avogadro : Advanced molecular editor that uses Qt4 and OpenGL ( http://avogadro.openmolecules.net/ )
avogadro2 : Advanced molecule editor and visualizer 2 ( http://www.openchemistry.org/ )
marvin : A free molecule editor written in Java ( https://www.chemaxon.com/download/marvin-suite/#marvin )
Add an ebuild in portage :
The ebuild is now in the portage tree.
You can also use layman : emerge layman then layman -a fusion809
For Paludis use this rsync : rsync://gentoo.zugaina.org/fusion809-portage
If you have a problem : ycarus(-at-)zugaina.org