\hypertarget{group__energy__parameters}{
\section{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}
\label{group__energy__parameters}\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
}


All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s).  


Collaboration diagram for Change and Precalculate Energy Parameter Sets and Boltzmann Factors:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=420pt]{group__energy__parameters}
\end{center}
\end{figure}
\subsection*{Modules}
\begin{DoxyCompactItemize}
\item 
\hyperlink{group__energy__parameters__rw}{Reading/Writing energy parameter sets from/to File}


\begin{DoxyCompactList}\small\item\em Read and Write energy parameter sets from and to text files. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Files}
\begin{DoxyCompactItemize}
\item 
file \hyperlink{params_8h}{params.h}
\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
\hyperlink{structparamT}{paramT} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\_\-parameters} (void)
\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \item\end{DoxyCompactList}\item 
\hyperlink{structparamT}{paramT} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md)
\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \item\end{DoxyCompactList}\item 
\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\_\-scaled\_\-pf\_\-parameters} (void)
\item 
\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\_\-boltzmann\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double betaScale, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_\-scale})
\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. \item\end{DoxyCompactList}\item 
\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\_\-boltzmann\_\-factor\_\-copy} (\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters)
\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \item\end{DoxyCompactList}\item 
\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{
\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{get\_\-scaled\_\-alipf\_\-parameters} (unsigned int n\_\-seq)}
\label{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}

\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant). \item\end{DoxyCompactList}\item 
\hypertarget{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}{
\hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$ \hyperlink{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}{get\_\-boltzmann\_\-factors\_\-ali} (unsigned int n\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double betaScale, \hyperlink{structmodel__detailsT}{model\_\-detailsT} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_\-scale})}
\label{group__energy__parameters_gaf0c74574b40f2778556535bf9d382828}

\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
All relevant functions to retrieve and copy precalculated energy parameter sets as well as reading/writing the energy parameter set from/to file(s). This module covers all relevant functions for precalculation of the energy parameters necessary for the folding routines provided by RNAlib. Furthermore, the energy parameter set in the RNAlib can be easily exchanged by a user-\/defined one. It is also possible to write the current energy parameter set into a text file. 

\subsection{Function Documentation}
\hypertarget{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{
\index{energy\_\-parameters@{energy\_\-parameters}!scale\_\-parameters@{scale\_\-parameters}}
\index{scale\_\-parameters@{scale\_\-parameters}!energy_parameters@{energy\_\-parameters}}
\subsubsection[{scale\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf paramT}$\ast$ scale\_\-parameters (void)}}
\label{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}


Get precomputed energy contributions for all the known loop types. \begin{DoxyNote}{Note}
OpenMP: This function relies on several global model settings variables and thus is not to be considered threadsafe. See \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\_\-scaled\_\-parameters()} for a completely threadsafe implementation.
\end{DoxyNote}
\begin{DoxyReturn}{Returns}
A set of precomputed energy contributions 
\end{DoxyReturn}
\hypertarget{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{
\index{energy\_\-parameters@{energy\_\-parameters}!get\_\-scaled\_\-parameters@{get\_\-scaled\_\-parameters}}
\index{get\_\-scaled\_\-parameters@{get\_\-scaled\_\-parameters}!energy_parameters@{energy\_\-parameters}}
\subsubsection[{get\_\-scaled\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf paramT}$\ast$ get\_\-scaled\_\-parameters (double {\em temperature}, \/  {\bf model\_\-detailsT} {\em md})}}
\label{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}


Get precomputed energy contributions for all the known loop types. Call this function to retrieve precomputed energy contributions, i.e. scaled according to the temperature passed. Furthermore, this function assumes a data structure that contains the model details as well, such that subsequent folding recursions are able to retrieve the correct model settings

\begin{DoxySeeAlso}{See also}
\hyperlink{structmodel__detailsT}{model\_\-detailsT}, \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\_\-model\_\-details()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em temperature}]The temperature in degrees Celcius \item[{\em md}]The model details \end{DoxyParams}
\begin{DoxyReturn}{Returns}
precomputed energy contributions and model settings 
\end{DoxyReturn}
\hypertarget{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{
\index{energy\_\-parameters@{energy\_\-parameters}!get\_\-scaled\_\-pf\_\-parameters@{get\_\-scaled\_\-pf\_\-parameters}}
\index{get\_\-scaled\_\-pf\_\-parameters@{get\_\-scaled\_\-pf\_\-parameters}!energy_parameters@{energy\_\-parameters}}
\subsubsection[{get\_\-scaled\_\-pf\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\_\-paramT}$\ast$ get\_\-scaled\_\-pf\_\-parameters (void)}}
\label{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}
get a datastructure of type \hyperlink{structpf__paramT}{pf\_\-paramT} which contains the Boltzmann weights of several energy parameters scaled according to the current temperature \begin{DoxyReturn}{Returns}
The datastructure containing Boltzmann weights for use in partition function calculations 
\end{DoxyReturn}
\hypertarget{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{
\index{energy\_\-parameters@{energy\_\-parameters}!get\_\-boltzmann\_\-factors@{get\_\-boltzmann\_\-factors}}
\index{get\_\-boltzmann\_\-factors@{get\_\-boltzmann\_\-factors}!energy_parameters@{energy\_\-parameters}}
\subsubsection[{get\_\-boltzmann\_\-factors}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\_\-paramT}$\ast$ get\_\-boltzmann\_\-factors (double {\em temperature}, \/  double {\em betaScale}, \/  {\bf model\_\-detailsT} {\em md}, \/  double {\em pf\_\-scale})}}
\label{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}


Get precomputed Boltzmann factors of the loop type dependent energy contributions with independent thermodynamic temperature. This function returns a data structure that contains all necessary precalculated Boltzmann factors for each loop type contribution.\par
 In contrast to \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\_\-scaled\_\-pf\_\-parameters()}, this function enables setting of independent temperatures for both, the individual energy contributions as well as the thermodynamic temperature used in $ exp(-\Delta G / kT) $

\begin{DoxySeeAlso}{See also}
\hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\_\-scaled\_\-pf\_\-parameters()}, \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\_\-boltzmann\_\-factor\_\-copy()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em temperature}]The temperature in degrees Celcius used for (re-\/)scaling the energy contributions \item[{\em betaScale}]A scaling value that is used as a multiplication factor for the absolute temperature of the system \item[{\em md}]The model details to be used \item[{\em pf\_\-scale}]The scaling factor for the Boltzmann factors \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A set of precomputed Boltzmann factors 
\end{DoxyReturn}
\hypertarget{group__energy__parameters_gacba212326a051734797e65987260fdd0}{
\index{energy\_\-parameters@{energy\_\-parameters}!get\_\-boltzmann\_\-factor\_\-copy@{get\_\-boltzmann\_\-factor\_\-copy}}
\index{get\_\-boltzmann\_\-factor\_\-copy@{get\_\-boltzmann\_\-factor\_\-copy}!energy_parameters@{energy\_\-parameters}}
\subsubsection[{get\_\-boltzmann\_\-factor\_\-copy}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\_\-paramT}$\ast$ get\_\-boltzmann\_\-factor\_\-copy ({\bf pf\_\-paramT} $\ast$ {\em parameters})}}
\label{group__energy__parameters_gacba212326a051734797e65987260fdd0}


Get a copy of already precomputed Boltzmann factors. \begin{DoxySeeAlso}{See also}
\hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\_\-boltzmann\_\-factors()}, \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\_\-scaled\_\-pf\_\-parameters()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em parameters}]The input data structure that shall be copied \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A copy of the provided Boltzmann factor dataset 
\end{DoxyReturn}
