binaries/src/ViennaRNA/doc/latex/part__func_8h.tex

   1 \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}
   2 \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}}
   3 }
   4
   5
   6 Partition function of single R\-N\-A sequences.
   7
   8
   9 Include dependency graph for part\-\_\-func.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{part__func_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 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)
  21 \begin{DoxyCompactList}\small\item\em Compute the partition function $Q$ for a given R\-N\-A sequence. \end{DoxyCompactList}\item
  22 float \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold} (const char $\ast$sequence, char $\ast$structure)
  23 \begin{DoxyCompactList}\small\item\em Compute the partition function $Q$ of an R\-N\-A sequence. \end{DoxyCompactList}\item
  24 float \hyperlink{group__pf__fold_ga819ce5fca8984004ac81c4a3b04cb735}{pf\-\_\-circ\-\_\-fold} (const char $\ast$sequence, char $\ast$structure)
  25 \begin{DoxyCompactList}\small\item\em Compute the partition function of a circular R\-N\-A sequence. \end{DoxyCompactList}\item
  26 char $\ast$ \hyperlink{group__subopt__stochbt_gac03ca6db186bb3bf0a2a326d7fb3ba03}{pbacktrack} (char $\ast$sequence)
  27 \begin{DoxyCompactList}\small\item\em Sample a secondary structure from the Boltzmann ensemble according its probability\par
  28 . \end{DoxyCompactList}\item
  29 char $\ast$ \hyperlink{group__subopt__stochbt_ga00474051204ac9ad576b3e45174d03ff}{pbacktrack\-\_\-circ} (char $\ast$sequence)
  30 \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
  31 void \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\-\_\-pf\-\_\-arrays} (void)
  32 \begin{DoxyCompactList}\small\item\em Free arrays for the partition function recursions. \end{DoxyCompactList}\item
  33 void \hyperlink{group__pf__fold_ga384e927890f9c034ff09fa66da102d28}{update\-\_\-pf\-\_\-params} (int length)
  34 \begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
  35 \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}
  36
  37 \begin{DoxyCompactList}\small\item\em Recalculate energy parameters. \end{DoxyCompactList}\item
  38 double $\ast$ \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\-\_\-bppm} (void)
  39 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array
  40
  41 Accessing the base pair probabilities for a pair (i,j) is achieved by. \end{DoxyCompactList}\item
  42 void \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr} (\hyperlink{structplist}{plist} $\ast$$\ast$pl, double $\ast$probs, int length, double cutoff)
  43 \begin{DoxyCompactList}\small\item\em Create a plist from a probability matrix. \end{DoxyCompactList}\item
  44 int \hyperlink{group__pf__fold_ga18607e79e106cad827f482eedd2f632e}{get\-\_\-pf\-\_\-arrays} (short $\ast$$\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)
  45 \begin{DoxyCompactList}\small\item\em Get the pointers to (almost) all relavant computation arrays used in partition function computation. \end{DoxyCompactList}\item
  46 \hypertarget{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{double \hyperlink{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}{get\-\_\-subseq\-\_\-\-F} (int i, int j)}\label{part__func_8h_a189e2a1ec6cc32c53ea72f7543b0441e}
  47
  48 \begin{DoxyCompactList}\small\item\em Get the free energy of a subsequence from the q\mbox{[}\mbox{]} array. \end{DoxyCompactList}\item
  49 char $\ast$ \hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\-\_\-centroid\-\_\-struct\-\_\-pl} (int length, double $\ast$dist, \hyperlink{structplist}{plist} $\ast$pl)
  50 \begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\item
  51 char $\ast$ \hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\-\_\-centroid\-\_\-struct\-\_\-pr} (int length, double $\ast$dist, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
  52 \begin{DoxyCompactList}\small\item\em Get the centroid structure of the ensemble. \end{DoxyCompactList}\item
  53 double \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\-\_\-bp\-\_\-distance} (int length)
  54 \begin{DoxyCompactList}\small\item\em Get the mean base pair distance of the last partition function computation. \end{DoxyCompactList}\item
  55 double \hyperlink{group__pf__fold_ga72d84525f0afd3a9d60d830a2f501fa5}{mean\-\_\-bp\-\_\-distance\-\_\-pr} (int length, double $\ast$\hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr})
  56 \begin{DoxyCompactList}\small\item\em Get the mean base pair distance in the thermodynamic ensemble. \end{DoxyCompactList}\item
  57 \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}
  58
  59 \begin{DoxyCompactList}\small\item\em Create a dot-\/bracket like structure string from base pair probability matrix. \end{DoxyCompactList}\item
  60 \hypertarget{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{char \hyperlink{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}{bppm\-\_\-symbol} (const float $\ast$x)}\label{part__func_8h_a49962ad6242b8c628de6ca16bb831c1d}
  61
  62 \begin{DoxyCompactList}\small\item\em Get a pseudo dot bracket notation for a given probability information. \end{DoxyCompactList}\item
  63 void \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\-\_\-pf\-\_\-fold} (int length)
  64 \begin{DoxyCompactList}\small\item\em Allocate space for \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()} \end{DoxyCompactList}\item
  65 char $\ast$ \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} (int length, double $\ast$dist)
  66 \item
  67 double \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\-\_\-bp\-\_\-dist} (int length)
  68 \item
  69 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)
  70 \item
  71 double \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{exp\-Hairpin\-Energy} (int u, int type, short si1, short sj1, const char $\ast$string)
  72 \end{DoxyCompactItemize}
  73 \subsection*{Variables}
  74 \begin{DoxyCompactItemize}
  75 \item
  76 int \hyperlink{group__subopt__stochbt_gacd79b1a570e6ad9be24cb11fe8cae30a}{st\-\_\-back}
  77 \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}
  78
  79
  80 \subsection{Detailed Description}
  81 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...
  82
  83 \subsection{Function Documentation}
  84 \hypertarget{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!init\-\_\-pf\-\_\-fold@{init\-\_\-pf\-\_\-fold}}
  85 \index{init\-\_\-pf\-\_\-fold@{init\-\_\-pf\-\_\-fold}!part_func.h@{part\-\_\-func.\-h}}
  86 \subsubsection[{init\-\_\-pf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}void init\-\_\-pf\-\_\-fold (
  87 \begin{DoxyParamCaption}
  88 \item[{int}]{length}
  89 \end{DoxyParamCaption}
  90 )}}\label{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}
  91
  92
  93 Allocate space for \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}
  94
  95 \begin{DoxyRefDesc}{Deprecated}
  96 \item[\hyperlink{deprecated__deprecated000011}{Deprecated}]This function is obsolete and will be removed soon! \end{DoxyRefDesc}
  97 \hypertarget{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!centroid@{centroid}}
  98 \index{centroid@{centroid}!part_func.h@{part\-\_\-func.\-h}}
  99 \subsubsection[{centroid}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ centroid (
 100 \begin{DoxyParamCaption}
 101 \item[{int}]{length, }
 102 \item[{double $\ast$}]{dist}
 103 \end{DoxyParamCaption}
 104 )}}\label{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}
 105 \begin{DoxyRefDesc}{Deprecated}
 106 \item[\hyperlink{deprecated__deprecated000012}{Deprecated}]This function is deprecated and should not be used anymore as it is not threadsafe! \end{DoxyRefDesc}
 107 \begin{DoxySeeAlso}{See Also}
 108 \hyperlink{group__centroid__fold_ga9aba0ba1433a6d259331e0fe9fc4a9a6}{get\-\_\-centroid\-\_\-struct\-\_\-pl()}, \hyperlink{group__centroid__fold_gacdabece4aa1e20c9eaa97acb4c4dcc38}{get\-\_\-centroid\-\_\-struct\-\_\-pr()}
 109 \end{DoxySeeAlso}
 110 \hypertarget{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!mean\-\_\-bp\-\_\-dist@{mean\-\_\-bp\-\_\-dist}}
 111 \index{mean\-\_\-bp\-\_\-dist@{mean\-\_\-bp\-\_\-dist}!part_func.h@{part\-\_\-func.\-h}}
 112 \subsubsection[{mean\-\_\-bp\-\_\-dist}]{\setlength{\rightskip}{0pt plus 5cm}double mean\-\_\-bp\-\_\-dist (
 113 \begin{DoxyParamCaption}
 114 \item[{int}]{length}
 115 \end{DoxyParamCaption}
 116 )}}\label{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}
 117 get the mean pair distance of ensemble
 118
 119 \begin{DoxyRefDesc}{Deprecated}
 120 \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}
 121 \hypertarget{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!exp\-Loop\-Energy@{exp\-Loop\-Energy}}
 122 \index{exp\-Loop\-Energy@{exp\-Loop\-Energy}!part_func.h@{part\-\_\-func.\-h}}
 123 \subsubsection[{exp\-Loop\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}double exp\-Loop\-Energy (
 124 \begin{DoxyParamCaption}
 125 \item[{int}]{u1, }
 126 \item[{int}]{u2, }
 127 \item[{int}]{type, }
 128 \item[{int}]{type2, }
 129 \item[{short}]{si1, }
 130 \item[{short}]{sj1, }
 131 \item[{short}]{sp1, }
 132 \item[{short}]{sq1}
 133 \end{DoxyParamCaption}
 134 )}}\label{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}
 135 \begin{DoxyRefDesc}{Deprecated}
 136 \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}
 137 \hypertarget{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{\index{part\-\_\-func.\-h@{part\-\_\-func.\-h}!exp\-Hairpin\-Energy@{exp\-Hairpin\-Energy}}
 138 \index{exp\-Hairpin\-Energy@{exp\-Hairpin\-Energy}!part_func.h@{part\-\_\-func.\-h}}
 139 \subsubsection[{exp\-Hairpin\-Energy}]{\setlength{\rightskip}{0pt plus 5cm}double exp\-Hairpin\-Energy (
 140 \begin{DoxyParamCaption}
 141 \item[{int}]{u, }
 142 \item[{int}]{type, }
 143 \item[{short}]{si1, }
 144 \item[{short}]{sj1, }
 145 \item[{const char $\ast$}]{string}
 146 \end{DoxyParamCaption}
 147 )}}\label{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}
 148 \begin{DoxyRefDesc}{Deprecated}
 149 \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}