OEBestOverlay

class OEBestOverlay

Note

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

This class is used to optimize the overlap between 2 molecules. Both molecules can contain one or more conformers. The reference molecule is held rigid and the fit molecule orientation is calculated to maximize overlap. Each conformer of the fit molecule is optimized against each conformer of the reference molecule, resulting in a large number of results that can be returned. The OEBestOverlayResults and OEBestOverlayScore classes are used to make handling this large amount of results easier.

Additionally, the reference or fit shape can be a grid instead of a molecule.

Since an OEBestOverlay optimization can result in numerous final results, one for each starting position, the OEBestOverlayResults class is a container to hold all the results for a fit conformer against a reference conformer. This class is essentially a container for one or more OEBestOverlayScore instances. The actual number of scores depends on the OEBOOrientation used in the OEBestOverlay.

For OEBOOrientation_Inertial, there will be 4, 8 or 20 scores per ref-fit conformer pair, depending on the symmetry of each conformer. For OEBOOrientation_AsIs, there will be just 1 OEBestOverlayScore inside each OEBestOverlayResults instance. And for OEBOOrientation_Random, then there will be 1 OEBestOverlayScore for each of the N random starts.

When dealing with the results from OEBestOverlay, the user can either use a double loop, i.e. loop over all the OEBestOverlayResults instances for each ref-fit conformer pair then loop over each OEBestOverlayScore inside each OEBestOverlayResults instance. In this case, the results also come out in conformer order.

for res in best.Overlay(fitmol):
    for score in res.GetScores():
        # do something with score

Or, there is a free function OESortOverlayScores, that takes an iterator of OEBestOverlayResults and returns a single, sorted iterator of OEBestOverlayScores that can be used in a single loop.

scoreiter = OEBestOverlayScoreIter()
OESortOverlayScores(scoreiter, best.Overlay(fitmol), OEHighestTanimotoCombo())
for score in scoreiter:
     # do something with score

Constructors

OEBestOverlay() -> OEBestOverlay
OEBestOverlay(refmol: OEMol) -> OEBestOverlay
OEBestOverlay(refgrid: OEScalarGrid, interpolate: float = 0.5) -> OEBestOverlay
OEBestOverlay(arg2: OEBestOverlay) -> OEBestOverlay

An empty OEBestOverlay class instance can be created, or a new instance can take the reference molecule or grid as an argument. Note that by default, grids that have a resolution larger that 0.5 Å will be interpolated to that resolution.

ClearColorForceField

ClearColorForceField() -> None

Clear out any color force field. No color scores will be calculated.

ClearUserStarts

ClearUserStarts() -> None

Set the number of User Starts back to zero.

GetCarbonRadius

GetCarbonRadius() -> float

Return the current value for the carbon radius approximation.

GetInitialOrientation

GetInitialOrientation() -> int

Get the current value for initial orientation. Possible values are from the OEBOOrientation namespace.

GetMaxRandomTranslation

GetMaxRandomTranslation() -> float

Get the value in Å of maximum random translation.

GetMethod

GetMethod() -> int

Return the current value of overlap method.

GetMinimizeType

GetMinimizeType() -> int

Get the current value for minimize type. Possible values are from the OEBOMinType namespace.

GetNumRandomStarts

GetNumRandomStarts() -> int

Get the current number of random starts.

GetNumUserStarts

GetNumUserStarts() -> int

Get the number of user starts currently set. Note that these are not actually used unless OEBOOrientation_UserInertialStarts is also set.

GetRadiiApproximation

GetRadiiApproximation() -> int

Return the current value of the radii approximation.

GetRandomSeed

GetRandomSeed() -> int

Get the current value of the random seed.

GetRefGrid

GetRefGrid() -> OEScalarGrid

GetRefMol

GetRefMol() -> OEMol

GetRefSelfColor

GetRefSelfColor() -> float

Return the self color score of the reference molecule.

GetRefSymmetry

GetRefSymmetry(confIdx: int) -> int

Return the current representation level.

GetSymmetryThreshold

GetSymmetryThreshold() -> float

GetUseHydrogens

GetUseHydrogens() -> bool

Return the status of hydrogen use in OEBestOverlay.

GetUserStarts

GetUserStarts(xyz: OEFloatArray) -> bool

Extract the coordinates of the user starts. xyz should be sized to 3 * GetNumUserStarts().

Overlay

Overlay(fitmol: OEMol) -> Iterable[OEBestOverlayResults]

Perform the calculation and return the an iterator of the results.

SetCarbonRadius

SetCarbonRadius(cradius: float) -> None

Set the radius to use when using OEOverlapRadii_Carbon. By default this is set to 1.7 Å.

SetColorForceField

SetColorForceField(type: int) -> bool
SetColorForceField(ifs: oeistream) -> bool
SetColorForceField(filename: str) -> bool
SetColorForceField(cff: OEColorForceField) -> bool

Set the color force field to be used. Once set, color scores will be calculated and included in the results. Color gradients will not be included in the optimization unless specifically set using SetColorOptimize(true).

SetColorOptimize

SetColorOptimize(state: bool) -> None

Add color gradients to shape gradients in the optimization. Has no effect unless a color force field is also set via OEBestOverlay.SetColorForceField.

SetInitialOrientation

SetInitialOrientation(orient: int) -> None

Determines the initial orientation (starting position) for each optimization. The default is OEBOOrientation_Inertial. Alternatives are defined in the OEBOOrientation namespace.

SetMaxRandomTranslation

SetMaxRandomTranslation(trans: float) -> None

If using random starts, this set the maximum distance (in Å) that the center of mass of the fit molecule will be moved away from the center calculated for inertial frame alignment.

SetMethod

SetMethod(method: int) -> None

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

SetMinimizeType

SetMinimizeType(type: int) -> None

Set the score to use in the optimization. Options are in the OEBOMinType namespace.

SetNumRandomStarts

SetNumRandomStarts(n: int) -> None

If SetInitialOrientation is set to OEBOOrientation_Random, this method sets the number of random starting positions that will be used.

SetRadiiApproximation

SetRadiiApproximation(type: int) -> None

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

SetRandomSeed

SetRandomSeed(seed: int) -> None

Set a random seed value to allow reproducible random searches.

SetRefGrid

SetRefGrid(refgrid: OEScalarGrid, interpolate: float = 0.5) -> bool

Set a reference grid for the calculation. OEBestOverlay makes an internal copy. Pre-existing reference molecules or grids are replaced.

SetRefMol

SetRefMol(refmol: OEMol) -> bool

Set a reference molecule for the calculation. OEBestOverlay makes an internal copy. Pre-existing reference molecules or grids are replaced.

SetSymmetryThreshold

SetSymmetryThreshold(threshold: float) -> None

SetUseHydrogens

SetUseHydrogens(state: bool) -> None

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

SetUserStarts

SetUserStarts(xyz: OEFloatArray, nstarts: int) -> None

Set a set of 3D coordinates for doing separate inertial starts. xyz should be 3 * nstarts. These are not used unless OEBOOrientation_UserInertialStarts is also set.