OEZap

class OEZap

This class represents OEZap.

Constructors

OEZap()
OEZap(const OEZap &rhs)

Default and copy constructors.

operator=

OEZap &operator=(const OEZap &rhs)

Assignment operator.

CalcAtomPotentials

bool CalcAtomPotentials(float *pot, bool no_grid=false)

Calculates the atom potentials and fills the float array with their values. The float array should be of length N, where N is the number of atoms.

CalcForces

bool CalcForces(float *forces)

Calculates the forces on the atoms and fills the float array with the values of their x, y, and z components. The float array should be of length 3N, where N is the number of atoms.

CalcPotentialGrid

bool CalcPotentialGrid(OESystem::OEScalarGrid &grid)

Calculates the potential grid and updates the OEScalarGrid with the values. The calculated electrostatic potential is a dimensionless value defined as eV/kT where eV is the electric work, in kcal/mol, of bringing an electron charge to the point with potential V, and kT = 0.59 kcal/mol (value of kT at room temperature).

CalcSolvationEnergy

float CalcSolvationEnergy()

Returns the solvation energy in kT of the molecule that has been set. This result does not include an area term.

ClearFocusTarget

void ClearFocusTarget()

Clears the target setting for focusing.

GetBoundarySpacing

float GetBoundarySpacing() const

Returns the boundary spacing setting, which is the amount of distance between the molecule and the edge of the grid. The default setting is 4.0.

GetDielectricModel

unsigned int GetDielectricModel() const

Returns an int representing the dielectric model being used. The two available models are OEZapDielectricModel.Gaussian and OEZapDielectricModel.Molecular.

GetError

float GetError() const

Returns the error setting. See OEZap.SetError.

GetFocusTarget

const OEChem::OEMolBase *GetFocusTarget() const

Returns a pointer to the molecule that has been set as the focus target.

GetGridSpacing

float GetGridSpacing() const

Returns the setting for the grid spacing. The default value is 0.5.

GetInnerDielectric

float GetInnerDielectric() const

Returns the setting for the internal dielectric constant. The default value is 1.0.

GetIterations

unsigned int GetIterations() const

Returns the maximum number of iterations allowed for the zap calculation. The default value is 10.

GetMolecule

const OEChem::OEMolBase *GetMolecule() const

Returns a pointer to the molecule that has been set to Zap.

GetOuterDielectric

float GetOuterDielectric() const

Returns the setting for the outer dielectric constant. The default value is 80.0.

GetProbeRadius

float GetProbeRadius() const

Returns the setting for the probe radius. The default value is 1.4.

GetVerbose

bool GetVerbose() const

Returns the setting for very low-level verbosity. The default value is false.

GetSaltConcentration

float GetSaltConcentration() const

Returns the setting for the salt concentration. The default value is 0.0.

IsFocusTargetSet

bool IsFocusTargetSet()

Returns a bool for whether the focus target is currently set. See the section of focusing for more information.

SetBoundarySpacing

bool SetBoundarySpacing(float spacing)

Sets the boundary spacing, which is the amount of distance between the molecule and the edge of the grid. The default setting is 4.0.

SetDielectricModel

bool SetDielectricModel(unsigned int model)

Sets the dielectric model. The two available models are OEZapDielectricModel.Gaussian and OEZapDielectricModel.Molecular. The default is the Gaussian model.

SetError

bool SetError(float zaperr)

Rather than setting the grid spacing, the acceptable error may be set instead using this method. The default value is set to 0.0, which means that the grid spacing is set explicitly.

SetFocusTarget

bool SetFocusTarget(const OEChem::OEMolBase &mol)

Sets the focus target. See the section of Focusing for more information.

SetGridSpacing

bool SetGridSpacing(float spacing)

Sets the grid spacing. The default value is 0.5.

SetInnerDielectric

bool SetInnerDielectric(float epsin)

Sets the internal dielectric constant. The default value is 1.0.

SetIterations

bool SetIterations(unsigned int iters)

Sets the maximum number of iterations allowed for the zap calculation. The default value is 10

SetMolecule

bool SetMolecule(const OEChem::OEMolBase &mol)

Sets the molecule to Zap. Partial charges, 3-D coordinates, and radii need to be set to the molecule before the molecule is set to Zap.

SetOuterDielectric

bool SetOuterDielectric(float epsout)

Sets the external dielectric constant. The default value is 80.0.

SetProbeRadius

bool SetProbeRadius(float radius)

Sets the probe radius, the default value is 1.4.

SetSaltConcentration

bool SetSaltConcentration(float conc)

Sets the salt concentration. The default value is 0.0.

SetVerbose

bool SetVerbose(bool verbose)

Sets very low-level verbosity. The default value is false.