OEGet2dPSA¶

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

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

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)

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)