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As one of the latest advanced techniques emerged from |
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object-oriented community, design patterns were applied in some of |
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the modern scientific software applications, such as JMol, {\sc |
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OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
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The following sections enumerates some of the patterns used in {\sc |
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OOPSE}. |
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OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005} |
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\textit{etc}. The following sections enumerates some of the patterns |
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used in {\sc OOPSE}. |
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|
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\subsection{\label{appendixSection:singleton}Singleton} |
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|
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diagram of Visitor patten.} \label{appendixFig:visitorUML} |
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\end{figure} |
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|
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%\begin{figure} |
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%\centering |
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%\includegraphics[width=\linewidth]{hierarchy.eps} |
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%\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
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%the class hierarchy. |
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%\begin{itemize} |
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%\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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%integrators and minimizers. |
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%\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
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%\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
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%\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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%DirectionalAtom}s which behaves as a single unit. |
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%\end{itemize} |
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%} \label{oopseFig:hierarchy} |
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%\end{figure} |
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{hierarchy.eps} |
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\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
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the class hierarchy. } \label{oopseFig:hierarchy} |
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\end{figure} |
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|
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\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
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|
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on the specifics of the simulation). The names of rigid bodies are |
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generated automatically. For example, the name of the first rigid |
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body in a DMPC molecule is DMPC\_RB\_0. |
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\begin{itemize} |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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+ |
integrators and minimizers. |
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+ |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
372 |
+ |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
373 |
+ |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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+ |
DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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|
|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
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The most general form of the select command is: {\tt select {\it |
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expression}}. This expression represents an arbitrary set of |
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StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
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composed of either name expressions, index expressions, predefined |
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sets, user-defined expressions, comparison operators, within |
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expressions, or logical combinations of the above expression types. |
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< |
Expressions can be combined using parentheses and the Boolean |
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< |
operators. |
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> |
{\sc OOPSE} provides a powerful selection utility to select |
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StuntDoubles. The most general form of the select command is: |
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|
|
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{\tt select {\it expression}}. |
383 |
+ |
|
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This expression represents an arbitrary set of StuntDoubles (Atoms |
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+ |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
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+ |
name expressions, index expressions, predefined sets, user-defined |
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+ |
expressions, comparison operators, within expressions, or logical |
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+ |
combinations of the above expression types. Expressions can be |
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+ |
combined using parentheses and the Boolean operators. |
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|
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\subsection{\label{appendixSection:logical}Logical expressions} |
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|
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The logical operators allow complex queries to be constructed out of |