75 |
|
|
76 |
|
Design patterns are optimal solutions to commonly-occurring problems |
77 |
|
in software design. Although they originated as an architectural |
78 |
< |
concept for buildings and towns by Christopher Alexander |
79 |
< |
\cite{Alexander1987}, design patterns first became popular in |
80 |
< |
software engineering with the wide acceptance of the book, Design |
81 |
< |
Patterns: Elements of Reusable Object-Oriented Software |
82 |
< |
\cite{Gamma1994}. Patterns reflect the experience, knowledge and |
83 |
< |
insights of developers who have successfully used these patterns in |
84 |
< |
their own work. Patterns are reusable. They provide a ready-made |
78 |
> |
concept for buildings and towns by Christopher |
79 |
> |
Alexander,\cite{Alexander1987} design patterns first became popular |
80 |
> |
in software engineering with the wide acceptance of the book, Design |
81 |
> |
Patterns: Elements of Reusable Object-Oriented |
82 |
> |
Software.\cite{Gamma1994} Patterns reflect the experience, knowledge |
83 |
> |
and insights of developers who have successfully used these patterns |
84 |
> |
in their own work. Patterns are reusable. They provide a ready-made |
85 |
|
solution that can be adapted to different problems as necessary. As |
86 |
|
one of the latest advanced techniques to emerge from object-oriented |
87 |
|
community, design patterns were applied in some of the modern |
88 |
|
scientific software applications, such as JMol, {\sc |
89 |
< |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}. |
90 |
< |
The following sections enumerates some of the patterns |
91 |
< |
used in {\sc OOPSE}. |
89 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004}. The |
90 |
> |
following sections enumerates some of the patterns used in {\sc |
91 |
> |
OOPSE}. |
92 |
|
|
93 |
|
\subsection{\label{appendixSection:singleton}Singletons} |
94 |
|
|
133 |
|
structure of a Visitor pattern which is used extensively in {\tt |
134 |
|
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
135 |
|
distinct operations are performed on different StuntDoubles (See the |
136 |
< |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the |
137 |
< |
declaration in Scheme.~\ref{appendixScheme:element}). Since the |
138 |
< |
hierarchies remain stable, it is easy to define a visit operation |
139 |
< |
(see Scheme.~\ref{appendixScheme:visitor}) for each class of |
140 |
< |
StuntDouble. Note that by using the Composite |
141 |
< |
pattern\cite{Gamma1994}, CompositeVisitor manages a priority visitor |
142 |
< |
list and handles the execution of every visitor in the priority list |
143 |
< |
on different StuntDoubles. |
136 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
137 |
> |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
138 |
> |
remain stable, it is easy to define a visit operation (see |
139 |
> |
Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
140 |
> |
Note that by using the Composite pattern,\cite{Gamma1994} |
141 |
> |
CompositeVisitor manages a priority visitor list and handles the |
142 |
> |
execution of every visitor in the priority list on different |
143 |
> |
StuntDoubles. |
144 |
|
|
145 |
|
\begin{figure} |
146 |
|
\centering |
668 |
|
|
669 |
|
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
670 |
|
which can be opened by other molecular dynamics viewers such as Jmol |
671 |
< |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
671 |
> |
and VMD.\cite{Humphrey1996} The options available for Dump2XYZ are |
672 |
|
as follows: |
673 |
|
|
674 |
|
\begin{longtable}[c]{|EFG|} |