\hypertarget{group__mfe__cofold}{
\section{MFE Structures of two hybridized Sequences}
\label{group__mfe__cofold}\index{MFE Structures of two hybridized Sequences@{MFE Structures of two hybridized Sequences}}
}


Collaboration diagram for MFE Structures of two hybridized Sequences:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=300pt]{group__mfe__cofold}
\end{center}
\end{figure}
\subsection*{Files}
\begin{DoxyCompactItemize}
\item 
file \hyperlink{cofold_8h}{cofold.h}


\begin{DoxyCompactList}\small\item\em MFE version of cofolding routines. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\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}\end{DoxyCompactItemize}


\subsection{Function Documentation}
\hypertarget{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{
\index{mfe\_\-cofold@{mfe\_\-cofold}!cofold@{cofold}}
\index{cofold@{cofold}!mfe_cofold@{mfe\_\-cofold}}
\subsubsection[{cofold}]{\setlength{\rightskip}{0pt plus 5cm}float cofold (const char $\ast$ {\em sequence}, \/  char $\ast$ {\em structure})}}
\label{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}


Compute the minimum free energy of two interacting RNA molecules. The code is analog to the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} function. If \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\_\-point} ==-\/1 results should be the same as with \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}.


\begin{DoxyParams}{Parameters}
\item[{\em sequence}]The two sequences concatenated \item[{\em structure}]Will hold the barcket dot structure of the dimer molecule \end{DoxyParams}
\begin{DoxyReturn}{Returns}
minimum free energy of the structure 
\end{DoxyReturn}
\hypertarget{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{
\index{mfe\_\-cofold@{mfe\_\-cofold}!export\_\-cofold\_\-arrays\_\-gq@{export\_\-cofold\_\-arrays\_\-gq}}
\index{export\_\-cofold\_\-arrays\_\-gq@{export\_\-cofold\_\-arrays\_\-gq}!mfe_cofold@{mfe\_\-cofold}}
\subsubsection[{export\_\-cofold\_\-arrays\_\-gq}]{\setlength{\rightskip}{0pt plus 5cm}void export\_\-cofold\_\-arrays\_\-gq (int $\ast$$\ast$ {\em f5\_\-p}, \/  int $\ast$$\ast$ {\em c\_\-p}, \/  int $\ast$$\ast$ {\em fML\_\-p}, \/  int $\ast$$\ast$ {\em fM1\_\-p}, \/  int $\ast$$\ast$ {\em fc\_\-p}, \/  int $\ast$$\ast$ {\em ggg\_\-p}, \/  int $\ast$$\ast$ {\em indx\_\-p}, \/  char $\ast$$\ast$ {\em ptype\_\-p})}}
\label{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}


Export the arrays of partition function cofold (with gquadruplex support). Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking


\begin{DoxyParams}{Parameters}
\item[{\em f5\_\-p}]A pointer to the 'f5' array, i.e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \item[{\em c\_\-p}]A pointer to the 'c' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \item[{\em fML\_\-p}]A pointer to the 'M' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \item[{\em fM1\_\-p}]A pointer to the 'M1' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \item[{\em fc\_\-p}]A pointer to the 'fc' array, i.e. array ... \item[{\em ggg\_\-p}]A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by \mbox{[}i,j\mbox{]} \item[{\em indx\_\-p}]A pointer to the indexing array used for accessing the energy matrices \item[{\em ptype\_\-p}]A pointer to the ptype array containing the base pair types for each possibility (i,j) \end{DoxyParams}
\hypertarget{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{
\index{mfe\_\-cofold@{mfe\_\-cofold}!export\_\-cofold\_\-arrays@{export\_\-cofold\_\-arrays}}
\index{export\_\-cofold\_\-arrays@{export\_\-cofold\_\-arrays}!mfe_cofold@{mfe\_\-cofold}}
\subsubsection[{export\_\-cofold\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void export\_\-cofold\_\-arrays (int $\ast$$\ast$ {\em f5\_\-p}, \/  int $\ast$$\ast$ {\em c\_\-p}, \/  int $\ast$$\ast$ {\em fML\_\-p}, \/  int $\ast$$\ast$ {\em fM1\_\-p}, \/  int $\ast$$\ast$ {\em fc\_\-p}, \/  int $\ast$$\ast$ {\em indx\_\-p}, \/  char $\ast$$\ast$ {\em ptype\_\-p})}}
\label{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}


Export the arrays of partition function cofold. Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking


\begin{DoxyParams}{Parameters}
\item[{\em f5\_\-p}]A pointer to the 'f5' array, i.e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \item[{\em c\_\-p}]A pointer to the 'c' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} given that i pairs with j \item[{\em fML\_\-p}]A pointer to the 'M' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for any multiloop segment with at least one stem \item[{\em fM1\_\-p}]A pointer to the 'M1' array, i.e. array containing best free energy in interval \mbox{[}i,j\mbox{]} for multiloop segment with exactly one stem \item[{\em fc\_\-p}]A pointer to the 'fc' array, i.e. array ... \item[{\em indx\_\-p}]A pointer to the indexing array used for accessing the energy matrices \item[{\em ptype\_\-p}]A pointer to the ptype array containing the base pair types for each possibility (i,j) \end{DoxyParams}
