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.