thesis.tex

\documentclass[final, notable, nolof, nolot, 11pt, nocover]{fithesis3}

%% The following section sets up the other used packages.
\usepackage[main=english]{babel}
\usepackage{graphicx}
\usepackage{algorithm}
\usepackage{algpseudocode}
\usepackage{algorithmicx}
\usepackage{amsmath}
\usepackage{mathptmx}
\usepackage{stfloats}
\usepackage{textcase}
\usepackage{esvect}
\usepackage{epstopdf}
\usepackage{wrapfig}
\usepackage{pdfpages}
\usepackage{subfigure}
\usepackage{makeidx}
\usepackage[textsize=small,colorinlistoftodos,disable]{todonotes}
\usepackage{textcomp}
\usepackage{chngcntr}


%\usepackage{verbatim}
%\usepackage{showframe}

%% The following section sets up the metadata of the thesis.
\thesissetup{
    university    = mu,
    faculty       = fi,
    type          = r,
    author        = Katarína Furmanová,
    gender        = m,
    advisor       = {prof. Jiří Sochor \\ \textbf{Co-Advisor:} assoc. prof. Barbora Kozlíková},
    title         = {Visualization and Visual Analysis of Intermolecular Interactions of Proteins},
    TeXtitle      = {Visualization and Visual Analysis of Intermolecular Interactions of Proteins},
    keywords      = {protein, protein-protein interactions, visualization, cavity, protein void, tunnel, trajectory, contact zone},
    TeXkeywords   = {protein, protein-protein interactions, visualization, cavity, protein void, tunnel, trajectory, contact zone},
}


\thesislong{abstract}{

}

\thesislong{thanks}{

}

%% The following section sets up the bibliography.
\usepackage{csquotes}
%\usepackage[             
%  backend=biber,         
%  bibstyle=numeric,          
%  citestyle=numeric-comp, 
%  sorting=none,           
%  sortlocale=auto,
%  maxnames=3,
%  firstinits=true         
%]{biblatex}  


%\renewbibmacro*{journal}{%
%  \iffieldundef{journaltitle}
%    {}
%    {\printtext[journaltitle]{%
%       \printfield[noformat]{journaltitle}%
%       \setunit{\subtitlepunct}%
%       \printfield[noformat]{journalsubtitle}}}}
       
%\renewbibmacro*{booktitle}{%
%  \iffieldundef{booktitle}
%    {}
%    {\printtext[booktitle]{%
%       \printfield[noformat]{booktitle}%
%       \setunit{\subtitlepunct}%
%       \printfield[noformat]{booksubtitle}}}}
%       
       
%\DeclareFieldFormat{titlecase}{\MakeSentenceCase{#1}}     
%\renewcommand*{\bibfont}{\small}
%\addbibresource{thesis.bib}

% Defines usefull commands.
\newcommand{\ie}{i.e.,~}
\newcommand{\eg}{e.g.,~}

% The following configures the algorithm package.
\renewcommand{\algorithmicrequire}{\textbf{Input:}}
\renewcommand{\algorithmicensure}{\textbf{Output:}}

\newcommand{\var}[1]{\textit{#1}}

% The following configures the subfigure.
\renewcommand{\thesubfigure}{(\Alph{subfigure})}

% The following section sets up the index.
\makeindex

\pdfminorversion=4

%\emergencystretch=1em

\begin{document}

%Makes the \part command work.
\pdfstringdefDisableCommands{%
	\let\MakeUppercase\relax
}

\listoftodos

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\label{Sec:Overview}

\input{includes/introduction.tex}
\input{includes/star.tex}
\input{includes/aims.tex}
\input{includes/results.tex}



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\renewcommand{\thesection}{\arabic{section}}
\input{includes/publications.tex}

%\printbibliography[title=References]
\bibliography{thesis}{}
\bibliographystyle{plain}        


\end{document}