--- /dev/null
+\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=350pt]{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. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Files}
+\begin{DoxyCompactItemize}
+\item
+file \hyperlink{params_8h}{params.\-h}
+\end{DoxyCompactItemize}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}{scale\-\_\-parameters} (void)
+\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item
+\hyperlink{structparamT}{param\-T} $\ast$ \hyperlink{group__energy__parameters_gac2f3ca440b7eaf4d999fb27da949fe72}{get\-\_\-scaled\-\_\-parameters} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md)
+\begin{DoxyCompactList}\small\item\em Get precomputed energy contributions for all the known loop types. \end{DoxyCompactList}\item
+\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{get\-\_\-scaled\-\_\-pf\-\_\-parameters} (void)
+\item
+\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_ga6fc2f3eef5a3024d44963ac59a42e39d}{get\-\_\-boltzmann\-\_\-factors} (double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} 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. \end{DoxyCompactList}\item
+\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gacba212326a051734797e65987260fdd0}{get\-\_\-boltzmann\-\_\-factor\-\_\-copy} (\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters)
+\begin{DoxyCompactList}\small\item\em Get a copy of already precomputed Boltzmann factors. \end{DoxyCompactList}\item
+\hypertarget{group__energy__parameters_gaa6a4297a2b91d6f7ae47dd61ca1862a0}{\hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \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) \end{DoxyCompactList}\item
+\hypertarget{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{P\-U\-B\-L\-I\-C \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$ \hyperlink{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}{get\-\_\-boltzmann\-\_\-factors\-\_\-ali} (unsigned int n\-\_\-seq, double \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}, double beta\-Scale, \hyperlink{structmodel__detailsT}{model\-\_\-details\-T} md, double \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\-\_\-scale})}\label{group__energy__parameters_gaaa049a8c9f1c2ed4398cb1b5a3d65a66}
+
+\begin{DoxyCompactList}\small\item\em Get precomputed Boltzmann factors of the loop type dependent energy contributions (alifold variant) with independent thermodynamic temperature. \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 R\-N\-Alib. Furthermore, the energy parameter set in the R\-N\-Alib 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{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!scale\-\_\-parameters@{scale\-\_\-parameters}}
+\index{scale\-\_\-parameters@{scale\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
+\subsubsection[{scale\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf param\-T}$\ast$ scale\-\_\-parameters (
+\begin{DoxyParamCaption}
+\item[{void}]{}
+\end{DoxyParamCaption}
+)}}\label{group__energy__parameters_ga527ef619cd8210b84d5d53be1e0e29b6}
+
+
+Get precomputed energy contributions for all the known loop types.
+
+\begin{DoxyNote}{Note}
+Open\-M\-P\-: 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{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-scaled\-\_\-parameters@{get\-\_\-scaled\-\_\-parameters}}
+\index{get\-\_\-scaled\-\_\-parameters@{get\-\_\-scaled\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
+\subsubsection[{get\-\_\-scaled\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf param\-T}$\ast$ get\-\_\-scaled\-\_\-parameters (
+\begin{DoxyParamCaption}
+\item[{double}]{temperature, }
+\item[{{\bf model\-\_\-details\-T}}]{md}
+\end{DoxyParamCaption}
+)}}\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\-\_\-details\-T}, \hyperlink{fold__vars_8h_a4c3257186a796182462f18a5480ac8b3}{set\-\_\-model\-\_\-details()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em temperature} & The temperature in degrees Celcius \\
+\hline
+{\em md} & The model details \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+precomputed energy contributions and model settings
+\end{DoxyReturn}
+\hypertarget{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-scaled\-\_\-pf\-\_\-parameters@{get\-\_\-scaled\-\_\-pf\-\_\-parameters}}
+\index{get\-\_\-scaled\-\_\-pf\-\_\-parameters@{get\-\_\-scaled\-\_\-pf\-\_\-parameters}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
+\subsubsection[{get\-\_\-scaled\-\_\-pf\-\_\-parameters}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-scaled\-\_\-pf\-\_\-parameters (
+\begin{DoxyParamCaption}
+\item[{void}]{}
+\end{DoxyParamCaption}
+)}}\label{group__energy__parameters_gab85f6b6da051f380371deb0d8921bdba}
+get a datastructure of type \hyperlink{structpf__paramT}{pf\-\_\-param\-T} 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{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-boltzmann\-\_\-factors@{get\-\_\-boltzmann\-\_\-factors}}
+\index{get\-\_\-boltzmann\-\_\-factors@{get\-\_\-boltzmann\-\_\-factors}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
+\subsubsection[{get\-\_\-boltzmann\-\_\-factors}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-boltzmann\-\_\-factors (
+\begin{DoxyParamCaption}
+\item[{double}]{temperature, }
+\item[{double}]{beta\-Scale, }
+\item[{{\bf model\-\_\-details\-T}}]{md, }
+\item[{double}]{pf\-\_\-scale}
+\end{DoxyParamCaption}
+)}}\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}
+{\em temperature} & The temperature in degrees Celcius used for (re-\/)scaling the energy contributions \\
+\hline
+{\em beta\-Scale} & A scaling value that is used as a multiplication factor for the absolute temperature of the system \\
+\hline
+{\em md} & The model details to be used \\
+\hline
+{\em pf\-\_\-scale} & The scaling factor for the Boltzmann factors \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A set of precomputed Boltzmann factors
+\end{DoxyReturn}
+\hypertarget{group__energy__parameters_gacba212326a051734797e65987260fdd0}{\index{Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}!get\-\_\-boltzmann\-\_\-factor\-\_\-copy@{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}}
+\index{get\-\_\-boltzmann\-\_\-factor\-\_\-copy@{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}!Change and Precalculate Energy Parameter Sets and Boltzmann Factors@{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}}
+\subsubsection[{get\-\_\-boltzmann\-\_\-factor\-\_\-copy}]{\setlength{\rightskip}{0pt plus 5cm}{\bf pf\-\_\-param\-T}$\ast$ get\-\_\-boltzmann\-\_\-factor\-\_\-copy (
+\begin{DoxyParamCaption}
+\item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters}
+\end{DoxyParamCaption}
+)}}\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}
+{\em parameters} & The input data structure that shall be copied \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+A copy of the provided Boltzmann factor dataset
+\end{DoxyReturn}
git://source.jalview.org / jabaws.git / blobdiff