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% API Documentation for nMOLDYN
% Module nMOLDYN.Core.Chemistry
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    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}|(}
\section{Module nMOLDYN.Core.Chemistry}

    \label{nMOLDYN:Core:Chemistry}
\begin{alltt}
This modules implements the functions and procedures that are related to chemistry.

Functions:
    * belongToAnAmine  : this function determine whether or not {\textbar}atom{\textbar} is part of an amine group.
    * belongToAHydroxy : this function determine whether or not {\textbar}atom{\textbar} is part of a hydroxy group.
    * belongToAMethyl  : this function determine whether or not {\textbar}atom{\textbar} is part of a mathyl group.
    * belongToAThiol   : this function determine whether or not {\textbar}atom{\textbar} is part of a thiol group.
\end{alltt}


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  \subsection{Functions}

    \label{nMOLDYN:Core:Chemistry:belongToAMethyl}
    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}!nMOLDYN.Core.Chemistry.belongToAMethyl \textit{(function)}}

    \vspace{0.5ex}

\hspace{.8\funcindent}\begin{boxedminipage}{\funcwidth}

    \raggedright \textbf{belongToAMethyl}(\textit{atom})

    \vspace{-1.5ex}

    \rule{\textwidth}{0.5\fboxrule}
\setlength{\parskip}{2ex}
    This function determine whether or not {\textbar}atom{\textbar} is part
    of a methyl group.

\setlength{\parskip}{1ex}
    \end{boxedminipage}

    \label{nMOLDYN:Core:Chemistry:belongToAnAmine}
    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}!nMOLDYN.Core.Chemistry.belongToAnAmine \textit{(function)}}

    \vspace{0.5ex}

\hspace{.8\funcindent}\begin{boxedminipage}{\funcwidth}

    \raggedright \textbf{belongToAnAmine}(\textit{atom})

    \vspace{-1.5ex}

    \rule{\textwidth}{0.5\fboxrule}
\setlength{\parskip}{2ex}
    This function determine whether or not {\textbar}atom{\textbar} is part
    of an amine group.

\setlength{\parskip}{1ex}
    \end{boxedminipage}

    \label{nMOLDYN:Core:Chemistry:belongToAThiol}
    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}!nMOLDYN.Core.Chemistry.belongToAThiol \textit{(function)}}

    \vspace{0.5ex}

\hspace{.8\funcindent}\begin{boxedminipage}{\funcwidth}

    \raggedright \textbf{belongToAThiol}(\textit{atom})

    \vspace{-1.5ex}

    \rule{\textwidth}{0.5\fboxrule}
\setlength{\parskip}{2ex}
    This function determine whether or not {\textbar}atom{\textbar} is part
    of a thiol group.

\setlength{\parskip}{1ex}
    \end{boxedminipage}

    \label{nMOLDYN:Core:Chemistry:belongToAHydroxy}
    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}!nMOLDYN.Core.Chemistry.belongToAHydroxy \textit{(function)}}

    \vspace{0.5ex}

\hspace{.8\funcindent}\begin{boxedminipage}{\funcwidth}

    \raggedright \textbf{belongToAHydroxy}(\textit{atom})

    \vspace{-1.5ex}

    \rule{\textwidth}{0.5\fboxrule}
\setlength{\parskip}{2ex}
    This function determine whether or not {\textbar}atom{\textbar} is part
    of a hydroxy group.

\setlength{\parskip}{1ex}
    \end{boxedminipage}

    \index{nMOLDYN \textit{(package)}!nMOLDYN.Core \textit{(package)}!nMOLDYN.Core.Chemistry \textit{(module)}|)}
