binaries/src/ViennaRNA/doc/latex/refman.tex

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  38 \usepackage[titles]{tocloft}
  39 \usepackage{doxygen}
  40 \lstset{language=C++,inputencoding=utf8,basicstyle=\footnotesize,breaklines=true,breakatwhitespace=true,tabsize=2,numbers=left }
  41 \makeindex
  42 \setcounter{tocdepth}{3}
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  49 \begin{document}
  50 \hypersetup{pageanchor=false,citecolor=blue}
  51 \begin{titlepage}
  52 \vspace*{7cm}
  53 \begin{center}
  54 {\Large R\-N\-Alib-\/2.1.2 }\\
  55 \vspace*{1cm}
  56 {\large Generated by Doxygen 1.8.3.1}\\
  57 \vspace*{0.5cm}
  58 {\small Thu Sep 5 2013 11:51:49}\\
  59 \end{center}
  60 \end{titlepage}
  61 \clearemptydoublepage
  62 \pagenumbering{roman}
  63 \tableofcontents
  64 \clearemptydoublepage
  65 \pagenumbering{arabic}
  66 \hypersetup{pageanchor=true,citecolor=blue}
  67 \chapter{Vienna\-R\-N\-A Package core -\/ R\-N\-Alib}
  68 \label{index}\hypertarget{index}{}\input{index}
  69 \chapter{Parsing and Comparing -\/ Functions to Manipulate Structures}
  70 \label{mp_parse}
  71 \hypertarget{mp_parse}{}
  72 \input{mp_parse}
  73 \chapter{Utilities -\/ Odds and Ends}
  74 \label{mp_utils}
  75 \hypertarget{mp_utils}{}
  76 \input{mp_utils}
  77 \chapter{Example -\/ A Small Example Program}
  78 \label{mp_example}
  79 \hypertarget{mp_example}{}
  80 \input{mp_example}
  81 \chapter{Deprecated List}
  82 \label{deprecated}
  83 \hypertarget{deprecated}{}
  84 \input{deprecated}
  85 \chapter{Module Index}
  86 \input{modules}
  87 \chapter{Data Structure Index}
  88 \input{annotated}
  89 \chapter{File Index}
  90 \input{files}
  91 \chapter{Module Documentation}
  92 \input{group__folding__routines}
  93 \include{group__mfe__fold}
  94 \include{group__pf__fold}
  95 \include{group__mea__fold}
  96 \include{group__centroid__fold}
  97 \include{group__subopt__fold}
  98 \include{group__subopt__zuker}
  99 \include{group__subopt__wuchty}
 100 \include{group__subopt__stochbt}
 101 \include{group__cofold}
 102 \include{group__mfe__cofold}
 103 \include{group__pf__cofold}
 104 \include{group__up__cofold}
 105 \include{group__consensus__fold}
 106 \include{group__consensus__mfe__fold}
 107 \include{group__consensus__pf__fold}
 108 \include{group__consensus__stochbt}
 109 \include{group__local__fold}
 110 \include{group__local__mfe__fold}
 111 \include{group__local__pf__fold}
 112 \include{group__local__consensus__fold}
 113 \include{group__energy__parameters}
 114 \include{group__energy__parameters__rw}
 115 \include{group__energy__parameters__convert}
 116 \include{group__eval}
 117 \include{group__inverse__fold}
 118 \include{group__class__fold}
 119 \include{group__kl__neighborhood}
 120 \include{group__kl__neighborhood__mfe}
 121 \include{group__kl__neighborhood__pf}
 122 \include{group__kl__neighborhood__stochbt}
 123 \include{group__dos}
 124 \include{group__parse}
 125 \chapter{Data Structure Documentation}
 126 \input{structbondT}
 127 \input{structbondTEn}
 128 \input{structcofoldF}
 129 \input{structConcEnt}
 130 \input{structconstrain}
 131 \input{structCOORDINATE}
 132 \input{structcpair}
 133 \input{structduplexT}
 134 \input{structdupVar}
 135 \input{structfolden}
 136 \input{structinteract}
 137 \input{structintermediate__t}
 138 \input{structINTERVAL}
 139 \input{structLIST}
 140 \input{structLST__BUCKET}
 141 \input{structmodel__detailsT}
 142 \input{structmove__t}
 143 \input{structPAIR}
 144 \input{structpair__info}
 145 \input{structpairpro}
 146 \input{structparamT}
 147 \input{structpath__t}
 148 \input{structpf__paramT}
 149 \input{structplist}
 150 \input{structPostorder__list}
 151 \input{structpu__contrib}
 152 \input{structpu__out}
 153 \input{structsect}
 154 \input{structsnoopT}
 155 \input{structSOLUTION}
 156 \input{structstruct__en}
 157 \input{structsvm__model}
 158 \input{structswString}
 159 \input{structTree}
 160 \input{structTwoDfold__solution}
 161 \input{structTwoDfold__vars}
 162 \input{structTwoDpfold__solution}
 163 \input{structTwoDpfold__vars}
 164 \chapter{File Documentation}
 165 \input{2Dfold_8h}
 166 \input{2Dpfold_8h}
 167 \input{alifold_8h}
 168 \input{cofold_8h}
 169 \input{convert__epars_8h}
 170 \input{data__structures_8h}
 171 \input{dist__vars_8h}
 172 \input{duplex_8h}
 173 \input{edit__cost_8h}
 174 \input{energy__const_8h}
 175 \input{findpath_8h}
 176 \input{fold_8h}
 177 \input{fold__vars_8h}
 178 \input{gquad_8h}
 179 \input{inverse_8h}
 180 \input{Lfold_8h}
 181 \input{loop__energies_8h}
 182 \input{LPfold_8h}
 183 \input{MEA_8h}
 184 \input{mm_8h}
 185 \input{naview_8h}
 186 \input{params_8h}
 187 \input{part__func_8h}
 188 \input{part__func__co_8h}
 189 \input{part__func__up_8h}
 190 \input{plot__layouts_8h}
 191 \input{profiledist_8h}
 192 \input{PS__dot_8h}
 193 \input{read__epars_8h}
 194 \input{RNAstruct_8h}
 195 \input{stringdist_8h}
 196 \input{subopt_8h}
 197 \input{treedist_8h}
 198 \input{utils_8h}
 199 \input{1_88_84__epars_8h}
 200 \input{1_88_84__intloops_8h}
 201 \newpage \bibliographystyle{plain}
 202 \bibliography{viennarna}
 203 \addcontentsline{toc}{part}{Index}
 204 \printindex
 205 \end{document}