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

   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}}
   3 }
   4
   5
   6 Contains functions related to stochastic backtracking from a specified distance class.
   7
   8
   9 Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=350pt]{group__kl__neighborhood__stochbt}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  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}
  24
  25
  26 \subsection{Detailed Description}
  27 Contains functions related to stochastic backtracking from a specified distance class.
  28
  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, }
  35 \item[{int}]{d1, }
  36 \item[{int}]{d2}
  37 \end{DoxyParamCaption}
  38 )}}\label{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}
  39
  40
  41 Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.
  42
  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.
  44
  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!
  47 \end{DoxyPrecond}
  48 \begin{DoxySeeAlso}{See Also}
  49 \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
  50 \end{DoxySeeAlso}
  51
  52 \begin{DoxyParams}[1]{Parameters}
  53 \mbox{\tt in}  & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
  54 \hline
  55 \mbox{\tt in}  & {\em d1} & the distance to reference1 (may be -\/1) \\
  56 \hline
  57 \mbox{\tt in}  & {\em d2} & the distance to reference2 \\
  58 \hline
  59 \end{DoxyParams}
  60 \begin{DoxyReturn}{Returns}
  61 A sampled secondary structure in dot-\/bracket notation
  62 \end{DoxyReturn}
  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, }
  68 \item[{int}]{d1, }
  69 \item[{int}]{d2, }
  70 \item[{unsigned int}]{length}
  71 \end{DoxyParamCaption}
  72 )}}\label{group__kl__neighborhood__stochbt_ga13430ac6a7f90df426774f131647d2c7}
  73
  74
  75 Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.
  76
  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
  78
  79 \begin{DoxyNote}{Note}
  80 This function does not work (since it makes no sense) for circular R\-N\-A sequences!
  81 \end{DoxyNote}
  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!
  84 \end{DoxyPrecond}
  85 \begin{DoxySeeAlso}{See Also}
  86 \hyperlink{group__kl__neighborhood__stochbt_gae251288f50dd4ae7d315af0085775f71}{Two\-Dpfold\-\_\-pbacktrack()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()}
  87 \end{DoxySeeAlso}
  88
  89 \begin{DoxyParams}[1]{Parameters}
  90 \mbox{\tt in}  & {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
  91 \hline
  92 \mbox{\tt in}  & {\em d1} & the distance to reference1 (may be -\/1) \\
  93 \hline
  94 \mbox{\tt in}  & {\em d2} & the distance to reference2 \\
  95 \hline
  96 \mbox{\tt in}  & {\em length} & the length of the structure beginning from the 5' end \\
  97 \hline
  98 \end{DoxyParams}
  99 \begin{DoxyReturn}{Returns}
 100 A sampled secondary structure in dot-\/bracket notation
 101 \end{DoxyReturn}