%% ============================================================================
% !Mode:: "TeX:UK:UTF-8"
% !TEX program = XeLaTeX
% -----------------------------------------------------------------------------
% Private XeLaTeX style for scientific texts
% copyright 2019 by Dr Engelbert Buxbaum <engelbert_buxbaum@web.de>
% This file may be shared under Gnu copyleft or the LaTeX the Project Public License.
\ProvidesPackage{manual}[2019/09/18 v1.01 standard packages for scientific texts]
\NeedsTeXFormat{LaTeX2e}
\RequirePackage{kpfonts-otf}
\usepackage{polyglossia}%foreign language support
\RequirePackage{acronym}%keep track of acronyms
%\RequirePackage{amssymb}%math symbols, not required with kpfonts-otf
\RequirePackage[backend=biber,bibencoding=UTF8,sorting=none,dateera=christian,style=numeric-comp]{biblatex}%bibliography
\RequirePackage{biochemistry-colors}%defines standard-conform colours for biochem entities
\RequirePackage{booktabs}%proper rules in tables
\RequirePackage{chemarrow}%arrows in chemical reactions
\RequirePackage{colortbl}%coloured background for tables
\RequirePackage{csquotes}%context-sensitive quotes, required for biblatex
\RequirePackage{css-colors}% defines web-safe colours
\RequirePackage{doi}%give DOIs as hyperlinks in bibliography
\RequirePackage{floatrow}%control float placement
\RequirePackage{fontspec}% font selecting commands
\RequirePackage{graphicx}%inclusion of images
\RequirePackage{hypcap} % anchors of captions
\RequirePackage[british]{isodate}%use international format for date and time
\RequirePackage{isotope}%correct typesetting of isotopes
\RequirePackage{letltxmacro}% change LaTeX commands with optional arguments
\RequirePackage{listings}%typeset computer code
\RequirePackage{lscape}%typeset wide material in lanscape mode
\RequirePackage{makeidx}%index generation
\RequirePackage{marvosym}%various symbols
\RequirePackage{mathbbol}%blackboard bold symbols (double line left)
\RequirePackage{mathtools}%extension of amsmath
\RequirePackage{media9}%include video or sound, currently doesn't work because flash-based
\RequirePackage{microtype}%micro-typesetting
\RequirePackage{multicol}%switching between one- and multicolumn
\RequirePackage{placeins}%allows FloatBarriers to be set
\RequirePackage{rotating}%rotate objects} sidewaystables/figures
\RequirePackage{siunitx}%correct typesetting of units
\RequirePackage[labelformat=empty,labelsep=none]{subfig}% several entries in one float
\RequirePackage{supertabular}%tables over several pages
\RequirePackage[breakable,skins,listings]{tcolorbox}%put text into coloured boxes
\RequirePackage[euler]{textgreek}%upright greek characters
\RequirePackage{ulem}%underlining and striking out
\RequirePackage{url}%typeset internet links (preloaded in beamer)
\RequirePackage{wasysym}
\RequirePackage{xcolor}%handle colours
%\RequirePackage{pdfcomment}% use pdf annotations
\RequirePackage{hyperref}%hyperrefs in PDF, must be last package called, preloaded in beamer
\hypersetup{final=true,
pdfauthor={Dr. Engelbert Buxbaum},
colorlinks=true,
citecolor=Blue,%bibliography, dark blue
linkcolor=Blue,%internal links, dark blue
urlcolor=DodgerBlue,%internet, middle blue
allbordercolors=White}
\newcommand{\EURO}{{\footnotesize{\EUR}}} % because \EUR is way too big
\DeclareSIUnit\angstrom{\text{��}}
\sisetup{% set-up for siunitx and XeTeX
print-unity-mantissa = false,
separate-uncertainty,
negative-color = red
}
% special chars in listings environment under XeTeX
\lstset{literate=%
{��}{{\"O}}1
{��}{{\"A}}1
{��}{{\"U}}1
{��}{{\ss}}1
{��}{{\"u}}1
{��}{{\"a}}1
{��}{{\"o}}1
{~}{{\textasciitilde}}1
}
\let\wasymale\male % start to undo overwriting of wasy by kpfonts_otf
\let\wasyfemale\female % complete after \begin{document}
% after \begin{document} add:
%\let\male\wasymale
%\let\female\wasyfemale
\setmainlanguage{en-GB}
\setotherlanguage{arabic}
\setotherlanguage{russian}
\setotherlanguage{greek}
\newfontfamily\arabicfont[Script=Arabic]{FreeSerif}
\newfontfamily\russianfont{FreeSerif}
\newfontfamily\greekfont{FreeSerif}
\newcommand{\Name}[1]{\textsc{#1}} % proper names
\newcommand{\Foreign}[1]{\textit{#1}} % words from foreign languages
\newcommand{\Species}[1]{\textit{#1}} % biological species
% Fonts for math-entities
\newcommand{\skalar}[1]{\ensuremath{#1}}
\newcommand{\Vector}[1]{\ensuremath{\vec{\mathfrak{#1}}}}
\newcommand{\AbsVec}[1]{\ensuremath{\mathfrak{#1}}}
\newcommand{\arr}[1]{\ensuremath{\mathcal{#1}}}
\newcommand{\tensor}[1]{\textsf{\bfseries{#1}}}
\newcommand{\set}[1]{\ensuremath{\mathbb{#1}}}
% move super- and subscripts to make them more readable
\makeatletter
\frozen@everymath={\check@mathfonts
\fontdimen16 \textfont2=\fontdimen17 \textfont2
\the\everymath}
\frozen@everydisplay={\check@mathfonts
\fontdimen16 \textfont2=\fontdimen17 \textfont2
\the\everymath}
\makeatother
%% "closed" sqrt sign, https://tex.stackexchange.com/questions/29834/closed-square-root-symbol
\LetLtxMacro{\OldSqrt}{\sqrt}
\newcommand{\ClosedSqrt}[1][\hphantom{3}]{\def\DHLindex{#1}\mathpalette\DHLhksqrt}
\makeatletter
\newcommand*\bold@name{bold}
\def\DHLhksqrt#1#2{%
\setbox0=\hbox{$#1\OldSqrt{#2\,}$}\dimen0=\ht0\relax%
\advance\dimen0-0.2\ht0\relax% size of the added box is still 0.2 times ht0
\setbox2=\hbox{\vrule height\ht0 depth -\dimen0}%
{\hbox{$#1\expandafter\OldSqrt\expandafter[\DHLindex]{#2\,}$}
\lower\ifx\math@version\bold@name0.6pt\else0.4pt\fi\box2}
}
% root index positioning and added space at the end, mostly noticeable in inline math mode
\renewcommand*{\sqrt}[2][\ ]{\ClosedSqrt[\leftroot{-2}\uproot{1}#1]{#2}\kern0.1em}
\makeatother
\DeclareMathOperator{\logit}{logit}
\DeclareMathOperator{\sgn}{sgn}
\DeclareMathOperator{\diag}{diag}
\DeclareMathOperator{\var}{var}
\DeclareMathOperator{\cov}{Cov}
\DeclareMathOperator{\trace}{tr}
\DeclareMathOperator{\abs}{abs}
\DeclareMathOperator{\rk}{rk}
\DeclareMathOperator{\svd}{svd}
\DeclareMathOperator{\median}{median}
\DeclareMathOperator{\dist}{dist}
\DeclareMathOperator{\ld}{ld}
\DeclareMathOperator{\modulo}{modulo}
% physicochemical entities
\newcommand{\ph}{\Foreign{p}H}
\newcommand{\poh}{\Foreign{p}OH}
\newcommand{\pka}{\Foreign{p}K\textsubscript{a}}
\newcommand{\pkb}{\Foreign{p}K\textsubscript{b}}
\newcommand{\pkw}{\Foreign{p}K\textsubscript{w}}
\newcommand{\pkr}{\Foreign{p}K\textsubscript{r}}
\newcommand{\pI}{\Foreign{p}I}
% Chemical formulas in text
\makeatletter
\DeclareRobustCommand{\single}{\raisebox{0.25ex}{$\m@th-$}}
\DeclareRobustCommand{\dotted}{\raisebox{0.6ex}{$\m@th.. $}}
\DeclareRobustCommand{\Lewis}{\raisebox{0.6ex}{$\m@th.$}}
\DeclareRobustCommand{\double}{\raisebox{0.25ex}{$\m@th=$}}
\DeclareRobustCommand{\triple}{\raisebox{0.25ex}{$\m@th\equiv$}}
\DeclareRobustCommand*{\Doth}{\LARGE{.}}
\DeclareRobustCommand{\radic}{\hspace{-0.1em}{\raisebox{1.4ex}{\Doth}}}
\DeclareRobustCommand{\chemical}[1]{%
{\(\m@th
\edef\resetfontdimens{\noexpand\)%
\fontdimen16 \textfont2=\the\fontdimen16 \textfont2
\fontdimen17 \textfont2=\the\fontdimen17 \textfont2 \relax}%
\fontdimen16 \textfont2=2.7pt \fontdimen17 \textfont2=2.7pt
\mathsf{#1}%
\resetfontdimens}}
\makeatother
\renewcommand{\isotopestyle}{\mathsf}% if package isotope is used
% use academic colours: philosophers blue, physicians green, lawyers red, theologists black
\newtcolorbox{advanced}[1]{colback=blue!5!white,colframe=blue!75!black,fonttitle=\bfseries,title=#1,breakable}
\newtcolorbox{medical}{colback=green!5!white,colframe=green!75!black,breakable}
\newtcolorbox{medtitle}[1]{colback=green!5!white,colframe=green!75!black,fonttitle=\bfseries,title=#1,breakable}
\newtcolorbox{rules}{colback=red!5!white,colframe=red!75!black,breakable}
\lstloadlanguages{[Borland6]Pascal,R,[x86masm]assembler}
\lstset{backgroundcolor=\color{Cornsilk},
language=[Borland6]Pascal,
alsolanguage=[x86masm]assembler,
alsolanguage=R,
extendedchars=false, % chars 128-255 not printed
breaklines=true, % long lines broken
breakatwhitespace=true, % ... but only at whitespace
numbers=left, numberstyle=\tiny, stepnumber=1, numbersep=0pt,
basicstyle=\ttfamily\small\color{black}, % print listing small monospaced
keywordstyle=\bfseries,
identifierstyle=\color{DarkRed}, %
morecomment=[l]{//}, % allow inline comments from Object Pascal
commentstyle=\color{Blue},
stringstyle=\color{DodgerBlue},
showstringspaces=false % no special string spaces
}
\defaultfontfeatures{Scale=MatchLowercase}
\setmonofont{Fantasque Sans Mono} % 0O, 1Il -~ clearly distinguished, Jany Belluz <jany.belluz@hotmail.fr>
% definitions for biblatex http://www.khirevich.com/latex/biblatex/, https://3d.bk.tudelft.nl/hledoux/blog/fiddling-biblatex/,
% moewe94@live.de on comp.text.tex, https://tex.stackexchange.com/questions/211199/changing-the-position-of-the-editor-with-biblatex-inbook
\DeclareNameAlias{sortname}{last-first}
\renewcommand{\multinamedelim}{\addcomma\space}
\renewcommand{\finalnamedelim}{\addspace\&\space}
\DefineBibliographyStrings{british}{%
andothers = {\textit{et\addabbrvspace al\adddot}},
editor = {(ed\adddot):},
editors = {(eds\adddot):},
byeditor = {(ed\adddot):},
}
\DefineBibliographyStrings{german}{%
andothers = {\textit{et\addabbrvspace al\adddot}},
editor = {(Hrsg.):},
editors = {(Hrsg.):},
byeditor = {(Hrsg.):},
}
%(ed.) after name list:
\renewbibmacro*{byeditor+others}{%
\ifnameundef{editor}
{}
{\printnames[byeditor][1-1]{editor}%
\setunit{\addspace}%
\usebibmacro{byeditor+othersstrg}%
\clearname{editor}%
\newunit}%
\usebibmacro{byeditorx}%
\usebibmacro{bytranslator+others}}
\renewcommand{\emph}[1]{\textnormal{\textit{#1}}}
\renewcommand*{\mkbibnamefamily}[1]{\textnormal{\textsc{#1}}} %
\renewcommand{\newunitpunct}{\addspace\midsentence}
\DeclareDelimFormat[bib]{nametitledelim}{\addcolon\space} %Doppelpunkt nach Namen, kein Punkt
\DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{\textnormal{#1}\addcomma} % keine Anf��hrungszeichen um Titel und kursiv
\DeclareFieldFormat{journaltitle}{\mkbibemph{#1}} % italic journal title, no comma
\DeclareFieldFormat[inbook,thesis]{title}{\mkbibemph{#1\addcomma}} % italic title with comma
\DeclareFieldFormat[article]{title}{#1\addcomma} % title of journal article is printed as normal text
\DeclareFieldFormat{titlecase}{#1} % keine ��berm����ig vielen Gro��buchstaben im Titel
\DeclareFieldFormat[article]{volume}{\mkbibbold{#1}} % Volume in bold
\DeclareFieldFormat[article]{number}{#1} % issue textnormal
\DeclareFieldFormat{pages}{#1} % Kein Pr��fix der Seitenzahlen
\renewbibmacro*{volume+number+eid}{%
\printfield{volume}%
\setunit{\addcolon}%
\printfield{number}%
}
\DeclareSourcemap{
\maps[datatype=bibtex]{
\map{
\step[fieldset=pagetotal, null]
}
}
}
\renewbibmacro{in:}{%
\ifentrytype{article}{}{\printtext{In\intitlepunct}}
}
% ------ setup for document
\floatsetup[table]{style=plaintop}
\setlength{\rotFPtop}{10pt plus 1fil} % quick fix for sidewaysfigures appearing to high, so that caption is cropped
\frenchspacing
\hyphenation{ATP-ase GTP-ase dia-be-tes phy-sio-logi-cal bio-lo-gy
pro-teo-ly-sis trans-cy-to-sis hy-dro-ly-sis telo-mere hy-dro-lysed
im-mu-no-glo-bu-lin Cali-for-nia mini-mum mini-ma phos-pha-ti-dyl pyro-phos-phate
phos-pho-pro-tein}
\makeatletter % \provideenvironment in analogy to \providecommand, https://tex.stackexchange.com/questions/20687/does-newenvironment-have-a-provideenvironment-cousin-as-newcommand-has-prov
\def\provideenvironment{\@star@or@long\provide@environment}
\def\provide@environment#1{%
\@ifundefined{#1}%
{\def\reserved@a{\newenvironment{#1}}}%
{\def\reserved@a{\renewenvironment{dummy@environ}}}%
\reserved@a
}
\def\dummy@environ{}
\makeatother
% Abstracts in book + scrbook
\providecommand\abstractname{Abstract}% doesn't change pre-existing command
\provideenvironment{abstract}[1]{%
\begin{center}\normalfont\bfseries\abstractname\end{center}
\begin{quotation} #1 \end{quotation}
}{%
\vspace{1cm}
}