--- /dev/null
+\hypertarget{part__func__co_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.h File Reference}
+\label{part__func__co_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/part\-\_\-func\-\_\-co.\-h}}
+}
+
+
+Partition function for two R\-N\-A sequences.
+
+
+Include dependency graph for part\-\_\-func\-\_\-co.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{part__func__co_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold} (char $\ast$sequence, char $\ast$structure)
+\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item
+\hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gabd873b450832ab5f21101fc5ab354d21}{co\-\_\-pf\-\_\-fold\-\_\-par} (char $\ast$sequence, char $\ast$structure, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained)
+\begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item
+double $\ast$ \hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\-\_\-co\-\_\-bppm} (void)
+\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item
+\hypertarget{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{void \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\-\_\-co\-\_\-pf\-\_\-arrays} (void)}\label{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}
+
+\begin{DoxyCompactList}\small\item\em Free the memory occupied by \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} \end{DoxyCompactList}\item
+void \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\-\_\-co\-\_\-pf\-\_\-params} (int length)
+\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
+void \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par} (int length, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)
+\begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
+void \hyperlink{group__pf__cofold_ga15ae04ac5ab84e876dcf0093120cb617}{compute\-\_\-probabilities} (double F\-A\-B, double F\-E\-A, double F\-E\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A\-B, struct \hyperlink{structplist}{plist} $\ast$pr\-A, struct \hyperlink{structplist}{plist} $\ast$pr\-B, int Alength)
+\begin{DoxyCompactList}\small\item\em Compute Boltzmann probabilities of dimerization without homodimers. \end{DoxyCompactList}\item
+\hyperlink{structConcEnt}{Conc\-Ent} $\ast$ \hyperlink{group__pf__cofold_ga5545cb936ac4ff93c7d699d46e72e8c7}{get\-\_\-concentrations} (double F\-E\-A\-B, double F\-E\-A\-A, double F\-E\-B\-B, double F\-E\-A, double F\-E\-B, double $\ast$startconc)
+\begin{DoxyCompactList}\small\item\em Given two start monomer concentrations a and b, compute the concentrations in thermodynamic equilibrium of all dimers and the monomers. \end{DoxyCompactList}\item
+\hyperlink{structplist}{plist} $\ast$ \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\-\_\-plist} (struct \hyperlink{structplist}{plist} $\ast$pl, int length, double cut\-\_\-off)
+\item
+void \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\-\_\-co\-\_\-pf\-\_\-fold} (int length)
+\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+\hypertarget{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{int \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog}}\label{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}
+
+\begin{DoxyCompactList}\small\item\em Toggles no intrabp in 2nd mol. \end{DoxyCompactList}\item
+\hypertarget{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{double \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\-\_\-monomer} \mbox{[}2\mbox{]}}\label{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}
+
+\begin{DoxyCompactList}\small\item\em Free energies of the two monomers. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Partition function for two R\-N\-A sequences. As for folding one R\-N\-A molecule, this computes the partition function of all possible structures and the base pair probabilities. Uses the same global \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale} variable to avoid overflows.
+
+To simplify the implementation the partition function computation is done internally in a null model that does not include the duplex initiation energy, i.\-e. the entropic penalty for producing a dimer from two monomers). The resulting free energies and pair probabilities are initially relative to that null model. In a second step the free energies can be corrected to include the dimerization penalty, and the pair probabilities can be divided into the conditional pair probabilities given that a re dimer is formed or not formed.
+
+After computing the partition functions of all possible dimeres one can compute the probabilities of base pairs, the concentrations out of start concentrations and sofar and soaway.
+
+Dimer formation is inherently concentration dependent. Given the free energies of the monomers A and B and dimers A\-B, A\-A, and B\-B one can compute the equilibrium concentrations, given input concentrations of A and B, see e.\-g. Dimitrov \& Zuker (2004)
+
+\subsection{Function Documentation}
+\hypertarget{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!get\-\_\-plist@{get\-\_\-plist}}
+\index{get\-\_\-plist@{get\-\_\-plist}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}}
+\subsubsection[{get\-\_\-plist}]{\setlength{\rightskip}{0pt plus 5cm}{\bf plist}$\ast$ get\-\_\-plist (
+\begin{DoxyParamCaption}
+\item[{struct {\bf plist} $\ast$}]{pl, }
+\item[{int}]{length, }
+\item[{double}]{cut\-\_\-off}
+\end{DoxyParamCaption}
+)}}\label{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}
+D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000016}{Deprecated}]\{ This function is deprecated and will be removed soon!\} use \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()} instead! \end{DoxyRefDesc}
+\hypertarget{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}}
+\index{init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}}
+\subsubsection[{init\-\_\-co\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-co\-\_\-pf\-\_\-fold (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}
+D\-O N\-O\-T U\-S\-E T\-H\-I\-S F\-U\-N\-C\-T\-I\-O\-N A\-N\-Y\-M\-O\-R\-E \begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000017}{Deprecated}]\{ This function is deprecated and will be removed soon!\} \end{DoxyRefDesc}
git://source.jalview.org / jabaws.git / blobdiff