1 \hypertarget{group__subopt__stochbt}{\section{Stochastic backtracking in the Ensemble}
2 \label{group__subopt__stochbt}\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
4 Collaboration diagram for Stochastic backtracking in the Ensemble\-:
9 \includegraphics[width=350pt]{group__subopt__stochbt}
13 \begin{DoxyCompactItemize}
15 \hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
17 \hyperlink{group__kl__neighborhood__stochbt}{Stochastic Backtracking of Structures from Distance Based Partitioning}
18 \begin{DoxyCompactList}\small\item\em Contains functions related to stochastic backtracking from a specified distance class. \end{DoxyCompactList}\end{DoxyCompactItemize}
19 \subsection*{Functions}
20 \begin{DoxyCompactItemize}
22 char $\ast$ \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack} (char $\ast$sequence)
23 \begin{DoxyCompactList}\small\item\em Sample a secondary structure from the Boltzmann ensemble according its probability\par
24 . \end{DoxyCompactList}\item
25 char $\ast$ \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ} (char $\ast$sequence)
26 \begin{DoxyCompactList}\small\item\em Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability. \end{DoxyCompactList}\end{DoxyCompactItemize}
27 \subsection*{Variables}
28 \begin{DoxyCompactItemize}
30 int \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\-\_\-back}
31 \begin{DoxyCompactList}\small\item\em Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. \end{DoxyCompactList}\end{DoxyCompactItemize}
34 \subsection{Detailed Description}
37 \subsection{Function Documentation}
38 \hypertarget{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack@{pbacktrack}}
39 \index{pbacktrack@{pbacktrack}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
40 \subsubsection[{pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack (
41 \begin{DoxyParamCaption}
42 \item[{char $\ast$}]{sequence}
43 \end{DoxyParamCaption}
44 )}}\label{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}
47 Sample a secondary structure from the Boltzmann ensemble according its probability\par
50 \begin{DoxyPrecond}{Precondition}
51 \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
54 \begin{DoxyParams}{Parameters}
55 {\em sequence} & The R\-N\-A sequence \\
58 \begin{DoxyReturn}{Returns}
59 A sampled secondary structure in dot-\/bracket notation
61 \hypertarget{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack\-\_\-circ@{pbacktrack\-\_\-circ}}
62 \index{pbacktrack\-\_\-circ@{pbacktrack\-\_\-circ}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
63 \subsubsection[{pbacktrack\-\_\-circ}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pbacktrack\-\_\-circ (
64 \begin{DoxyParamCaption}
65 \item[{char $\ast$}]{sequence}
66 \end{DoxyParamCaption}
67 )}}\label{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}
70 Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability.
72 This function does the same as \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()} but assumes the R\-N\-A molecule to be circular
74 \begin{DoxyPrecond}{Precondition}
75 \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\-\_\-fold\-\_\-par()} or pf\-\_\-fold\-\_\-circ() have to be called first to fill the partition function matrices
78 \begin{DoxyParams}{Parameters}
79 {\em sequence} & The R\-N\-A sequence \\
82 \begin{DoxyReturn}{Returns}
83 A sampled secondary structure in dot-\/bracket notation
87 \subsection{Variable Documentation}
88 \hypertarget{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{\index{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!st\-\_\-back@{st\-\_\-back}}
89 \index{st\-\_\-back@{st\-\_\-back}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}}
90 \subsubsection[{st\-\_\-back}]{\setlength{\rightskip}{0pt plus 5cm}int st\-\_\-back}}\label{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}
93 Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.
95 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
97 \begin{DoxySeeAlso}{See Also}
98 \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()}, \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ}