\hypertarget{subopt_8h}{
\section{H/subopt.h File Reference}
\label{subopt_8h}\index{H/subopt.h@{H/subopt.h}}
}


RNAsubopt and density of states declarations.  
Include dependency graph for subopt.h:\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{subopt_8h_ac7f749cb177da547798509ebe021884c}{subopt} (char $\ast$seq, char $\ast$sequence, int delta, FILE $\ast$fp)
\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \item\end{DoxyCompactList}\item 
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{subopt_8h_a8634516e4740e0b6c9a46d2bae940340}{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{subopt_8h_a873cf8ed69e0437f8efa8b1fec854a0e}{
int \hyperlink{subopt_8h_a873cf8ed69e0437f8efa8b1fec854a0e}{subopt\_\-sorted}}
\label{subopt_8h_a873cf8ed69e0437f8efa8b1fec854a0e}

\begin{DoxyCompactList}\small\item\em Sort output by energy. \item\end{DoxyCompactList}\item 
\hypertarget{subopt_8h_a5e57d914bcb5feeecdf520e25313fcfe}{
double \hyperlink{subopt_8h_a5e57d914bcb5feeecdf520e25313fcfe}{print\_\-energy}}
\label{subopt_8h_a5e57d914bcb5feeecdf520e25313fcfe}

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


\subsection{Detailed Description}
RNAsubopt and density of states declarations. 

\subsection{Function Documentation}
\hypertarget{subopt_8h_ac7f749cb177da547798509ebe021884c}{
\index{subopt.h@{subopt.h}!subopt@{subopt}}
\index{subopt@{subopt}!subopt.h@{subopt.h}}
\subsubsection[{subopt}]{\setlength{\rightskip}{0pt plus 5cm}{\bf SOLUTION}$\ast$ subopt (char $\ast$ {\em seq}, \/  char $\ast$ {\em sequence}, \/  int {\em delta}, \/  FILE $\ast$ {\em fp})}}
\label{subopt_8h_ac7f749cb177da547798509ebe021884c}


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

\end{DoxyReturn}
\hypertarget{subopt_8h_a8634516e4740e0b6c9a46d2bae940340}{
\index{subopt.h@{subopt.h}!subopt\_\-circ@{subopt\_\-circ}}
\index{subopt\_\-circ@{subopt\_\-circ}!subopt.h@{subopt.h}}
\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{subopt_8h_a8634516e4740e0b6c9a46d2bae940340}


Returns list of circular subopt structures or writes to fp. This function is similar to \hyperlink{subopt_8h_ac7f749cb177da547798509ebe021884c}{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}
