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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / structmodel__detailsT.tex

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+\hypertarget{structmodel__detailsT}{\section{model\-\_\-details\-T Struct Reference}
+\label{structmodel__detailsT}\index{model\-\_\-details\-T@{model\-\_\-details\-T}}
+}
+
+
+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) \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. \end{DoxyCompactList}\item 
+\hypertarget{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{int \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{no\-L\-P}}\label{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}
+
+\begin{DoxyCompactList}\small\item\em Only consider canonical structures, i.\-e. no 'lonely' base pairs. \end{DoxyCompactList}\item 
+\hypertarget{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{int \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{no\-G\-U}}\label{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}
+
+\begin{DoxyCompactList}\small\item\em Do not allow G\-U pairs. \end{DoxyCompactList}\item 
+\hypertarget{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{int \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{no\-G\-Uclosure}}\label{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}
+
+\begin{DoxyCompactList}\small\item\em Do not allow loops to be closed by G\-U pair. \end{DoxyCompactList}\item 
+\hypertarget{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{int \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{log\-M\-L}}\label{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}
+
+\begin{DoxyCompactList}\small\item\em Use logarithmic scaling for multi loops. \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. \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. \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\-\_\-details\-T@{model\-\_\-details\-T}!dangles@{dangles}}
+\index{dangles@{dangles}!model_detailsT@{model\-\_\-details\-T}}
+\subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int model\-\_\-details\-T\-::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 
+/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/\hyperlink{data__structures_8h}{data\-\_\-structures.\-h}\end{DoxyCompactItemize}