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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / group__subopt__wuchty.tex

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+\hypertarget{group__subopt__wuchty}{\section{Suboptimal structures within an energy band arround the M\-F\-E}
+\label{group__subopt__wuchty}\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}}
+}
+Collaboration diagram for Suboptimal structures within an energy band arround the M\-F\-E\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=348pt]{group__subopt__wuchty}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{subopt} (char $\ast$seq, char $\ast$structure, int delta, F\-I\-L\-E $\ast$fp)
+\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item 
+\hypertarget{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}{subopt\-\_\-par} (char $\ast$seq, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int delta, int is\-\_\-constrained, int is\-\_\-circular, F\-I\-L\-E $\ast$fp)}\label{group__subopt__wuchty_ga554dedfcdb249fdf151caade58666e4d}
+
+\begin{DoxyCompactList}\small\item\em Returns list of subopt structures or writes to fp. \end{DoxyCompactList}\item 
+\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{subopt\-\_\-circ} (char $\ast$seq, char $\ast$sequence, int delta, F\-I\-L\-E $\ast$fp)
+\begin{DoxyCompactList}\small\item\em Returns list of circular subopt structures or writes to fp. \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. \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 log\-M\-L \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__subopt__wuchty_ga700f662506a233e42dd7fda74fafd40e}{\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}!subopt@{subopt}}
+\index{subopt@{subopt}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\-F\-E}}
+\subsubsection[{subopt}]{\setlength{\rightskip}{0pt plus 5cm}{\bf S\-O\-L\-U\-T\-I\-O\-N}$\ast$ subopt (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{seq, }
+\item[{char $\ast$}]{structure, }
+\item[{int}]{delta, }
+\item[{F\-I\-L\-E $\ast$}]{fp}
+\end{DoxyParamCaption}
+)}}\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 N\-U\-L\-L), or (fp==N\-U\-L\-L) returned in a \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ list terminated by an entry were the 'structure' pointer is N\-U\-L\-L.
+
+
+\begin{DoxyParams}{Parameters}
+{\em seq} & \\
+\hline
+{\em structure} & \\
+\hline
+{\em delta} & \\
+\hline
+{\em fp} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}
+\hypertarget{group__subopt__wuchty_ga8634516e4740e0b6c9a46d2bae940340}{\index{Suboptimal structures within an energy band arround the M\-F\-E@{Suboptimal structures within an energy band arround the M\-F\-E}!subopt\-\_\-circ@{subopt\-\_\-circ}}
+\index{subopt\-\_\-circ@{subopt\-\_\-circ}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\-F\-E}}
+\subsubsection[{subopt\-\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}{\bf S\-O\-L\-U\-T\-I\-O\-N}$\ast$ subopt\-\_\-circ (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{seq, }
+\item[{char $\ast$}]{sequence, }
+\item[{int}]{delta, }
+\item[{F\-I\-L\-E $\ast$}]{fp}
+\end{DoxyParamCaption}
+)}}\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 R\-N\-A sequence to be circular instead of linear
+
+
+\begin{DoxyParams}{Parameters}
+{\em seq} & \\
+\hline
+{\em sequence} & \\
+\hline
+{\em delta} & \\
+\hline
+{\em fp} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+
+\end{DoxyReturn}