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

   1 \hypertarget{group__kl__neighborhood__pf}{\section{Calculate Partition Functions of a Distance Based Partitioning}
   2 \label{group__kl__neighborhood__pf}\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}}
   3 }
   4
   5
   6 Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures.
   7
   8
   9 Collaboration diagram for Calculate Partition Functions of a Distance Based Partitioning\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=350pt]{group__kl__neighborhood__pf}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Files}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 file \hyperlink{2Dpfold_8h}{2\-Dpfold.\-h}
  21 \end{DoxyCompactItemize}
  22 \subsection*{Functions}
  23 \begin{DoxyCompactItemize}
  24 \item
  25 \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables} (const char $\ast$seq, const char $\ast$structure1, char $\ast$structure2, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
  26 \begin{DoxyCompactList}\small\item\em Get a datastructure containing all necessary attributes and global folding switches. \end{DoxyCompactList}\item
  27 \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$ \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E} (\hyperlink{structTwoDfold__vars}{Two\-Dfold\-\_\-vars} $\ast$mfe\-\_\-vars)
  28 \begin{DoxyCompactList}\small\item\em Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure. \end{DoxyCompactList}\item
  29 void \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars)
  30 \begin{DoxyCompactList}\small\item\em Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure. \end{DoxyCompactList}\item
  31 \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution} $\ast$ \hyperlink{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{Two\-Dpfold\-List} (\hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} $\ast$vars, int max\-Distance1, int max\-Distance2)
  32 \begin{DoxyCompactList}\small\item\em Compute the partition function for all distance classes. \end{DoxyCompactList}\end{DoxyCompactItemize}
  33
  34
  35 \subsection{Detailed Description}
  36 Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures.
  37
  38 \subsection{Function Documentation}
  39 \hypertarget{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\-\_\-\-Two\-Dpfold\-\_\-variables@{get\-\_\-\-Two\-Dpfold\-\_\-variables}}
  40 \index{get\-\_\-\-Two\-Dpfold\-\_\-variables@{get\-\_\-\-Two\-Dpfold\-\_\-variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}}
  41 \subsubsection[{get\-\_\-\-Two\-Dpfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-vars}$\ast$ get\-\_\-\-Two\-Dpfold\-\_\-variables (
  42 \begin{DoxyParamCaption}
  43 \item[{const char $\ast$}]{seq, }
  44 \item[{const char $\ast$}]{structure1, }
  45 \item[{char $\ast$}]{structure2, }
  46 \item[{int}]{circ}
  47 \end{DoxyParamCaption}
  48 )}}\label{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}
  49
  50
  51 Get a datastructure containing all necessary attributes and global folding switches.
  52
  53 This function prepares all necessary attributes and matrices etc which are needed for a call of Two\-Dpfold\-List. A snapshot of all current global model switches (dangles, temperature and so on) is done and stored in the returned datastructure. Additionally, all matrices that will hold the partition function values are prepared.
  54
  55
  56 \begin{DoxyParams}{Parameters}
  57 {\em seq} & the R\-N\-A sequence in uppercase format with letters from the alphabet \{A\-U\-C\-G\} \\
  58 \hline
  59 {\em structure1} & the first reference structure in dot-\/bracket notation \\
  60 \hline
  61 {\em structure2} & the second reference structure in dot-\/bracket notation \\
  62 \hline
  63 {\em circ} & a switch indicating if the sequence is linear (0) or circular (1) \\
  64 \hline
  65 \end{DoxyParams}
  66 \begin{DoxyReturn}{Returns}
  67 the datastructure containing all necessary partition function attributes
  68 \end{DoxyReturn}
  69 \hypertarget{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E@{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}}
  70 \index{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E@{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}}
  71 \subsubsection[{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-vars}$\ast$ get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E (
  72 \begin{DoxyParamCaption}
  73 \item[{{\bf Two\-Dfold\-\_\-vars} $\ast$}]{mfe\-\_\-vars}
  74 \end{DoxyParamCaption}
  75 )}}\label{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}
  76
  77
  78 Get the datastructure containing all necessary attributes and global folding switches from a pre-\/filled mfe-\/datastructure.
  79
  80 This function actually does the same as get\-\_\-\-Two\-Dpfold\-\_\-variables but takes its switches and settings from a pre-\/filled M\-F\-E equivalent datastructure
  81
  82 \begin{DoxySeeAlso}{See Also}
  83 \hyperlink{group__kl__neighborhood__mfe_gac9284f132cf0eaa0a2f43590eda05488}{get\-\_\-\-Two\-Dfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}
  84 \end{DoxySeeAlso}
  85
  86 \begin{DoxyParams}{Parameters}
  87 {\em mfe\-\_\-vars} & the pre-\/filled mfe datastructure \\
  88 \hline
  89 \end{DoxyParams}
  90 \begin{DoxyReturn}{Returns}
  91 the datastructure containing all necessary partition function attributes
  92 \end{DoxyReturn}
  93 \hypertarget{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!destroy\-\_\-\-Two\-Dpfold\-\_\-variables@{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}}
  94 \index{destroy\-\_\-\-Two\-Dpfold\-\_\-variables@{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}}
  95 \subsubsection[{destroy\-\_\-\-Two\-Dpfold\-\_\-variables}]{\setlength{\rightskip}{0pt plus 5cm}void destroy\-\_\-\-Two\-Dpfold\-\_\-variables (
  96 \begin{DoxyParamCaption}
  97 \item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars}
  98 \end{DoxyParamCaption}
  99 )}}\label{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}
 100
 101
 102 Free all memory occupied by a \hyperlink{structTwoDpfold__vars}{Two\-Dpfold\-\_\-vars} datastructure.
 103
 104 This function free's all memory occupied by a datastructure obtained from from \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()} or \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()}
 105
 106 \begin{DoxySeeAlso}{See Also}
 107 \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gacc2f66da7ee62096cab629fce7112216}{get\-\_\-\-Two\-Dpfold\-\_\-variables\-\_\-from\-\_\-\-M\-F\-E()}
 108 \end{DoxySeeAlso}
 109
 110 \begin{DoxyParams}{Parameters}
 111 {\em vars} & the datastructure to be free'd \\
 112 \hline
 113 \end{DoxyParams}
 114 \hypertarget{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}{\index{Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}!Two\-Dpfold\-List@{Two\-Dpfold\-List}}
 115 \index{Two\-Dpfold\-List@{Two\-Dpfold\-List}!Calculate Partition Functions of a Distance Based Partitioning@{Calculate Partition Functions of a Distance Based Partitioning}}
 116 \subsubsection[{Two\-Dpfold\-List}]{\setlength{\rightskip}{0pt plus 5cm}{\bf Two\-Dpfold\-\_\-solution}$\ast$ Two\-Dpfold\-List (
 117 \begin{DoxyParamCaption}
 118 \item[{{\bf Two\-Dpfold\-\_\-vars} $\ast$}]{vars, }
 119 \item[{int}]{max\-Distance1, }
 120 \item[{int}]{max\-Distance2}
 121 \end{DoxyParamCaption}
 122 )}}\label{group__kl__neighborhood__pf_ga3e1cd3b24eb635c65181182cbb4ae3eb}
 123
 124
 125 Compute the partition function for all distance classes.
 126
 127 This function computes the partition functions for all distance classes according the two reference structures specified in the datastructure 'vars'. Similar to \hyperlink{group__kl__neighborhood__mfe_ga47da790166020558d27323aef489703e}{Two\-Dfold\-List()} the arguments max\-Distance1 and max\-Distance2 specify the maximum distance to both reference structures. A value of '-\/1' in either of them makes the appropriate distance restrictionless, i.\-e. all basepair distancies to the reference are taken into account during computation. In case there is a restriction, the returned solution contains an entry where the attribute k=l=-\/1 contains the partition function for all structures exceeding the restriction. A values of \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F} in the attribute 'k' of the returned list denotes the end of the list
 128
 129 \begin{DoxySeeAlso}{See Also}
 130 \hyperlink{group__kl__neighborhood__pf_ga1aca740e2a75ab2b2951538266e53d64}{get\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{group__kl__neighborhood__pf_gafe994291458ee2ac34d3eb825ef62a15}{destroy\-\_\-\-Two\-Dpfold\-\_\-variables()}, \hyperlink{structTwoDpfold__solution}{Two\-Dpfold\-\_\-solution}
 131 \end{DoxySeeAlso}
 132
 133 \begin{DoxyParams}{Parameters}
 134 {\em vars} & the datastructure containing all necessary folding attributes and matrices \\
 135 \hline
 136 {\em max\-Distance1} & the maximum basepair distance to reference1 (may be -\/1) \\
 137 \hline
 138 {\em max\-Distance2} & the maximum basepair distance to reference2 (may be -\/1) \\
 139 \hline
 140 \end{DoxyParams}
 141 \begin{DoxyReturn}{Returns}
 142 a list of partition funtions for the appropriate distance classes
 143 \end{DoxyReturn}