OEOverlap

class OEOverlap

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.

GetCarbonRadius

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.

GetRadiiApproximation

unsigned int GetRadiiApproximation() const

Return the current value of the radii approximation.

GetRepresentationLevel

unsigned int GetRepresentationLevel() const

Return the current representation level.

GetUseHydrogens

bool GetUseHydrogens() const

Return the status of hydrogen use in OEOverlap.

Overlap

bool Overlap(OEOverlapResults &res, float *atomOverlaps=0)
bool Overlap(const OESystem::OEScalarGrid &fitgrid, OEOverlapResults &res)
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.

SetCarbonRadius

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.

SetFitGrid

bool SetFitGrid(const OESystem::OEScalarGrid &fitgrid)

Set grid to be used as fit object.

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.

SetRadiiApproximation

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.

SetRepresentationLevel

bool SetRepresentationLevel(unsigned int type)

Set the representation level for the Gaussians in OEOverlap. The default is OEOverlapRepresentation.Atomic. Alternatives are defined in the OEOverlapRepresentation namespace.

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.