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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / part__func__up_8h.tex

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+\hypertarget{part__func__up_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.h File Reference}
+\label{part__func__up_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-up.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-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=250pt]{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. \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. \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()}. \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()}. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Partition Function Cofolding as stepwise process. In this approach to cofolding the interaction between two R\-N\-A 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. 
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