Subsections

7.19 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.

7.19.1 Constructors

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

Default and copy constructors.

7.19.2 operator=

OEOverlap &operator=(const OEOverlap &rhs)

Assignment operator. The contents of the passed OEColorOverlap reference are copied into an OEColorOverlap instance.

7.19.3 GetCarbonRadius

float GetCarbonRadius() const

Return the current value for the carbon radius approximation.

7.19.4 GetHandle

int GetHandle() const

7.19.5 GetMethod

unsigned int GetMethod() const

Return the current value of overlap method.

7.19.6 GetRadiiApproximation

unsigned int GetRadiiApproximation() const

Return the current value of the radii approximation.

7.19.7 GetRepresentationLevel

unsigned int GetRepresentationLevel() const

Return the current representation level.

7.19.8 GetUseHydrogens

bool GetUseHydrogens() const

Return the status of hydrogen use in OEOverlap.

7.19.9 Overlap

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

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

7.19.10 SetCarbonRadius

bool SetCarbonRadius(float cradius)

Set the radius to use when using OEOverlapRadii::Carbon. By default this is set to 1.7Å.

7.19.11 SetFitGrid

bool SetFitGrid(const OESystem::OEScalarGrid &fitgrid)

7.19.12 SetFitMol

bool SetFitMol(const OEChem::OEMolBase &fitmol)

7.19.13 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 (section 9.4).

7.19.14 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 (section 9.5).

7.19.15 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.

7.19.16 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.

7.19.17 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 (section 9.6).

7.19.18 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.

				Shape Toolkit Java Programming Manual

				Shape Toolkit Java Programming Manual