Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas.
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convertl effect is very good, but there are some problems in converting to *.xyz file.
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The Chemistry Development Kit (CDK) is a Java library for bio- and chemoInformatics and computational chemistry. It is the basis of other projects like JChemPaint, SENECA and NMRShiftDB, and used in many, many other projects.
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