Add missing doc files

[jabaws.git] / binaries / src / ViennaRNA / doc / latex / energy__const_8h.tex

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+\hypertarget{energy__const_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.h File Reference}
+\label{energy__const_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/energy\-\_\-const.\-h}}
+}
+Include dependency graph for energy\-\_\-const.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{energy__const_8h__incl}
+\end{center}
+\end{figure}
+This graph shows which files directly or indirectly include this file\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{energy__const_8h__dep__incl}
+\end{center}
+\end{figure}
+\subsection*{Macros}
+\begin{DoxyCompactItemize}
+\item 
+\#define \hyperlink{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{G\-A\-S\-C\-O\-N\-S\-T}~1.\-98717  /$\ast$ in \mbox{[}cal/K\mbox{]} $\ast$/
+\item 
+\#define \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0}~273.\-15
+\item 
+\#define \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{I\-N\-F}~10000000 /$\ast$ (I\-N\-T\-\_\-\-M\-A\-X/10) $\ast$/
+\item 
+\#define \hyperlink{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{F\-O\-R\-B\-I\-D\-D\-E\-N}~9999
+\item 
+\#define \hyperlink{energy__const_8h_a96a9822fa134450197dd454b1478a193}{B\-O\-N\-U\-S}~10000
+\item 
+\#define \hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{N\-B\-P\-A\-I\-R\-S}~7
+\item 
+\#define \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{T\-U\-R\-N}~3
+\item 
+\#define \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{M\-A\-X\-L\-O\-O\-P}~30
+\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+energy constants 
+
+\subsection{Macro Definition Documentation}
+\hypertarget{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!G\-A\-S\-C\-O\-N\-S\-T@{G\-A\-S\-C\-O\-N\-S\-T}}
+\index{G\-A\-S\-C\-O\-N\-S\-T@{G\-A\-S\-C\-O\-N\-S\-T}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{G\-A\-S\-C\-O\-N\-S\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define G\-A\-S\-C\-O\-N\-S\-T~1.\-98717  /$\ast$ in \mbox{[}cal/K\mbox{]} $\ast$/}}\label{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}
+The gas constant \hypertarget{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!K0@{K0}}
+\index{K0@{K0}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{K0}]{\setlength{\rightskip}{0pt plus 5cm}\#define K0~273.\-15}}\label{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}
+0 deg Celsius in Kelvin \hypertarget{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!I\-N\-F@{I\-N\-F}}
+\index{I\-N\-F@{I\-N\-F}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{I\-N\-F}]{\setlength{\rightskip}{0pt plus 5cm}\#define I\-N\-F~10000000 /$\ast$ (I\-N\-T\-\_\-\-M\-A\-X/10) $\ast$/}}\label{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}
+Infinity as used in minimization routines \hypertarget{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!F\-O\-R\-B\-I\-D\-D\-E\-N@{F\-O\-R\-B\-I\-D\-D\-E\-N}}
+\index{F\-O\-R\-B\-I\-D\-D\-E\-N@{F\-O\-R\-B\-I\-D\-D\-E\-N}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{F\-O\-R\-B\-I\-D\-D\-E\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-O\-R\-B\-I\-D\-D\-E\-N~9999}}\label{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}
+forbidden \hypertarget{energy__const_8h_a96a9822fa134450197dd454b1478a193}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!B\-O\-N\-U\-S@{B\-O\-N\-U\-S}}
+\index{B\-O\-N\-U\-S@{B\-O\-N\-U\-S}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{B\-O\-N\-U\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define B\-O\-N\-U\-S~10000}}\label{energy__const_8h_a96a9822fa134450197dd454b1478a193}
+bonus contribution \hypertarget{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!N\-B\-P\-A\-I\-R\-S@{N\-B\-P\-A\-I\-R\-S}}
+\index{N\-B\-P\-A\-I\-R\-S@{N\-B\-P\-A\-I\-R\-S}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{N\-B\-P\-A\-I\-R\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define N\-B\-P\-A\-I\-R\-S~7}}\label{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}
+The number of distinguishable base pairs \hypertarget{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!T\-U\-R\-N@{T\-U\-R\-N}}
+\index{T\-U\-R\-N@{T\-U\-R\-N}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{T\-U\-R\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define T\-U\-R\-N~3}}\label{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}
+The minimum loop length \hypertarget{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{\index{energy\-\_\-const.\-h@{energy\-\_\-const.\-h}!M\-A\-X\-L\-O\-O\-P@{M\-A\-X\-L\-O\-O\-P}}
+\index{M\-A\-X\-L\-O\-O\-P@{M\-A\-X\-L\-O\-O\-P}!energy_const.h@{energy\-\_\-const.\-h}}
+\subsubsection[{M\-A\-X\-L\-O\-O\-P}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X\-L\-O\-O\-P~30}}\label{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}
+The maximum loop length 
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