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

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+\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=350pt]{group__kl__neighborhood__stochbt}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-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. \end{DoxyCompactList}\item 
+char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{Two\-Dpfold\-\_\-pbacktrack5} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-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. \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{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\-Dpfold\-\_\-pbacktrack@{Two\-Dpfold\-\_\-pbacktrack}}
+\index{Two\-Dpfold\-\_\-pbacktrack@{Two\-Dpfold\-\_\-pbacktrack}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
+\subsubsection[{Two\-Dpfold\-\_\-pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack (
+\begin{DoxyParamCaption}
+\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
+\item[{int}]{d1, }
+\item[{int}]{d2}
+\end{DoxyParamCaption}
+)}}\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}{Two\-Dpfold\-List()} preceding this function is mandatory!
+\end{DoxyPrecond}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}[1]{Parameters}
+\mbox{\tt in}  & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
+\hline
+\mbox{\tt in}  & {\em d1} & the distance to reference1 (may be -\/1) \\
+\hline
+\mbox{\tt in}  & {\em d2} & the distance to reference2 \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A sampled secondary structure in dot-\/bracket notation 
+\end{DoxyReturn}
+\hypertarget{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}{\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}!Two\-Dpfold\-\_\-pbacktrack5@{Two\-Dpfold\-\_\-pbacktrack5}}
+\index{Two\-Dpfold\-\_\-pbacktrack5@{Two\-Dpfold\-\_\-pbacktrack5}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
+\subsubsection[{Two\-Dpfold\-\_\-pbacktrack5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack5 (
+\begin{DoxyParamCaption}
+\item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
+\item[{int}]{d1, }
+\item[{int}]{d2, }
+\item[{unsigned int}]{length}
+\end{DoxyParamCaption}
+)}}\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 Two\-Dpfold\-\_\-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 R\-N\-A 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}{Two\-Dpfold\-List()} preceding this function is mandatory!
+\end{DoxyPrecond}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}[1]{Parameters}
+\mbox{\tt in}  & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
+\hline
+\mbox{\tt in}  & {\em d1} & the distance to reference1 (may be -\/1) \\
+\hline
+\mbox{\tt in}  & {\em d2} & the distance to reference2 \\
+\hline
+\mbox{\tt in}  & {\em length} & the length of the structure beginning from the 5' end \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A sampled secondary structure in dot-\/bracket notation 
+\end{DoxyReturn}