OESzmapEngineOptions¶

class OESzmapEngineOptions


This class represents OESzmapEngineOptions, an object used to set one or more options when constructing an OESzmapEngine.

opt.SetProbe(24).SetMaskCutoff(999.99);


When returned by OESzmapEngine.GetOptions, can be used to determine the settings used for a given set of calculations.

OESzmapEngineOptions opts = sz.GetOptions();
System.out.println("norient= " + opts.NumOrientations());
System.out.println("name   = " + opts.GetProbeName());
System.out.format("cutoff = %.3f%n", opts.GetMaskCutoff());


Constructors¶

OESzmapEngineOptions()
OESzmapEngineOptions(const OESzmapEngineOptions &rhs)


Default and copy constructors. The default OESzmapEngineOptions object defines the probe to be a standard SZMAP water with 60 orientations.

OESzmapEngineOptions opt = new OESzmapEngineOptions();


operator=¶

OESzmapEngineOptions &operator=(const OESzmapEngineOptions &rhs)


Assignment operator.

double GetMaskCutoff() const


Returns the energy cutoff (in kcal/mol) defining a clash (by default, 0.0; see OEIsClashing and OESzmapEngineOptions.SetMaskCutoff). A clash means every orientation of the probe had a combined OEComponent.Interaction + OEComponent.VDW energy total greater than the cutoff.

GetProbe¶

const OEChem::OEMCMolBase &GetProbe() const


Returns a reference to the current multi-conformer probe molecule (see OESzmapEngineOptions.SetProbe).

OEMCMolBase p = opt.GetProbe();
System.out.println("probe nconf = " + p.NumConfs());


GetProbeMol¶

void GetProbeMol(OEChem::OEMolBase &outputMol,
unsigned int orientation=0u) const


Updates outputMol to contain a specific orientation of the current multi-conformer probe (see OESzmapEngineOptions.SetProbe). By default, the first orientation is returned.

OEGraphMol mol = new OEGraphMol();
opt.GetProbeMol(mol);


GetProbeName¶

const char *GetProbeName() const


Returns the standard name of the current probe type (e.g. "water").

NumOrientations¶

unsigned int NumOrientations() const


Returns the number of orientations for the current probe (see OESzmapEngineOptions.SetProbe).

OESzmapEngineOptions &SetMaskCutoff(double cutoff)


Set the energy cutoff (in kcal/mol) defining a clash (by default, 0.0; see OEIsClashing and OESzmapEngineOptions.GetMaskCutoff). A clash means every orientation of the probe had a combined OEComponent.Interaction + OEComponent.VDW energy total greater than the cutoff.

SetProbe¶

OESzmapEngineOptions &SetProbe(unsigned int numOrientations)


Define the current multi-conformation probe molecule to be a standard SZMAP water molecule with the specified number of orientations (see The Szmap TK Standard Water Model for more information on the geometry and charges used).

If numOrientations is set to 24, 60, 216, 360, or 648 then the set of orientations will be symmetric. Otherwise, it will include random orientations and may have lopsided gaps in coverage. For most purposes, 60 is the minimum required for reliable energy calculations and 360 generates higher-precision results, although with a speed penalty due to the additional Zap calculations.

opt.SetProbe(360);


The default OESzmapEngineOptions standard SZMAP water has 60 orientations.