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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 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.

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Am I reading this right, you have chemical formulas and want to get a set of 3D coordinates (of the energy-minimized conformation)? – Mad Scientist Mar 11 '13 at 10:12
@MadScientist yes that's correct but its not possible for all molecules just some – user1357 Mar 12 '13 at 5:03
up vote 3 down vote accepted

Did you try to use Bioclipse:

Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. Bioclipse supports editing in 2D, processing large collections of molecules in tables, calculation of various types of properties, and much more cheminformatics functionality. The Jmol application is integrated in Bioclipse as an editor, and provides advanced interactive 3D visualizations.

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