--- trunk/tengDissertation/Appendix.tex	2006/06/08 20:10:36	2828
+++ trunk/tengDissertation/Appendix.tex	2006/06/08 20:24:39	2829
@@ -290,23 +290,26 @@ class RigidBody: public StuntDouble {
 };
 
 \end{lstlisting}
-\section{\label{appendixSection:concepts}Concepts}
 
-\begin{figure}
-\centering
-\includegraphics[width=\linewidth]{heirarchy.eps}
-\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class
-heirarchy of StuntDoubles in {\sc OOPSE}.}
-\label{oopseFig:heirarchy}
-\end{figure}
+\section{\label{appendixSection:concepts}Concepts}
 
 OOPSE manipulates both traditional atoms as well as some objects
 that {\it behave like atoms}.  These objects can be rigid
 collections of atoms or atoms which have orientational degrees of
 freedom.  A diagram of the class heirarchy is illustrated in
-Fig.~\ref{oopseFig:heirarchy}.
-
-
+Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and
+DirectionalAtom in {\sc OOPSE} have their own names which are
+specified in the {\tt .md} file. In contrast, RigidBodies are
+denoted by their membership and index inside a particular molecule:
+[MoleculeName]\_RB\_[index] (the contents inside the brackets depend
+on the specifics of the simulation). The names of rigid bodies are
+generated automatically. For example, the name of the first rigid
+body in a DMPC molecule is DMPC\_RB\_0.
+\begin{figure}
+\centering
+\includegraphics[width=\linewidth]{heirarchy.eps}
+\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class
+heirarchy of StuntDoubles in {\sc OOPSE}.
 \begin{itemize}
 \item A {\bf StuntDouble} is {\it any} object that can be manipulated by the
 integrators and minimizers.
@@ -315,14 +318,8 @@ DirectionalAtom}s which behaves as a single unit.
 \item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf
 DirectionalAtom}s which behaves as a single unit.
 \end{itemize}
-
-Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their
-own names which are specified in the {\tt .md} file. In contrast,
-RigidBodies are denoted by their membership and index inside a
-particular molecule: [MoleculeName]\_RB\_[index] (the contents
-inside the brackets depend on the specifics of the simulation). The
-names of rigid bodies are generated automatically. For example, the
-name of the first rigid body in a DMPC molecule is DMPC\_RB\_0.
+} \label{oopseFig:heirarchy}
+\end{figure}
 
 \section{\label{appendixSection:syntax}Syntax of the Select Command}