OEArea¶
class OEArea
This class represents OEArea. OEArea is a simple object that calculates surface area using the same grid-based Gaussians that Zap uses. This class is mostly used for calculating the area term in solvation calculations or the buried area term in bind calculations.
GetArea¶
float GetArea(const OEChem::OEMolBase &mol)
bool GetArea(const OEChem::OEMolBase &mol, float *atomArea)
Calculate the surface area of the passed-in molecule. The first
version calculates the surface area of the entire molecule. The
second version takes an array sized by
OEMolBase::GetMaxAtomIdx
to return the contribution of each
atom to the total surface area.
Note that whether or not hydrogens are included in these calculations is
controlled by OEArea.SetUseHydrogens
which is set to false
by default.
The following demonstrates how to calculate the area of a molecule:
Example of calculating the surface area of a molecule
area = oezap.OEArea()
a = area.GetArea(mol)
print("Molecule area =", a)
The following demonstrates how to retrieve the individual atom contributions to the surface area:
Example of calculating the surface area contribution of individual atoms
atomArea = oechem.OEFloatArray(mol.GetMaxAtomIdx())
area = oezap.OEArea()
area.GetArea(mol, atomArea)
for atom in mol.GetAtoms():
idx = atom.GetIdx()
print(idx, atomArea[idx])
GetMethod¶
unsigned int GetMethod() const
Returns an int
indicating the method that is used to model
the area of the molecule. The two possible return values are
OEAreaMethod_Gaussian
and OEAreaMethod_Discrete
.
GetUseHydrogens¶
bool GetUseHydrogens() const
Returns a bool
where true
means explicit hydrogens are
turned on and false
means they are turned off for the area
calculation.
SetMethod¶
bool SetMethod(const unsigned int method)
Takes an int
with the value of
OEAreaMethod_Gaussian
of
OEAreaMethod_Discrete
SetUseHydrogens¶
bool SetUseHydrogens(bool state)
This method takes a bool
where true
turns on explicit
hydrogens for calculating area and false
turn them off.