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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / group__folding__routines.tex

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+\hypertarget{group__folding__routines}{\section{R\-N\-A Secondary Structure Folding}
+\label{group__folding__routines}\index{R\-N\-A Secondary Structure Folding@{R\-N\-A Secondary Structure Folding}}
+}
+
+
+This module contains all functions related to thermodynamic folding of R\-N\-As.  
+
+
+Collaboration diagram for R\-N\-A Secondary Structure Folding\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__folding__routines}
+\end{center}
+\end{figure}
+\subsection*{Modules}
+\begin{DoxyCompactItemize}
+\item 
+\hyperlink{group__mfe__fold}{Calculating Minimum Free Energy (\-M\-F\-E) Structures}
+\begin{DoxyCompactList}\small\item\em This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. \end{DoxyCompactList}\item 
+\hyperlink{group__pf__fold}{Calculating Partition Functions and Pair Probabilities}
+\begin{DoxyCompactList}\small\item\em This section provides information about all functions and variables related to the calculation of the partition function and base pair probabilities. \end{DoxyCompactList}\item 
+\hyperlink{group__subopt__fold}{Enumerating Suboptimal Structures}
+\item 
+\hyperlink{group__cofold}{Calculate Secondary Structures of two R\-N\-As upon Dimerization}
+\begin{DoxyCompactList}\small\item\em Predict structures formed by two molecules upon hybridization. \end{DoxyCompactList}\item 
+\hyperlink{group__consensus__fold}{Predicting Consensus Structures from Alignment(s)}
+\begin{DoxyCompactList}\small\item\em compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments \end{DoxyCompactList}\item 
+\hyperlink{group__local__fold}{Predicting Locally stable structures of large sequences}
+\item 
+\hyperlink{group__energy__parameters}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}
+\begin{DoxyCompactList}\small\item\em All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s). \end{DoxyCompactList}\item 
+\hyperlink{group__eval}{Energy evaluation}
+\begin{DoxyCompactList}\small\item\em This module contains all functions and variables related to energy evaluation of sequence/structure pairs. \end{DoxyCompactList}\item 
+\hyperlink{group__inverse__fold}{Searching Sequences for Predefined Structures}
+\item 
+\hyperlink{group__class__fold}{Classified Dynamic Programming}
+\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+This module contains all functions related to thermodynamic folding of R\-N\-As. 
\ No newline at end of file