binaries/src/ViennaRNA/doc/latex/part__func__co_8h.tex

   1 \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}
   2 \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}}
   3 }
   4
   5
   6 Partition function for two R\-N\-A sequences.
   7
   8
   9 Include dependency graph for part\-\_\-func\-\_\-co.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{part__func__co_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 \hyperlink{structcofoldF}{cofold\-F} \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold} (char $\ast$sequence, char $\ast$structure)
  21 \begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item
  22 \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)
  23 \begin{DoxyCompactList}\small\item\em Calculate partition function and base pair probabilities. \end{DoxyCompactList}\item
  24 double $\ast$ \hyperlink{group__pf__cofold_ga11f0252c1d2c4697253ff4b5bd392d3c}{export\-\_\-co\-\_\-bppm} (void)
  25 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item
  26 \hypertarget{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{void \hyperlink{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}{free\-\_\-co\-\_\-pf\-\_\-arrays} (void)}\label{group__pf__cofold_gade3ce34ae8214811374b1d28a40dc247}
  27
  28 \begin{DoxyCompactList}\small\item\em Free the memory occupied by \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} \end{DoxyCompactList}\item
  29 void \hyperlink{group__pf__cofold_ga6e0f36c1f9b7d9dd4bfbad914c1119e5}{update\-\_\-co\-\_\-pf\-\_\-params} (int length)
  30 \begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
  31 void \hyperlink{group__pf__cofold_ga117d880df45bef444d5e2785ffa40a53}{update\-\_\-co\-\_\-pf\-\_\-params\-\_\-par} (int length, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)
  32 \begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
  33 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)
  34 \begin{DoxyCompactList}\small\item\em Compute Boltzmann probabilities of dimerization without homodimers. \end{DoxyCompactList}\item
  35 \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)
  36 \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
  37 \hyperlink{structplist}{plist} $\ast$ \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\-\_\-plist} (struct \hyperlink{structplist}{plist} $\ast$pl, int length, double cut\-\_\-off)
  38 \item
  39 void \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\-\_\-co\-\_\-pf\-\_\-fold} (int length)
  40 \end{DoxyCompactItemize}
  41 \subsection*{Variables}
  42 \begin{DoxyCompactItemize}
  43 \item
  44 \hypertarget{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{int \hyperlink{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}{mirnatog}}\label{group__pf__cofold_gaff27888c4088cc1f60fd59cbd589474c}
  45
  46 \begin{DoxyCompactList}\small\item\em Toggles no intrabp in 2nd mol. \end{DoxyCompactList}\item
  47 \hypertarget{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{double \hyperlink{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}{F\-\_\-monomer} \mbox{[}2\mbox{]}}\label{group__pf__cofold_gac2d1851a710a8561390861155ca988fe}
  48
  49 \begin{DoxyCompactList}\small\item\em Free energies of the two monomers. \end{DoxyCompactList}\end{DoxyCompactItemize}
  50
  51
  52 \subsection{Detailed Description}
  53 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.
  54
  55 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.
  56
  57 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.
  58
  59 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)
  60
  61 \subsection{Function Documentation}
  62 \hypertarget{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!get\-\_\-plist@{get\-\_\-plist}}
  63 \index{get\-\_\-plist@{get\-\_\-plist}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}}
  64 \subsubsection[{get\-\_\-plist}]{\setlength{\rightskip}{0pt plus 5cm}{\bf plist}$\ast$ get\-\_\-plist (
  65 \begin{DoxyParamCaption}
  66 \item[{struct {\bf plist} $\ast$}]{pl, }
  67 \item[{int}]{length, }
  68 \item[{double}]{cut\-\_\-off}
  69 \end{DoxyParamCaption}
  70 )}}\label{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}
  71 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}
  72 \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}
  73 \hypertarget{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{\index{part\-\_\-func\-\_\-co.\-h@{part\-\_\-func\-\_\-co.\-h}!init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}}
  74 \index{init\-\_\-co\-\_\-pf\-\_\-fold@{init\-\_\-co\-\_\-pf\-\_\-fold}!part_func_co.h@{part\-\_\-func\-\_\-co.\-h}}
  75 \subsubsection[{init\-\_\-co\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-co\-\_\-pf\-\_\-fold (
  76 \begin{DoxyParamCaption}
  77 \item[{int}]{length}
  78 \end{DoxyParamCaption}
  79 )}}\label{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}
  80 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}
  81 \item[\hyperlink{deprecated__deprecated000017}{Deprecated}]\{ This function is deprecated and will be removed soon!\} \end{DoxyRefDesc}