-\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}}
+\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
+Include dependency graph for part\_\-func\_\-up.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=250pt]{part__func__up_8h__incl}
+\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. \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}
+\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()}. \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_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()}. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\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 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.
\ No newline at end of file
+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.
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff