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
OEOverlap(refmol: OEScalarGrid) -> OEOverlap
OEOverlap(rhs: OEOverlap) -> OEOverlap
OEOverlap(refmol: Union[OEGraphMol,OEMol,OEQMol]) -> OEOverlap

Default and copy constructors.

GetCarbonRadius

GetCarbonRadius() -> float

Return the current value for the carbon radius approximation.

GetGridSpacing

GetGridSpacing() -> float

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

GetMethod() -> int

Return the current value of overlap method.

GetRadiiApproximation

GetRadiiApproximation() -> int

Return the current value of the radii approximation.

GetUseHydrogens

GetUseHydrogens() -> bool

Return the status of hydrogen use in OEOverlap.

Overlap

Overlap(res: OEOverlapResults, atomOverlaps: OEFloatArray = None) -> bool
Overlap(fitmol: Union[OEGraphMol,OEMol,OEQMol],
        res: OEOverlapResults, atomOverlaps: OEFloatArray = None) -> bool

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

SetCarbonRadius

SetCarbonRadius(cradius: float) -> bool

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

SetFitMol

SetFitMol(fitmol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Set molecule to be used as fit object.

SetGridSpacing

SetGridSpacing(spacing: float) -> bool

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

SetMethod(m: int) -> bool

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

SetRadiiApproximation

SetRadiiApproximation(type: int) -> bool

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

SetRefGrid

SetRefGrid(refgrid: OEScalarGrid) -> bool

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

SetRefMol

SetRefMol(refmol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

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

SetUseHydrogens

SetUseHydrogens(state: bool) -> bool

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