--- /dev/null
+\hypertarget{part__func_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.h File Reference}
+\label{part__func_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func.\-h}}
+}
+
+
+Partition function of single R\-N\-A sequences.
+
+
+Include dependency graph for part\-\_\-func.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{part__func_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+float \hyperlink{group__pf__fold_ga1839c61275760944b3a007c41d5c0823}{pf\-\_\-fold\-\_\-par} (const char $\ast$sequence, char $\ast$structure, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular)
+\begin{DoxyCompactList}\small\item\em Compute the partition function $Q$ for a given R\-N\-A sequence. \end{DoxyCompactList}\item
+float \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold} (const char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute the partition function $Q$ of an R\-N\-A sequence. \end{DoxyCompactList}\item
+float \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf\-\_\-circ\-\_\-fold} (const char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Compute the partition function of a circular R\-N\-A sequence. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack} (char $\ast$sequence)
+\begin{DoxyCompactList}\small\item\em Sample a secondary structure from the Boltzmann ensemble according its probability\par
+. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ} (char $\ast$sequence)
+\begin{DoxyCompactList}\small\item\em Sample a secondary structure of a circular R\-N\-A from the Boltzmann ensemble according its probability. \end{DoxyCompactList}\item
+void \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\-\_\-pf\-\_\-arrays} (void)
+\begin{DoxyCompactList}\small\item\em Free arrays for the partition function recursions. \end{DoxyCompactList}\item
+void \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\-\_\-pf\-\_\-params} (int length)
+\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
+\hypertarget{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{void \hyperlink{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}{update\-\_\-pf\-\_\-params\-\_\-par} (int length, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)}\label{group__pf__fold_ga0733527a94de3b79eee3c3c03c99c1bc}
+
+\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
+double $\ast$ \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\-\_\-bppm} (void)
+\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array
+
+Accessing the base pair probabilities for a pair (i,j) is achieved by. \end{DoxyCompactList}\item
+void \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr} (\hyperlink{structplist}{plist} $\ast$$\ast$pl, double $\ast$probs, int length, double cutoff)
+\begin{DoxyCompactList}\small\item\em Create a plist from a probability matrix. \end{DoxyCompactList}\item
+int \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get\-\_\-pf\-\_\-arrays} (short $\ast$$\ast$S\-\_\-p, short $\ast$$\ast$S1\-\_\-p, char $\ast$$\ast$ptype\-\_\-p, double $\ast$$\ast$qb\-\_\-p, double $\ast$$\ast$qm\-\_\-p, double $\ast$$\ast$q1k\-\_\-p, double $\ast$$\ast$qln\-\_\-p)
+\begin{DoxyCompactList}\small\item\em Get the pointers to (almost) all relavant computation arrays used in partition function computation. \end{DoxyCompactList}\item
+\hypertarget{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{double \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get\-\_\-subseq\-\_\-\-F} (int i, int j)}\label{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}
+
+\begin{DoxyCompactList}\small\item\em Get the free energy of a subsequence from the q\mbox{[}\mbox{]} array. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\-\_\-centroid\-\_\-struct\-\_\-pl} (int length, double $\ast$dist, \hyperlink{structplist}{plist} $\ast$pl)
+\begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\-\_\-centroid\-\_\-struct\-\_\-pr} (int length, double $\ast$dist, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
+\begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\item
+double \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\-\_\-bp\-\_\-distance} (int length)
+\begin{DoxyCompactList}\small\item\em Get the mean base pair distance of the last partition function computation. \end{DoxyCompactList}\item
+double \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean\-\_\-bp\-\_\-distance\-\_\-pr} (int length, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
+\begin{DoxyCompactList}\small\item\em Get the mean base pair distance in the thermodynamic ensemble. \end{DoxyCompactList}\item
+\hypertarget{part__func_8h_a1f562d463c14d4703d9656056200eb38}{void \hyperlink{part__func_8h_a1f562d463c14d4703d9656056200eb38}{bppm\-\_\-to\-\_\-structure} (char $\ast$structure, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr}, unsigned int length)}\label{part__func_8h_a1f562d463c14d4703d9656056200eb38}
+
+\begin{DoxyCompactList}\small\item\em Create a dot-\/bracket like structure string from base pair probability matrix. \end{DoxyCompactList}\item
+\hypertarget{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{char \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm\-\_\-symbol} (const float $\ast$x)}\label{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}
+
+\begin{DoxyCompactList}\small\item\em Get a pseudo dot bracket notation for a given probability information. \end{DoxyCompactList}\item
+void \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\-\_\-pf\-\_\-fold} (int length)
+\begin{DoxyCompactList}\small\item\em Allocate space for \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} \end{DoxyCompactList}\item
+char $\ast$ \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} (int length, double $\ast$dist)
+\item
+double \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\-\_\-bp\-\_\-dist} (int length)
+\item
+double \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{exp\-Loop\-Energy} (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)
+\item
+double \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{exp\-Hairpin\-Energy} (int u, int type, short si1, short sj1, const char $\ast$string)
+\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+int \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\-\_\-back}
+\begin{DoxyCompactList}\small\item\em Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Partition function of single R\-N\-A sequences. This file includes (almost) all function declarations within the {\bfseries R\-N\-Alib} that are related to Partion function folding...
+
+\subsection{Function Documentation}
+\hypertarget{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!init\-\_\-pf\-\_\-fold@{init\-\_\-pf\-\_\-fold}}
+\index{init\-\_\-pf\-\_\-fold@{init\-\_\-pf\-\_\-fold}!part_func.h@{part\-\_\-func.\-h}}
+\subsubsection[{init\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-pf\-\_\-fold (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}
+
+
+Allocate space for \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}
+
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000011}{Deprecated}]This function is obsolete and will be removed soon! \end{DoxyRefDesc}
+\hypertarget{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!centroid@{centroid}}
+\index{centroid@{centroid}!part_func.h@{part\-\_\-func.\-h}}
+\subsubsection[{centroid}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ centroid (
+\begin{DoxyParamCaption}
+\item[{int}]{length, }
+\item[{double $\ast$}]{dist}
+\end{DoxyParamCaption}
+)}}\label{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000012}{Deprecated}]This function is deprecated and should not be used anymore as it is not threadsafe! \end{DoxyRefDesc}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\-\_\-centroid\-\_\-struct\-\_\-pl()}, \hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\-\_\-centroid\-\_\-struct\-\_\-pr()}
+\end{DoxySeeAlso}
+\hypertarget{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!mean\-\_\-bp\-\_\-dist@{mean\-\_\-bp\-\_\-dist}}
+\index{mean\-\_\-bp\-\_\-dist@{mean\-\_\-bp\-\_\-dist}!part_func.h@{part\-\_\-func.\-h}}
+\subsubsection[{mean\-\_\-bp\-\_\-dist}]{\setlength{\rightskip}{0pt plus 5cm}double mean\-\_\-bp\-\_\-dist (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}
+get the mean pair distance of ensemble
+
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000013}{Deprecated}]This function is not threadsafe and should not be used anymore. Use \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\-\_\-bp\-\_\-distance()} instead! \end{DoxyRefDesc}
+\hypertarget{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!exp\-Loop\-Energy@{exp\-Loop\-Energy}}
+\index{exp\-Loop\-Energy@{exp\-Loop\-Energy}!part_func.h@{part\-\_\-func.\-h}}
+\subsubsection[{exp\-Loop\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}double exp\-Loop\-Energy (
+\begin{DoxyParamCaption}
+\item[{int}]{u1, }
+\item[{int}]{u2, }
+\item[{int}]{type, }
+\item[{int}]{type2, }
+\item[{short}]{si1, }
+\item[{short}]{sj1, }
+\item[{short}]{sp1, }
+\item[{short}]{sq1}
+\end{DoxyParamCaption}
+)}}\label{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000014}{Deprecated}]Use \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\-\_\-\-E\-\_\-\-Int\-Loop()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead \end{DoxyRefDesc}
+\hypertarget{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!exp\-Hairpin\-Energy@{exp\-Hairpin\-Energy}}
+\index{exp\-Hairpin\-Energy@{exp\-Hairpin\-Energy}!part_func.h@{part\-\_\-func.\-h}}
+\subsubsection[{exp\-Hairpin\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}double exp\-Hairpin\-Energy (
+\begin{DoxyParamCaption}
+\item[{int}]{u, }
+\item[{int}]{type, }
+\item[{short}]{si1, }
+\item[{short}]{sj1, }
+\item[{const char $\ast$}]{string}
+\end{DoxyParamCaption}
+)}}\label{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000015}{Deprecated}]Use \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\-\_\-\-E\-\_\-\-Hairpin()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead \end{DoxyRefDesc}
git://source.jalview.org / jabaws.git / blobdiff