\hypertarget{group__subopt__stochbt}{
\section{Stochastic backtracking in the Ensemble}
\label{group__subopt__stochbt}\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
}


Collaboration diagram for Stochastic backtracking in the Ensemble:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=420pt]{group__subopt__stochbt}
\end{center}
\end{figure}
\subsection*{Modules}
\begin{DoxyCompactItemize}
\item 
\hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
\item 
\hyperlink{group__kl__neighborhood__stochbt}{Stochastic Backtracking of Structures from Distance Based Partitioning}


\begin{DoxyCompactList}\small\item\em Contains functions related to stochastic backtracking from a specified distance class. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
char $\ast$ \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack} (char $\ast$sequence)
\begin{DoxyCompactList}\small\item\em Sample a secondary structure from the Boltzmann ensemble according its probability\par
. \item\end{DoxyCompactList}\item 
char $\ast$ \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_\-circ} (char $\ast$sequence)
\begin{DoxyCompactList}\small\item\em Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
int \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\_\-back}
\begin{DoxyCompactList}\small\item\em Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Function Documentation}
\hypertarget{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{
\index{subopt\_\-stochbt@{subopt\_\-stochbt}!pbacktrack@{pbacktrack}}
\index{pbacktrack@{pbacktrack}!subopt_stochbt@{subopt\_\-stochbt}}
\subsubsection[{pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack (char $\ast$ {\em sequence})}}
\label{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}


Sample a secondary structure from the Boltzmann ensemble according its probability\par
. \begin{DoxyPrecond}{Precondition}
\hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\_\-fold\_\-par()} or \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()} have to be called first to fill the partition function matrices
\end{DoxyPrecond}

\begin{DoxyParams}{Parameters}
\item[{\em sequence}]The RNA sequence \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation 
\end{DoxyReturn}
\hypertarget{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{
\index{subopt\_\-stochbt@{subopt\_\-stochbt}!pbacktrack\_\-circ@{pbacktrack\_\-circ}}
\index{pbacktrack\_\-circ@{pbacktrack\_\-circ}!subopt_stochbt@{subopt\_\-stochbt}}
\subsubsection[{pbacktrack\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack\_\-circ (char $\ast$ {\em sequence})}}
\label{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}


Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. This function does the same as \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()} but assumes the RNA molecule to be circular

\begin{DoxyPrecond}{Precondition}
\hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\_\-fold\_\-par()} or pf\_\-fold\_\-circ() have to be called first to fill the partition function matrices
\end{DoxyPrecond}

\begin{DoxyParams}{Parameters}
\item[{\em sequence}]The RNA sequence \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation 
\end{DoxyReturn}


\subsection{Variable Documentation}
\hypertarget{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{
\index{subopt\_\-stochbt@{subopt\_\-stochbt}!st\_\-back@{st\_\-back}}
\index{st\_\-back@{st\_\-back}!subopt_stochbt@{subopt\_\-stochbt}}
\subsubsection[{st\_\-back}]{\setlength{\rightskip}{0pt plus 5cm}int {\bf st\_\-back}}}
\label{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}


Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. Set this variable to 1 prior to a call of \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()} to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions

\begin{DoxySeeAlso}{See also}
\hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()}, \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\_\-circ} 
\end{DoxySeeAlso}
