\label{deprecated__deprecated000008}
\hypertarget{deprecated__deprecated000008}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\_\-pair} ]Do not use this variable anymore! 
\end{DoxyDescription}

\label{deprecated__deprecated000012}
\hypertarget{deprecated__deprecated000012}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} ]This function is deprecated and should not be used anymore as it is not threadsafe! 
\end{DoxyDescription}

\label{deprecated__deprecated000007}
\hypertarget{deprecated__deprecated000007}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\_\-of\_\-circ\_\-struct} ]This function is deprecated and should not be used in future programs Use \hyperlink{fold_8h_aeb14f3664aec67fc03268ac75253f0f8}{energy\_\-of\_\-circ\_\-structure()} instead!


\end{DoxyDescription}

\label{deprecated__deprecated000005}
\hypertarget{deprecated__deprecated000005}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\_\-of\_\-struct} ]This function is deprecated and should not be used in future programs! Use \hyperlink{fold_8h_af93986cb3cb29770ec9cca69c9fab8cf}{energy\_\-of\_\-structure()} instead!


\end{DoxyDescription}

\label{deprecated__deprecated000006}
\hypertarget{deprecated__deprecated000006}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\_\-of\_\-struct\_\-pt} ]This function is deprecated and should not be used in future programs! Use \hyperlink{fold_8h_a8831445966b761417e713360791299d8}{energy\_\-of\_\-structure\_\-pt()} instead!


\end{DoxyDescription}

\label{deprecated__deprecated000015}
\hypertarget{deprecated__deprecated000015}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy} ]Use \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\_\-E\_\-Hairpin()} from \hyperlink{loop__energies_8h}{loop\_\-energies.h} instead 
\end{DoxyDescription}

\label{deprecated__deprecated000014}
\hypertarget{deprecated__deprecated000014}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy} ]Use \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\_\-E\_\-IntLoop()} from \hyperlink{loop__energies_8h}{loop\_\-energies.h} instead 
\end{DoxyDescription}

\label{deprecated__deprecated000016}
\hypertarget{deprecated__deprecated000016}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\_\-plist} ]\{ This function is deprecated and will be removed soon!\} use \hyperlink{part__func_8h_a2f29542659beb5ebd176631a3da11580}{assign\_\-plist\_\-from\_\-pr()} instead! 
\end{DoxyDescription}

\label{deprecated__deprecated000003}
\hypertarget{deprecated__deprecated000003}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE} ]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_\-Hairpin()} instead!\} 
\end{DoxyDescription}

\label{deprecated__deprecated000010}
\hypertarget{deprecated__deprecated000010}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx} ]Do not use this variable anymore! 
\end{DoxyDescription}

\label{deprecated__deprecated000017}
\hypertarget{deprecated__deprecated000017}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\_\-co\_\-pf\_\-fold} ]\{ This function is deprecated and will be removed soon!\} 
\end{DoxyDescription}

\label{deprecated__deprecated000011}
\hypertarget{deprecated__deprecated000011}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\_\-pf\_\-fold} ]This function is obsolete and will be removed soon! 
\end{DoxyDescription}

\label{deprecated__deprecated000001}
\hypertarget{deprecated__deprecated000001}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\_\-cofold} ]\{This function is obsolete and will be removed soon!\} 
\end{DoxyDescription}

\label{deprecated__deprecated000004}
\hypertarget{deprecated__deprecated000004}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\_\-fold} ]\{This function is deprecated and will be removed soon!\}


\end{DoxyDescription}

\label{deprecated__deprecated000002}
\hypertarget{deprecated__deprecated000002}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy} ]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_\-IntLoop()} instead!\} 
\end{DoxyDescription}

\label{deprecated__deprecated000018}
\hypertarget{deprecated__deprecated000018}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\_\-bp\_\-profile} ]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a3dff26e707a2a2e65a0f759caabde6e7}{Make\_\-bp\_\-profile\_\-bppm()} for a replacement


\end{DoxyDescription}

\label{deprecated__deprecated000013}
\hypertarget{deprecated__deprecated000013}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_\-bp\_\-dist} ]This function is not threadsafe and should not be used anymore. Use \hyperlink{part__func_8h_a79cbc375af65f11609feb6b055269e7d}{mean\_\-bp\_\-distance()} instead! 
\end{DoxyDescription}

\label{deprecated__deprecated000009}
\hypertarget{deprecated__deprecated000009}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{fold__vars_8h_ac98ec419070aee6831b44e5c700f090f}{pr} ]Do not use this variable anymore! 
\end{DoxyDescription}

\label{deprecated__deprecated000019}
\hypertarget{deprecated__deprecated000019}{}
 
\begin{DoxyDescription}
\item[Global \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{PS\_\-dot\_\-plot} ]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_\-dot\_\-plot\_\-list()} instead! 
\end{DoxyDescription}