\documentclass[10pt]{book}

\usepackage{html}
\usepackage{verbatimfiles}
\usepackage{makeidx}
\usepackage{jmb}
\usepackage{epsf}
\usepackage{cite}
\usepackage{rotating}
\usepackage{afterpage}
\usepackage{supertabular}

\makeindex

\input{macros.tex}       % macro definitions
\input{defs.tex}         % general format definitions
\input{title.tex}        % page 1 definition (title, address)

\begin{document}

% \latexonly{\sf}

\frontmatter

\begin{titlepage}
  \maketitle
\end{titlepage}

\tableofcontents
\listoffigures
\listoftables
\newpage

\chapter{Copyright notice}
\input{copyright.tex}
\newpage

\chapter{Acknowledgments}
\input{acknowl.tex}

\mainmatter

\chapter{Introduction}

    \input{preface.tex}
    \newpage

    \input{bib_main.tex}
    \newpage

    \input{distribution.tex}
    \newpage

    \input{install.tex}
    \newpage

    \input{bug.tex}
    \newpage

    \input{outline.tex}
    \clearpage

    \input{primer.tex}
    \clearpage

    \input{tutorial.tex}
    \clearpage

    \input{faq.tex}
    \clearpage

    \input{changes.tex}


\chapter{\MODELLER\ commands} \label{CHAPTERMODELLER}

    \input{mod_intro.tex}
    \clearpage

    \section{Stereochemical parameters and molecular topology}
    \label{SECTION:topology}
    \input{topol.opt}
    \clearpage

    \section{Handling of atomic coordinates}
    \label{SECTION:model}
    \input{model.opt}
    \clearpage

    \section{Comparison and searching of sequences and structures}
    \label{SECTION:compare}
    \input{compare-cmds.opt}
    \clearpage

    \section{Calculation of spatial restraints}
    \label{SECTION:restraints}
    \input{restraints-desc.tex}
    \input{restraints-cmds.opt}
    \clearpage

    \section{Optimization of the model}
    \label{SECTION:energy}
    \input{energy-cmds.opt}



\chapter{\MODELLER\ scripts} \label{CHAPTERSCRIPTS}
    \input{scripts.tex}



\chapter{\TOP, \MODELLER\ scripting language} \label{CHAPTERTOP}

    \input{top_incl.opt}



\chapter{Methods}
    \label{CHAPTER:methods}

    \vspace{2cm}

    \section{Dynamic programming for sequence and structure
             comparison and searching}
    \label{SECTION:comparedesc}
    \input{compare-desc.tex}

    \section{Optimization of the objective function by \MODELLER}
    \label{SECTION:energydesc}
    \input{energy-desc.tex}

    \section{Equations used in the derivation of the molecular pdf}
    \label{SECTION:eqs}
    \input{eqs.tex}

    \section{List of commands, arguments, and default values}
    \label{SECTION:topini}
 
    The {\tt top.ini} file contains the list of all 
    \MODELLER\ commands, arguments, and default values of arguments.

    {\small
    \verbatimfile{../src/main/top.ini}
    }

\clearpage
\backmatter

% \addcontentsline{toc}{chapter}{Bibliography}
\nocite{TitlesOn}
\bibliographystyle{jmb}
\bibliography{AS}

% \addcontentsline{toc}{chapter}{Index}
\printindex

\end{document}
