OWL Java library for Structural Bioinformatics
OWL is a Java library and a set of command line tools for the analysis of biological macromolecules. It provides functionality for analysing protein sequences and structures using built-in algorithms and interfaces to external tools. Particular emphasis is put on the analysis of proteins as contact graphs.
A lot of the functionality in OWL has now been ported to the https://github.com/biojava/biojava project and it is available in Biojava 4.0 and newer releases.