JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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Chemical Descriptors Library (CDL)
CDL provides a generic C++ framework to write algorithms for the calculation of molecular descriptors. CDL provides efficient substructure search, fingerprints and pharmacophore algorithms, and many more for the calculation molecular descriptors.
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