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MayaChemTools - MayaChemTools provides a variety of scripts - some straightforward and others a bit more involved - to work with SD files, CSV/TSV text files, and databases: splitting, joining, merging, and sorting SD and text files; merging text files into SD files; splitting SD files into MDL MOL files; generating HTML files from SD and text files; exporting data from MySQL and Oracle tables into text files.
xeo - xeo is a free (GPL) open project management for nanostructures using Java
Java CML Filter Library (JCFL) - Java import and export filters to convert CML to and from various internal formats for display
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