OEGet2dPSAΒΆ

OEGet2dPSA(OEMolBase mol, OEFloatArray atomPSA=None, bool SandP=False) -> float

Returns the topological polar surface area for a given molecule as described in the Polar Surface Area section. The SandP parameter controls whether sulfur and phosphorus should be counted towards the total surface area. See example in Figure: Example of depicting the atom contributions of the polar surface area.

Warning

TPSA values are mildly sensitive to the protonation state of a molecule.

The atomPSA parameter can be used to retrieve the contribution of each atom to the total polar surface area as shown in Listing 1.

Listing 1: Example of retrieving individual atom contributions to PSA

atomPSA = OEFloatArray(mol.GetMaxAtomIdx())
psa = OEGet2dPSA(mol, atomPSA)

print("PSA =", psa)
for atom in mol.GetAtoms():
    idx = atom.GetIdx()
    print(idx, atomPSA[idx])
../../_images/OEGet2dPSA.png

Example of depicting the atom contributions of the polar surface area (ignoring S and P atoms)

(Darker colors and longer spikes indicate larger PSA atom contributions)
../../_images/OEGet2dPSA-SAndP.png

Example of depicting the atom contributions of the polar surface area (considering S and P atoms)

(Darker colors and longer spikes indicate larger PSA atom contributions)

See also

The Python script that visualizes the polar surface area of a molecule can be downloaded from the OpenEye Python Cookbook

See also

Polar Surface Area section