binaries/src/ViennaRNA/doc/latex/cofold_8h.tex

   1 \hypertarget{cofold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/cofold.h File Reference}
   2 \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}}
   3 }
   4
   5
   6 M\-F\-E version of cofolding routines.
   7
   8
   9 Include dependency graph for cofold.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{cofold_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 float \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold} (const char $\ast$sequence, char $\ast$structure)
  21 \begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item
  22 \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}
  23
  24 \begin{DoxyCompactList}\small\item\em Compute the minimum free energy of two interacting R\-N\-A molecules. \end{DoxyCompactList}\item
  25 \hypertarget{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{void \hyperlink{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}{free\-\_\-co\-\_\-arrays} (void)}\label{group__mfe__cofold_gaafb33d7473eb9af9d1b168ca8761c41a}
  26
  27 \begin{DoxyCompactList}\small\item\em Free memory occupied by \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()} \end{DoxyCompactList}\item
  28 \hypertarget{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{void \hyperlink{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}{update\-\_\-cofold\-\_\-params} (void)}\label{group__mfe__cofold_ga4fcbf34e77b99bfbb2333d2ab0c41a57}
  29
  30 \begin{DoxyCompactList}\small\item\em Recalculate parameters. \end{DoxyCompactList}\item
  31 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)
  32 \begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold (with gquadruplex support) \end{DoxyCompactList}\item
  33 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)
  34 \begin{DoxyCompactList}\small\item\em Export the arrays of partition function cofold. \end{DoxyCompactList}\item
  35 \hyperlink{structSOLUTION}{S\-O\-L\-U\-T\-I\-O\-N} $\ast$ \hyperlink{group__subopt__zuker_ga0d5104e3ecf119d8eabd40aa5fe47f90}{zukersubopt} (const char $\ast$string)
  36 \begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \end{DoxyCompactList}\item
  37 \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}
  38
  39 \begin{DoxyCompactList}\small\item\em Compute Zuker type suboptimal structures. \end{DoxyCompactList}\item
  40 void \hyperlink{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{get\-\_\-monomere\-\_\-mfes} (float $\ast$e1, float $\ast$e2)
  41 \begin{DoxyCompactList}\small\item\em get\-\_\-monomer\-\_\-free\-\_\-energies \end{DoxyCompactList}\item
  42 void \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\-\_\-cofold} (int length)
  43 \end{DoxyCompactItemize}
  44
  45
  46 \subsection{Detailed Description}
  47 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.
  48
  49 \subsection{Function Documentation}
  50 \hypertarget{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}{\index{cofold.\-h@{cofold.\-h}!get\-\_\-monomere\-\_\-mfes@{get\-\_\-monomere\-\_\-mfes}}
  51 \index{get\-\_\-monomere\-\_\-mfes@{get\-\_\-monomere\-\_\-mfes}!cofold.h@{cofold.\-h}}
  52 \subsubsection[{get\-\_\-monomere\-\_\-mfes}]{\setlength{\rightskip}{0pt plus 5cm}void get\-\_\-monomere\-\_\-mfes (
  53 \begin{DoxyParamCaption}
  54 \item[{float $\ast$}]{e1, }
  55 \item[{float $\ast$}]{e2}
  56 \end{DoxyParamCaption}
  57 )}}\label{cofold_8h_a4958b517c613e4d2afd5bce6c1060a79}
  58
  59
  60 get\-\_\-monomer\-\_\-free\-\_\-energies
  61
  62 Export monomer free energies out of cofold arrays
  63
  64
  65 \begin{DoxyParams}{Parameters}
  66 {\em e1} & A pointer to a variable where the energy of molecule A will be written to \\
  67 \hline
  68 {\em e2} & A pointer to a variable where the energy of molecule B will be written to \\
  69 \hline
  70 \end{DoxyParams}
  71 \hypertarget{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{\index{cofold.\-h@{cofold.\-h}!initialize\-\_\-cofold@{initialize\-\_\-cofold}}
  72 \index{initialize\-\_\-cofold@{initialize\-\_\-cofold}!cofold.h@{cofold.\-h}}
  73 \subsubsection[{initialize\-\_\-cofold}]{\setlength{\rightskip}{0pt plus 5cm}void initialize\-\_\-cofold (
  74 \begin{DoxyParamCaption}
  75 \item[{int}]{length}
  76 \end{DoxyParamCaption}
  77 )}}\label{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}
  78 allocate arrays for folding \begin{DoxyRefDesc}{Deprecated}
  79 \item[\hyperlink{deprecated__deprecated000001}{Deprecated}]\{This function is obsolete and will be removed soon!\} \end{DoxyRefDesc}