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.

GetMaskCutoff

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).

SetMaskCutoff

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.