--- /dev/null
+\hypertarget{group__mfe__fold}{\section{Calculating Minimum Free Energy (M\-F\-E) Structures}
+\label{group__mfe__fold}\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}}
+}
+
+
+This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences.
+
+
+Collaboration diagram for Calculating Minimum Free Energy (M\-F\-E) Structures\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__mfe__fold}
+\end{center}
+\end{figure}
+\subsection*{Modules}
+\begin{DoxyCompactItemize}
+\item
+\hyperlink{group__mfe__cofold}{M\-F\-E Structures of two hybridized Sequences}
+\item
+\hyperlink{group__consensus__mfe__fold}{M\-F\-E Consensus Structures for Sequence Alignment(s)}
+\item
+\hyperlink{group__local__mfe__fold}{Local M\-F\-E structure Prediction and Z-\/scores}
+\item
+\hyperlink{group__kl__neighborhood__mfe}{Calculating M\-F\-E representatives of a Distance Based Partitioning}
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy (M\-F\-E) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+float \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained, int is\-\_\-circular)
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item
+float \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold} (const char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence. \end{DoxyCompactList}\item
+float \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold} (const char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence. \end{DoxyCompactList}\item
+\hypertarget{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{void \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\-\_\-arrays} (void)}\label{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}
+
+\begin{DoxyCompactList}\small\item\em Free arrays for mfe folding. \end{DoxyCompactList}\item
+\hypertarget{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{void \hyperlink{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}{update\-\_\-fold\-\_\-params} (void)}\label{group__mfe__fold_ga41bf8f6fa15b94471f7095cad9f0ccf3}
+
+\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. This section covers all functions and variables related to the calculation of minimum free energy (M\-F\-E) structures.
+
+The library provides a fast dynamic programming minimum free energy folding algorithm as described by Zuker \& Stiegler (1981).
+
+The library provides a fast dynamic programming minimum free energy folding algorithm as described in\cite{zuker:1981}. All relevant parts that directly implement the \char`\"{}\-Zuker \& Stiegler\char`\"{} algorithm for single sequences are described in this section.
+
+Folding of circular R\-N\-A sequences is handled as a post-\/processing step of the forward recursions. See\cite{hofacker:2006} for further details.
+
+Nevertheless, the R\-N\-Alib also provides interfaces for the prediction of consensus M\-F\-E structures of sequence alignments, M\-F\-E structure for two hybridized sequences, local optimal structures and many more. For those more specialized variants of M\-F\-E folding routines, please consult the appropriate subsections (Modules) as listed above.
+
+\subsection{Function Documentation}
+\hypertarget{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!fold\-\_\-par@{fold\-\_\-par}}
+\index{fold\-\_\-par@{fold\-\_\-par}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}}
+\subsubsection[{fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float fold\-\_\-par (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{sequence, }
+\item[{char $\ast$}]{structure, }
+\item[{{\bf param\-T} $\ast$}]{parameters, }
+\item[{int}]{is\-\_\-constrained, }
+\item[{int}]{is\-\_\-circular}
+\end{DoxyParamCaption}
+)}}\label{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}
+
+
+Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence.
+
+The first parameter given, the R\-N\-A sequence, must be {\itshape uppercase} and should only contain an alphabet $\Sigma$ that is understood by the R\-N\-Alib\par
+ (e.\-g. $ \Sigma = \{A,U,C,G\} $)\par
+
+
+The second parameter, {\itshape structure}, must always point to an allocated block of memory with a size of at least $\mathrm{strlen}(\mathrm{sequence})+1$
+
+If the third parameter is N\-U\-L\-L, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used.
+
+The fourth parameter indicates whether a secondary structure constraint in enhanced dot-\/bracket notation is passed through the structure parameter or not. If so, the characters \char`\"{} $|$ x $<$ $>$ \char`\"{} are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets \char`\"{} ( ) \char`\"{} denote base pairs, dots \char`\"{}.\char`\"{} are used for unconstrained bases.
+
+To indicate that the R\-N\-A sequence is circular and thus has to be post-\/processed, set the last parameter to non-\/zero
+
+After a successful call of \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, a backtracked secondary structure (in dot-\/bracket notation) that exhibits the minimum of free energy will be written to the memory {\itshape structure} is pointing to. The function returns the minimum of free energy for any fold of the sequence given.
+
+\begin{DoxyNote}{Note}
+Open\-M\-P\-: Passing N\-U\-L\-L to the 'parameters' argument involves access to several global model detail variables and thus is not to be considered threadsafe
+\end{DoxyNote}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T}, set\-\_\-energy\-\_\-model(), \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & R\-N\-A sequence \\
+\hline
+{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\
+\hline
+{\em parameters} & A data structure containing the prescaled energy contributions and the model details. (N\-U\-L\-L may be passed, see Open\-M\-P notes above) \\
+\hline
+{\em is\-\_\-constrained} & Switch to indicate that a structure contraint is passed via the structure argument (0==off) \\
+\hline
+{\em is\-\_\-circular} & Switch to (de-\/)activate postprocessing steps in case R\-N\-A sequence is circular (0==off)\\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the minimum free energy (M\-F\-E) in kcal/mol
+\end{DoxyReturn}
+\hypertarget{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!fold@{fold}}
+\index{fold@{fold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}}
+\subsubsection[{fold}]{\setlength{\rightskip}{0pt plus 5cm}float fold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{sequence, }
+\item[{char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}
+
+
+Compute minimum free energy and an appropriate secondary structure of an R\-N\-A sequence.
+
+This function essentially does the same thing as \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}. However, it takes its model details, i.\-e. \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}, \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}, \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}, \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}, \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs} from the current global settings within the library
+
+Use \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()} for a completely threadsafe variant
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & R\-N\-A sequence \\
+\hline
+{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the minimum free energy (M\-F\-E) in kcal/mol
+\end{DoxyReturn}
+\hypertarget{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{\index{Calculating Minimum Free Energy (\-M\-F\-E) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}!circfold@{circfold}}
+\index{circfold@{circfold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\-M\-F\-E) Structures}}
+\subsubsection[{circfold}]{\setlength{\rightskip}{0pt plus 5cm}float circfold (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{sequence, }
+\item[{char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}
+
+
+Compute minimum free energy and an appropriate secondary structure of a circular R\-N\-A sequence.
+
+This function essentially does the same thing as \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}. However, it takes its model details, i.\-e. \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{fold__vars_8h_a72b511ed1201f7e23ec437e468790d74}{dangles}, \hyperlink{fold__vars_8h_a4f6265bdf0ead7ff4628a360adbfd77e}{tetra\-\_\-loop}, \hyperlink{fold__vars_8h_abf380d09e4f1ab94fc6af57cf0ad5d32}{no\-G\-U}, \hyperlink{fold__vars_8h_aa8d1c7b92489179e1eafa562b7bdd259}{no\-\_\-closing\-G\-U}, \hyperlink{fold__vars_8h_a0afc287c2464866d94858c39175154af}{fold\-\_\-constrained}, \hyperlink{fold__vars_8h_a097eccaabd6ae8b4fef83cccff85bb5d}{no\-Lonely\-Pairs} from the current global settings within the library
+
+Use \hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()} for a completely threadsafe variant
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__mfe__fold_gadb973133c241d57c04b253df35e4d34e}{fold\-\_\-par()}, \hyperlink{group__mfe__fold_ga4ac63ab3e8d9a80ced28b8052d94e423}{circfold()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & R\-N\-A sequence \\
+\hline
+{\em structure} & A pointer to the character array where the secondary structure in dot-\/bracket notation will be written to \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the minimum free energy (M\-F\-E) in kcal/mol
+\end{DoxyReturn}
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