\batchmode
\documentclass[a4paper]{book}
\usepackage{makeidx}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{float}
\usepackage{listings}
\usepackage{color}
\usepackage{textcomp}
\usepackage{alltt}
\usepackage{times}
\usepackage{ifpdf}
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\usepackage[utf8]{inputenc}
\usepackage{doxygen}
\lstset{language=C++,inputencoding=utf8,basicstyle=\footnotesize,breaklines=true,breakatwhitespace=true,tabsize=2,numbers=left }
\makeindex
\setcounter{tocdepth}{3}
\renewcommand{\footrulewidth}{0.4pt}
\begin{document}
\hypersetup{pageanchor=false}
\begin{titlepage}
\vspace*{7cm}
\begin{center}
{\Large RNAlib-\/2.1.2 }\\
\vspace*{1cm}
{\large Generated by Doxygen 1.6.1}\\
\vspace*{0.5cm}
{\small Tue Apr 11 12:10:08 2017}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
\hypersetup{pageanchor=true}
\chapter{ViennaRNA Package core -\/ RNAlib}
\label{index}\hypertarget{index}{}\input{main}
\chapter{Parsing and Comparing -\/ Functions to Manipulate Structures}
\label{mp_parse}
\hypertarget{mp_parse}{}
\include{mp_parse}
\chapter{Utilities -\/ Odds and Ends}
\label{mp_utils}
\hypertarget{mp_utils}{}
\include{mp_utils}
\chapter{Example -\/ A Small Example Program}
\label{mp_example}
\hypertarget{mp_example}{}
\include{mp_example}
\chapter{Deprecated List}
\label{deprecated}
\hypertarget{deprecated}{}
\include{deprecated}
\chapter{Module Index}
\input{modules}
\chapter{Data Structure Index}
\input{annotated}
\chapter{File Index}
\input{files}
\chapter{Module Documentation}
\input{group__folding__routines}
\include{group__mfe__fold}
\include{group__pf__fold}
\include{group__mea__fold}
\include{group__centroid__fold}
\include{group__subopt__fold}
\include{group__subopt__zuker}
\include{group__subopt__wuchty}
\include{group__subopt__stochbt}
\include{group__cofold}
\include{group__mfe__cofold}
\include{group__pf__cofold}
\include{group__up__cofold}
\include{group__consensus__fold}
\include{group__consensus__mfe__fold}
\include{group__consensus__pf__fold}
\include{group__consensus__stochbt}
\include{group__local__fold}
\include{group__local__mfe__fold}
\include{group__local__pf__fold}
\include{group__local__consensus__fold}
\include{group__energy__parameters}
\include{group__energy__parameters__rw}
\include{group__energy__parameters__convert}
\include{group__eval}
\include{group__inverse__fold}
\include{group__class__fold}
\include{group__kl__neighborhood}
\include{group__kl__neighborhood__mfe}
\include{group__kl__neighborhood__pf}
\include{group__kl__neighborhood__stochbt}
\include{group__dos}
\include{group__parse}
\chapter{Data Structure Documentation}
\input{structbondT}
\include{structbondTEn}
\include{structcofoldF}
\include{structConcEnt}
\include{structconstrain}
\include{structCOORDINATE}
\include{structcpair}
\include{structduplexT}
\include{structdupVar}
\include{structfolden}
\include{structinteract}
\include{structintermediate__t}
\include{structINTERVAL}
\include{structLIST}
\include{structLST__BUCKET}
\include{structmodel__detailsT}
\include{structmove__t}
\include{structPAIR}
\include{structpair__info}
\include{structpairpro}
\include{structparamT}
\include{structpath__t}
\include{structpf__paramT}
\include{structplist}
\include{structPostorder__list}
\include{structpu__contrib}
\include{structpu__out}
\include{structsect}
\include{structsnoopT}
\include{structSOLUTION}
\include{structstruct__en}
\include{structsvm__model}
\include{structswString}
\include{structTree}
\include{structTwoDfold__solution}
\include{structTwoDfold__vars}
\include{structTwoDpfold__solution}
\include{structTwoDpfold__vars}
\chapter{File Documentation}
\input{2Dfold_8h}
\include{2Dpfold_8h}
\include{alifold_8h}
\include{cofold_8h}
\include{convert__epars_8h}
\include{data__structures_8h}
\include{dist__vars_8h}
\include{duplex_8h}
\include{edit__cost_8h}
\include{energy__const_8h}
\include{findpath_8h}
\include{fold_8h}
\include{fold__vars_8h}
\include{gquad_8h}
\include{inverse_8h}
\include{Lfold_8h}
\include{loop__energies_8h}
\include{LPfold_8h}
\include{MEA_8h}
\include{mm_8h}
\include{naview_8h}
\include{params_8h}
\include{part__func_8h}
\include{part__func__co_8h}
\include{part__func__up_8h}
\include{plot__layouts_8h}
\include{profiledist_8h}
\include{PS__dot_8h}
\include{read__epars_8h}
\include{RNAstruct_8h}
\include{stringdist_8h}
\include{subopt_8h}
\include{treedist_8h}
\include{utils_8h}
\include{1_88_84__epars_8h}
\include{1_88_84__intloops_8h}
\printindex
\end{document}
