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mabib0573.tex
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mabib0573.tex
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\documentclass{article}
\usepackage[letterpaper, total={6.75in, 9in}]{geometry} % good with line numbers
%\usepackage[top=0.5in,bottom=0.5in,left=0.5in,right=0.5in]{geometry} % Reduce the size of the margin to save paper
\usepackage{booktabs}
\usepackage{graphicx}
\usepackage{xurl} % permit line breaks in urls
\usepackage[luatex,plainpages=false]{hyperref}
\usepackage{lineno}
\usepackage{datetime2}
\usepackage{breakcites} % allow citatation to wrap
\usepackage{makeidx} % allows index generation
\usepackage[utf8]{inputenc}
%\usepackage{setspace} \doublespacing
%\doublespacing % turn on doublespacing for the whole document.
\usepackage{parskip} % add a blank line between paragraphs upon export to PDF.
\usepackage[T1]{fontenc}
\usepackage{authblk}
\usepackage[labelfont=bf]{caption}
\DeclareCaptionType{equ}[][] % provide equ environment to add captions to equations
\usepackage[bottom]{footmisc}% places footnotes at page bottom
\usepackage{amsfonts, mathtools, amssymb, amssymb} % For math fonts, symbols and environments
\usepackage{booktabs} % Needed for fancy tables
\usepackage{threeparttable}
\usepackage{graphicx}
\usepackage{wrapfig} % Allows in-line images
\usepackage[labelfont=bf]{caption} % Make figure numbering in captions bold
% \usepackage{minted} invoke -shell-escape flag
%Print page numbers in the upper right corner rather than the bottom center.
\pagestyle{myheadings}
\usepackage{lastpage}
\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{} % Clear all header and footer fields
\fancyhead[L]{\today}
\fancyhead[C]{0573 Crystal detection} % Center header
\fancyhead[R]{\thepage\ / \pageref{LastPage}}
% Three glossaries, the order matters here
\usepackage[acronym]{glossaries}
\newglossary[nlg]{notation}{not}{ntn}{Notation}
\makeglossaries
\setacronymstyle{long-short}
\loadglsentries{glossaries/acronyms}
\loadglsentries{glossaries/glossary}
\loadglsentries{glossaries/notation}
%backmatter
\bibliographystyle{cell}
\makeindex
% The following command produces a single column author index.
\RequirePackage{authorindex}
% Use this, if you want hyperlinks back from list of author entry to page
% where the citation was placed
\def\theaipage{\string\hyperpage{\thepage}}
\newcommand{\listofauthorsname}{List of Authors}%
\newcommand{\listofauthors}% {%\section*{\listofauthorsname}%
% %\begin{multicols*}{2}
% \phantomsection%
% \addcontentsline{toc}{chapter}{\listofauthorsname}%
% \noindent%
\printauthorindex%
% Set the depth of the table of contents
\setcounter{tocdepth}{2} % 1 for sections, 2 for subsections, 3 for subsubsections, etc.
% Rename Reference section
\renewcommand{\refname}{Literature Cited}
% Create a code float environment to enclosed minted environments so that captions can be added to code listings.
\newenvironment{code}{\captionsetup{type=listing}}{}
% Approximate Arial font. To save ink by returning to a sans serif font, comment the next two lines.
\usepackage{helvet}
\renewcommand{\familydefault}{\sfdefault}
\modulolinenumbers[1]
\setlength{\parindent}{0pt} % Remove automatic indent of paragraphs.
\author[1]{Graduate Student}
\author[2]{Senior Collaborator}
\author[3]{Staff Scientist}
\author[1,2,3]{Blaine Mooers\thanks{blaine-mooers at ouhsc.edu, phone: 405-271-8XXX, FAX: 405-271-3X3X}}
\affil[1]{Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States 73104}
\affil[2]{Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States 73104}
\affil[3]{Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States 73104}
\title{An \gls{annotated bibliography}: Molecular graphics}
\usepackage{bibentry}
\nobibliography*
\begin{document}
\maketitle
\tableofcontents
% If the sections are unnumbered, they are invisible to the table of contents unless you use the addcontentsline command.
\section*{Illustrated and annotated bibliography}
\addcontentsline{toc}{section}{Illustrated and annotated bibliography}
\subsection*{\bibentry{Mooers2020ShortcutsForFasterImageCreationInPyMOL}}
\addcontentsline{toc}{subsection}{Mooers2020ShortcutsForFasterImageCreationInPyMOL}
\input{bibNotes/Mooers2020ShortcutsForFasterImageCreationInPyMOL.tex}
\subsection*{\bibentry{Mooers2021TemplatesForWritingPyMOLScripts}}
\addcontentsline{toc}{subsection}{Mooers2021TemplatesForWritingPyMOLScripts}
\input{bibNotes/Mooers2021TemplatesForWritingPyMOLScripts.tex}
\newpage
\addcontentsline{toc}{section}{Acronyms}
\printglossary[type=\acronymtype] % Print the acronym list
\clearpage
\addcontentsline{toc}{section}{Glossary}
\printglossary % Print the main glossary
\clearpage
\addcontentsline{toc}{section}{Mathematical Notation}
\glsaddall[types={notation}] % add all entries, not just those used.
\printglossary[type=notation, title=Mathematical Notation]
\clearpage
\addcontentsline{toc}{section}{Literature Cited}
\bibliography{mabib0573}
\clearpage
\addcontentsline{toc}{section}{Index}
\printindex
%\listofauthors
\end{document}