\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
\begin{figure}[H]
\begin{center}
\leavevmode
\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 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}

\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{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 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}
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()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\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{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 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()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\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{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 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()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\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{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 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_gab5169ea4f72f250e43811463a33f4e40}{energy\_\-of\_\-struct\_\-par()}, \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\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{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 RNA. If verbosity level is set to a value $>$0, energies of structure elements are printed to stdout

\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_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()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\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{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}


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}
\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}
