-\hypertarget{group__energy__parameters__convert}{\section{Converting energy parameter files}
+\hypertarget{group__energy__parameters__convert}{
+\section{Converting energy parameter files}
\label{group__energy__parameters__convert}\index{Converting energy parameter files@{Converting energy parameter files}}
}
Convert energy parameter files into the latest format.
-Collaboration diagram for Converting energy parameter files\-:
-\nopagebreak
+Collaboration diagram for Converting energy parameter files:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__energy__parameters__convert}
+\includegraphics[width=248pt]{group__energy__parameters__convert}
\end{center}
\end{figure}
\subsection*{Files}
\begin{DoxyCompactItemize}
\item
-file \hyperlink{convert__epars_8h}{convert\-\_\-epars.\-h}
-\begin{DoxyCompactList}\small\item\em Functions and definitions for energy parameter file format conversion. \end{DoxyCompactList}\end{DoxyCompactItemize}
-\subsection*{Macros}
+file \hyperlink{convert__epars_8h}{convert\_\-epars.h}
+
+
+\begin{DoxyCompactList}\small\item\em Functions and definitions for energy parameter file format conversion. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Defines}
\begin{DoxyCompactItemize}
\item
-\#define \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}~1\-U
+\#define \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}~1U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}~2\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}~2U
\item
-\#define \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}~4\-U
+\#define \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}~4U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}~8\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}~8U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}~16\-U
+\#define \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}~16U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}~32\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}~32U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}~64\-U
+\#define \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}~64U
\item
-\#define \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}~128\-U
+\#define \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}~128U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}~256\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}~256U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}~512\-U
+\#define \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}~512U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}~1024\-U
+\#define \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}~1024U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}~2048\-U
+\#define \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}~2048U
\item
-\#define \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}~4096\-U
+\#define \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}~4096U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}~8192\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}~8192U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}~16384\-U
+\#define \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}~16384U
\item
-\#define \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}~32768\-U
+\#define \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}~32768U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}~65536\-U
+\#define \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}~65536U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}~131072\-U
+\#define \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}~131072U
\item
-\#define \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}~262144\-U
+\#define \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}~262144U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}~524288\-U
+\#define \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}~524288U
\item
-\#define \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}~1048576\-U
+\#define \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}~1048576U
\item
-\#define \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}~2097152\-U
+\#define \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}~2097152U
\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item
-void \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\-\_\-parameter\-\_\-file} (const char $\ast$iname, const char $\ast$oname, unsigned int options)
+void \hyperlink{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{convert\_\-parameter\_\-file} (const char $\ast$iname, const char $\ast$oname, unsigned int options)
\end{DoxyCompactItemize}
\subsection{Detailed Description}
-Convert energy parameter files into the latest format. To preserve some backward compatibility the R\-N\-Alib also provides functions to convert energy parameter files from the format used in version 1.\-4-\/1.\-8 into the new format used since version 2.\-0
+Convert energy parameter files into the latest format. To preserve some backward compatibility the RNAlib also provides functions to convert energy parameter files from the format used in version 1.4-\/1.8 into the new format used since version 2.0
-\subsection{Macro Definition Documentation}
-\hypertarget{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L~1\-U}}\label{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}
-Flag to indicate printing of a complete parameter set \hypertarget{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P~2\-U}}\label{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}
-Flag to indicate printing of hairpin contributions \hypertarget{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K~4\-U}}\label{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}
-Flag to indicate printing of base pair stack contributions \hypertarget{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P~8\-U}}\label{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}
-Flag to indicate printing of hairpin mismatch contribution \hypertarget{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T~16\-U}}\label{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}
-Flag to indicate printing of interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N~32\-U}}\label{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}
-Flag to indicate printing of 1\-:n interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23~64\-U}}\label{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}
-Flag to indicate printing of 2\-:3 interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I~128\-U}}\label{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}
-Flag to indicate printing of multi loop mismatch contribution \hypertarget{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T~256\-U}}\label{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}
-Flag to indicate printing of exterior loop mismatch contribution \hypertarget{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5~512\-U}}\label{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}
-Flag to indicate printing of 5' dangle conctribution \hypertarget{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3~1024\-U}}\label{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}
-Flag to indicate printing of 3' dangle contribution \hypertarget{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11~2048\-U}}\label{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}
-Flag to indicate printing of 1\-:1 interior loop contribution \hypertarget{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21~4096\-U}}\label{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}
-Flag to indicate printing of 2\-:1 interior loop contribution \hypertarget{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22~8192\-U}}\label{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}
-Flag to indicate printing of 2\-:2 interior loop contribution \hypertarget{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E~16384\-U}}\label{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}
-Flag to indicate printing of bulge loop contribution \hypertarget{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T~32768\-U}}\label{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}
-Flag to indicate printing of interior loop contribution \hypertarget{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L~65536\-U}}\label{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}
-Flag to indicate printing of multi loop contribution \hypertarget{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C~131072\-U}}\label{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}
-Flag to indicate printing of misc contributions (such as terminal\-A\-U) \hypertarget{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P~262144\-U}}\label{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}
-Flag to indicate printing of special hairpin contributions (tri-\/, tetra-\/, hexa-\/loops) \hypertarget{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A~524288\-U}}\label{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}
+\subsection{Define Documentation}
+\hypertarget{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL@{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL@{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL~1U}}
+\label{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}
+Flag to indicate printing of a complete parameter set \hypertarget{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-HP~2U}}
+\label{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}
+Flag to indicate printing of hairpin contributions \hypertarget{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK@{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK@{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK~4U}}
+\label{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}
+Flag to indicate printing of base pair stack contributions \hypertarget{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP~8U}}
+\label{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}
+Flag to indicate printing of hairpin mismatch contribution \hypertarget{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT~16U}}
+\label{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}
+Flag to indicate printing of interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N~32U}}
+\label{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}
+Flag to indicate printing of 1:n interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23~64U}}
+\label{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}
+Flag to indicate printing of 2:3 interior loop mismatch contribution \hypertarget{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI~128U}}
+\label{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}
+Flag to indicate printing of multi loop mismatch contribution \hypertarget{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT~256U}}
+\label{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}
+Flag to indicate printing of exterior loop mismatch contribution \hypertarget{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5~512U}}
+\label{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}
+Flag to indicate printing of 5' dangle conctribution \hypertarget{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3~1024U}}
+\label{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}
+Flag to indicate printing of 3' dangle contribution \hypertarget{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11~2048U}}
+\label{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}
+Flag to indicate printing of 1:1 interior loop contribution \hypertarget{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21~4096U}}
+\label{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}
+Flag to indicate printing of 2:1 interior loop contribution \hypertarget{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22~8192U}}
+\label{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}
+Flag to indicate printing of 2:2 interior loop contribution \hypertarget{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE@{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE@{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE~16384U}}
+\label{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}
+Flag to indicate printing of bulge loop contribution \hypertarget{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-INT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT@{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-INT~32768U}}
+\label{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}
+Flag to indicate printing of interior loop contribution \hypertarget{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-ML@{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML@{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-ML~65536U}}
+\label{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}
+Flag to indicate printing of multi loop contribution \hypertarget{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC@{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC~131072U}}
+\label{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}
+Flag to indicate printing of misc contributions (such as terminalAU) \hypertarget{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP~262144U}}
+\label{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}
+Flag to indicate printing of special hairpin contributions (tri-\/, tetra-\/, hexa-\/loops) \hypertarget{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA@{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA@{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA~524288U}}
+\label{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}
Flag to indicate printing of given parameters only\par
\begin{DoxyNote}{Note}
-This option overrides all other output options, except \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P} !
+This option overrides all other output options, except \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP} !
\end{DoxyNote}
-\hypertarget{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O~1048576\-U}}\label{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}
-Flag to indicate printing of interior loop asymmetry contribution \hypertarget{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{\index{Converting energy parameter files@{Converting energy parameter files}!V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}}
-\index{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P@{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P~2097152\-U}}\label{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}
+\hypertarget{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO@{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO@{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO~1048576U}}
+\label{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}
+Flag to indicate printing of interior loop asymmetry contribution \hypertarget{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}}
+\index{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP@{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}]{\setlength{\rightskip}{0pt plus 5cm}\#define VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP~2097152U}}
+\label{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}
Flag to indicate dumping the energy contributions from the library instead of an input file
\subsection{Function Documentation}
-\hypertarget{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{\index{Converting energy parameter files@{Converting energy parameter files}!convert\-\_\-parameter\-\_\-file@{convert\-\_\-parameter\-\_\-file}}
-\index{convert\-\_\-parameter\-\_\-file@{convert\-\_\-parameter\-\_\-file}!Converting energy parameter files@{Converting energy parameter files}}
-\subsubsection[{convert\-\_\-parameter\-\_\-file}]{\setlength{\rightskip}{0pt plus 5cm}void convert\-\_\-parameter\-\_\-file (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{iname, }
-\item[{const char $\ast$}]{oname, }
-\item[{unsigned int}]{options}
-\end{DoxyParamCaption}
-)}}\label{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}
-Convert/dump a Vienna 1.\-8.\-4 formatted energy parameter file
+\hypertarget{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}{
+\index{energy\_\-parameters\_\-convert@{energy\_\-parameters\_\-convert}!convert\_\-parameter\_\-file@{convert\_\-parameter\_\-file}}
+\index{convert\_\-parameter\_\-file@{convert\_\-parameter\_\-file}!energy_parameters_convert@{energy\_\-parameters\_\-convert}}
+\subsubsection[{convert\_\-parameter\_\-file}]{\setlength{\rightskip}{0pt plus 5cm}void convert\_\-parameter\_\-file (const char $\ast$ {\em iname}, \/ const char $\ast$ {\em oname}, \/ unsigned int {\em options})}}
+\label{group__energy__parameters__convert_gafbe538bc4eb2cf2a33326e1010005f8a}
+Convert/dump a Vienna 1.8.4 formatted energy parameter file
The options argument allows to control the different output modes.\par
- Currently available options are\-:\par
- \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-A\-L\-L}, \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-H\-P}, \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-T\-A\-C\-K}\par
- \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-H\-P}, \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T}, \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-1\-N}\par
- \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-I\-N\-T\-\_\-23}, \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-M\-U\-L\-T\-I}, \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-M\-\_\-\-E\-X\-T}\par
- \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E5}, \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-A\-N\-G\-L\-E3}, \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-11}\par
- \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-21}, \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T\-\_\-22}, \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-B\-U\-L\-G\-E}\par
- \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-I\-N\-T}, \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-L}, \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-M\-I\-S\-C}\par
- \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-S\-P\-E\-C\-I\-A\-L\-\_\-\-H\-P}, \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-V\-A\-N\-I\-L\-L\-A}, \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-N\-I\-N\-I\-O}\par
- \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{V\-R\-N\-A\-\_\-\-C\-O\-N\-V\-E\-R\-T\-\_\-\-O\-U\-T\-P\-U\-T\-\_\-\-D\-U\-M\-P}
+ Currently available options are:\par
+ \hyperlink{group__energy__parameters__convert_ga8dc6aee5a806c49b71557152f9616bc4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ALL}, \hyperlink{group__energy__parameters__convert_gaf66fe2cb11dfcfd32d791049c254a8a4}{VRNA\_\-CONVERT\_\-OUTPUT\_\-HP}, \hyperlink{group__energy__parameters__convert_gad23522d63f8d4c50d5a5deee9bee3ef2}{VRNA\_\-CONVERT\_\-OUTPUT\_\-STACK}\par
+ \hyperlink{group__energy__parameters__convert_gaa892c7b4957459090f3e08da298cc347}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-HP}, \hyperlink{group__energy__parameters__convert_ga4ff223fb1f9c62cd92d9ab811ad03d55}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT}, \hyperlink{group__energy__parameters__convert_gaf5d3743219f83c6348155cd81e755bbb}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-1N}\par
+ \hyperlink{group__energy__parameters__convert_ga78382ec622ba99e0ac2262317bdd7316}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-INT\_\-23}, \hyperlink{group__energy__parameters__convert_gae67af9f1cdf7baf2865481282a5d1034}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-MULTI}, \hyperlink{group__energy__parameters__convert_gaf14ead7ef1fdbe725ade653750fc51e3}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MM\_\-EXT}\par
+ \hyperlink{group__energy__parameters__convert_ga036ffd996d8c8a9acf631760dd1da24b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE5}, \hyperlink{group__energy__parameters__convert_ga34a8a5479ef885834ef32f3fb43d79bc}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DANGLE3}, \hyperlink{group__energy__parameters__convert_ga079aafefd5f8ab57ee5120099a34bd25}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-11}\par
+ \hyperlink{group__energy__parameters__convert_gacf770881d9034431ebe741642342a1f9}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-21}, \hyperlink{group__energy__parameters__convert_gaa307671e2631cdacad9cbe4c6583b05f}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT\_\-22}, \hyperlink{group__energy__parameters__convert_ga7092fe0be4de6f02cc0bf08e81af726a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-BULGE}\par
+ \hyperlink{group__energy__parameters__convert_gac5c2289fdf8ff1b980976d1613ff943a}{VRNA\_\-CONVERT\_\-OUTPUT\_\-INT}, \hyperlink{group__energy__parameters__convert_gaf2c8755d64eff3852aa45df9ac80a4fe}{VRNA\_\-CONVERT\_\-OUTPUT\_\-ML}, \hyperlink{group__energy__parameters__convert_ga46d5b1535ae86060b6317565b7c6b40b}{VRNA\_\-CONVERT\_\-OUTPUT\_\-MISC}\par
+ \hyperlink{group__energy__parameters__convert_gaa1ff48a79642d69579d1766561ec6db6}{VRNA\_\-CONVERT\_\-OUTPUT\_\-SPECIAL\_\-HP}, \hyperlink{group__energy__parameters__convert_ga0d4e8a836bb4864ab5129c085dbf592d}{VRNA\_\-CONVERT\_\-OUTPUT\_\-VANILLA}, \hyperlink{group__energy__parameters__convert_ga2eb0462f16939ddacdaf751a88d675ce}{VRNA\_\-CONVERT\_\-OUTPUT\_\-NINIO}\par
+ \hyperlink{group__energy__parameters__convert_gac86976e9c2a55b3a6481ea60044f6098}{VRNA\_\-CONVERT\_\-OUTPUT\_\-DUMP}
-The defined options are fine for bitwise compare-\/ and assignment-\/operations, e. g.\-: pass a collection of options as a single value like this\-: \begin{DoxyVerb}convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) \end{DoxyVerb}
+The defined options are fine for bitwise compare-\/ and assignment-\/operations, e. g.: pass a collection of options as a single value like this: \begin{DoxyVerb}convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) \end{DoxyVerb}
\begin{DoxyParams}{Parameters}
-{\em iname} & The input file name (If N\-U\-L\-L input is read from stdin) \\
-\hline
-{\em oname} & The output file name (If N\-U\-L\-L output is written to stdout) \\
-\hline
-{\em options} & The options (as described above) \\
-\hline
-\end{DoxyParams}
+\item[{\em iname}]The input file name (If NULL input is read from stdin) \item[{\em oname}]The output file name (If NULL output is written to stdout) \item[{\em options}]The options (as described above) \end{DoxyParams}
git://source.jalview.org / jabaws.git / blobdiff