\hypertarget{structmodel__detailsT}{
\section{model\_\-detailsT Struct Reference}
\label{structmodel__detailsT}\index{model\_\-detailsT@{model\_\-detailsT}}
}


The data structure that contains the complete model details used throughout the calculations.  
\subsection*{Data Fields}
\begin{DoxyCompactItemize}
\item 
int \hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}
\begin{DoxyCompactList}\small\item\em Specifies the dangle model used in any energy evaluation (0,1,2 or 3). \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{
int \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\_\-hp}}
\label{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}

\begin{DoxyCompactList}\small\item\em Include special hairpin contributions for tri, tetra and hexaloops. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{
int \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{noLP}}
\label{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}

\begin{DoxyCompactList}\small\item\em Only consider canonical structures, i.e. no 'lonely' base pairs. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{
int \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{noGU}}
\label{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}

\begin{DoxyCompactList}\small\item\em Do not allow GU pairs. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{
int \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{noGUclosure}}
\label{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}

\begin{DoxyCompactList}\small\item\em Do not allow loops to be closed by GU pair. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{
int \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{logML}}
\label{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}

\begin{DoxyCompactList}\small\item\em Use logarithmic scaling for multi loops. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{
int \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ}}
\label{structmodel__detailsT_a55f083dad18c216505805a8062e63074}

\begin{DoxyCompactList}\small\item\em Assume molecule to be circular. \item\end{DoxyCompactList}\item 
\hypertarget{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{
int \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad}}
\label{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}

\begin{DoxyCompactList}\small\item\em Include G-\/quadruplexes in structure prediction. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
The data structure that contains the complete model details used throughout the calculations. 

\subsection{Field Documentation}
\hypertarget{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{
\index{model\_\-detailsT@{model\_\-detailsT}!dangles@{dangles}}
\index{dangles@{dangles}!model_detailsT@{model\_\-detailsT}}
\subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int {\bf model\_\-detailsT::dangles}}}
\label{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}


Specifies the dangle model used in any energy evaluation (0,1,2 or 3). \begin{DoxyNote}{Note}
Some function do not implement all dangle model but only a subset of (0,1,2,3). Read the documentaion of the particular recurrences or energy evaluation function for information about the provided dangle model. 
\end{DoxyNote}


The documentation for this struct was generated from the following file:\begin{DoxyCompactItemize}
\item 
/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/\hyperlink{data__structures_8h}{data\_\-structures.h}\end{DoxyCompactItemize}
