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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (version 1.7.0_03) on Sun Jun 24 05:11:54 UTC 2012 -->
<title>All Classes</title>
<meta name="date" content="2012-06-24">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
</head>
<body>
<h1 class="bar">All Classes</h1>
<div class="indexContainer">
<ul>
<li><a href="jgromacs/data/Alignment.html" title="class in jgromacs.data" target="classFrame">Alignment</a></li>
<li><a href="jgromacs/data/Angle.html" title="class in jgromacs.data" target="classFrame">Angle</a></li>
<li><a href="jgromacs/analysis/Angles.html" title="class in jgromacs.analysis" target="classFrame">Angles</a></li>
<li><a href="jgromacs/ui/Application.html" title="class in jgromacs.ui" target="classFrame">Application</a></li>
<li><a href="jgromacs/data/Atom.html" title="class in jgromacs.data" target="classFrame">Atom</a></li>
<li><a href="jgromacs/db/AtomType.html" title="class in jgromacs.db" target="classFrame">AtomType</a></li>
<li><a href="jgromacs/analysis/Distances.html" title="class in jgromacs.analysis" target="classFrame">Distances</a></li>
<li><a href="jgromacs/analysis/Dynamics.html" title="class in jgromacs.analysis" target="classFrame">Dynamics</a></li>
<li><a href="jgromacs/data/FrameIndexSet.html" title="class in jgromacs.data" target="classFrame">FrameIndexSet</a></li>
<li><a href="jgromacs/analysis/GNM.html" title="class in jgromacs.analysis" target="classFrame">GNM</a></li>
<li><a href="jgromacs/data/IndexSet.html" title="class in jgromacs.data" target="classFrame">IndexSet</a></li>
<li><a href="jgromacs/data/IndexSetList.html" title="class in jgromacs.data" target="classFrame">IndexSetList</a></li>
<li><a href="jgromacs/io/IOData.html" title="class in jgromacs.io" target="classFrame">IOData</a></li>
<li><a href="jgromacs/io/IOMath.html" title="class in jgromacs.io" target="classFrame">IOMath</a></li>
<li><a href="jgromacs/data/Point3D.html" title="class in jgromacs.data" target="classFrame">Point3D</a></li>
<li><a href="jgromacs/data/PointList.html" title="class in jgromacs.data" target="classFrame">PointList</a></li>
<li><a href="jgromacs/data/Residue.html" title="class in jgromacs.data" target="classFrame">Residue</a></li>
<li><a href="jgromacs/db/ResidueType.html" title="class in jgromacs.db" target="classFrame">ResidueType</a></li>
<li><a href="jgromacs/data/Sequence.html" title="class in jgromacs.data" target="classFrame">Sequence</a></li>
<li><a href="jgromacs/data/SequencePosition.html" title="class in jgromacs.data" target="classFrame">SequencePosition</a></li>
<li><a href="jgromacs/analysis/Similarity.html" title="class in jgromacs.analysis" target="classFrame">Similarity</a></li>
<li><a href="jgromacs/data/Structure.html" title="class in jgromacs.data" target="classFrame">Structure</a></li>
<li><a href="jgromacs/analysis/Superposition.html" title="class in jgromacs.analysis" target="classFrame">Superposition</a></li>
<li><a href="jgromacs/ui/TemplateApplication.html" title="class in jgromacs.ui" target="classFrame">TemplateApplication</a></li>
<li><a href="jgromacs/data/Trajectory.html" title="class in jgromacs.data" target="classFrame">Trajectory</a></li>
</ul>
</div>
</body>
</html>