--- /dev/null
+\hypertarget{group__mfe__cofold}{\section{M\-F\-E Structures of two hybridized Sequences}
+\label{group__mfe__cofold}\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
+}
+Collaboration diagram for M\-F\-E Structures of two hybridized Sequences\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__mfe__cofold}
+\end{center}
+\end{figure}
+\subsection*{Files}
+\begin{DoxyCompactItemize}
+\item
+file \hyperlink{cofold_8h}{cofold.\-h}
+\begin{DoxyCompactList}\small\item\em M\-F\-E version of cofolding routines. \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 R\-N\-A molecules. \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}{param\-T} $\ast$parameters, int is\-\_\-constrained)}\label{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}
+
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \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()} \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. \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$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-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) \end{DoxyCompactList}\item
+void \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\-\_\-cofold\-\_\-arrays} (int $\ast$$\ast$f5\-\_\-p, int $\ast$$\ast$c\-\_\-p, int $\ast$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-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. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+
+
+\subsection{Function Documentation}
+\hypertarget{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!cofold@{cofold}}
+\index{cofold@{cofold}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
+\subsubsection[{cofold}]{\setlength{\rightskip}{0pt plus 5cm}float cofold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{sequence, }
+\item[{char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}
+
+
+Compute the minimum free energy of two interacting R\-N\-A 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}
+{\em sequence} & The two sequences concatenated \\
+\hline
+{\em structure} & Will hold the barcket dot structure of the dimer molecule \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+minimum free energy of the structure
+\end{DoxyReturn}
+\hypertarget{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!export\-\_\-cofold\-\_\-arrays\-\_\-gq@{export\-\_\-cofold\-\_\-arrays\-\_\-gq}}
+\index{export\-\_\-cofold\-\_\-arrays\-\_\-gq@{export\-\_\-cofold\-\_\-arrays\-\_\-gq}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
+\subsubsection[{export\-\_\-cofold\-\_\-arrays\-\_\-gq}]{\setlength{\rightskip}{0pt plus 5cm}void export\-\_\-cofold\-\_\-arrays\-\_\-gq (
+\begin{DoxyParamCaption}
+\item[{int $\ast$$\ast$}]{f5\-\_\-p, }
+\item[{int $\ast$$\ast$}]{c\-\_\-p, }
+\item[{int $\ast$$\ast$}]{f\-M\-L\-\_\-p, }
+\item[{int $\ast$$\ast$}]{f\-M1\-\_\-p, }
+\item[{int $\ast$$\ast$}]{fc\-\_\-p, }
+\item[{int $\ast$$\ast$}]{ggg\-\_\-p, }
+\item[{int $\ast$$\ast$}]{indx\-\_\-p, }
+\item[{char $\ast$$\ast$}]{ptype\-\_\-p}
+\end{DoxyParamCaption}
+)}}\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}
+{\em f5\-\_\-p} & A pointer to the 'f5' array, i.\-e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \\
+\hline
+{\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 \\
+\hline
+{\em f\-M\-L\-\_\-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 \\
+\hline
+{\em f\-M1\-\_\-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 \\
+\hline
+{\em fc\-\_\-p} & A pointer to the 'fc' array, i.\-e. array ... \\
+\hline
+{\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{]} \\
+\hline
+{\em indx\-\_\-p} & A pointer to the indexing array used for accessing the energy matrices \\
+\hline
+{\em ptype\-\_\-p} & A pointer to the ptype array containing the base pair types for each possibility (i,j) \\
+\hline
+\end{DoxyParams}
+\hypertarget{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{\index{M\-F\-E Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}!export\-\_\-cofold\-\_\-arrays@{export\-\_\-cofold\-\_\-arrays}}
+\index{export\-\_\-cofold\-\_\-arrays@{export\-\_\-cofold\-\_\-arrays}!MFE Structures of two hybridized Sequences@{M\-F\-E Structures of two hybridized Sequences}}
+\subsubsection[{export\-\_\-cofold\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void export\-\_\-cofold\-\_\-arrays (
+\begin{DoxyParamCaption}
+\item[{int $\ast$$\ast$}]{f5\-\_\-p, }
+\item[{int $\ast$$\ast$}]{c\-\_\-p, }
+\item[{int $\ast$$\ast$}]{f\-M\-L\-\_\-p, }
+\item[{int $\ast$$\ast$}]{f\-M1\-\_\-p, }
+\item[{int $\ast$$\ast$}]{fc\-\_\-p, }
+\item[{int $\ast$$\ast$}]{indx\-\_\-p, }
+\item[{char $\ast$$\ast$}]{ptype\-\_\-p}
+\end{DoxyParamCaption}
+)}}\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}
+{\em f5\-\_\-p} & A pointer to the 'f5' array, i.\-e. array conatining best free energy in interval \mbox{[}1,j\mbox{]} \\
+\hline
+{\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 \\
+\hline
+{\em f\-M\-L\-\_\-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 \\
+\hline
+{\em f\-M1\-\_\-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 \\
+\hline
+{\em fc\-\_\-p} & A pointer to the 'fc' array, i.\-e. array ... \\
+\hline
+{\em indx\-\_\-p} & A pointer to the indexing array used for accessing the energy matrices \\
+\hline
+{\em ptype\-\_\-p} & A pointer to the ptype array containing the base pair types for each possibility (i,j) \\
+\hline
+\end{DoxyParams}
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