I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but 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.
Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction. http://www.mti.univ-paris-diderot.fr/fr/downloads.html