Victor
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The Victor library (Virtual Construction Toolkit for Proteins) is an open-source project dedicated to providing tools for analyzing and manipulating protein structures. It contains methods that will allow you to representate one aminoacidic string in a efficient way.
For a general introduction, tutorial and usage examples please visit the following wiki http://protein.bio.unipd.it/victor
In the Victor wiki you will also find instructions to run the implemented Unit tests.