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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / cofold_8h.tex

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+\hypertarget{cofold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.h File Reference}
+\label{cofold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.\-h}}
+}
+
+
+M\-F\-E version of cofolding routines.  
+
+
+Include dependency graph for cofold.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{cofold_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+float \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold} (const char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item 
+\hypertarget{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{float \hyperlink{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}{cofold\-\_\-par} (const char $\ast$string, char $\ast$structure, \hyperlink{structparamT}{param\-T} $\ast$parameters, int is\-\_\-constrained)}\label{group__mfe__cofold_gafe430060533f14b11fc611f60b3f1f6f}
+
+\begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item 
+\hypertarget{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{void \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\-\_\-co\-\_\-arrays} (void)}\label{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}
+
+\begin{DoxyCompactList}\small\item\em Free memory occupied by \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()} \end{DoxyCompactList}\item 
+\hypertarget{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{void \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\-\_\-cofold\-\_\-params} (void)}\label{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}
+
+\begin{DoxyCompactList}\small\item\em Recalculate parameters. \end{DoxyCompactList}\item 
+void \hyperlink{group__mfe__cofold_ga5f5bf4df35d0554f6ace9579f8744c48}{export\-\_\-cofold\-\_\-arrays\-\_\-gq} (int $\ast$$\ast$f5\-\_\-p, int $\ast$$\ast$c\-\_\-p, int $\ast$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-p, int $\ast$$\ast$fc\-\_\-p, int $\ast$$\ast$ggg\-\_\-p, int $\ast$$\ast$indx\-\_\-p, char $\ast$$\ast$ptype\-\_\-p)
+\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold (with gquadruplex support) \end{DoxyCompactList}\item 
+void \hyperlink{group__mfe__cofold_ga5cb6b59983f1f74ccc00b9b9c4e84482}{export\-\_\-cofold\-\_\-arrays} (int $\ast$$\ast$f5\-\_\-p, int $\ast$$\ast$c\-\_\-p, int $\ast$$\ast$f\-M\-L\-\_\-p, int $\ast$$\ast$f\-M1\-\_\-p, int $\ast$$\ast$fc\-\_\-p, int $\ast$$\ast$indx\-\_\-p, char $\ast$$\ast$ptype\-\_\-p)
+\begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold. \end{DoxyCompactList}\item 
+\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__zuker_ga0d5104e3ecf119d8eabd40aa5fe47f90}{zukersubopt} (const char $\ast$string)
+\begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \end{DoxyCompactList}\item 
+\hypertarget{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{\hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}{zukersubopt\-\_\-par} (const char $\ast$string, \hyperlink{structparamT}{param\-T} $\ast$parameters)}\label{group__subopt__zuker_ga6d98a9450d1affadf144ac79f543da8c}
+
+\begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \end{DoxyCompactList}\item 
+void \hyperlink{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{get\-\_\-monomere\-\_\-mfes} (float $\ast$e1, float $\ast$e2)
+\begin{DoxyCompactList}\small\item\em get\-\_\-monomer\-\_\-free\-\_\-energies \end{DoxyCompactList}\item 
+void \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\-\_\-cofold} (int length)
+\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+M\-F\-E version of cofolding routines. This file includes (almost) all function declarations within the {\bfseries R\-N\-Alib} that are related to M\-F\-E Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines. 
+
+\subsection{Function Documentation}
+\hypertarget{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{\index{cofold.\-h@{cofold.\-h}!get\-\_\-monomere\-\_\-mfes@{get\-\_\-monomere\-\_\-mfes}}
+\index{get\-\_\-monomere\-\_\-mfes@{get\-\_\-monomere\-\_\-mfes}!cofold.h@{cofold.\-h}}
+\subsubsection[{get\-\_\-monomere\-\_\-mfes}]{\setlength{\rightskip}{0pt plus 5cm}void get\-\_\-monomere\-\_\-mfes (
+\begin{DoxyParamCaption}
+\item[{float $\ast$}]{e1, }
+\item[{float $\ast$}]{e2}
+\end{DoxyParamCaption}
+)}}\label{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}
+
+
+get\-\_\-monomer\-\_\-free\-\_\-energies 
+
+Export monomer free energies out of cofold arrays
+
+
+\begin{DoxyParams}{Parameters}
+{\em e1} & A pointer to a variable where the energy of molecule A will be written to \\
+\hline
+{\em e2} & A pointer to a variable where the energy of molecule B will be written to \\
+\hline
+\end{DoxyParams}
+\hypertarget{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{\index{cofold.\-h@{cofold.\-h}!initialize\-\_\-cofold@{initialize\-\_\-cofold}}
+\index{initialize\-\_\-cofold@{initialize\-\_\-cofold}!cofold.h@{cofold.\-h}}
+\subsubsection[{initialize\-\_\-cofold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\-\_\-cofold (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}
+allocate arrays for folding \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000001}{Deprecated}]\{This function is obsolete and will be removed soon!\} \end{DoxyRefDesc}