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% API Documentation for nMOLDYN
% Package nMOLDYN
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% Generated by epydoc 3.0.1
% [Thu Oct  8 16:59:58 2009]
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    \index{nMOLDYN \textit{(package)}|(}
\section{Package nMOLDYN}

    \label{nMOLDYN}

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%%                                Modules                                %%
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\subsection{Modules}

\begin{itemize}
\setlength{\parskip}{0ex}
\item \textbf{Analysis}
  \textit{(Section \ref{nMOLDYN:Analysis}, p.~\pageref{nMOLDYN:Analysis})}

  \begin{itemize}
\setlength{\parskip}{0ex}
    \item \textbf{Analysis}: This modules implements the base class for all the analysis available in 
nMOLDYN.



  \textit{(Section \ref{nMOLDYN:Analysis:Analysis}, p.~\pageref{nMOLDYN:Analysis:Analysis})}

    \item \textbf{Dynamics}: Collections of classes for the determination of dynamics-related properties.



  \textit{(Section \ref{nMOLDYN:Analysis:Dynamics}, p.~\pageref{nMOLDYN:Analysis:Dynamics})}

    \item \textbf{NMR}: Collections of classes for the determination of NMR-related properties.



  \textit{(Section \ref{nMOLDYN:Analysis:NMR}, p.~\pageref{nMOLDYN:Analysis:NMR})}

    \item \textbf{Scattering}: Collections of classes for the determination of scattering-related properties.



  \textit{(Section \ref{nMOLDYN:Analysis:Scattering}, p.~\pageref{nMOLDYN:Analysis:Scattering})}

    \item \textbf{Slave}: This modules contains the functions used by Pyro slave to perform analysis remotely.



  \textit{(Section \ref{nMOLDYN:Analysis:Slave}, p.~\pageref{nMOLDYN:Analysis:Slave})}

    \item \textbf{Structure}: Collections of classes for the determination of structure-related properties.



  \textit{(Section \ref{nMOLDYN:Analysis:Structure}, p.~\pageref{nMOLDYN:Analysis:Structure})}

    \item \textbf{Template}: This modules implements the estimate, serial and parrallel templates for 
all analysis.



  \textit{(Section \ref{nMOLDYN:Analysis:Template}, p.~\pageref{nMOLDYN:Analysis:Template})}

  \end{itemize}
\item \textbf{Core}
  \textit{(Section \ref{nMOLDYN:Core}, p.~\pageref{nMOLDYN:Core})}

  \begin{itemize}
\setlength{\parskip}{0ex}
    \item \textbf{Chemistry}: This modules implements the functions and procedures that are related to chemistry.



  \textit{(Section \ref{nMOLDYN:Core:Chemistry}, p.~\pageref{nMOLDYN:Core:Chemistry})}

    \item \textbf{Config}: 
This modules implements the procedures that handles nMOLDYN PREFERENCES.



  \textit{(Section \ref{nMOLDYN:Core:Config}, p.~\pageref{nMOLDYN:Core:Config})}

    \item \textbf{Error}
  \textit{(Section \ref{nMOLDYN:Core:Error}, p.~\pageref{nMOLDYN:Core:Error})}

    \item \textbf{IOFiles}: This module implements IO-related classes, functions and procedures.



  \textit{(Section \ref{nMOLDYN:Core:IOFiles}, p.~\pageref{nMOLDYN:Core:IOFiles})}

    \item \textbf{Logger}: This module implements the classes used to handle the nMOLDYN logger.



  \textit{(Section \ref{nMOLDYN:Core:Logger}, p.~\pageref{nMOLDYN:Core:Logger})}

    \item \textbf{Mathematics}: This modules implements the mathematics-related classes, functions and procedures.



  \textit{(Section \ref{nMOLDYN:Core:Mathematics}, p.~\pageref{nMOLDYN:Core:Mathematics})}

    \item \textbf{Misc}: This modules implements the functions and procedures that can not be classified anywhere else in 
the library.



  \textit{(Section \ref{nMOLDYN:Core:Misc}, p.~\pageref{nMOLDYN:Core:Misc})}

    \item \textbf{Preferences}: This modules stores some the nMOLDYN PREFERENCES variables that will be 
used throughout all nMOLDYN code.



  \textit{(Section \ref{nMOLDYN:Core:Preferences}, p.~\pageref{nMOLDYN:Core:Preferences})}

  \end{itemize}
\item \textbf{GUI}
  \textit{(Section \ref{nMOLDYN:GUI}, p.~\pageref{nMOLDYN:GUI})}

  \begin{itemize}
\setlength{\parskip}{0ex}
    \item \textbf{ASCIIToNetCDFConversionDialog}: This modules implements I\{File--{\textgreater}Convert ASCII to NetCDF\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:ASCIIToNetCDFConversionDialog}, p.~\pageref{nMOLDYN:GUI:ASCIIToNetCDFConversionDialog})}

    \item \textbf{AnalysisBenchmarkDialog}: This modules implements I\{Help--{\textgreater}nMOLDYN benchmark\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:AnalysisBenchmarkDialog}, p.~\pageref{nMOLDYN:GUI:AnalysisBenchmarkDialog})}

    \item \textbf{AnalysisDialog}: This modules implements I\{Analysis--{\textgreater}selected analysis\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:AnalysisDialog}, p.~\pageref{nMOLDYN:GUI:AnalysisDialog})}

    \item \textbf{AnimationDialog}: This modules implements I\{View--{\textgreater}Animation\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:AnimationDialog}, p.~\pageref{nMOLDYN:GUI:AnimationDialog})}

    \item \textbf{CheckJobsStatusDialog}: This modules implements I\{Help--{\textgreater}Check job status\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:CheckJobsStatusDialog}, p.~\pageref{nMOLDYN:GUI:CheckJobsStatusDialog})}

    \item \textbf{GeneralInformationsDialog}: This modules implements I\{Help--{\textgreater}About nMOLDYN\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:GeneralInformationsDialog}, p.~\pageref{nMOLDYN:GUI:GeneralInformationsDialog})}

    \item \textbf{HTMLReader}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader}, p.~\pageref{nMOLDYN:GUI:HTMLReader})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{mfxtools}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:mfxtools}, p.~\pageref{nMOLDYN:GUI:HTMLReader:mfxtools})}

        \item \textbf{mfxutil}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:mfxutil}, p.~\pageref{nMOLDYN:GUI:HTMLReader:mfxutil})}

        \item \textbf{tkconst}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkconst}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkconst})}

        \item \textbf{tkfont}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkfont}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkfont})}

        \item \textbf{tkhtml}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkhtml}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkhtml})}

        \item \textbf{tkinit}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkinit}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkinit})}

        \item \textbf{tkutil}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkutil}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkutil})}

        \item \textbf{tkwidget}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:tkwidget}, p.~\pageref{nMOLDYN:GUI:HTMLReader:tkwidget})}

        \item \textbf{util}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:util}, p.~\pageref{nMOLDYN:GUI:HTMLReader:util})}

        \item \textbf{version}
  \textit{(Section \ref{nMOLDYN:GUI:HTMLReader:version}, p.~\pageref{nMOLDYN:GUI:HTMLReader:version})}

      \end{itemize}
    \item \textbf{MainDialog}: This is where the main window of nMOLDYN is defined.



  \textit{(Section \ref{nMOLDYN:GUI:MainDialog}, p.~\pageref{nMOLDYN:GUI:MainDialog})}

    \item \textbf{NetCDFToASCIIConversionDialog}: This modules implements I\{File--{\textgreater}Convert NetCDF to ASCII\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:NetCDFToASCIIConversionDialog}, p.~\pageref{nMOLDYN:GUI:NetCDFToASCIIConversionDialog})}

    \item \textbf{PDBSnapshotGeneratorDialog}: This modules implements I\{File--{\textgreater}Frame snapshot\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:PDBSnapshotGeneratorDialog}, p.~\pageref{nMOLDYN:GUI:PDBSnapshotGeneratorDialog})}

    \item \textbf{PlotNetCDFVariableDialog}: This modules implements I\{View--{\textgreater}Plot\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:PlotNetCDFVariableDialog}, p.~\pageref{nMOLDYN:GUI:PlotNetCDFVariableDialog})}

    \item \textbf{PreferencesDialog}: This modules implements I\{File--{\textgreater}Preferences\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:PreferencesDialog}, p.~\pageref{nMOLDYN:GUI:PreferencesDialog})}

    \item \textbf{PyroServerDialog}: This modules implements I\{View--{\textgreater}Animation\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:PyroServerDialog}, p.~\pageref{nMOLDYN:GUI:PyroServerDialog})}

    \item \textbf{SelectionDialog}: This modules implements the atom selection dialog used in almost all nMOLDYN analysis.



  \textit{(Section \ref{nMOLDYN:GUI:SelectionDialog}, p.~\pageref{nMOLDYN:GUI:SelectionDialog})}

    \item \textbf{Tags}
  \textit{(Section \ref{nMOLDYN:GUI:Tags}, p.~\pageref{nMOLDYN:GUI:Tags})}

    \item \textbf{TrajectoryConversionDialog}: This modules implements I\{File --{\textgreater} Trajectory conversion --{\textgreater} converter\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:TrajectoryConversionDialog}, p.~\pageref{nMOLDYN:GUI:TrajectoryConversionDialog})}

    \item \textbf{ViewEffectiveModeDialog}: This modules implements I\{View --{\textgreater} Effective Mode\} dialog.



  \textit{(Section \ref{nMOLDYN:GUI:ViewEffectiveModeDialog}, p.~\pageref{nMOLDYN:GUI:ViewEffectiveModeDialog})}

    \item \textbf{Widgets}: This module implements all classes used for the generation of combo widgets. 


  \textit{(Section \ref{nMOLDYN:GUI:Widgets}, p.~\pageref{nMOLDYN:GUI:Widgets})}

  \end{itemize}
\item \textbf{Tests}
  \textit{(Section \ref{nMOLDYN:Tests}, p.~\pageref{nMOLDYN:Tests})}

  \begin{itemize}
\setlength{\parskip}{0ex}
    \item \textbf{ARA}
  \textit{(Section \ref{nMOLDYN:Tests:ARA}, p.~\pageref{nMOLDYN:Tests:ARA})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:ARA:TestsContents}, p.~\pageref{nMOLDYN:Tests:ARA:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:ARA:runTests}, p.~\pageref{nMOLDYN:Tests:ARA:runTests})}

      \end{itemize}
    \item \textbf{AVACF}
  \textit{(Section \ref{nMOLDYN:Tests:AVACF}, p.~\pageref{nMOLDYN:Tests:AVACF})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:AVACF:TestsContents}, p.~\pageref{nMOLDYN:Tests:AVACF:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:AVACF:runTests}, p.~\pageref{nMOLDYN:Tests:AVACF:runTests})}

      \end{itemize}
    \item \textbf{AnalysisTests}: Test cases for analysis modules.



  \textit{(Section \ref{nMOLDYN:Tests:AnalysisTests}, p.~\pageref{nMOLDYN:Tests:AnalysisTests})}

    \item \textbf{BuildTestCases}
  \textit{(Section \ref{nMOLDYN:Tests:BuildTestCases}, p.~\pageref{nMOLDYN:Tests:BuildTestCases})}

    \item \textbf{DCSF}
  \textit{(Section \ref{nMOLDYN:Tests:DCSF}, p.~\pageref{nMOLDYN:Tests:DCSF})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:DCSF:TestsContents}, p.~\pageref{nMOLDYN:Tests:DCSF:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:DCSF:runTests}, p.~\pageref{nMOLDYN:Tests:DCSF:runTests})}

      \end{itemize}
    \item \textbf{DISF}
  \textit{(Section \ref{nMOLDYN:Tests:DISF}, p.~\pageref{nMOLDYN:Tests:DISF})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:DISF:TestsContents}, p.~\pageref{nMOLDYN:Tests:DISF:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:DISF:runTests}, p.~\pageref{nMOLDYN:Tests:DISF:runTests})}

      \end{itemize}
    \item \textbf{DISFG}
  \textit{(Section \ref{nMOLDYN:Tests:DISFG}, p.~\pageref{nMOLDYN:Tests:DISFG})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:DISFG:TestsContents}, p.~\pageref{nMOLDYN:Tests:DISFG:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:DISFG:runTests}, p.~\pageref{nMOLDYN:Tests:DISFG:runTests})}

      \end{itemize}
    \item \textbf{DOS}
  \textit{(Section \ref{nMOLDYN:Tests:DOS}, p.~\pageref{nMOLDYN:Tests:DOS})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:DOS:TestsContents}, p.~\pageref{nMOLDYN:Tests:DOS:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:DOS:runTests}, p.~\pageref{nMOLDYN:Tests:DOS:runTests})}

      \end{itemize}
    \item \textbf{EISF}
  \textit{(Section \ref{nMOLDYN:Tests:EISF}, p.~\pageref{nMOLDYN:Tests:EISF})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:EISF:TestsContents}, p.~\pageref{nMOLDYN:Tests:EISF:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:EISF:runTests}, p.~\pageref{nMOLDYN:Tests:EISF:runTests})}

      \end{itemize}
    \item \textbf{MSD}
  \textit{(Section \ref{nMOLDYN:Tests:MSD}, p.~\pageref{nMOLDYN:Tests:MSD})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:MSD:TestsContents}, p.~\pageref{nMOLDYN:Tests:MSD:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:MSD:runTests}, p.~\pageref{nMOLDYN:Tests:MSD:runTests})}

      \end{itemize}
    \item \textbf{StabilityTests}: 
Test cases for stability of the current version of nMOLDYN versus nMoldyn v2.1.0, the last stable release 
of nMoldyn.



  \textit{(Section \ref{nMOLDYN:Tests:StabilityTests}, p.~\pageref{nMOLDYN:Tests:StabilityTests})}

    \item \textbf{VACF}
  \textit{(Section \ref{nMOLDYN:Tests:VACF}, p.~\pageref{nMOLDYN:Tests:VACF})}

      \begin{itemize}
    \setlength{\parskip}{0ex}
        \item \textbf{TestsContents}
  \textit{(Section \ref{nMOLDYN:Tests:VACF:TestsContents}, p.~\pageref{nMOLDYN:Tests:VACF:TestsContents})}

        \item \textbf{runTests}
  \textit{(Section \ref{nMOLDYN:Tests:VACF:runTests}, p.~\pageref{nMOLDYN:Tests:VACF:runTests})}

      \end{itemize}
  \end{itemize}
\item \textbf{\_\_pkginfo\_\_}
  \textit{(Section \ref{nMOLDYN:__pkginfo__}, p.~\pageref{nMOLDYN:__pkginfo__})}

\end{itemize}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%                               Variables                               %%
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  \subsection{Variables}

    \vspace{-1cm}
\hspace{\varindent}\begin{longtable}{|p{\varnamewidth}|p{\vardescrwidth}|l}
\cline{1-2}
\cline{1-2} \centering \textbf{Name} & \centering \textbf{Description}& \\
\cline{1-2}
\endhead\cline{1-2}\multicolumn{3}{r}{\small\textit{continued on next page}}\\\endfoot\cline{1-2}
\endlastfoot\raggedright n\-m\-o\-l\-d\-y\-n\-\_\-p\-a\-c\-k\-a\-g\-e\-\_\-p\-a\-t\-h\- & \raggedright \textbf{Value:} 
{\tt os.path.split(\_\_file\_\_) [0]}&\\
\cline{1-2}
\raggedright f\-i\-l\-e\-H\-a\-n\-d\-l\-e\-r\- & \raggedright \textbf{Value:} 
{\tt LogToFile(os.path.join(PREFERENCES.logfile\_path, 'nMOLDYN\texttt{...}}&\\
\cline{1-2}
\raggedright c\-o\-n\-s\-o\-l\-e\-H\-a\-n\-d\-l\-e\-r\- & \raggedright \textbf{Value:} 
{\tt LogToConsole()}&\\
\cline{1-2}
\raggedright d\-i\-a\-l\-o\-g\-H\-a\-n\-d\-l\-e\-r\- & \raggedright \textbf{Value:} 
{\tt LogToGUI()}&\\
\cline{1-2}
\end{longtable}

    \index{nMOLDYN \textit{(package)}|)}
