Silicos provides shape-it - a C++ program for doing shape matching using gaussian volume.

To compile under Ubuntu 12.04:

sudo apt-get install libopenbabel-dev libopenbabel4 openbabel

export BABEL_INCLUDEDIR=/usr/include/openbabel-2.0/openbabel
export BABEL_LIBDIR=/usr/lib/openbabel/2.3.1/
export BABEL_DATADIR=/usr/share/openbabel/openbabel/2.3.1/