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

   1 \hypertarget{group__inverse__fold}{\section{Searching Sequences for Predefined Structures}
   2 \label{group__inverse__fold}\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
   3 }
   4 Collaboration diagram for Searching Sequences for Predefined Structures\-:
   5 \nopagebreak
   6 \begin{figure}[H]
   7 \begin{center}
   8 \leavevmode
   9 \includegraphics[width=350pt]{group__inverse__fold}
  10 \end{center}
  11 \end{figure}
  12 \subsection*{Files}
  13 \begin{DoxyCompactItemize}
  14 \item
  15 file \hyperlink{inverse_8h}{inverse.\-h}
  16 \begin{DoxyCompactList}\small\item\em Inverse folding routines. \end{DoxyCompactList}\end{DoxyCompactItemize}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 float \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold} (char $\ast$start, const char $\ast$target)
  21 \begin{DoxyCompactList}\small\item\em Find sequences with predefined structure. \end{DoxyCompactList}\item
  22 float \hyperlink{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{inverse\-\_\-pf\-\_\-fold} (char $\ast$start, const char $\ast$target)
  23 \begin{DoxyCompactList}\small\item\em Find sequence that maximizes probability of a predefined structure. \end{DoxyCompactList}\end{DoxyCompactItemize}
  24 \subsection*{Variables}
  25 \begin{DoxyCompactItemize}
  26 \item
  27 \hypertarget{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}{char $\ast$ \hyperlink{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}{symbolset}}\label{group__inverse__fold_ga8f791e7740a5a28b9f6fafb4e60301d9}
  28
  29 \begin{DoxyCompactList}\small\item\em This global variable points to the allowed bases, initially \char`\"{}\-A\-U\-G\-C\char`\"{}. It can be used to design sequences from reduced alphabets. \end{DoxyCompactList}\item
  30 float \hyperlink{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c}{final\-\_\-cost}
  31 \item
  32 int \hyperlink{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{give\-\_\-up}
  33 \item
  34 int \hyperlink{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63}{inv\-\_\-verbose}
  35 \end{DoxyCompactItemize}
  36
  37
  38 \subsection{Detailed Description}
  39 We provide two functions that search for sequences with a given structure, thereby inverting the folding routines.
  40
  41 \subsection{Function Documentation}
  42 \hypertarget{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\-\_\-fold@{inverse\-\_\-fold}}
  43 \index{inverse\-\_\-fold@{inverse\-\_\-fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
  44 \subsubsection[{inverse\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float inverse\-\_\-fold (
  45 \begin{DoxyParamCaption}
  46 \item[{char $\ast$}]{start, }
  47 \item[{const char $\ast$}]{target}
  48 \end{DoxyParamCaption}
  49 )}}\label{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}
  50
  51
  52 Find sequences with predefined structure.
  53
  54 This function searches for a sequence with minimum free energy structure provided in the parameter 'target', starting with sequence 'start'. It returns 0 if the search was successful, otherwise a structure distance in terms of the energy difference between the search result and the actual target 'target' is returned. The found sequence is returned in 'start'. If \hyperlink{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{give\-\_\-up} is set to 1, the function will return as soon as it is clear that the search will be unsuccessful, this speeds up the algorithm if you are only interested in exact solutions.
  55
  56
  57 \begin{DoxyParams}{Parameters}
  58 {\em start} & The start sequence \\
  59 \hline
  60 {\em target} & The target secondary structure in dot-\/bracket notation \\
  61 \hline
  62 \end{DoxyParams}
  63 \begin{DoxyReturn}{Returns}
  64 The distance to the target in case a search was unsuccessful, 0 otherwise
  65 \end{DoxyReturn}
  66 \hypertarget{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inverse\-\_\-pf\-\_\-fold@{inverse\-\_\-pf\-\_\-fold}}
  67 \index{inverse\-\_\-pf\-\_\-fold@{inverse\-\_\-pf\-\_\-fold}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
  68 \subsubsection[{inverse\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float inverse\-\_\-pf\-\_\-fold (
  69 \begin{DoxyParamCaption}
  70 \item[{char $\ast$}]{start, }
  71 \item[{const char $\ast$}]{target}
  72 \end{DoxyParamCaption}
  73 )}}\label{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}
  74
  75
  76 Find sequence that maximizes probability of a predefined structure.
  77
  78 This function searches for a sequence with maximum probability to fold into the provided structure 'target' using the partition function algorithm. It returns $-kT \cdot \log(p)$ where $p$ is the frequency of 'target' in the ensemble of possible structures. This is usually much slower than \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()}.
  79
  80
  81 \begin{DoxyParams}{Parameters}
  82 {\em start} & The start sequence \\
  83 \hline
  84 {\em target} & The target secondary structure in dot-\/bracket notation \\
  85 \hline
  86 \end{DoxyParams}
  87 \begin{DoxyReturn}{Returns}
  88 The distance to the target in case a search was unsuccessful, 0 otherwise
  89 \end{DoxyReturn}
  90
  91
  92 \subsection{Variable Documentation}
  93 \hypertarget{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!final\-\_\-cost@{final\-\_\-cost}}
  94 \index{final\-\_\-cost@{final\-\_\-cost}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
  95 \subsubsection[{final\-\_\-cost}]{\setlength{\rightskip}{0pt plus 5cm}float final\-\_\-cost}}\label{group__inverse__fold_ga7f17d3b169af048d32bb185039a9c09c}
  96 when to stop \hyperlink{group__inverse__fold_gaeef52ecbf2a2450ad585a344f9826806}{inverse\-\_\-pf\-\_\-fold()} \hypertarget{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!give\-\_\-up@{give\-\_\-up}}
  97 \index{give\-\_\-up@{give\-\_\-up}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
  98 \subsubsection[{give\-\_\-up}]{\setlength{\rightskip}{0pt plus 5cm}int give\-\_\-up}}\label{group__inverse__fold_ga7ec4ba51f86e1717a1e174264e4a75ce}
  99 default 0\-: try to minimize structure distance even if no exact solution can be found \hypertarget{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63}{\index{Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}!inv\-\_\-verbose@{inv\-\_\-verbose}}
 100 \index{inv\-\_\-verbose@{inv\-\_\-verbose}!Searching Sequences for Predefined Structures@{Searching Sequences for Predefined Structures}}
 101 \subsubsection[{inv\-\_\-verbose}]{\setlength{\rightskip}{0pt plus 5cm}int inv\-\_\-verbose}}\label{group__inverse__fold_gafcfc65fba01b9cca5946726ed9057a63}
 102 print out substructure on which \hyperlink{group__inverse__fold_ga7af026de55d4babad879f2c92559cbbc}{inverse\-\_\-fold()} fails