binaries/src/ViennaRNA/doc/latex/structmodel__detailsT.tex

   1 \hypertarget{structmodel__detailsT}{\section{model\-\_\-details\-T Struct Reference}
   2 \label{structmodel__detailsT}\index{model\-\_\-details\-T@{model\-\_\-details\-T}}
   3 }
   4
   5
   6 The data structure that contains the complete model details used throughout the calculations.
   7
   8
   9 \subsection*{Data Fields}
  10 \begin{DoxyCompactItemize}
  11 \item
  12 int \hyperlink{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{dangles}
  13 \begin{DoxyCompactList}\small\item\em Specifies the dangle model used in any energy evaluation (0,1,2 or 3) \end{DoxyCompactList}\item
  14 \hypertarget{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{int \hyperlink{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}{special\-\_\-hp}}\label{structmodel__detailsT_a9d73fde17b0465311a80f607faa85617}
  15
  16 \begin{DoxyCompactList}\small\item\em Include special hairpin contributions for tri, tetra and hexaloops. \end{DoxyCompactList}\item
  17 \hypertarget{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{int \hyperlink{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}{no\-L\-P}}\label{structmodel__detailsT_a6fb076173d2cbc4259606ce23eedf17d}
  18
  19 \begin{DoxyCompactList}\small\item\em Only consider canonical structures, i.\-e. no 'lonely' base pairs. \end{DoxyCompactList}\item
  20 \hypertarget{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{int \hyperlink{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}{no\-G\-U}}\label{structmodel__detailsT_a0f982e6904d012e4fe41e99daa797f5d}
  21
  22 \begin{DoxyCompactList}\small\item\em Do not allow G\-U pairs. \end{DoxyCompactList}\item
  23 \hypertarget{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{int \hyperlink{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}{no\-G\-Uclosure}}\label{structmodel__detailsT_ae9cedf375cd904e5fb8e56cf3f64bcd9}
  24
  25 \begin{DoxyCompactList}\small\item\em Do not allow loops to be closed by G\-U pair. \end{DoxyCompactList}\item
  26 \hypertarget{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{int \hyperlink{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}{log\-M\-L}}\label{structmodel__detailsT_a415556dc150e02d108be81ecc5c48e85}
  27
  28 \begin{DoxyCompactList}\small\item\em Use logarithmic scaling for multi loops. \end{DoxyCompactList}\item
  29 \hypertarget{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{int \hyperlink{structmodel__detailsT_a55f083dad18c216505805a8062e63074}{circ}}\label{structmodel__detailsT_a55f083dad18c216505805a8062e63074}
  30
  31 \begin{DoxyCompactList}\small\item\em Assume molecule to be circular. \end{DoxyCompactList}\item
  32 \hypertarget{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{int \hyperlink{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}{gquad}}\label{structmodel__detailsT_aa1ecdce7bc3f375bd8a9a7b738abc0ea}
  33
  34 \begin{DoxyCompactList}\small\item\em Include G-\/quadruplexes in structure prediction. \end{DoxyCompactList}\end{DoxyCompactItemize}
  35
  36
  37 \subsection{Detailed Description}
  38 The data structure that contains the complete model details used throughout the calculations.
  39
  40 \subsection{Field Documentation}
  41 \hypertarget{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}{\index{model\-\_\-details\-T@{model\-\_\-details\-T}!dangles@{dangles}}
  42 \index{dangles@{dangles}!model_detailsT@{model\-\_\-details\-T}}
  43 \subsubsection[{dangles}]{\setlength{\rightskip}{0pt plus 5cm}int model\-\_\-details\-T\-::dangles}}\label{structmodel__detailsT_a89f9df217a4a7f4351a642655976376b}
  44
  45
  46 Specifies the dangle model used in any energy evaluation (0,1,2 or 3)
  47
  48 \begin{DoxyNote}{Note}
  49 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.
  50 \end{DoxyNote}
  51
  52
  53 The documentation for this struct was generated from the following file\-:\begin{DoxyCompactItemize}
  54 \item
  55 /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}