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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.
[jabaws.git] / binaries / src / ViennaRNA / doc / latex / energy__const_8h.tex
diff --git a/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex b/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex
index 68d9c6d..7228573 100644 (file)
--- a/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex
+++ b/binaries/src/ViennaRNA/doc/latex/energy__const_8h.tex
@@ -1,69 +1,84 @@
-\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}}
+\hypertarget{energy__const_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\-const.h File Reference}
+\label{energy__const_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\-const.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/energy\_\-const.h}}
 }
-Include dependency graph for energy\-\_\-const.\-h\-:
-\nopagebreak
+Include dependency graph for energy\_\-const.h:\nopagebreak
 \begin{figure}[H]
 \begin{center}
 \leavevmode
-\includegraphics[width=250pt]{energy__const_8h__incl}
+\includegraphics[width=225pt]{energy__const_8h__incl}
 \end{center}
 \end{figure}
-This graph shows which files directly or indirectly include this file\-:
-\nopagebreak
+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}
+\includegraphics[width=420pt]{energy__const_8h__dep__incl}
 \end{center}
 \end{figure}
-\subsection*{Macros}
+\subsection*{Defines}
 \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{]} $\ast$/
+\#define \hyperlink{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{GASCONST}~1.98717
 \item 
-\#define \hyperlink{energy__const_8h_a307c72605e3713972b4f4fb2d53ea20e}{K0}~273.\-15
+\#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) $\ast$/
+\#define \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}~10000000
 \item 
-\#define \hyperlink{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{F\-O\-R\-B\-I\-D\-D\-E\-N}~9999
+\#define \hyperlink{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{FORBIDDEN}~9999
 \item 
-\#define \hyperlink{energy__const_8h_a96a9822fa134450197dd454b1478a193}{B\-O\-N\-U\-S}~10000
+\#define \hyperlink{energy__const_8h_a96a9822fa134450197dd454b1478a193}{BONUS}~10000
 \item 
-\#define \hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{N\-B\-P\-A\-I\-R\-S}~7
+\#define \hyperlink{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{NBPAIRS}~7
 \item 
-\#define \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{T\-U\-R\-N}~3
+\#define \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{TURN}~3
 \item 
-\#define \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{M\-A\-X\-L\-O\-O\-P}~30
+\#define \hyperlink{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{MAXLOOP}~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}
+\subsection{Define Documentation}
+\hypertarget{energy__const_8h_ab1e4a8d82f24ed5db01dde5f25269cf1}{
+\index{energy\_\-const.h@{energy\_\-const.h}!GASCONST@{GASCONST}}
+\index{GASCONST@{GASCONST}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{GASCONST}]{\setlength{\rightskip}{0pt plus 5cm}\#define GASCONST~1.98717}}
+\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}!INF@{INF}}
+\index{INF@{INF}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{INF}]{\setlength{\rightskip}{0pt plus 5cm}\#define INF~10000000}}
+\label{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}
+Infinity as used in minimization routines \hypertarget{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}{
+\index{energy\_\-const.h@{energy\_\-const.h}!FORBIDDEN@{FORBIDDEN}}
+\index{FORBIDDEN@{FORBIDDEN}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{FORBIDDEN}]{\setlength{\rightskip}{0pt plus 5cm}\#define FORBIDDEN~9999}}
+\label{energy__const_8h_a5064c29ab2d1e20c2304b3c67562774d}
+forbidden \hypertarget{energy__const_8h_a96a9822fa134450197dd454b1478a193}{
+\index{energy\_\-const.h@{energy\_\-const.h}!BONUS@{BONUS}}
+\index{BONUS@{BONUS}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{BONUS}]{\setlength{\rightskip}{0pt plus 5cm}\#define BONUS~10000}}
+\label{energy__const_8h_a96a9822fa134450197dd454b1478a193}
+bonus contribution \hypertarget{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}{
+\index{energy\_\-const.h@{energy\_\-const.h}!NBPAIRS@{NBPAIRS}}
+\index{NBPAIRS@{NBPAIRS}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{NBPAIRS}]{\setlength{\rightskip}{0pt plus 5cm}\#define NBPAIRS~7}}
+\label{energy__const_8h_a5e75221c779d618eab81e096f37e32ce}
+The number of distinguishable base pairs \hypertarget{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{
+\index{energy\_\-const.h@{energy\_\-const.h}!TURN@{TURN}}
+\index{TURN@{TURN}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{TURN}]{\setlength{\rightskip}{0pt plus 5cm}\#define TURN~3}}
+\label{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}
+The minimum loop length \hypertarget{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}{
+\index{energy\_\-const.h@{energy\_\-const.h}!MAXLOOP@{MAXLOOP}}
+\index{MAXLOOP@{MAXLOOP}!energy_const.h@{energy\_\-const.h}}
+\subsubsection[{MAXLOOP}]{\setlength{\rightskip}{0pt plus 5cm}\#define MAXLOOP~30}}
+\label{energy__const_8h_ad1bd6eabac419670ddd3c9ed82145988}
 The maximum loop length 
\ No newline at end of file