As I understood, you want to draw the chemical structures. You can use ChemSketch, ChemDraw, MarvinSketch, Sybyl in windows. In Linux, this would be easily done by Gabedit software. Chemsketch is free and you can download the freeware version from acdlabs website. Hope this will be helpful for you.
http://www.simbiosys.ca/caesa/ CAESA: Compter Assisted Estimation of Synthetic Accessibility is a paid software through which you can predict the possible ways of chemical synthesis of your compound. Also you can look for ChemAxon webhttp://www.chemaxon.com/ for their product list. They also have such activity software.