\hypertarget{group__kl__neighborhood__stochbt}{
\section{Stochastic Backtracking of Structures from Distance Based Partitioning}
\label{group__kl__neighborhood__stochbt}\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
}


Contains functions related to stochastic backtracking from a specified distance class.  


Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=354pt]{group__kl__neighborhood__stochbt}
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\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2)
\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\item 
char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{TwoDpfold\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{TwoDpfold\_\-vars} $\ast$vars, int d1, int d2, unsigned int length)
\begin{DoxyCompactList}\small\item\em Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
Contains functions related to stochastic backtracking from a specified distance class. 

\subsection{Function Documentation}
\hypertarget{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{
\index{kl\_\-neighborhood\_\-stochbt@{kl\_\-neighborhood\_\-stochbt}!TwoDpfold\_\-pbacktrack@{TwoDpfold\_\-pbacktrack}}
\index{TwoDpfold\_\-pbacktrack@{TwoDpfold\_\-pbacktrack}!kl_neighborhood_stochbt@{kl\_\-neighborhood\_\-stochbt}}
\subsubsection[{TwoDpfold\_\-pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ TwoDpfold\_\-pbacktrack ({\bf TwoDpfold\_\-vars} $\ast$ {\em vars}, \/  int {\em d1}, \/  int {\em d2})}}
\label{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}


Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. If the argument 'd1' is set to '-\/1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.

\begin{DoxyPrecond}{Precondition}
The argument 'vars' must contain precalculated partition function matrices, i.e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()} preceding this function is mandatory!
\end{DoxyPrecond}
\begin{DoxySeeAlso}{See also}
\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[\mbox{$\leftarrow$} {\em vars}]the datastructure containing all necessary folding attributes and matrices \item[\mbox{$\leftarrow$} {\em d1}]the distance to reference1 (may be -\/1) \item[\mbox{$\leftarrow$} {\em d2}]the distance to reference2 \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation 
\end{DoxyReturn}
\hypertarget{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{
\index{kl\_\-neighborhood\_\-stochbt@{kl\_\-neighborhood\_\-stochbt}!TwoDpfold\_\-pbacktrack5@{TwoDpfold\_\-pbacktrack5}}
\index{TwoDpfold\_\-pbacktrack5@{TwoDpfold\_\-pbacktrack5}!kl_neighborhood_stochbt@{kl\_\-neighborhood\_\-stochbt}}
\subsubsection[{TwoDpfold\_\-pbacktrack5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ TwoDpfold\_\-pbacktrack5 ({\bf TwoDpfold\_\-vars} $\ast$ {\em vars}, \/  int {\em d1}, \/  int {\em d2}, \/  unsigned int {\em length})}}
\label{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}


Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. This function does essentially the same as TwoDpfold\_\-pbacktrack with the only difference that partial structures, i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked

\begin{DoxyNote}{Note}
This function does not work (since it makes no sense) for circular RNA sequences! 
\end{DoxyNote}
\begin{DoxyPrecond}{Precondition}
The argument 'vars' must contain precalculated partition function matrices, i.e. a call to \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()} preceding this function is mandatory!
\end{DoxyPrecond}
\begin{DoxySeeAlso}{See also}
\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{TwoDpfold\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{TwoDpfoldList()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[\mbox{$\leftarrow$} {\em vars}]the datastructure containing all necessary folding attributes and matrices \item[\mbox{$\leftarrow$} {\em d1}]the distance to reference1 (may be -\/1) \item[\mbox{$\leftarrow$} {\em d2}]the distance to reference2 \item[\mbox{$\leftarrow$} {\em length}]the length of the structure beginning from the 5' end \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled secondary structure in dot-\/bracket notation 
\end{DoxyReturn}
