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+\hypertarget{structTwoDpfold__vars}{\section{Two\-Dpfold\-\_\-vars Struct Reference}
+\label{structTwoDpfold__vars}\index{Two\-Dpfold\-\_\-vars@{Two\-Dpfold\-\_\-vars}}
+}
+
+
+Variables compound for 2\-Dfold partition function folding.  
+
+
+
+
+Collaboration diagram for Two\-Dpfold\-\_\-vars\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=184pt]{structTwoDpfold__vars__coll__graph}
+\end{center}
+\end{figure}
+\subsection*{Data Fields}
+\begin{DoxyCompactItemize}
+\item 
+\hypertarget{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{char $\ast$ \hyperlink{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}{ptype}}\label{structTwoDpfold__vars_a67f37b8901b8d0a049c216d4c6241b07}
+
+\begin{DoxyCompactList}\small\item\em Precomputed array of pair types. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{char $\ast$ \hyperlink{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}{sequence}}\label{structTwoDpfold__vars_a32c15a1e31856588259556c9020f32c6}
+
+\begin{DoxyCompactList}\small\item\em The input sequence. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{short $\ast$ \hyperlink{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}{S1}}\label{structTwoDpfold__vars_a240311ae1e8e121441651d6101e187ac}
+
+\begin{DoxyCompactList}\small\item\em The input sequences in numeric form. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{unsigned int \hyperlink{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}{max\-D1}}\label{structTwoDpfold__vars_a7292b6cbc1ee5bacf55e842f316c4bef}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to first reference. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{unsigned int \hyperlink{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}{max\-D2}}\label{structTwoDpfold__vars_a8900622d91454d2d037242e290e42834}
+
+\begin{DoxyCompactList}\small\item\em Maximum allowed base pair distance to second reference. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{int $\ast$ \hyperlink{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}{my\-\_\-iindx}}\label{structTwoDpfold__vars_ac2d3e6abf0cb0e1df363904fc938076e}
+
+\begin{DoxyCompactList}\small\item\em Index for moving in quadratic distancy dimensions. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{int $\ast$ \hyperlink{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}{jindx}}\label{structTwoDpfold__vars_a0699e194a797532c91b284ab10272384}
+
+\begin{DoxyCompactList}\small\item\em Index for moving in the triangular matrix qm1. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}{reference\-B\-Ps1}}\label{structTwoDpfold__vars_aea15706d27b6b0fc19f5773919f43a8a}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure1 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}{reference\-B\-Ps2}}\label{structTwoDpfold__vars_a1221396d712bf76b7f35297f2ab35a9f}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing number of basepairs of reference structure2 in interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}{bpdist}}\label{structTwoDpfold__vars_accef8eaa05fa57ca33aa22cbc7b7aaff}
+
+\begin{DoxyCompactList}\small\item\em Matrix containing base pair distance of reference structure 1 and 2 on interval \mbox{[}i,j\mbox{]}. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}{mm1}}\label{structTwoDpfold__vars_a7c9e9af6224d4696118e05835441863d}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 1 disallowed. \end{DoxyCompactList}\item 
+\hypertarget{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{unsigned int $\ast$ \hyperlink{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}{mm2}}\label{structTwoDpfold__vars_affb913470783f9edb12a0bfc22466269}
+
+\begin{DoxyCompactList}\small\item\em Maximum matching matrix, reference struct 2 disallowed. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Variables compound for 2\-Dfold partition function folding. 
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List()} 
+\end{DoxySeeAlso}
+
+
+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}