I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction are there any programs which will go from formula to structure with optimal geometry of random small chemicals say 30 atoms ? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a command line unix program which computes mols from formulas. 
thank you