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

diff --git a/binaries/src/ViennaRNA/doc/latex/structmodel__detailsT.tex b/binaries/src/ViennaRNA/doc/latex/structmodel__detailsT.tex
index bb423bb..501741d 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/structmodel__detailsT.tex
+++ b/binaries/src/ViennaRNA/doc/latex/structmodel__detailsT.tex
@@ -1,55 +1,68 @@
-\hypertarget{structmodel__detailsT}{\section{model\-\_\-details\-T Struct Reference}
-\label{structmodel__detailsT}\index{model\-\_\-details\-T@{model\-\_\-details\-T}}
+\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) \end{DoxyCompactList}\item 
-\hypertarget{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{int \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\-\_\-hp}}\label{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}
+\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. \end{DoxyCompactList}\item 
-\hypertarget{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{int \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{no\-L\-P}}\label{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}
+\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. \end{DoxyCompactList}\item 
-\hypertarget{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{int \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{no\-G\-U}}\label{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}
+\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 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 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 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 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. \end{DoxyCompactList}\item 
-\hypertarget{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{int \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ}}\label{structmodel__detailsT_a55f083dad18c216505805a8062e63074}
+\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. \end{DoxyCompactList}\item 
-\hypertarget{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{int \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad}}\label{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}
+\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. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\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\-\_\-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}
-
+\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}
+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}
+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}
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/\hyperlink{data__structures_8h}{data\_\-structures.h}\end{DoxyCompactItemize}