-\hypertarget{group__eval}{\section{Energy evaluation}
+\hypertarget{group__eval}{
+\section{Energy evaluation}
\label{group__eval}\index{Energy evaluation@{Energy evaluation}}
}
This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
-Collaboration diagram for Energy evaluation\-:
-\nopagebreak
+Collaboration diagram for Energy evaluation:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=336pt]{group__eval}
+\includegraphics[width=173pt]{group__eval}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\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}\end{DoxyCompactItemize}
+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}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item
-\hypertarget{group__eval_ga567530678f6260a1a649a5beca5da4c5}{int \hyperlink{group__eval_ga567530678f6260a1a649a5beca5da4c5}{eos\-\_\-debug}}\label{group__eval_ga567530678f6260a1a649a5beca5da4c5}
+\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}
This module contains all functions and variables related to energy evaluation of sequence/structure pairs.
\subsection{Function Documentation}
-\hypertarget{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}}
-\index{energy\-\_\-of\-\_\-structure@{energy\-\_\-of\-\_\-structure}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-structure (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{const char $\ast$}]{structure, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}
+\hypertarget{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{
+\index{eval@{eval}!energy\_\-of\_\-structure@{energy\_\-of\_\-structure}}
+\index{energy\_\-of\_\-structure@{energy\_\-of\_\-structure}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-structure (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}
-Calculate the free energy of an already folded R\-N\-A using global model detail settings.
-
-If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+Calculate the free energy of an already folded RNA using global model detail settings. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
\begin{DoxyNote}{Note}
-Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
+OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()} for a completely threadsafe implementation.
\end{DoxyNote}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()}, \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_\-of\_\-circ\_\-structure()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em string} & R\-N\-A sequence \\
-\hline
-{\em structure} & secondary structure in dot-\/bracket notation \\
-\hline
-{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
-\hline
-\end{DoxyParams}
+\item[{\em string}]RNA sequence \item[{\em structure}]secondary structure in dot-\/bracket notation \item[{\em verbosity\_\-level}]a flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
the free energy of the input structure given the input sequence in kcal/mol
\end{DoxyReturn}
-\hypertarget{group__eval_gab5169ea4f72f250e43811463a33f4e40}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}}
-\index{energy\-\_\-of\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-struct\-\_\-par (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{const char $\ast$}]{structure, }
-\item[{{\bf param\-T} $\ast$}]{parameters, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_gab5169ea4f72f250e43811463a33f4e40}
-
+\hypertarget{group__eval_gab5169ea4f72f250e43811463a33f4e40}{
+\index{eval@{eval}!energy\_\-of\_\-struct\_\-par@{energy\_\-of\_\-struct\_\-par}}
+\index{energy\_\-of\_\-struct\_\-par@{energy\_\-of\_\-struct\_\-par}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-struct\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-struct\_\-par (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure}, \/ {\bf paramT} $\ast$ {\em parameters}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_gab5169ea4f72f250e43811463a33f4e40}
-Calculate the free energy of an already folded R\-N\-A.
-If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+Calculate the free energy of an already folded RNA. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()}, \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_\-of\_\-circ\_\-structure()}, \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\_\-of\_\-structure\_\-pt()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em string} & R\-N\-A sequence in uppercase letters \\
-\hline
-{\em structure} & Secondary structure in dot-\/bracket notation \\
-\hline
-{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
-\hline
-{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
-\hline
-\end{DoxyParams}
+\item[{\em string}]RNA sequence in uppercase letters \item[{\em structure}]Secondary structure in dot-\/bracket notation \item[{\em parameters}]A data structure containing the prescaled energy contributions and the model details. \item[{\em verbosity\_\-level}]A flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy of the input structure given the input sequence in kcal/mol
\end{DoxyReturn}
-\hypertarget{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}}
-\index{energy\-\_\-of\-\_\-circ\-\_\-structure@{energy\-\_\-of\-\_\-circ\-\_\-structure}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-structure (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{const char $\ast$}]{structure, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}
-
+\hypertarget{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{
+\index{eval@{eval}!energy\_\-of\_\-circ\_\-structure@{energy\_\-of\_\-circ\_\-structure}}
+\index{energy\_\-of\_\-circ\_\-structure@{energy\_\-of\_\-circ\_\-structure}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-circ\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-circ\_\-structure (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}
-Calculate the free energy of an already folded circular R\-N\-A.
-\begin{DoxyNote}{Note}
-Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()} for a completely threadsafe implementation.
+Calculate the free energy of an already folded circular RNA. \begin{DoxyNote}{Note}
+OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_\-of\_\-circ\_\-struct\_\-par()} for a completely threadsafe implementation.
\end{DoxyNote}
If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{energy\_\-of\_\-circ\_\-struct\_\-par()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em string} & R\-N\-A sequence \\
-\hline
-{\em structure} & Secondary structure in dot-\/bracket notation \\
-\hline
-{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
-\hline
-\end{DoxyParams}
+\item[{\em string}]RNA sequence \item[{\em structure}]Secondary structure in dot-\/bracket notation \item[{\em verbosity\_\-level}]A flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy of the input structure given the input sequence in kcal/mol
\end{DoxyReturn}
-\hypertarget{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}}
-\index{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par@{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-circ\-\_\-struct\-\_\-par (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{const char $\ast$}]{structure, }
-\item[{{\bf param\-T} $\ast$}]{parameters, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}
+\hypertarget{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}{
+\index{eval@{eval}!energy\_\-of\_\-circ\_\-struct\_\-par@{energy\_\-of\_\-circ\_\-struct\_\-par}}
+\index{energy\_\-of\_\-circ\_\-struct\_\-par@{energy\_\-of\_\-circ\_\-struct\_\-par}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-circ\_\-struct\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-circ\_\-struct\_\-par (const char $\ast$ {\em string}, \/ const char $\ast$ {\em structure}, \/ {\bf paramT} $\ast$ {\em parameters}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_ga75dc765ee4a1177832bc817c94cf88e5}
-Calculate the free energy of an already folded circular R\-N\-A.
+Calculate the free energy of an already folded circular RNA. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
-If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
-
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em string} & R\-N\-A sequence \\
-\hline
-{\em structure} & Secondary structure in dot-\/bracket notation \\
-\hline
-{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
-\hline
-{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
-\hline
-\end{DoxyParams}
+\item[{\em string}]RNA sequence \item[{\em structure}]Secondary structure in dot-\/bracket notation \item[{\em parameters}]A data structure containing the prescaled energy contributions and the model details. \item[{\em verbosity\_\-level}]A flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy of the input structure given the input sequence in kcal/mol
\end{DoxyReturn}
-\hypertarget{group__eval_ga8831445966b761417e713360791299d8}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}}
-\index{energy\-\_\-of\-\_\-structure\-\_\-pt@{energy\-\_\-of\-\_\-structure\-\_\-pt}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-structure\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-structure\-\_\-pt (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{short $\ast$}]{ptable, }
-\item[{short $\ast$}]{s, }
-\item[{short $\ast$}]{s1, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_ga8831445966b761417e713360791299d8}
-
+\hypertarget{group__eval_ga8831445966b761417e713360791299d8}{
+\index{eval@{eval}!energy\_\-of\_\-structure\_\-pt@{energy\_\-of\_\-structure\_\-pt}}
+\index{energy\_\-of\_\-structure\_\-pt@{energy\_\-of\_\-structure\_\-pt}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-structure\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int energy\_\-of\_\-structure\_\-pt (const char $\ast$ {\em string}, \/ short $\ast$ {\em ptable}, \/ short $\ast$ {\em s}, \/ short $\ast$ {\em s1}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_ga8831445966b761417e713360791299d8}
-Calculate the free energy of an already folded R\-N\-A.
-If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+Calculate the free energy of an already folded RNA. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
\begin{DoxyNote}{Note}
-Open\-M\-P\-: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()} for a completely threadsafe implementation.
+OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\_\-of\_\-struct\_\-pt\_\-par()} for a completely threadsafe implementation.
\end{DoxyNote}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par()}
+\begin{DoxySeeAlso}{See also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_\-pair\_\-table()}, \hyperlink{group__eval_gada4701dd7519b29da75ceac147601f4e}{energy\_\-of\_\-struct\_\-pt\_\-par()}
\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
-{\em verbosity\-\_\-level} & a flag to turn verbose output on/off \\
-\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 \item[{\em verbosity\_\-level}]a flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
the free energy of the input structure given the input sequence in 10kcal/mol
\end{DoxyReturn}
-\hypertarget{group__eval_gada4701dd7519b29da75ceac147601f4e}{\index{Energy evaluation@{Energy evaluation}!energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}}
-\index{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par@{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}!Energy evaluation@{Energy evaluation}}
-\subsubsection[{energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}int energy\-\_\-of\-\_\-struct\-\_\-pt\-\_\-par (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{string, }
-\item[{short $\ast$}]{ptable, }
-\item[{short $\ast$}]{s, }
-\item[{short $\ast$}]{s1, }
-\item[{{\bf param\-T} $\ast$}]{parameters, }
-\item[{int}]{verbosity\-\_\-level}
-\end{DoxyParamCaption}
-)}}\label{group__eval_gada4701dd7519b29da75ceac147601f4e}
-
-
-Calculate the free energy of an already folded R\-N\-A.
+\hypertarget{group__eval_gada4701dd7519b29da75ceac147601f4e}{
+\index{eval@{eval}!energy\_\-of\_\-struct\_\-pt\_\-par@{energy\_\-of\_\-struct\_\-pt\_\-par}}
+\index{energy\_\-of\_\-struct\_\-pt\_\-par@{energy\_\-of\_\-struct\_\-pt\_\-par}!eval@{eval}}
+\subsubsection[{energy\_\-of\_\-struct\_\-pt\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}int energy\_\-of\_\-struct\_\-pt\_\-par (const char $\ast$ {\em string}, \/ short $\ast$ {\em ptable}, \/ short $\ast$ {\em s}, \/ short $\ast$ {\em s1}, \/ {\bf paramT} $\ast$ {\em parameters}, \/ int {\em verbosity\_\-level})}}
+\label{group__eval_gada4701dd7519b29da75ceac147601f4e}
-If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\-\_\-of\-\_\-struct\-\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters()}
+Calculate the free energy of an already folded RNA. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_\-pair\_\-table()}, \hyperlink{group__eval_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em string} & R\-N\-A sequence in uppercase letters \\
-\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
-{\em parameters} & A data structure containing the prescaled energy contributions and the model details. \\
-\hline
-{\em verbosity\-\_\-level} & A flag to turn verbose output on/off \\
-\hline
-\end{DoxyParams}
+\item[{\em string}]RNA sequence in uppercase letters \item[{\em ptable}]The pair table of the secondary structure \item[{\em s}]Encoded RNA sequence \item[{\em s1}]Encoded RNA sequence \item[{\em parameters}]A data structure containing the prescaled energy contributions and the model details. \item[{\em verbosity\_\-level}]A flag to turn verbose output on/off \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy of the input structure given the input sequence in 10kcal/mol
\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff