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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / modules.tex

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+\section{Modules}
+Here is a list of all modules\-:\begin{DoxyCompactList}
+\item \contentsline{section}{R\-N\-A Secondary Structure Folding}{\pageref{group__folding__routines}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Calculating Minimum Free Energy (M\-F\-E) Structures}{\pageref{group__mfe__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{M\-F\-E Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
+\item \contentsline{section}{M\-F\-E Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
+\item \contentsline{section}{Local M\-F\-E structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
+\item \contentsline{section}{Calculating M\-F\-E representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Calculating Partition Functions and Pair Probabilities}{\pageref{group__pf__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Compute the structure with maximum expected accuracy (M\-E\-A)}{\pageref{group__mea__fold}}{}
+\item \contentsline{section}{Compute the centroid structure}{\pageref{group__centroid__fold}}{}
+\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
+\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
+\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
+\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
+\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Enumerating Suboptimal Structures}{\pageref{group__subopt__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Suboptimal structures according to Zuker et al. 1989}{\pageref{group__subopt__zuker}}{}
+\item \contentsline{section}{Suboptimal structures within an energy band arround the M\-F\-E}{\pageref{group__subopt__wuchty}}{}
+\item \contentsline{section}{Stochastic backtracking in the Ensemble}{\pageref{group__subopt__stochbt}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
+\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
+\end{DoxyCompactList}
+\end{DoxyCompactList}
+\item \contentsline{section}{Calculate Secondary Structures of two R\-N\-As upon Dimerization}{\pageref{group__cofold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{M\-F\-E Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
+\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
+\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Predicting Consensus Structures from Alignment(s)}{\pageref{group__consensus__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{M\-F\-E Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
+\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
+\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
+\item \contentsline{section}{Local M\-F\-E consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Predicting Locally stable structures of large sequences}{\pageref{group__local__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Local M\-F\-E structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
+\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
+\item \contentsline{section}{Local M\-F\-E consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{\pageref{group__energy__parameters}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Reading/\-Writing energy parameter sets from/to File}{\pageref{group__energy__parameters__rw}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Converting energy parameter files}{\pageref{group__energy__parameters__convert}}{}
+\end{DoxyCompactList}
+\end{DoxyCompactList}
+\item \contentsline{section}{Energy evaluation}{\pageref{group__eval}}{}
+\item \contentsline{section}{Searching Sequences for Predefined Structures}{\pageref{group__inverse__fold}}{}
+\item \contentsline{section}{Classified Dynamic Programming}{\pageref{group__class__fold}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Distance based partitioning of the Secondary Structure Space}{\pageref{group__kl__neighborhood}}{}
+\begin{DoxyCompactList}
+\item \contentsline{section}{Calculating M\-F\-E representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
+\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
+\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
+\end{DoxyCompactList}
+\item \contentsline{section}{Compute the Density of States}{\pageref{group__dos}}{}
+\end{DoxyCompactList}
+\end{DoxyCompactList}
+\item \contentsline{section}{Parsing and Comparing -\/ Functions to Manipulate Structures}{\pageref{group__parse}}{}
+\end{DoxyCompactList}