\hypertarget{part__func__up_8h}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\-func\_\-up.h File Reference}
\label{part__func__up_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\-func\_\-up.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part\_\-func\_\-up.h}}
}


Partition Function Cofolding as stepwise process.  
Include dependency graph for part\_\-func\_\-up.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=222pt]{part__func__up_8h__incl}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
\hyperlink{structpu__contrib}{pu\_\-contrib} $\ast$ \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\_\-unstru} (char $\ast$sequence, int max\_\-w)
\begin{DoxyCompactList}\small\item\em Calculate the partition function over all unpaired regions of a maximal length. \item\end{DoxyCompactList}\item 
\hyperlink{structinteract}{interact} $\ast$ \hyperlink{group__up__cofold_ga1aa0aa02bc3a724f87360c03097afd00}{pf\_\-interact} (const char $\ast$s1, const char $\ast$s2, \hyperlink{structpu__contrib}{pu\_\-contrib} $\ast$p\_\-c, \hyperlink{structpu__contrib}{pu\_\-contrib} $\ast$p\_\-c2, int max\_\-w, char $\ast$cstruc, int incr3, int incr5)
\begin{DoxyCompactList}\small\item\em Calculates the probability of a local interaction between two sequences. \item\end{DoxyCompactList}\item 
\hypertarget{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}{
void \hyperlink{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}{free\_\-interact} (\hyperlink{structinteract}{interact} $\ast$pin)}
\label{group__up__cofold_gadde308fd5f696dc271b1532aa96fd12f}

\begin{DoxyCompactList}\small\item\em Frees the output of function \hyperlink{group__up__cofold_ga1aa0aa02bc3a724f87360c03097afd00}{pf\_\-interact()}. \item\end{DoxyCompactList}\item 
\hypertarget{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}{
void \hyperlink{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}{free\_\-pu\_\-contrib\_\-struct} (\hyperlink{structpu__contrib}{pu\_\-contrib} $\ast$pu)}
\label{group__up__cofold_gac20bd61824981d45ce0dc9934aa56df8}

\begin{DoxyCompactList}\small\item\em Frees the output of function \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\_\-unstru()}. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
Partition Function Cofolding as stepwise process. In this approach to cofolding the interaction between two RNA molecules is seen as a stepwise process. In a first step, the target molecule has to adopt a structure in which a binding site is accessible. In a second step, the ligand molecule will hybridize with a region accessible to an interaction. Consequently the algorithm is designed as a two step process: The first step is the calculation of the probability that a region within the target is unpaired, or equivalently, the calculation of the free energy needed to expose a region. In the second step we compute the free energy of an interaction for every possible binding site. 