\hypertarget{cofold_8h}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h File Reference}
\label{cofold_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h}}
}


MFE version of cofolding routines.  
Include dependency graph for cofold.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=209pt]{cofold_8h__incl}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
float \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold} (const char $\ast$sequence, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting RNA molecules. \item\end{DoxyCompactList}\item 
\hypertarget{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{
float \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold\_\-par} (const char $\ast$string, char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int is\_\-constrained)}
\label{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}

\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting RNA molecules. \item\end{DoxyCompactList}\item 
\hypertarget{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{
void \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\_\-co\_\-arrays} (void)}
\label{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}

\begin{DoxyCompactList}\small\item\em Free memory occupied by \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()}. \item\end{DoxyCompactList}\item 
\hypertarget{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{
void \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\_\-cofold\_\-params} (void)}
\label{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}

\begin{DoxyCompactList}\small\item\em Recalculate parameters. \item\end{DoxyCompactList}\item 
void \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export\_\-cofold\_\-arrays\_\-gq} (int $\ast$$\ast$f5\_\-p, int $\ast$$\ast$c\_\-p, int $\ast$$\ast$fML\_\-p, int $\ast$$\ast$fM1\_\-p, int $\ast$$\ast$fc\_\-p, int $\ast$$\ast$ggg\_\-p, int $\ast$$\ast$indx\_\-p, char $\ast$$\ast$ptype\_\-p)
\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold (with gquadruplex support). \item\end{DoxyCompactList}\item 
void \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\_\-cofold\_\-arrays} (int $\ast$$\ast$f5\_\-p, int $\ast$$\ast$c\_\-p, int $\ast$$\ast$fML\_\-p, int $\ast$$\ast$fM1\_\-p, int $\ast$$\ast$fc\_\-p, int $\ast$$\ast$indx\_\-p, char $\ast$$\ast$ptype\_\-p)
\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold. \item\end{DoxyCompactList}\item 
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__zuker_ga0d5104e3ecf119d8eabd40aa5fe47f90}{zukersubopt} (const char $\ast$string)
\begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \item\end{DoxyCompactList}\item 
\hypertarget{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{
\hyperlink{structSOLUTION}{SOLUTION} $\ast$ \hyperlink{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{zukersubopt\_\-par} (const char $\ast$string, \hyperlink{structparamT}{paramT} $\ast$parameters)}
\label{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}

\begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \item\end{DoxyCompactList}\item 
void \hyperlink{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{get\_\-monomere\_\-mfes} (float $\ast$e1, float $\ast$e2)
\begin{DoxyCompactList}\small\item\em get\_\-monomer\_\-free\_\-energies \item\end{DoxyCompactList}\item 
void \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\_\-cofold} (int length)
\end{DoxyCompactItemize}


\subsection{Detailed Description}
MFE version of cofolding routines. This file includes (almost) all function declarations within the {\bfseries RNAlib} that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines. 

\subsection{Function Documentation}
\hypertarget{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{
\index{cofold.h@{cofold.h}!get\_\-monomere\_\-mfes@{get\_\-monomere\_\-mfes}}
\index{get\_\-monomere\_\-mfes@{get\_\-monomere\_\-mfes}!cofold.h@{cofold.h}}
\subsubsection[{get\_\-monomere\_\-mfes}]{\setlength{\rightskip}{0pt plus 5cm}void get\_\-monomere\_\-mfes (float $\ast$ {\em e1}, \/  float $\ast$ {\em e2})}}
\label{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}


get\_\-monomer\_\-free\_\-energies Export monomer free energies out of cofold arrays


\begin{DoxyParams}{Parameters}
\item[{\em e1}]A pointer to a variable where the energy of molecule A will be written to \item[{\em e2}]A pointer to a variable where the energy of molecule B will be written to \end{DoxyParams}
\hypertarget{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{
\index{cofold.h@{cofold.h}!initialize\_\-cofold@{initialize\_\-cofold}}
\index{initialize\_\-cofold@{initialize\_\-cofold}!cofold.h@{cofold.h}}
\subsubsection[{initialize\_\-cofold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\_\-cofold (int {\em length})}}
\label{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}
allocate arrays for folding \begin{Desc}
\item[\hyperlink{deprecated__deprecated000001}{Deprecated}]\{This function is obsolete and will be removed soon!\} \end{Desc}
