OEZap

class OEZap

The principal interface for Poisson-Boltzmann electrostatics calculations. Stores a molecule and computes solvation energies, potential grids, and atomic potentials using an implicit solvent model. See OEZap.SetMolecule for molecule preparation requirements.

Constructors

OEZap() -> OEZap
OEZap(rhs: OEZap) -> OEZap

Default and copy constructors.

CalcAtomPotentials

CalcAtomPotentials(pot: OEFloatArray, no_grid: bool = False) -> bool

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

CalcForces(forces: OEFloatArray) -> bool

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

CalcPotentialGrid(grid: OEScalarGrid) -> bool

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

CalcSolvationEnergy() -> float

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

ClearFocusTarget

ClearFocusTarget() -> None

Clears the target setting for focusing.

GetBoundarySpacing

GetBoundarySpacing() -> float

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

GetDielectricModel() -> int

Returns an int representing the dielectric model being used. The two available models are OEZapDielectricModel_Gaussian and OEZapDielectricModel_Molecular.

GetError

GetError() -> float

Returns the error setting. See OEZap.SetError.

GetFocusTarget

GetFocusTarget() -> OEGraphMol

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

GetGridSpacing

GetGridSpacing() -> float

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

GetInnerDielectric

GetInnerDielectric() -> float

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

GetIterations

GetIterations() -> int

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

GetMolecule

GetMolecule() -> OEGraphMol

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

GetOuterDielectric

GetOuterDielectric() -> float

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

GetProbeRadius

GetProbeRadius() -> float

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

GetVerbose

GetVerbose() -> bool

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

GetSaltConcentration

GetSaltConcentration() -> float

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

IsFocusTargetSet

IsFocusTargetSet() -> bool

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

SetBoundarySpacing

SetBoundarySpacing(spacing: float) -> bool

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

SetDielectricModel(model: int) -> bool

Sets the dielectric model. The two available models are OEZapDielectricModel_Gaussian and OEZapDielectricModel_Molecular. The default is the Gaussian model.

SetError

SetError(zaperr: float) -> bool

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

SetFocusTarget(mol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

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

SetGridSpacing

SetGridSpacing(spacing: float) -> bool

Sets the grid spacing. The default value is 0.5.

SetInnerDielectric

SetInnerDielectric(epsin: float) -> bool

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

SetIterations

SetIterations(iters: int) -> bool

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

SetMolecule

SetMolecule(mol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

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

SetOuterDielectric(epsout: float) -> bool

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

SetProbeRadius

SetProbeRadius(radius: float) -> bool

Sets the probe radius, the default value is 1.4.

SetSaltConcentration

SetSaltConcentration(conc: float) -> bool

Sets the salt concentration. The default value is 0.0.

SetVerbose

SetVerbose(verbose: bool)

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