OESzmapEngine

class OESzmapEngine

It stores the context molecule, the configuration options (including the probe molecule), and an OEZap object used to perform the Poisson-Boltzmann electrostatics calculations by OECalcSzmapResults, OECalcSzmapValue, and OEIsClashing. A OESzmapEngine may cache the results of a calculation at a given 3D point to improve efficiency.

Constructors

OESzmapEngine(opt: OESzmapEngineOptions = OESzmapEngineOptions()) -> OESzmapEngine
OESzmapEngine(rhs: OESzmapEngine) -> OESzmapEngine
OESzmapEngine(context: Union[OEGraphMol,OEMol,OEQMol],
              opt: OESzmapEngineOptions = OESzmapEngineOptions()) -> OESzmapEngine

Default and copy constructors, along with constructors that take a context molecule (typically a properly prepared protein, see OESzmapEngine.SetContext) and/or a OESzmapEngineOptions object.

sz = oeszmap.OESzmapEngine(prot, opt)

operator bool

IsValid() -> bool

Returns true if this object is valid for use in OESzmap calculations. A context molecule—either at construction or through a call to OESzmapEngine.SetContext— must be provided to establish validity.

CheckAtomTypes

CheckAtomTypes() -> bool

Returns true if atom types could be applied to the molecular context and probe molecules.

GetContext

GetContext() -> OEGraphMol

Returns a reference to the molecular context for OESzmap calculations (see OESzmapEngine.SetContext).

mol = sz.GetContext()
print("context mol: %s" % mol.GetTitle())

GetOptions

GetOptions() -> OESzmapEngineOptions

Returns a reference to the OESzmapEngineOptions used to construct this OESzmapEngine. It can be used to construct another OESzmapEngine object and to access details of the probe and other settings.

SetContext

SetContext(context: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Updates the molecular context used for any OESzmap calculations based on this object (see OESzmapEngine.SetContext and OESzmapEngine.operator bool). The context molecule must have 3D coordinates assigned and partial charges associated with each atom. Atomic radii are also necessary, but will be generated if not supplied.

Returns true if the context molecule is acceptable, with 3D coordinates and partial charges.