\hypertarget{group__subopt__wuchty}{
\section{Suboptimal structures within an energy band arround the MFE}
\label{group__subopt__wuchty}\index{Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the MFE}}
}


Collaboration diagram for Suboptimal structures within an energy band arround the MFE:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=272pt]{group__subopt__wuchty}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (char $\ast$seq, char $\ast$structure, int delta, FILE $\ast$fp)
\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \item\end{DoxyCompactList}\item 
\hypertarget{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\_\-par} (char $\ast$seq, char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int delta, int is\_\-constrained, int is\_\-circular, FILE $\ast$fp)}
\label{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}

\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \item\end{DoxyCompactList}\item 
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\_\-circ} (char $\ast$seq, char $\ast$sequence, int delta, FILE $\ast$fp)
\begin{DoxyCompactList}\small\item\em Returns list of circular subopt structures or writes to fp. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
\hypertarget{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{
int \hyperlink{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}{subopt\_\-sorted}}
\label{group__subopt__wuchty_ga873cf8ed69e0437f8efa8b1fec854a0e}

\begin{DoxyCompactList}\small\item\em Sort output by energy. \item\end{DoxyCompactList}\item 
\hypertarget{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{
double \hyperlink{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}{print\_\-energy}}
\label{group__subopt__wuchty_ga5e57d914bcb5feeecdf520e25313fcfe}

\begin{DoxyCompactList}\small\item\em printing threshold for use with logML \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Function Documentation}
\hypertarget{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{
\index{subopt\_\-wuchty@{subopt\_\-wuchty}!subopt@{subopt}}
\index{subopt@{subopt}!subopt_wuchty@{subopt\_\-wuchty}}
\subsubsection[{subopt}]{\setlength{\rightskip}{0pt plus 5cm}{\bf SOLUTION}$\ast$ subopt (char $\ast$ {\em seq}, \/  char $\ast$ {\em structure}, \/  int {\em delta}, \/  FILE $\ast$ {\em fp})}}
\label{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}


Returns list of subopt structures or writes to fp. This function produces {\bfseries all} suboptimal secondary structures within 'delta' $\ast$ 0.01 kcal/mol of the optimum. The results are either directly written to a 'fp' (if 'fp' is not NULL), or (fp==NULL) returned in a \hyperlink{structSOLUTION}{SOLUTION} $\ast$ list terminated by an entry were the 'structure' pointer is NULL.


\begin{DoxyParams}{Parameters}
\item[{\em seq}]\item[{\em structure}]\item[{\em delta}]\item[{\em fp}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{
\index{subopt\_\-wuchty@{subopt\_\-wuchty}!subopt\_\-circ@{subopt\_\-circ}}
\index{subopt\_\-circ@{subopt\_\-circ}!subopt_wuchty@{subopt\_\-wuchty}}
\subsubsection[{subopt\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}{\bf SOLUTION}$\ast$ subopt\_\-circ (char $\ast$ {\em seq}, \/  char $\ast$ {\em sequence}, \/  int {\em delta}, \/  FILE $\ast$ {\em fp})}}
\label{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}


Returns list of circular subopt structures or writes to fp. This function is similar to \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt()} but calculates secondary structures assuming the RNA sequence to be circular instead of linear


\begin{DoxyParams}{Parameters}
\item[{\em seq}]\item[{\em sequence}]\item[{\em delta}]\item[{\em fp}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
