--- /dev/null
+\hypertarget{fold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.h File Reference}
+\label{fold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/fold.\-h}}
+}
+
+
+M\-F\-E calculations and energy evaluations for single R\-N\-A sequences.
+
+
+Include dependency graph for fold.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{fold_8h__incl}
+\end{center}
+\end{figure}
+\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
+float \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A using global model detail settings. \end{DoxyCompactList}\item
+float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
+float \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure} (const char $\ast$string, const char $\ast$structure, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
+float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular R\-N\-A. \end{DoxyCompactList}\item
+int \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \end{DoxyCompactList}\item
+int \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1, \hyperlink{structparamT}{param\-T} $\ast$parameters, int verbosity\-\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded R\-N\-A. \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
+void \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\-\_\-structure} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length)
+\begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack. \end{DoxyCompactList}\item
+void \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\-\_\-zuker} (char $\ast$structure, \hyperlink{structbondT}{bond\-T} $\ast$bp, int length)
+\begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c. \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}\item
+float \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move} (const char $\ast$string, const char $\ast$structure, int m1, int m2)
+\begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item
+int \hyperlink{fold_8h_a49e0ee561be69faf0568213546f6a53f}{energy\-\_\-of\-\_\-move\-\_\-pt} (short $\ast$pt, short $\ast$s, short $\ast$s1, int m1, int m2)
+\begin{DoxyCompactList}\small\item\em Calculate energy of a move (closing or opening of a base pair) \end{DoxyCompactList}\item
+int \hyperlink{fold_8h_a507d4fd93f4b398d793ba2402731388d}{loop\-\_\-energy} (short $\ast$ptable, short $\ast$s, short $\ast$s1, int i)
+\begin{DoxyCompactList}\small\item\em Calculate energy of a loop. \end{DoxyCompactList}\item
+void \hyperlink{fold_8h_adaa59b81664e2e36cb9932e891558fae}{assign\-\_\-plist\-\_\-from\-\_\-db} (\hyperlink{structplist}{plist} $\ast$$\ast$pl, const char $\ast$struc, float \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
+\begin{DoxyCompactList}\small\item\em Create a plist from a dot-\/bracket string. \end{DoxyCompactList}\item
+int \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{Loop\-Energy} (int n1, int n2, int type, int type\-\_\-2, int si1, int sj1, int sp1, int sq1)
+\item
+int \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{Hairpin\-E} (int size, int type, int si1, int sj1, const char $\ast$string)
+\item
+void \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length)
+\item
+float \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct} (const char $\ast$string, const char $\ast$structure)
+\item
+int \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1)
+\item
+float \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct} (const char $\ast$string, const char $\ast$structure)
+\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+\hypertarget{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{int \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{log\-M\-L}}\label{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}
+
+\begin{DoxyCompactList}\small\item\em if nonzero use logarithmic M\-L energy in energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\item
+\hypertarget{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{int \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\-\_\-\-M\-L}}\label{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}
+
+\begin{DoxyCompactList}\small\item\em do M\-L decomposition uniquely (for subopt) \end{DoxyCompactList}\item
+\hypertarget{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{int \hyperlink{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point}}\label{fold_8h_ab9b2c3a37a5516614c06d0ab54b97cda}
+
+\begin{DoxyCompactList}\small\item\em set to first pos of second seq for cofolding \end{DoxyCompactList}\item
+\hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5}
+
+\begin{DoxyCompactList}\small\item\em verbose info from energy\-\_\-of\-\_\-struct \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+M\-F\-E calculations and energy evaluations for single R\-N\-A sequences. This file includes (almost) all function declarations within the R\-N\-Alib that are related to M\-F\-E folding...
+
+\subsection{Function Documentation}
+\hypertarget{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-structure@{parenthesis\-\_\-structure}}
+\index{parenthesis\-\_\-structure@{parenthesis\-\_\-structure}!fold.h@{fold.\-h}}
+\subsubsection[{parenthesis\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-structure (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{structure, }
+\item[{{\bf bond\-T} $\ast$}]{bp, }
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}
+
+
+Create a dot-\/backet/parenthesis structure from backtracking stack.
+
+\begin{DoxyNote}{Note}
+This function is threadsafe
+\end{DoxyNote}
+\hypertarget{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{\index{fold.\-h@{fold.\-h}!parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}}
+\index{parenthesis\-\_\-zuker@{parenthesis\-\_\-zuker}!fold.h@{fold.\-h}}
+\subsubsection[{parenthesis\-\_\-zuker}]{\setlength{\rightskip}{0pt plus 5cm}void parenthesis\-\_\-zuker (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{structure, }
+\item[{{\bf bond\-T} $\ast$}]{bp, }
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a325f3835c68f34fe833b2b7a5828857f}
+
+
+Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c.
+
+\begin{DoxyNote}{Note}
+This function is threadsafe
+\end{DoxyNote}
+\hypertarget{fold_8h_a539ecaed89730f7644c202f304d7529b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}}
+\index{energy\-\_\-of\-\_\-move@{energy\-\_\-of\-\_\-move}!fold.h@{fold.\-h}}
+\subsubsection[{energy\-\_\-of\-\_\-move}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-move (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure, }
+\item[{int}]{m1, }
+\item[{int}]{m2}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a539ecaed89730f7644c202f304d7529b}
+
+
+Calculate energy of a move (closing or opening of a base pair)
+
+If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & secondary structure in dot-\/bracket notation \\
+\hline
+{\em m1} & first coordinate of base pair \\
+\hline
+{\em m2} & second coordinate of base pair \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+energy change of the move in kcal/mol
+\end{DoxyReturn}
+\hypertarget{fold_8h_a49e0ee561be69faf0568213546f6a53f}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}}
+\index{energy\-\_\-of\-\_\-move\-\_\-pt@{energy\-\_\-of\-\_\-move\-\_\-pt}!fold.h@{fold.\-h}}
+\subsubsection[{energy\-\_\-of\-\_\-move\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-move\-\_\-pt (
+\begin{DoxyParamCaption}
+\item[{short $\ast$}]{pt, }
+\item[{short $\ast$}]{s, }
+\item[{short $\ast$}]{s1, }
+\item[{int}]{m1, }
+\item[{int}]{m2}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a49e0ee561be69faf0568213546f6a53f}
+
+
+Calculate energy of a move (closing or opening of a base pair)
+
+If the parameters m1 and m2 are negative, it is deletion (opening) of a base pair, otherwise it is insertion (opening).
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{fold_8h_a539ecaed89730f7644c202f304d7529b}{energy\-\_\-of\-\_\-move()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em pt} & the pair table of the secondary structure \\
+\hline
+{\em s} & encoded R\-N\-A sequence \\
+\hline
+{\em s1} & encoded R\-N\-A sequence \\
+\hline
+{\em m1} & first coordinate of base pair \\
+\hline
+{\em m2} & second coordinate of base pair \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+energy change of the move in 10cal/mol
+\end{DoxyReturn}
+\hypertarget{fold_8h_a507d4fd93f4b398d793ba2402731388d}{\index{fold.\-h@{fold.\-h}!loop\-\_\-energy@{loop\-\_\-energy}}
+\index{loop\-\_\-energy@{loop\-\_\-energy}!fold.h@{fold.\-h}}
+\subsubsection[{loop\-\_\-energy}]{\setlength{\rightskip}{0pt plus 5cm}int loop\-\_\-energy (
+\begin{DoxyParamCaption}
+\item[{short $\ast$}]{ptable, }
+\item[{short $\ast$}]{s, }
+\item[{short $\ast$}]{s1, }
+\item[{int}]{i}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a507d4fd93f4b398d793ba2402731388d}
+
+
+Calculate energy of a loop.
+
+
+\begin{DoxyParams}{Parameters}
+{\em ptable} & the pair table of the secondary structure \\
+\hline
+{\em s} & encoded R\-N\-A sequence \\
+\hline
+{\em s1} & encoded R\-N\-A sequence \\
+\hline
+{\em i} & position of covering base pair \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+free energy of the loop in 10cal/mol
+\end{DoxyReturn}
+\hypertarget{fold_8h_adaa59b81664e2e36cb9932e891558fae}{\index{fold.\-h@{fold.\-h}!assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}}
+\index{assign\-\_\-plist\-\_\-from\-\_\-db@{assign\-\_\-plist\-\_\-from\-\_\-db}!fold.h@{fold.\-h}}
+\subsubsection[{assign\-\_\-plist\-\_\-from\-\_\-db}]{\setlength{\rightskip}{0pt plus 5cm}void assign\-\_\-plist\-\_\-from\-\_\-db (
+\begin{DoxyParamCaption}
+\item[{{\bf plist} $\ast$$\ast$}]{pl, }
+\item[{const char $\ast$}]{struc, }
+\item[{float}]{pr}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_adaa59b81664e2e36cb9932e891558fae}
+
+
+Create a plist from a dot-\/bracket string.
+
+The dot-\/bracket string is parsed and for each base pair an entry in the plist is created. The probability of each pair in the list is set by a function parameter.
+
+The end of the plist is marked by sequence positions i as well as j equal to 0. This condition should be used to stop looping over its entries
+
+This function is threadsafe
+
+
+\begin{DoxyParams}{Parameters}
+{\em pl} & A pointer to the plist that is to be created \\
+\hline
+{\em struc} & The secondary structure in dot-\/bracket notation \\
+\hline
+{\em pr} & The probability for each base pair \\
+\hline
+\end{DoxyParams}
+\hypertarget{fold_8h_a2163034a25c6115d894b199e97e03f6c}{\index{fold.\-h@{fold.\-h}!Loop\-Energy@{Loop\-Energy}}
+\index{Loop\-Energy@{Loop\-Energy}!fold.h@{fold.\-h}}
+\subsubsection[{Loop\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}int Loop\-Energy (
+\begin{DoxyParamCaption}
+\item[{int}]{n1, }
+\item[{int}]{n2, }
+\item[{int}]{type, }
+\item[{int}]{type\-\_\-2, }
+\item[{int}]{si1, }
+\item[{int}]{sj1, }
+\item[{int}]{sp1, }
+\item[{int}]{sq1}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a2163034a25c6115d894b199e97e03f6c}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000002}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\-\_\-\-Int\-Loop()} instead!\} \end{DoxyRefDesc}
+\hypertarget{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{\index{fold.\-h@{fold.\-h}!Hairpin\-E@{Hairpin\-E}}
+\index{Hairpin\-E@{Hairpin\-E}!fold.h@{fold.\-h}}
+\subsubsection[{Hairpin\-E}]{\setlength{\rightskip}{0pt plus 5cm}int Hairpin\-E (
+\begin{DoxyParamCaption}
+\item[{int}]{size, }
+\item[{int}]{type, }
+\item[{int}]{si1, }
+\item[{int}]{sj1, }
+\item[{const char $\ast$}]{string}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000003}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\-\_\-\-Hairpin()} instead!\} \end{DoxyRefDesc}
+\hypertarget{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{\index{fold.\-h@{fold.\-h}!initialize\-\_\-fold@{initialize\-\_\-fold}}
+\index{initialize\-\_\-fold@{initialize\-\_\-fold}!fold.h@{fold.\-h}}
+\subsubsection[{initialize\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\-\_\-fold (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_ac3f0a28d9cb609d388b155445073fd20}
+Allocate arrays for folding\par
+ \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000004}{Deprecated}]\{This function is deprecated and will be removed soon!\}\end{DoxyRefDesc}
+\hypertarget{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}}
+\index{energy\-\_\-of\-\_\-struct@{energy\-\_\-of\-\_\-struct}!fold.h@{fold.\-h}}
+\subsubsection[{energy\-\_\-of\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}
+Calculate the free energy of an already folded R\-N\-A
+
+\begin{DoxyNote}{Note}
+This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
+
+\end{DoxyNote}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000005}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} instead!\end{DoxyRefDesc}
+
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure}, \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & secondary structure in dot-\/bracket notation \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the free energy of the input structure given the input sequence in kcal/mol
+\end{DoxyReturn}
+\hypertarget{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}}
+\index{energy\-\_\-of\-\_\-struct\-\_\-pt@{energy\-\_\-of\-\_\-struct\-\_\-pt}!fold.h@{fold.\-h}}
+\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{short $\ast$}]{ptable, }
+\item[{short $\ast$}]{s, }
+\item[{short $\ast$}]{s1}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}
+Calculate the free energy of an already folded R\-N\-A
+
+\begin{DoxyNote}{Note}
+This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
+
+\end{DoxyNote}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000006}{Deprecated}]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()} instead!\end{DoxyRefDesc}
+
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em ptable} & the pair table of the secondary structure \\
+\hline
+{\em s} & encoded R\-N\-A sequence \\
+\hline
+{\em s1} & encoded R\-N\-A sequence \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the free energy of the input structure given the input sequence in 10kcal/mol
+\end{DoxyReturn}
+\hypertarget{fold_8h_a657222e2758c46bf13b416ef3032e417}{\index{fold.\-h@{fold.\-h}!energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}}
+\index{energy\-\_\-of\-\_\-circ\-\_\-struct@{energy\-\_\-of\-\_\-circ\-\_\-struct}!fold.h@{fold.\-h}}
+\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{string, }
+\item[{const char $\ast$}]{structure}
+\end{DoxyParamCaption}
+)}}\label{fold_8h_a657222e2758c46bf13b416ef3032e417}
+Calculate the free energy of an already folded circular R\-N\-A
+
+\begin{DoxyNote}{Note}
+This function is not entirely threadsafe! Depending on the state of the global variable \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug} it prints energy information to stdout or not...\par
+
+\end{DoxyNote}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000007}{Deprecated}]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} instead!\end{DoxyRefDesc}
+
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct()}, \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em string} & R\-N\-A sequence \\
+\hline
+{\em structure} & secondary structure in dot-\/bracket notation \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+the free energy of the input structure given the input sequence in kcal/mol
+\end{DoxyReturn}
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