OEEonPBFunc

Attention

This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.

class OEEonPBFunc : public OEMolPotential::OEMolFunc0

This class enables computation of electrostatic potential similarity.

The OEEonPBFunc defines the following public methods:

Setup

SetupRef

NumVar

GetFComponents

operator()

Overlap

CreateCopy

Public methods inherited from the parent class can be found in the OEMolPotential::OEMolFunc0.

Constructors

Default, copy constructors:

OEEonPBFunc(opts: OEEonPBOptions = OEEonPBOptions()) -> OEEonPBFunc
OEEonPBFunc(arg2: OEEonPBFunc) -> OEEonPBFunc

Destructor

~OEEonPBFunc()

Setup

Setup(fitMol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Sets up the fit molecule for Poisson-Boltzmann overlap calculations. The molecule must have 3D coordinates and partial charges assigned.

SetupRef

SetupRef(refMol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Sets up the reference molecule for Poisson-Boltzmann overlap calculations. The molecule must have 3D coordinates and partial charges assigned.

NumVar

NumVar() -> int

Returns the number of variables (degrees of freedom) for the current fit molecule.

CreateCopy

CreateCopy() -> OEEonPBFunc

Creates and returns a deep copy of this object.

GetFComponents

GetFComponents(coords: float) -> Iterable[OEFComponent]

Returns an iterator over the force components at the given coordinates. The fit molecule must have been set up via Setup.

operator()

__call__(coords: OEDoubleArray) -> float

Evaluates the Poisson-Boltzmann potential overlap function at the given coordinates. The fit molecule must have been set up via Setup.

Overlap

Overlap(coords: OEDoubleArray, results: OEEonPBResults) -> bool
Overlap(fitMol: Union[OEGraphMol,OEMol,OEQMol],
        results: OEEonPBResults) -> bool

These methods compute Poisson–Boltzmann (PB) potential overlap between reference and fit molecules. The first one assumes that the fit molecule has already been set up using Setup method. The second one directly inputs the fit molecule and does this setup internally.