Dear All

I have a problem I'm trying to solve, and I'm not having much luck on my own.

I have a library of compounds based on a common scaffold that I have docked into a receptor. I would like to be able to calculate a solvent accesibility for a particular atom in the docked ligand structures. My problem is how to identify the atom of interest when atom naming is not consistent. Would this be a job for the Perl molecular toolkit?

Any ideas would be welcome.

Regards
Hassan