\hypertarget{group__folding__routines}{
\section{RNA Secondary Structure Folding}
\label{group__folding__routines}\index{RNA Secondary Structure Folding@{RNA Secondary Structure Folding}}
}


This module contains all functions related to thermodynamic folding of RNAs.  


Collaboration diagram for RNA Secondary Structure Folding:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=297pt]{group__folding__routines}
\end{center}
\end{figure}
\subsection*{Modules}
\begin{DoxyCompactItemize}
\item 
\hyperlink{group__mfe__fold}{Calculating Minimum Free Energy (MFE) 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. \item\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. \item\end{DoxyCompactList}\item 
\hyperlink{group__subopt__fold}{Enumerating Suboptimal Structures}
\item 
\hyperlink{group__cofold}{Calculate Secondary Structures of two RNAs upon Dimerization}


\begin{DoxyCompactList}\small\item\em Predict structures formed by two molecules upon hybridization. \item\end{DoxyCompactList}\item 
\hyperlink{group__consensus__fold}{Predicting Consensus Structures from Alignment(s)}


\begin{DoxyCompactList}\small\item\em compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments \item\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). \item\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. \item\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 RNAs. 