-\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}}
+\hypertarget{fold_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h File Reference}
+\label{fold_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/fold.h}}
}
-M\-F\-E calculations and energy evaluations for single R\-N\-A sequences.
-
-
-Include dependency graph for fold.\-h\-:
-\nopagebreak
+MFE calculations and energy evaluations for single RNA sequences.
+Include dependency graph for fold.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=250pt]{fold_8h__incl}
+\includegraphics[width=203pt]{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_gadb973133c241d57c04b253df35e4d34e}{fold\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int is\_\-constrained, int is\_\-circular)
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an RNA sequence. \item\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
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of an RNA sequence. \item\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)
+\begin{DoxyCompactList}\small\item\em Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence. \item\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 RNA using global model detail settings. \item\end{DoxyCompactList}\item
+float \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int verbosity\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded RNA. \item\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 RNA. \item\end{DoxyCompactList}\item
+float \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_\-of\_\-circ\_\-struct\_\-par} (const char $\ast$string, const char $\ast$structure, \hyperlink{structparamT}{paramT} $\ast$parameters, int verbosity\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded circular RNA. \item\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 RNA. \item\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}{paramT} $\ast$parameters, int verbosity\_\-level)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of an already folded RNA. \item\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. \item\end{DoxyCompactList}\item
+void \hyperlink{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}{parenthesis\_\-structure} (char $\ast$structure, \hyperlink{structbondT}{bondT} $\ast$bp, int length)
+\begin{DoxyCompactList}\small\item\em Create a dot-\/backet/parenthesis structure from backtracking stack. \item\end{DoxyCompactList}\item
+void \hyperlink{fold_8h_a325f3835c68f34fe833b2b7a5828857f}{parenthesis\_\-zuker} (char $\ast$structure, \hyperlink{structbondT}{bondT} $\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. \item\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. \item\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). \item\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). \item\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. \item\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 \hyperlink{structplist}{plist} from a dot-\/bracket string. \item\end{DoxyCompactList}\item
+int \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy} (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)
+int \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE} (int size, int type, int si1, int sj1, const char $\ast$string)
\item
-void \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length)
+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)
+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)
+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)
+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}
+\hypertarget{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{
+int \hyperlink{fold_8h_a80c3c5fd35e7479704cc91d2d0367743}{logML}}
+\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 if nonzero use logarithmic ML energy in energy\_\-of\_\-struct \item\end{DoxyCompactList}\item
+\hypertarget{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{
+int \hyperlink{fold_8h_a6c5655c8b272e3e6cab74dd0f540294f}{uniq\_\-ML}}
+\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 do ML decomposition uniquely (for subopt) \item\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 set to first pos of second seq for cofolding \item\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}
+\begin{DoxyCompactList}\small\item\em verbose info from energy\_\-of\_\-struct \item\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...
+MFE calculations and energy evaluations for single RNA sequences. This file includes (almost) all function declarations within the RNAlib that are related to MFE 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}
-
+\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 (char $\ast$ {\em structure}, \/ {\bf bondT} $\ast$ {\em bp}, \/ int {\em length})}}
+\label{fold_8h_a87b7869bd1d8dc79c60775c74e009e9b}
-Create a dot-\/backet/parenthesis structure from backtracking stack.
-\begin{DoxyNote}{Note}
+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}
-
+\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 (char $\ast$ {\em structure}, \/ {\bf bondT} $\ast$ {\em bp}, \/ int {\em length})}}
+\label{fold_8h_a325f3835c68f34fe833b2b7a5828857f}
-Create a dot-\/backet/parenthesis structure from backtracking stack obtained by zuker suboptimal calculation in cofold.\-c.
-\begin{DoxyNote}{Note}
+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}
-
+\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 (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure}, \/ int {\em m1}, \/ int {\em m2})}}
+\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).
+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()}
+\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}
+\item[{\em string}]RNA sequence \item[{\em structure}]secondary structure in dot-\/bracket notation \item[{\em m1}]first coordinate of base pair \item[{\em m2}]second coordinate of base pair \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}
+\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 (short $\ast$ {\em pt}, \/ short $\ast$ {\em s}, \/ short $\ast$ {\em s1}, \/ int {\em m1}, \/ int {\em m2})}}
+\label{fold_8h_a49e0ee561be69faf0568213546f6a53f}
-Calculate energy of a move (closing or opening of a base pair)
+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).
-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()}
+\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}
+\item[{\em pt}]the pair table of the secondary structure \item[{\em s}]encoded RNA sequence \item[{\em s1}]encoded RNA sequence \item[{\em m1}]first coordinate of base pair \item[{\em m2}]second coordinate of base pair \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}
+\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 (short $\ast$ {\em ptable}, \/ short $\ast$ {\em s}, \/ short $\ast$ {\em s1}, \/ int {\em i})}}
+\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}
+\item[{\em ptable}]the pair table of the secondary structure \item[{\em s}]encoded RNA sequence \item[{\em s1}]encoded RNA sequence \item[{\em i}]position of covering base pair \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$$\ast$}]{pl, }
-\item[{const char $\ast$}]{struc, }
-\item[{float}]{pr}
-\end{DoxyParamCaption}
-)}}\label{fold_8h_adaa59b81664e2e36cb9932e891558fae}
-
+\hypertarget{fold_8h_adaa59b81664e2e36cb9932e891558fae}{
+\index{fold.h@{fold.h}!assign\_\-plist\_\-from\_\-db@{assign\_\-plist\_\-from\_\-db}}
+\index{assign\_\-plist\_\-from\_\-db@{assign\_\-plist\_\-from\_\-db}!fold.h@{fold.h}}
+\subsubsection[{assign\_\-plist\_\-from\_\-db}]{\setlength{\rightskip}{0pt plus 5cm}void assign\_\-plist\_\-from\_\-db ({\bf plist} $\ast$$\ast$ {\em pl}, \/ const char $\ast$ {\em struc}, \/ float {\em pr})}}
+\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.
+Create a \hyperlink{structplist}{plist} from a dot-\/bracket string. The dot-\/bracket string is parsed and for each base pair an entry in the \hyperlink{structplist}{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
+The end of the \hyperlink{structplist}{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}
+\item[{\em pl}]A pointer to the \hyperlink{structplist}{plist} that is to be created \item[{\em struc}]The secondary structure in dot-\/bracket notation \item[{\em pr}]The probability for each base pair \end{DoxyParams}
+\hypertarget{fold_8h_a2163034a25c6115d894b199e97e03f6c}{
+\index{fold.h@{fold.h}!LoopEnergy@{LoopEnergy}}
+\index{LoopEnergy@{LoopEnergy}!fold.h@{fold.h}}
+\subsubsection[{LoopEnergy}]{\setlength{\rightskip}{0pt plus 5cm}int LoopEnergy (int {\em n1}, \/ int {\em n2}, \/ int {\em type}, \/ int {\em type\_\-2}, \/ int {\em si1}, \/ int {\em sj1}, \/ int {\em sp1}, \/ int {\em sq1})}}
+\label{fold_8h_a2163034a25c6115d894b199e97e03f6c}
+\begin{Desc}
+\item[\hyperlink{deprecated__deprecated000002}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_\-IntLoop()} instead!\} \end{Desc}
+\hypertarget{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{
+\index{fold.h@{fold.h}!HairpinE@{HairpinE}}
+\index{HairpinE@{HairpinE}!fold.h@{fold.h}}
+\subsubsection[{HairpinE}]{\setlength{\rightskip}{0pt plus 5cm}int HairpinE (int {\em size}, \/ int {\em type}, \/ int {\em si1}, \/ int {\em sj1}, \/ const char $\ast$ {\em string})}}
+\label{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}
+\begin{Desc}
+\item[\hyperlink{deprecated__deprecated000003}{Deprecated}]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_\-Hairpin()} instead!\} \end{Desc}
+\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 (int {\em length})}}
+\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{Desc}
+\item[\hyperlink{deprecated__deprecated000004}{Deprecated}]\{This function is deprecated and will be removed soon!\}\end{Desc}
+\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 (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure})}}
+\label{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}
+Calculate the free energy of an already folded RNA
\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
+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()}
+\begin{Desc}
+\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{Desc}
+\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}
+\item[{\em string}]RNA sequence \item[{\em structure}]secondary structure in dot-\/bracket notation \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
+\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 (const char $\ast$ {\em string}, \/ short $\ast$ {\em ptable}, \/ short $\ast$ {\em s}, \/ short $\ast$ {\em s1})}}
+\label{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}
+Calculate the free energy of an already folded RNA
\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
+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()}
+\begin{Desc}
+\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{Desc}
+\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}
+\item[{\em string}]RNA sequence \item[{\em ptable}]the pair table of the secondary structure \item[{\em s}]encoded RNA sequence \item[{\em s1}]encoded RNA sequence \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
+\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 (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure})}}
+\label{fold_8h_a657222e2758c46bf13b416ef3032e417}
+Calculate the free energy of an already folded circular RNA
\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
+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()}
+\begin{Desc}
+\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{Desc}
+\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}
+\item[{\em string}]RNA sequence \item[{\em structure}]secondary structure in dot-\/bracket notation \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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