1 \hypertarget{group__kl__neighborhood__stochbt}{\section{Stochastic Backtracking of Structures from Distance Based Partitioning}
2 \label{group__kl__neighborhood__stochbt}\index{Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
6 Contains functions related to stochastic backtracking from a specified distance class.
9 Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning\-:
14 \includegraphics[width=350pt]{group__kl__neighborhood__stochbt}
17 \subsection*{Functions}
18 \begin{DoxyCompactItemize}
20 char $\ast$ \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int d1, int d2)
21 \begin{DoxyCompactList}\small\item\em Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. \end{DoxyCompactList}\item
22 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)
23 \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}
26 \subsection{Detailed Description}
27 Contains functions related to stochastic backtracking from a specified distance class.
29 \subsection{Function Documentation}
30 \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}}
31 \index{Two\-Dpfold\-\_\-pbacktrack@{Two\-Dpfold\-\_\-pbacktrack}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
32 \subsubsection[{Two\-Dpfold\-\_\-pbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack (
33 \begin{DoxyParamCaption}
34 \item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
37 \end{DoxyParamCaption}
38 )}}\label{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}
41 Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.
43 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.
45 \begin{DoxyPrecond}{Precondition}
46 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!
48 \begin{DoxySeeAlso}{See Also}
49 \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
52 \begin{DoxyParams}[1]{Parameters}
53 \mbox{\tt in} & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
55 \mbox{\tt in} & {\em d1} & the distance to reference1 (may be -\/1) \\
57 \mbox{\tt in} & {\em d2} & the distance to reference2 \\
60 \begin{DoxyReturn}{Returns}
61 A sampled secondary structure in dot-\/bracket notation
63 \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}}
64 \index{Two\-Dpfold\-\_\-pbacktrack5@{Two\-Dpfold\-\_\-pbacktrack5}!Stochastic Backtracking of Structures from Distance Based Partitioning@{Stochastic Backtracking of Structures from Distance Based Partitioning}}
65 \subsubsection[{Two\-Dpfold\-\_\-pbacktrack5}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ Two\-Dpfold\-\_\-pbacktrack5 (
66 \begin{DoxyParamCaption}
67 \item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
70 \item[{unsigned int}]{length}
71 \end{DoxyParamCaption}
72 )}}\label{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}
75 Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.
77 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
79 \begin{DoxyNote}{Note}
80 This function does not work (since it makes no sense) for circular R\-N\-A sequences!
82 \begin{DoxyPrecond}{Precondition}
83 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!
85 \begin{DoxySeeAlso}{See Also}
86 \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
89 \begin{DoxyParams}[1]{Parameters}
90 \mbox{\tt in} & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
92 \mbox{\tt in} & {\em d1} & the distance to reference1 (may be -\/1) \\
94 \mbox{\tt in} & {\em d2} & the distance to reference2 \\
96 \mbox{\tt in} & {\em length} & the length of the structure beginning from the 5' end \\
99 \begin{DoxyReturn}{Returns}
100 A sampled secondary structure in dot-\/bracket notation