\hypertarget{group__consensus__pf__fold}{
\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
\label{group__consensus__pf__fold}\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
}


Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=334pt]{group__consensus__pf__fold}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\_\-fold\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters, int calculate\_\-bppm, int is\_\-constrained, int is\_\-circular)
\item 
float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\_\-info} structs. The list is terminated by the first entry with pi.i = 0. \item\end{DoxyCompactList}\item 
float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\item 
FLT\_\-OR\_\-DBL $\ast$ \hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export\_\-ali\_\-bppm} (void)
\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Function Documentation}
\hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{
\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}}
\index{alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
\subsubsection[{alipf\_\-fold\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold\_\-par (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl}, \/  {\bf pf\_\-paramT} $\ast$ {\em parameters}, \/  int {\em calculate\_\-bppm}, \/  int {\em is\_\-constrained}, \/  int {\em is\_\-circular})}}
\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}

\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\item[{\em parameters}]\item[{\em calculate\_\-bppm}]\item[{\em is\_\-constrained}]\item[{\em is\_\-circular}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{
\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold@{alipf\_\-fold}}
\index{alipf\_\-fold@{alipf\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
\subsubsection[{alipf\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}


The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\_\-info} structs. The list is terminated by the first entry with pi.i = 0. 
\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{
\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}}
\index{alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
\subsubsection[{alipf\_\-circ\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-circ\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}

\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{
\index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}}
\index{export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
\subsubsection[{export\_\-ali\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}FLT\_\-OR\_\-DBL$\ast$ export\_\-ali\_\-bppm (void)}}
\label{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}


Get a pointer to the base pair probability array. Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}


\begin{DoxySeeAlso}{See also}
\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_\-iindx()} 
\end{DoxySeeAlso}
\begin{DoxyReturn}{Returns}
A pointer to the base pair probability array 
\end{DoxyReturn}
