OEGet2dPSAΒΆ

bool OEGet2dPSA(const OEChem::OEMolBase &mol, float &psa, float *atomPSA=0,
                bool SandP=false)

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

  // declare an array for atom values
  float * atomPSA = new float[mol.GetMaxAtomIdx()];
  float psa;
  OEGet2dPSA(mol, psa, atomPSA);

  std::cout << "PSA = " << psa << std::endl;
  for (OEIter<OEAtomBase> atom=mol.GetAtoms();atom;++atom)
  {
    unsigned int idx = atom->GetIdx();
    std::cout << idx << " " << atomPSA[idx] << std::endl;
  }

  // clean up
  delete [] atomPSA;
../../_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