacing() const


Return the current value for the grid spacing to use for the OEOverlapMethod::Grid method of calculating overlaps. Is not used by any other overlap method. Defaults to 0.25.

## GetMethod¶

unsigned int GetMethod() const


Return the current value of overlap method.

unsigned int GetRadiiApproximation() const


Return the current value of the radii approximation.

## GetUseHydrogens¶

bool GetUseHydrogens() const


Return the status of hydrogen use in OEOverlap.

## Overlap¶

bool Overlap(OEOverlapResults &res, float *atomOverlaps=0)
bool Overlap(const OEChem::OEMolBase &fitmol, OEOverlapResults &res,
float *atomOverlaps=0)


Calculate the overlap of the passed in fit molecule or fit grid and place the results into the passed instance of OEOverlapResults.

bool SetCarbonRadius(float cradius)


Set the radius to use when using OEOverlapRadii::Carbon. By default this is set to 1.7 Angstroms. See OEBestOverlay::GetCarbonRadius.

## SetFitMol¶

bool SetFitMol(const OEChem::OEMolBase &fitmol)


Set molecule to be used as fit object.

## SetGridSpacing¶

bool SetGridSpacing(float spacing)


Set the grid spacing to use for the OEOverlapMethod::Grid method of calculating overlaps. Smaller values typically lead to more accurate results when considering large numbers of compounds, though not necessarily more accurate results in individual cases. This method will only accept values between 0.125 and 1.0 inclusive. The default is 0.25 angstroms for a balance of performance and reproducibility. Larger values may lead to better performance on some platforms.

## SetMethod¶

bool SetMethod(unsigned int m)


Set the method used to calculate overlap. The default for OEOverlap is OEOverlapMethod::Exact. Alternatives are defined in the OEOverlapMethod namespace.

bool SetRadiiApproximation(unsigned int type)


Set the radius approximation used to calculate overlap. The default for OEOverlap is OEOverlapRadii::Carbon. Alternatives are defined in the OEOverlapRadii namespace.

## SetRefGrid¶

bool SetRefGrid(const OESystem::OEScalarGrid &refgrid)


Set a reference grid for the calculation. An internal copy is made. Any previous reference molecule or grid is cleared.

## SetRefMol¶

bool SetRefMol(const OEChem::OEMolBase &refmol)


Set a reference molecule for the calculation. An internal copy is made. Any previous reference molecule or grid is cleared.

## SetUseHydrogens¶

bool SetUseHydrogens(bool state)


Boolean to determine whether hydrogens are included in the shape calculation. By default this is false and hydrogens are ignored.