1 \hypertarget{group__folding__routines}{\section{R\-N\-A Secondary Structure Folding}
2 \label{group__folding__routines}\index{R\-N\-A Secondary Structure Folding@{R\-N\-A Secondary Structure Folding}}
6 This module contains all functions related to thermodynamic folding of R\-N\-As.
9 Collaboration diagram for R\-N\-A Secondary Structure Folding\-:
14 \includegraphics[width=350pt]{group__folding__routines}
18 \begin{DoxyCompactItemize}
20 \hyperlink{group__mfe__fold}{Calculating Minimum Free Energy (\-M\-F\-E) Structures}
21 \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
22 \hyperlink{group__pf__fold}{Calculating Partition Functions and Pair Probabilities}
23 \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
24 \hyperlink{group__subopt__fold}{Enumerating Suboptimal Structures}
26 \hyperlink{group__cofold}{Calculate Secondary Structures of two R\-N\-As upon Dimerization}
27 \begin{DoxyCompactList}\small\item\em Predict structures formed by two molecules upon hybridization. \end{DoxyCompactList}\item
28 \hyperlink{group__consensus__fold}{Predicting Consensus Structures from Alignment(s)}
29 \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
30 \hyperlink{group__local__fold}{Predicting Locally stable structures of large sequences}
32 \hyperlink{group__energy__parameters}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}
33 \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
34 \hyperlink{group__eval}{Energy evaluation}
35 \begin{DoxyCompactList}\small\item\em This module contains all functions and variables related to energy evaluation of sequence/structure pairs. \end{DoxyCompactList}\item
36 \hyperlink{group__inverse__fold}{Searching Sequences for Predefined Structures}
38 \hyperlink{group__class__fold}{Classified Dynamic Programming}
39 \end{DoxyCompactItemize}
42 \subsection{Detailed Description}
43 This module contains all functions related to thermodynamic folding of R\-N\-As.