Ncbs Tifr Thesis

% !TeX spellcheck = en_US
\documentclass[
12pt,
a4paper, 
%oneside, % Uncomment this for digital
twoside  % Use twoside for printing.
openright % Uncomment this for printing
]{book}

% If you use twoside, it will leave different margin for left and right. 
% Initially you think it is unintutive but it is actually how book margins are left. 
% See this for further infomation -- https://tex.stackexchange.com/a/319146/105124

%\usepackage{showframe} % This is to check margin area, you dont need it in general

\usepackage[utf8x]{inputenc}

% Footnote related
\usepackage[bottom]{footmisc} %Footnotes in Tables. Load this before hyperref

\author{Rohit Suratekar}
\usepackage[pdftex,
pdfauthor={Rohit Suratekar},
pdftitle ={Understanding structure and dynamics of the Drosophila PI(4,5)P2 cycle with mathematical models.},
pdfsubject={Computational Cell Biology},
pdfkeywords={PIP2 Cycle, Mathematical Model, PIP2, Thesis}, hidelinks]{hyperref} %References and hyperlinks 
% Remove Hidelinks option from above if you want links

\usepackage{graphicx, float, tikz-cd, xcolor, subcaption, chemfig} %Figures and Graphics
\usepackage{caption, tabularx, multirow, threeparttable, float} %Tables related
\usepackage{amsmath, amsfonts, amssymb, mathtools, calc} %Maths and Equations
\usepackage{standalone} % load only in the main file
\usepackage{fancyhdr} %For header
\usepackage{emptypage} % Removes header from empty pages
\usepackage{longtable} % Multipage Tables
\usepackage{makeidx} %To make index page
\usepackage[totoc]{idxlayout} %To get index into TOC
\usepackage[acronym,toc]{glossaries} %Acronyms, TOC option will add it to TOC
\usepackage[titletoc,title]{appendix} %For Appendix


\usepackage[version=3]{mhchem} %Chemistry reactions

%Tikz-cd setup
\usetikzlibrary{decorations.text}
\usetikzlibrary{positioning}

% To order citation within multiple citations
\usepackage[sort]{natbib}  %Need for sectionbib
\usepackage[sectionbib]{chapterbib} %References on each chapter

\allowdisplaybreaks %Allows equations to break page
\usepackage[final]{pdfpages} %Include PDF page

% Need to remove section numbers of appendix from TOC
\usepackage{etoolbox}
\appto\appendix{\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}}
% reinstate the correct level for list of tables and figures
\appto\listoffigures{\addtocontents{lof}{\protect\setcounter{tocdepth}{1}}}
\appto\listoftables{\addtocontents{lot}{\protect\setcounter{tocdepth}{1}}}


%Create new style to add header on each page
\pagestyle{fancy}
\renewcommand{\sectionmark}[1]{\markright{#1}}
\fancyhf{}
\makeatletter
\rhead{\fancyplain{}{\if@mainmatter \slshape\nouppercase{\leftmark}} \fi}
\makeatother
\lhead{\fancyplain{}{}} 
\cfoot{\fancyplain{}{\thepage}}

% Comment following Hypersetup during printing
\hypersetup{ 
	colorlinks   = true, %Colours links instead of ugly boxes
	urlcolor     = blue, %Colour for external hyperlinks
	linkcolor    = blue, %Colour of internal links
	citecolor   = red %Colour of citations
}

% Footnote related command
\newcommand\pubnote[1]{%
	\begingroup
	\renewcommand\thefootnote{}\footnote{#1}%
	\addtocounter{footnote}{-1}%
	\endgroup
}

\makeindex %Makes index file.
\makeglossaries %Make glossary file

\input{helpers/acronym} %Include add acronyms

% For generating random text. You don't need it 
\usepackage{blindtext}


% Following new definition to align table text to left in case of multi-row and multi-column
\usepackage{array}
\newcolumntype{L}[1]{>{\raggedright\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}

% Appendix related. Remove appendix sections from appearning in table of content
\usepackage{etoolbox}
\appto\appendix{\addtocontents{toc}{\protect\setcounter{tocdepth}{0}}}
\appto\listoffigures{\addtocontents{lof}{\protect\setcounter{tocdepth}{1}}}
\appto\listoftables{\addtocontents{lot}{\protect\setcounter{tocdepth}{1}}}

\begin{document}
	\frontmatter
	\input{front_matter/cover_page}
	\input{front_matter/declaration}
	\input{front_matter/certificate}
	\input{front_matter/publications}
	\input{front_matter/acknowledgment}
	\input{front_matter/dedication}
	
	\printglossary[type=\acronymtype,title={Abbreviations}, style=alttree]
	\phantomsection
	\addcontentsline{toc}{chapter}{\listfigurename}
	\listoffigures
	\phantomsection
	\addcontentsline{toc}{chapter}{\listtablename}
	\listoftables
	\tableofcontents
	
	\mainmatter
	\include{chapters/chapter1}
	\include{chapters/chapter2}
	
	
	% Switch off Caption
	\captionsetup{list=no}
	\include{appendix/appendix1}
	\printindex
\end{document}