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Open Babel - The Open Source Chemistry Toolbox

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Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It is an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas.

It can
  • Read, write and convert over 90 chemical file formats
  • Filter and search molecular files using SMARTS and other methods
  • Supports molecular modeling, cheminformatics, bioinformatics
  • Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry
http://openbabel.org/wiki/
https://sourceforge.net/projects/openbabel/
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