Dear Rdkit Team,

I wonder whether you can advise me as to how best approach calculating apolar 
surface area (APSA) and the fraction that this contributes towards the total 
surface area, please?

(I am happy with topological approximations of atomic contributions.)

At first, I thought this might be achieved via identifying the indices of 
apolar atoms based on zero contributions to _CalcTPSAContribs(mol) and then 
summing the atomic contributions to the surface area for those apolar atoms, to 
give APSA, which could then be divided by the summation over all atoms to give 
the fractional value.

However, as far as I can see, it is not possible to obtain the corresponding 
atomic contributions to surface area for all atoms - at least not in Python.

The values returned via _CalcLabuteASAContribs(mol) do not appear consistent 
with the non-zero _CalcTPSAContribs(mol) for the examples I have looked at.

Please excuse me if I am overlooking something here.

Best regards,


Check out the vibrant tech community on one of the world's most
engaging tech sites,!
Rdkit-discuss mailing list

Reply via email to