binaries/src/ViennaRNA/doc/latex/group__subopt__stochbt.tex

   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}}
   3 }
   4 Collaboration diagram for Stochastic backtracking in the Ensemble\-:
   5 \nopagebreak
   6 \begin{figure}[H]
   7 \begin{center}
   8 \leavevmode
   9 \includegraphics[width=350pt]{group__subopt__stochbt}
  10 \end{center}
  11 \end{figure}
  12 \subsection*{Modules}
  13 \begin{DoxyCompactItemize}
  14 \item
  15 \hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
  16 \item
  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}
  21 \item
  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}
  29 \item
  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}
  32
  33
  34 \subsection{Detailed Description}
  35
  36
  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}
  45
  46
  47 Sample a secondary structure from the Boltzmann ensemble according its probability\par
  48 .
  49
  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
  52 \end{DoxyPrecond}
  53
  54 \begin{DoxyParams}{Parameters}
  55 {\em sequence} & The R\-N\-A sequence \\
  56 \hline
  57 \end{DoxyParams}
  58 \begin{DoxyReturn}{Returns}
  59 A sampled secondary structure in dot-\/bracket notation
  60 \end{DoxyReturn}
  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}
  68
  69
  70 Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability.
  71
  72 This function does the same as \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()} but assumes the R\-N\-A molecule to be circular
  73
  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
  76 \end{DoxyPrecond}
  77
  78 \begin{DoxyParams}{Parameters}
  79 {\em sequence} & The R\-N\-A sequence \\
  80 \hline
  81 \end{DoxyParams}
  82 \begin{DoxyReturn}{Returns}
  83 A sampled secondary structure in dot-\/bracket notation
  84 \end{DoxyReturn}
  85
  86
  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}
  91
  92
  93 Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.
  94
  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
  96
  97 \begin{DoxySeeAlso}{See Also}
  98 \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack()}, \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ}
  99 \end{DoxySeeAlso}