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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Javaapplications.
Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.