There are quite a lot libraries that can be used in chemoinformatics. In Python one should mention
- Open Babel, http://openbabel.org/wiki/Main_Page
For people in the Computational/Quantum chemistry this library is usually connected with molecular file conversion. But it offers a lot more. The library is natively written in C++, but it has a very convenient SWIG wrapping that makes it available from Python and Perl.