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diff --git a/macros/latex/contrib/mychemistry/mychemistry_en.tex b/macros/latex/contrib/mychemistry/mychemistry_en.tex new file mode 100644 index 0000000000..269b8fecbf --- /dev/null +++ b/macros/latex/contrib/mychemistry/mychemistry_en.tex @@ -0,0 +1,1724 @@ +% arara: pdflatex +% arara: pdflatex +% arara: makeindex: { sort: on, style: mychemistry_en.ist } +% arara: pdflatex +% -------------------------------------------------------------------------- +% the MYCHEMISTRY package +% +% create reaction schemes with LaTeX and chemfig +% +% -------------------------------------------------------------------------- +% Clemens Niederberger +% Web: https://www.bitbucket.org/cgnieder/mychemistry +% E-Mail: contact@mychemistry.eu +% -------------------------------------------------------------------------- +% If you have any ideas, questions, suggestions or bugs to report, please +% feel free to contact me. +% -------------------------------------------------------------------------- +% Copyright 2011--2012 Clemens Niederberger +% +% This work may be distributed and/or modified under the +% conditions of the LaTeX Project Public License, either version 1.3 +% of this license or (at your option) any later version. +% The latest version of this license is in +% http://www.latex-project.org/lppl.txt +% and version 1.3 or later is part of all distributions of LaTeX +% version 2005/12/01 or later. +% +% This work has the LPPL maintenance status `maintained'. +% +% The Current Maintainer of this work is Clemens Niederberger. +% +% This work consists of the files modiagram.sty, modiagram_en.tex, +% README and the derived file modiagram_en.pdf. +% -------------------------------------------------------------------------- +% \errorcontextlines=999 +\documentclass[toc=index,DIV10]{cnpkgdoc} +\docsetup{ + pkg = [draft]mychemistry, + subtitle = Create Reaction Schemes with \LaTeXe\ and Chemfig , + code-box = { + skipbelow = .5\baselineskip plus .5ex minus .5ex , + skipabove = .5\baselineskip plus .5ex minus .5ex , + roundcorner = 3pt , + innerleftmargin = 1.5em , + innerrightmargin = 1.5em + } +} + +\usepackage{chemnum} +\usepackage{fnpct} +\usepackage{booktabs} +\usepackage{siunitx} + +\chemsetup[chemformula]{format=\libertineLF} + +\addcmds{ + @addtoreset, + anywhere, + arrow, + branch, + celsius, + ch, + chemabove, + chemand, + chembelow, + chemfig, + chemname, + cmpd, + colorlet, + command, + draw, + elmove, + floatstyle, + fpch, + fplus, + fscrm, + fscrp, + Hpl, + iupac, + lewis, + Lewis, + listof, + makeinvisible, + makevisible, + marrow, + mch, + mCsetup, + mech, + mesomeric, + N, + node, + para, + pch, + phantom, + reactant, + restylefloat, + setarrowlabel, + setarrowlength, + setarrowline, + setatomsep, + setatomsize, + setbondlength, + setbondshape, + setcrambond, + setmergelength, + setrcndist, + setrxnalign, + setschemealign, + setschemename, + SI, + text, + therxnscheme, + tikzset, + trans, + transition +} + +\usepackage{makeidx} +\usepackage{filecontents} +\begin{filecontents*}{\jobname.ist} + heading_prefix "{\\bfseries " + heading_suffix "\\hfil}\\nopagebreak\n" + headings_flag 1 + delim_0 "\\dotfill " + delim_1 "\\dotfill " + delim_2 "\\dotfill " + delim_r "\\nohyperpage{\\textendash}" + suffix_2p "\\nohyperpage{\\,f.}" + suffix_3p "\\nohyperpage{\\,ff.}" +\end{filecontents*} + +\makeindex + +\begin{document} +\section{Licence and Requirements}\label{ssec:voraussetzungen} +Permission is granted to copy, distribute and/or modify this software under the +terms of the LaTeX Project Public License, version 1.3 or later +(\url{http://www.latex-project.org/lppl.txt}). This package has the status +``maintained.'' + +\mychemistry needs and loads the packages \paket{etoolbox}, \paket{float}, +\paket{xkeyval}, \paket{chemmacros} and \paket{chemfig}. It also loads the +TikZ-libraries \code{arrows}, \code{positioning}, \code{decorations.pathmorphing}, +\code{shapes}, \code{calc}, \code{matrix}, \code{chains}, \code{scopes} and +\code{intersections}. + +\mychemistry also loads \paket*{translations}\footnote{Part of the +\paket*{exsheets} package} for proper language support. + +\section{Changes} +With v1.99 (=v2.0beta) package dependencies have changed so that \mychemistry +loads noticably less packages than before. Most important for you: it does \emph{not} +load \paket{mhchem} any more. This documentation uses \paket{chemmacros} instead +which is loaded by \mychemistry. + +There are now considerably less package options as most of them are not needed +any more. + +\mychemistry now provides proper language support, \eg, when used together with +\paket{babel}. + +New is the command \cmd{setelmove}. The command \cmd{makevisible} now only has +an effect if the new option \key{draft} is used. + +\section{Background} +\mychemistry provides two environments within which the mechanisms are created. +Both environments basically are \code{tikzpicture} environments. When this package +first was written \paket{chemfig} lacked the possibility of creating reaction +schemes itself. This was the motivation for me to get started on \mychemistry +which then rapidly grew and until now has its users. + +The background has changed in August 2011, though. Then \paket{chemfig} v1.0 was +published and now provides simple but powerful macros to create reactions schemes. +They don't seem to to be used very often but I am advertising as much as I can. +Anyway, since then \mychemistry can be considered obsolete and is not actively +developed any more. The current release 1.99 (= 2.0beta) was due to an +incompatibilty with \paket{pdfpages} and a complete robustification of various +parts of the code. + +\emph{Other than bug fixes this package will very likely \emph{not} be updated +any more}! + +\section{Package options}\label{sec:paketoptionen} +\mychemistry has a few package options. +\begin{beschreibung} + \option{strict} With this option all warning messages are turned into error + messages. + \option{draft} This option is an alias to \key{strict}. Additionally it enables + the \cmd{makevisible} command. + \option{final} This option is the opposite to \key{draft}, \ie, most error + messages will be issued as warnings. It also disables the \cmd{makevisible} + command. + \option{placement}{<value>} Changes the default floating behaviour of \env{rxnscheme}, + see section~\ref{ssec:rxnscheme}. +\end{beschreibung} + +\section{Usage} +\subsection{Basic Principle} +Within the \code{tikzpicture} reactants and arrows are placed as nodes on a +\code{chain}\footnote{Provided by the tikzlibrary `chains'}. + +\begin{beispiel} + \begin{tikzpicture}[start chain] + \node [on chain] {A}; + \node [on chain] {B}; + \node [on chain] {C}; + \end{tikzpicture} +\end{beispiel} +This way there are several possibilities to place the nodes relative to the others. +\begin{beispiel} + \begin{tikzpicture}[start chain=going right,node distance=5mm] + \node [draw,on chain] {Hello}; + \node [draw,on chain] {World}; + \node [draw,continue chain=going below,on chain] {,}; + \node [draw,on chain] {this}; + \node [draw,on chain] {is}; + \end{tikzpicture} +\end{beispiel} + +Above all \mychemistry uses the possibility of creating branches to the chain. +\begin{beispiel} + \begin{tikzpicture}[start chain=going right,node distance=5mm] + \node [draw,on chain] {A}; + \node [draw,on chain] {B}; + { [start branch] + \node [on chain=going below] {1}; + \node [on chain=going below] {2}; + } + { [start branch] + \node [on chain=going above] {$\alpha$}; + \node [on chain=going above] {$\beta$}; + } + \node [draw,on chain] {C}; + \end{tikzpicture} +\end{beispiel} +You don't have to understand that mechanism in detail but you should remember the +placement commands in the last example, because \mychemistry uses them in the same +way. + +In some of the examples in this documentation the nodes are boxed with a coloured +frame (see section~\ref{ssec:makevisible}). This is done so one can see, which size +they have and which impact changes of the alignment have on them. + +\subsection{How does it work?} +\subsubsection{Basic Commands} +There are two basic commands: +\begin{beschreibung} + \Befehl{reactant}[<pos>,<name>,<tikz>]{<formula>} + \Befehl{arrow}[<pos>,<type>,<length factor>,<name>,both,<tikz>]{<above>}\ma{<below>} +\end{beschreibung} + +Schemes are created within the \env{rxn}{} environment. There you place reactants +and arrows. +\begin{beispiel} + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow{Ox.}{} + \reactant{ \chemfig{-[::30]=_[::-60]O} } + \end{rxn} +\end{beispiel} + +When you don't use options reactants and arrows always are put to the right of +the last object. With the option \code{<pos>} you can change this behaviour. +\begin{beispiel} + % positioning using key words + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow[below]{Ox.}{} + \reactant[below]{ \chemfig{-[::30]=_[::-60]O} } + \end{rxn} + % positioning using an angle + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow[180]{}{Ox.} + \reactant[180]{ \chemfig{-[::30]=_[::-60]O} } + \end{rxn} +\end{beispiel} + +\begin{table} + \centering + \begin{tabular}{>{\ttfamily}l*{2}{>{$}r<{$}}} + \toprule + {\normalfont key word} & \text{pos. angle} & \text{neg. angle} \\ + \midrule + right & 0 & \pm 360 \\ + right above & 45 & -315 \\ + above & 90 & -270 \\ + above left & 135 & -225 \\ + left & 180 & -180 \\ + below left & 225 & -135 \\ + below & 270 & -90 \\ + below right & 315 & -45 \\ + \bottomrule + \end{tabular} + \caption{key words for positioning}\label{tab:keywords} +\end{table} + +You can see in the last example that positioning can be realized through key +words (see table~\ref{tab:keywords}) like \code{below} or by using the angle +relative to the horizontal line. Every angle from the interval +$[\ang{-360};\ang{360}]$. \ang{0} corresponds to \code{right} which is the default +value. \emph{Positive angles} mean a turn \emph{counter clockwise}, negative ones +a turn clockwise -- like you're used to in mathematics. + +\begin{beispiel} + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow[20]{Ox.}{} + \reactant[20]{ \chemfig{-[::30]=_[::-60]O} } + \end{rxn} + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow[-20]{Ox.}{} + \reactant[-20]{ \chemfig{-[::30]=_[::-60]O} } + \end{rxn} +\end{beispiel} + +\subsubsection{Positioning} +Reactants and arrows cannot only be positioned through key words and angles. They +can refer to another reactant or arrow. +\begin{beispiel} + \begin{rxn} + \reactant[,start]{ \chemfig{R-[::30](-[::60]R|^1) (-[::-120]R|^2)-[::-60]OH} } + \arrow[40]{\tiny$\text{R}^1=\text{H}$} {\tiny$\text{R}^2=\text{H}$} + \reactant[40]{ \chemfig{R-[::30]=_[::-60]O} } + \arrow[start.0]{\tiny$\text{R}^1=\text{alkyl}$} {\tiny$\text{R}^2=\text{H}$} + \reactant{ \chemfig{R-[::30](-[::60]R)=_[::-60]O} } + \arrow[start.-40,-|>]{\tiny$\text{R}^1=\text{alkyl}$} {\tiny$\text{R}^2=\text{Alkyl}$} + \end{rxn} +\end{beispiel} +In the last example the first reactant got the \code{<name>} \code{start}. The +arrows in lines 5 and 7 now could refer to it. A \emph{previously given name} can +act as an anchor for later reactants or arrows, if the positioning is written like +\code{<anchor>.<angle>}. + +Arrows can be given names, too. The anchor point of an arrow always is in the +middle of the arrow line and has \emph{no} size. +\begin{beispiel} + \begin{rxn} + \reactant{\chemfig{[:60]-(-[::60])=[::-60](-[::-60])-}} + \arrow[,,,arrow]{}{} + \reactant[arrow.90]{\ch{H2O}} + \end{rxn} +\end{beispiel} + +Using this kind of positioning does \emph{not} break the chain. +\begin{beispiel}[code only] + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \reactant{B} + \arrow[a.-90]{}{} + \reactant[-90]{C} + \arrow[a.180]{}{} + \reactant[180]{D} + \end{rxn} +\end{beispiel} + +All seven objects of this example are logically speaking part of the same chain. +The next object is placed to the right of the last one if no positioning is used. +\begin{rxn} + \tikzset{nummer/.style={circle,fill=gray!30,draw=gray,minimum size=3.5mm}} + \reactant[,a]{A}\arrow[,,,pa]{}{}\reactant[,b]{B} + \arrow[a.-90,,,pb]{}{}\reactant[-90,c]{C} + \arrow[a.180,,,pc]{}{}\reactant[180,d]{D} + \anywhere{a.45,,nummer}{1} + \anywhere{pa.90,,nummer}{2} + \anywhere{b.45,,nummer}{3} + \anywhere{pb.0,,nummer}{4} + \anywhere{c.45,,nummer}{5} + \anywhere{pc.90,,nummer}{6} + \anywhere{d.45,,nummer}{7} +\end{rxn} + +\subsubsection{Branches} +To break a chain you use the command +\begin{beschreibung} + \Befehl{branch}[<pos>,<name>,<tikz>]{<formulae>} +\end{beschreibung} +The positioning of a branch is slightly different from earlier objects, although +the syntax is similar. A branch has two additional ways of positioning. Every +positioning that refers to an anchor cause that the branch is not a part of the +chain but is a real branch. +\begin{description} + \item[\code{<angle>}] on the chain + \item[\code{<key>}] on the chain + \item[\code{<anchor>.<angle>}] not on the chain + \item[\code{on chain=going <key>}]on the chain + \item[\code{<key>=of <anchor>}] not on the chain +\end{description} +As \code{<key>} you again use the values from table~\ref{tab:keywords}. + +\begin{beispiel} + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow{}{} + \reactant[,carbonyl]{ \chemfig{-[::30]=_[::-60]O} } + \branch[carbonyl.-90]{ + \arrow[-90,<=>]{\ch{NH2R}}{} + \reactant[-90]{ \chemfig{-[::30]=_[::-60]N(-[6]H)-[::60]R} } + } + \arrow{}{} + \reactant{ \chemfig{-[::30](-[::60]OH)=_[::-60]O} } + \end{rxn} +\end{beispiel} + +Please note that in the last example the arrow and the reactant placed after +branch continue the original chain. +\begin{beispiel}[code only] + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \reactant{B} + \branch[a.-90]{ + \arrow[-90]{}{} + \reactant[-90]{C} + } + \arrow[a.180]{}{} + \reactant[180]{D} + \end{rxn} +\end{beispiel} + +The chain is broken by the branch which starts a new chain itself. +\begin{rxn} + \tikzset{nummer/.style={circle,fill=gray!30,draw=gray,minimum size=3.5mm,overlay}} + \reactant[,a]{A}\arrow[,,,pa]{}{}\reactant[,b]{B} + \branch[a.-90]{ + \arrow[-90,,,pb]{}{}\reactant[-90,c]{C} + \anywhere{pb.0,,nummer}{a} + \anywhere{c.45,,nummer}{b} + } + \arrow[a.180,,,pc]{}{}\reactant[180,d]{D} + \anywhere{a.45,,nummer}{1} + \anywhere{pa.90,,nummer}{2} + \anywhere{b.45,,nummer}{3} + \anywhere{pc.90,,nummer}{4} + \anywhere{d.45,,nummer}{5} +\end{rxn} + +Using \cmd{branch} allows to create schemes with several branches: +\begin{beispiel} + \begin{rxn} + \reactant{ \chemfig{-[::30]-[::-60]OH} } + \arrow{}{} + \reactant[,carbonyl]{ \chemfig{-[::30]=_[::-60]O} } + \arrow[-90]{}{} + \reactant[-90]{ \chemfig{-[::30](-[::60]OH)=_[::-60]O} } + \branch[right=of carbonyl]{ + \arrow[,<=>,1.12]{\ch{NH2R}}{} + \reactant{ \chemfig{-[::30]=_[::-60]N(-[6]H)-[::60]R} } + } + \branch[below right=of carbonyl]{ + \arrow[-45,<=>,1.12]{ \chemfig{[,.75]-[::30]-[::-60]OH} }{} + \reactant[-45]{ \chemfig{-[::30](-[::60]O-[::-60]-[::-60])-[::-60]OH} } + } + \arrow[carbonyl.90]{ \chemfig{[,.75]-[::30]=_[::-60]O}/\Hpl }{} + \reactant[90]{ \chemfig{-[::30](-[::60]OH)-[::-60]-[::60]=[::60]O} } + \arrow{$-\ch{H2O}$}{} + \reactant{ \chemfig{-[::30]=[::-60]-[::60]=[::60]O} } + \end{rxn} +\end{beispiel} + +\subsubsection{Numbered Schemes} +There is another environment to create schemes. +\begin{beschreibung} + \Umg{rxnscheme}[<label>,<placement>,<alignment>,<skale factor>,<title>]{<caption>} +\end{beschreibung} + +This is a floating environment for scheme, which can be given a \code{<caption>}, +a \code{<label>} and the common placement identifiers like \code{htp} (default). +\begin{beispiel}[code and float] +\begin{rxnscheme}{Keto-Enol-tautomerism} + \reactant{ \chemfig{=[::30]-[::-60]OH} } + \arrow[,<=>]{}{} + \reactant{ \chemfig{-[::30]=[::-60]O} } +\end{rxnscheme} +\end{beispiel} + +\subsection{Predefined Values} +There are some predefined values that are basically due to my personal taste. But +of course you can change them according to your requirements. For \paket{chemfig}% +-formul\ae\ \emph{inside of \mychemistry environments} some values are predefined +as follows: +\begin{beispiel}[code only] + \setatomsep{1.8em} + \setcrambond{3pt}{0.5pt}{1pt} +\end{beispiel} +Outside the \mychemistry environments the defaults of \paket{chemfig} still are +set. +\begin{beispiel} + \begin{rxn} + \reactant{\chemfig{**6(------)}} + \end{rxn} + \chemfig{**6(------)} +\end{beispiel} + +\mychemistry's defaults can be changed with these commands: +\begin{beschreibung} + \Befehl{setbondlength}{<length>} + \Befehl{setbondshape}{<base length>}\ma{<dash thickness>}\ma{<dash spacing>} + \Befehl{setatomsize}{<font size>} +\end{beschreibung} +With these commands the parameters are changed \emph{for all following} +\mychemistry environments. If you leave the arguments empty default values are +restored. Default for \cmd{setatomsize} is \cmd{small}. + +\begin{beispiel} + \setbondlength{2.1em}\setbondshape{5pt}{1pt}{2pt}\setatomsize{\Large} + \begin{rxn} + \reactant{\chemfig{-[::30](<[::60])-[::-60](<:[::-60])-[::60]A}} + \end{rxn} + \setbondlength{}\setbondshape{}{}{}\setatomsize{} + \begin{rxn} + \reactant{\chemfig{-[::30](<[::60])-[::-60](<:[::-60])-[::60]A}} + \end{rxn} +\end{beispiel} + +If you only want to change the parameters of a single environment you can use +\paket{chemfig}'s commands and \LaTeX's fontsize commands \emph{inside the +environment}. +\begin{beispiel} + \begin{rxn} + \setatomsep{2.1em}\setcrambond{5pt}{1pt}{2pt}\Large + \reactant{\chemfig{-[::30](<[::60])-[::-60](<:[::-60])-[::60]A}} + \end{rxn} + \begin{rxn} + \reactant{\chemfig{-[::30](<[::60])-[::-60](<:[::-60])-[::60]A}} + \end{rxn} +\end{beispiel} + +The default length of reaction arrows is \SI{4}{em}, the default line width is +\code{semithick} and the default label distance is \SI{0.2}{em}. You can change +these default values with the commands +\begin{beschreibung} + \Befehl{setarrowlength}{<length>} + \Befehl{setarrowline}{<line width>} + \Befehl{setarrowlabel}{<label distance>} +\end{beschreibung} +or with +\begin{beschreibung} + \befehl{mCsetup}{<options>} valid options are: + \Option{arrowlength}{<length>} + \Option{arrowline}{<line width>} + \Option{arrowlabel}{<label distance>} +\end{beschreibung} + +\section{Advanced Usage, Usage with \TikZ} +The biggest problem with \mychemistry usually is the correct positioning of +reactants and arrows. Section~\ref{ssec:ausrichtungsfrage} looks a little bit +into this topic. + +Some of the commands can be given \TikZ code as third optional argument. More +precisely you can use the same \TikZ keys there as you would with a \cmd{node} +inside a \code{tikzpicture}. If a node is placed with \cmd{node}\oa{<tikz>}% +\da{<placement>}\ma{<anything>} then \code{<tikz>} is about the same in \eg +\cmd{reactant}[,,<tikz>]{}. With this you can customize your scheme in many ways. + +\subsection{The Alignment Question}\label{ssec:ausrichtungsfrage} +Since reactants, arrows and branches are aligned centered to the referred object +the default alignment not always produces nice results. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \cmpd{benzene}} } + \arrow{}{} + \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \cmpd{bromobenzene}} } + \end{rxn} +\end{beispiel} +As you can see both reactants are not aligned equally to the arrow as far as the +benzene ring is concerned. The first reactant seems to be shifted up. Trying to +solve this with \TikZ code fails: + +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,,yshift=-1em]{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \cmpd{benzene}} } + \arrow{}{} + \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \cmpd{bromobenzene}} } + \end{rxn} +\end{beispiel} +This is, because the first reactant is shifted with the respect to the object it +refers to. Since it is the first object on the chain itself it isn't shifted a +all. The following arrow always is centered to the object before. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant{A} + \chemand + \reactant[,,yshift=1em]{B} + \arrow{}{} + \end{rxn} +\end{beispiel} +Since there is no possibility to change the alignment of the arrow itself what +you can do is put it inside a branch. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant{A} + \chemand + \reactant[,,yshift=1em]{B} + \branch[,,yshift=-1em]{\arrow{}{}} + \end{rxn} + \begin{rxn} + \reactant{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \cmpd{benzene}} } + \branch[,,yshift=1em]{\arrow{}{}} + \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \cmpd{bromobenzene}} } + \end{rxn} +\end{beispiel} +For the last example this isn't the best solution though because exact alignment +needs lots of tries until you get the required result. There is another solution: +an invisible bromine to the first benzene. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant{ \chemname{\chemfig{*6(-=-=(-[,,,,draw=none]\phantom{Br})-=)}}{benzene \cmpd{benzene}} } + \arrow{}{} + \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \cmpd{bromobenzene}} } + \end{rxn} +\end{beispiel} +In other cases, too, an invisible substituent should be preferred over \TikZ code +since it's easier and more precise: +\begin{beispiel} + \makevisible + default: + \begin{rxn} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]OH}} + \chemand + \reactant{\chemfig{HO-[:30]-[:-30]-[:30]}} + \arrow{[\Hpl]}{\SI{200}{\celsius}} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]O-[:30]-[:-30]-[:30]}} + \end{rxn} + hydroxy groups at the same height through TikZ: + \begin{rxn} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]OH}} + \chemand[,,yshift=-1.2em] + \reactant[,,yshift=.12em]{\chemfig{HO-[:30]-[:-30]-[:30]}} + \branch[,,yshift=1.08em]{\arrow{[\Hpl]}{\SI{200}{\celsius}}} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]O-[:30]-[:-30]-[:30]}} + \end{rxn} + hydroxy groups at the same height through an invisible substituent: + \begin{rxn} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]OH}} + \chemand + \reactant{\chemfig{HO-[:30](=[2,,,,draw=none]\phantom{O})-[:-30]-[:30]}} + \arrow{[\Hpl]}{\SI{200}{\celsius}} + \reactant{\chemfig{-[:-30]-[:30](=[2]O)-[:-30]O-[:30]-[:-30]-[:30]}} + \end{rxn} +\end{beispiel} + +I'm afraid that in many other cases you'll have to play with \code{xshift} and +\code{yshift}, though, until the scheme looks the way you want. + +\subsection{Using \TikZ to Achieve Other Results} +You could, just for fun?, change the looks of a molecule with \TikZ. +\begin{beispiel} + \begin{rxn} + \reactant[,,->,green!45!blue!55]{ \chemfig{*6(---(-)---)} } + \end{rxn} + \chemfig[->,green!45!blue!55]{*6(---(-)---)} +\end{beispiel} +The last example is not very good, of course, since you can achieve the same result +using \paket{chemfig}'s own possibilities. But other cases are imaginable: for +example one could define a style with which reactants are shown: +\begin{beispiel} + \colorlet{mCgreen}{green!50!gray} + \colorlet{mCblue}{cyan!50!gray} + \colorlet{mCred}{magenta!50!gray} + \colorlet{mCyellow}{yellow!50!gray} + \begin{rxn} + \tikzset{reactant/.style={draw=#1,fill=#1!10,inner sep=1em,minimum height=10em,minimum width=12em,rounded corners}} + \reactant[,cytosine,reactant=mCred]{\chemfig{H-[:30]N*6(-(=O)-N=(-NH_2)-=-)}} + \anywhere{cytosine.-90,,yshift=-2mm}{Cytosine} + \reactant[,thymine,reactant=mCyellow]{\chemfig{H-[:30]N*6(-(=O)-N(-H)-(=O)-(-CH_3)=-)}} + \anywhere{thymine.-90,,yshift=-2mm}{Thymine} + \reactant[cytosine.-90,adenine,yshift=-2em,reactant=mCblue]{\chemfig{[:-36]*5(-N(-H)-*6(-N=-N=(-NH_2)--)--N=)}} + \anywhere{adenine.-90,Guanin,yshift=-2mm}{Adenine} + \reactant[,guanine,reactant=mCgreen]{\chemfig{[:-36]*5(-N(-H)-*6(-N=(-NH_2)-N(-H)-(=O)--)--N=)}} + \anywhere{guanine.-90,,yshift=-2mm}{Guanine} + \end{rxn} +\end{beispiel} +This way certain parts of a scheme could be emphasized: +\begin{beispiel} + \begin{rxn} + \setatomsep{1.5em} + \colorlet{mCgreen}{green!50!gray} + \tikzset{emph/.style={draw=mCgreen,fill=mCgreen!10,inner sep=1em}} + \reactant[,lineOne]{\chemfig{R^1-[:30](=[@{b1}2]O)-[:-30]O-H}} + \arrow[,<=>]{\chemfig{@{Hpl1}\Hpl}}{} + \branch[,,emph]{ + \reactant{\chemfig{R^1-[:30]@{C1}(-[2]O-[:30]H)(-[6,.5,,,draw=none]\fplus)-[:-30]O-H}} + \arrow[,<=>,2]{\chemfig{[:30]H-@{O1}O-[::-60]-R^2}}{} + \reactant{\chemfig{R^1-[:30](-[2]O-[:30]H)(-[6]@{O2}O-[:-150]H)-[:-30]@{O3}\chemabove{O}{\fplus}(-[@{b2}6]H)-[:30]-[:-30]R^2}} + } + \anywhere{lineOne.-90,lineTwo,xshift=-3em,yshift=-7em}{} + \arrow[lineTwo.0,<=>]{$-$\Hpl/\chemfig{@{Hpl2}\Hpl}}{} + \reactant{\chemfig{R^1-[:30](-[@{b3}2]O-[@{b4}:30]H)(-[@{b5}6]@{O4}\chembelow{O}{\fplus}(-[:-30]H)-[:-150]H)-[:-30]O-[:30]-[:-30]R^2}} + \arrow[,<=>,2]{$- \ch{H+} - \ch{H2O}$}{} + \reactant{\chemfig{R^1-[:30](=[2]O)-[:-30]O-[:30]-[:-30]R^2}} + \anywhere{lineTwo.-90}{ + \elmove{b1}{10:5mm}{Hpl1}{135:1cm} + \elmove{O1}{135:1.5cm}{C1}{30:5mm} + \elmove{O2}{-90:3cm}{Hpl2}{90:2cm} + \elmove{b2}{0:5mm}{O3}{-10:5mm} + \elmove{b4}{-40:5mm}{b3}{0:5mm} + \elmove{b5}{-30:5mm}{O4}{-10:5mm} + } + \end{rxn} +\end{beispiel} + +\section{Alphabetical Command Reference} +In the following section every command is explained. + +\subsection{anywhere}\label{ssec:anywhere} +Sometimes it might be useful to be able to place a reactant or anything else off +the chain. +\begin{beschreibung} + \Befehl{anywhere}{<pos>,<name>,<tikz>}\ma{<something>} +\end{beschreibung} +For this case there's \cmd{anywhere}. It is positioned with \code{<pos>} similar +to \cmd{branch}. +\begin{description} + \item[\code{<anchor>.<angle>}] not on the chain + \item[\code{on chain=going <key>}] on the chain + \item[\code{<key>=of <anchor>}] not on the chain +\end{description} +Please be aware that \code{<pos>} cannot be left empty. + +\begin{beispiel} + \begin{rxn} + \reactant[,carbonyl_A]{\chemfig{R_2C=O}} + \anywhere{above=of carbonyl_A}{\chemfig{H-[:-30]O-[:30]H}}; + \end{rxn} +\end{beispiel} +You can use this command \eg for placing labels next to reactants. +\begin{beispiel} + \begin{rxn} + \reactant[,ketone]{\chemfig{H-\chemabove{C}{\hspace*{5mm}\scriptstyle\alpha}(-[2]H)(-[6,,,2]{}|{\textcolor{blue}H})-C(=[:60]\lewis{02,O})-[:-60]C|H_3}} + \anywhere{below=of ketone}{$+ \ch[format=\color{blue}]{OH-}$} + \arrow[,<=>]{\tiny slow}{} + \mesomeric[,mesomer]{ + \reactant[,carbanion]{\chemfig{H_2|\chemabove[3pt]{\lewis{2,C}}{\fscrm}-C(=[:60]\lewis{02,O})-[:-60]C|H_3}} + \marrow + \reactant[,enolate]{\chemfig{H_2C=C(-[:60]\chemabove{\lewis{024,O}}{\hspace*{5mm}\fscrm})-[:-60]C|H_3}} + } + \anywhere{above=of enolate}{\tiny enolate ion} + \anywhere{above=of carbanion}{\tiny carbanion} + \anywhere{below=of mesomer}{$+ \ch[format=\color{blue}]{H2O}$} + \end{rxn} +\end{beispiel} +You can find many further examples for the usage of \cmd{anywhere} in \code{examples.tex} +or \code{examples.pdf}, respectively. + +\subsection{\cmd{arrow}}\label{ssec:arrow} +Reaction arrows are created with \cmd{arrow}. +\begin{beschreibung} + \Befehl{arrow}[<pos>,<type>,<length factor>,<name>,both,<tikz>]{<above>}\ma{<below>} +\end{beschreibung} + +\subsubsection{Options} +There are a number of options to customize the arrows. The options must be used +in the right order, separated with commas. +\begin{enumerate} +\item\code{<pos>} -- possible values: + \begin{rxn} + \setarrowlength{2.5em} + \dummy[a] + \arrow{}{}\reactant{right = \ang{0}} + \branch[above right=of a]{\arrow[above right]{}{}\reactant[above right,,overlay]{above right = \ang{45}}} + \branch[above=of a]{\arrow[above]{}{}\reactant[above,,overlay]{above = \ang{90}}} + \branch[above left=of a]{\arrow[above left]{}{}\reactant[above left,,overlay]{above left = \ang{135}}} + \branch[left=of a]{\arrow[left]{}{}\reactant[left,,overlay]{left = \ang{180} = \ang{-180}}} + \branch[below left=of a]{\arrow[below left]{}{}\reactant[below left,,overlay,xshift=-2em]{below left = \ang{225} = \ang{-135}}} + \branch[below=of a]{\arrow[below]{}{}\reactant[below,,overlay]{below = \ang{270} = \ang{-90}}} + \branch[below right=of a]{\arrow[below right]{}{}\reactant[below right,,overlay,xshift=2em]{below right = \ang{315} = \ang{-45}}} + \end{rxn} + Additionally you can use every angle from the interval $[\ang{-360};\ang{360}]$. + + You can also use an angle with respect to an object that's been named with + \code{<name>}: \code{<name>.<angle>}. This means the arrow is placed in an + angle of \code{<angle>} next to \code{<name>}. You can find lots of examples in + \code{examples.tex} or\code{examples.pdf}, respectively. +\item\code{<type>} -- possible values: + \begin{rxn} + \dummy[a] + \branch[below=of a,b,yshift=.5em]{\arrow{}{}\reactant{\ttfamily -\textgreater}} + \branch[below=of b,c,yshift=.5em]{\arrow[,<-]{}{}\reactant{\ttfamily \textless-}} + \branch[below=of c,d,xshift=.25em,yshift=.5em]{\arrow[,<->]{}{}\reactant{\ttfamily \textless-\textgreater}} + \branch[below=of d,e,yshift=.5em]{\arrow[,<=>]{}{}\reactant{\ttfamily \textless=\textgreater}} + \branch[below=of e,f,xshift=.25em,yshift=.5em]{\arrow[,<=>>]{}{}\reactant{\ttfamily \textless=\textgreater{}\textgreater}} + \branch[below=of f,g,yshift=.5em]{\arrow[,<<=>]{}{}\reactant{\ttfamily \textless{}\textless=\textgreater}} + \branch[below=of g,h,xshift=-.25em,yshift=.5em]{\arrow[,-|>]{}{}\reactant{\ttfamily -\textbar\textgreater}} + \branch[below=of h,,yshift=.5em]{\arrow[,-+>]{ }{ }\reactant{\ttfamily -+\textgreater}} + \end{rxn} +\item\code{<length factor>} -- this factor multiplies with the arrow length + (\SI{4}{em} with factor = $1.0$, default) +\item\code{<name>} -- can be used to give the arrow an anchor, to which another + object can refer. +\item\code{both}-- this gives both nodes within which the labels are written the + same size. +\item\code{<tikz>} -- you can modify the arrow with \TikZ keys. Not all \TikZ + keys have an effect, though. You can't shift arrows with \code{shift=<coord>}, + for example. +\end{enumerate} +\begin{beispiel} + \begin{rxn} + \arrow[,,.25]{M}{}\arrow[,,.5]{MM}{}\arrow[,,.75]{MMM}{}\arrow{MMMM}{}\arrow[,,1.125]{MMMMM}{}\arrow[,,1.25]{MMMMM}{} + \end{rxn} +\end{beispiel} +Please note, that the labels \code{<above>} and \code{<below>} are rotated with +the arrow. At an angle of \ang{180} \code{<above>} actually is \emph{below} the arrow. +\begin{beispiel} + \begin{rxn} + \setarrowlength{2.5em} + \dummy[a] + \arrow{a}{b} + \arrow[a.45]{a}{b} + \arrow[a.90]{a}{b} + \arrow[a.135]{a}{b} + \arrow[a.180]{a}{b} + \arrow[a.225]{a}{b} + \arrow[a.270]{a}{b} + \arrow[a.315]{a}{b} + \end{rxn} +\end{beispiel} + +You need to be aware of one or two points, when using the arrow type \code{-+>}: +if you leave the labels empty, the arrow is the same as \code{->}. The first label +is the one added to the reaction, the second the one subtracted. If you use only +one of the labels only the corresponding arrow part is drawn. +\begin{beispiel} + corresponds \verb"->": + \begin{rxn} + \arrow[,-+>]{}{} + \end{rxn} + add: + \begin{rxn} + \arrow[,-+>]{a}{} + \end{rxn} + subtract: + \begin{rxn} + \arrow[,-+>]{}{b} + \end{rxn} + both add and subtract: + \begin{rxn} + \arrow[,-+>]{a}{b} + \end{rxn} + Blanks are \emph{not} an empty label: + \begin{rxn} + \arrow[,-+>]{ }{ } + \end{rxn} +\end{beispiel} + +You can change the appearance of an arrow with \TikZ keys: +\begin{beispiel} + \begin{rxn} + \mCsetup{arrowlabel=.7em,arrowlength=6em} + \reactant{A} + \arrow[20,,,,,decorate,decoration=snake,blue]{a}{b} + \reactant[20]{A$^*$} + \end{rxn} +\end{beispiel} + +\subsubsection{Alignment} +If an arrow is placed inside a branch the alignment of the branch may be +determined by the size of the label nodes. If the two labels have a different +size, alignment can go wrong. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \branch[below=of a]{ + \arrow[-90]{\chemfig{-[::30]-[::-60]OH}}{} + } + \end{rxn} + \makeinvisible +\end{beispiel} +By using the option \code{both} both nodes get the same size. This can correct +the alignment. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \branch[below=of a]{ + \arrow[-90,,,,both]{\chemfig{-[::30]-[::-60]OH}}{} + } + \end{rxn} + \makeinvisible +\end{beispiel} +There's more to the question of alignment in section~\ref{sssec:branch_ausrichtung}. + +\subsubsection{Appearance} +You can change the general appearance of arrows with \cmd{setarrowlength} +(section~\ref{ssec:setarrowlength}) and \cmd{setarrowline} (section~\ref{ssec:setarrowline}). + +\subsection{\cmd{branch}}\label{ssec:branch} +\cmd{branch} is used to, well, create a branch to a reaction. +\begin{beschreibung} + \Befehl{branch}[<pos>,<anchor>,<tikz>]{<branch code>} +\end{beschreibung} +For \cmd{branch} positioning an anchor is important. Let's take a look at an example: +\begin{beispiel} + \begin{rxn} + \reactant[,start]{\chemfig{-[::30]=_[::-60](-[::-60])-[::60]}} + \arrow[,,.75]{\ch{HCl}}{} + \reactant{\chemfig{-[::30]-[::-60](-[::120]Cl)(-[::-60])-[::60]}} + \chemand + \reactant{\chemfig{-[::30](-[::60]Cl)-[::-60](-[::-60])-[::60]}} + \branch[below right=of start]{ + \arrow[-45,,.75]{\ch{H2O}}{} + \reactant[-45]{\chemfig{-[::30]-[::-60](-[::120]OH)(-[::-60])-[::60]}} + \chemand + \reactant{\chemfig{-[::30](-[::60]OH)-[::-60](-[::-60])-[::60]}} + } + \end{rxn} +\end{beispiel} +The first reactant got the anchor \code{start} (line 2, also see +section~\ref{ssec:reactant}). \cmd{branch} now refers to it in its alignment +(line 7). If you don't use the alignment reference to an anchor you automatically +refer to the last \cmd{reactant} or \cmd{arrow}. If you don't use alignment at all, +then the branch is aligned to the right of the last \cmd{reactant} or \cmd{arrow}. +\begin{beispiel} + \begin{rxn} + \reactant{ \chemfig{CH_2=CH-OH} } + \arrow[,<=>,.5]{}{} + \branch{ \reactant{ \chemfig{CH_3-CH=O} } } + \end{rxn} +\end{beispiel} + +\subsubsection{Positioning}\label{sssec:branch_positionierung} +There are several ways to position a branch. It can either be part of the chain +or be a real branch. +\begin{description} + \item[\code{<angle>}] on the chain + \item[\code{<key>}] on the chain + \item[\code{<anchor>.<angle>}] not on the chain + \item[\code{on chain=going <key>}] on the chain + \item[\code{<key>=of <anchor>}] not on the chain +\end{description} + +The default behaviour is equal to \cmd{branch}[0]{}. In different situations +different ways can be favoured. For example if you want to use \cmd{branch} to +shift an arrow it can still be part of the chain. +\begin{beispiel} + \begin{rxn} + \reactant{A} + \branch[,,yshift=1em]{\arrow{}{}} + \reactant[,,yshift=-1em]{B} + \end{rxn} +\end{beispiel} + +If you like to start a real branch it \emph{does} matter which way you use. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a]{\chemfig{[:30]--[::-60]-OH}} + \arrow{}{} + \branch[a.-45]{\arrow[-45]{}{}} + \end{rxn} + \begin{rxn} + \reactant[,a]{\chemfig{[:30]--[::-60]-OH}} + \arrow{}{} + \branch[below right=of a]{\arrow[-45]{}{}} + \end{rxn} +\end{beispiel} + +If a reactant isn't squared or circled \ang{-45} does not mean the same as +``below right.'' +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a,circle]{\chemfig{[:30]--[::-60]-OH}} + \arrow{}{} + \branch[a.-45]{\arrow[-45]{}{}} + \end{rxn} + \begin{rxn} + \reactant[,a,circle]{\chemfig{[:30]--[::-60]-OH}} + \arrow{}{} + \branch[below right=of a]{\arrow[-45]{}{}} + \end{rxn} +\end{beispiel} + +\subsubsection{Alignment problems}\label{sssec:branch_ausrichtung} +If an arrow has two arguments with different sizes and is placed inside a branch +the alignment of the branch can go wrong. In this case the \cmd{arrow} key +\code{both} isn't a solution since the smaller argument then is not placed next +to the arrow but is centered in its node. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \branch[below=of a]{ + \arrow[below,,,,both]{\chemfig{-[::30]-[::-60]OH}}{\Hpl} + } + \end{rxn} +\end{beispiel} + +What you have to do is shift the branch using the \TikZ keys \code{xshift} and +\code{yshift}. +\begin{beispiel} + \makevisible + \begin{rxn} + \reactant[,a]{A} + \arrow{}{} + \branch[below=of a,,xshift=-1.35em]{ + \arrow[below]{\chemfig{-[::30]-[::-60]OH}}{\Hpl} + } + \end{rxn} +\end{beispiel} + +\subsection{\cmd{chemand}}\label{ssec:chemand} +The command +\begin{beschreibung} + \Befehl{chemand}[<alignment>,<anchor>,<tikz>] +\end{beschreibung} +produces and places a $+$ in the same way \cmd{reactant} places arbitrary text. +\begin{beispiel} + \begin{rxn} + \reactant{\chemfig{*6(------)}} + \chemand + \reactant{\ch{Br2}} + \arrow{$h\nu$}{} + \reactant{\chemfig{*6(--(-Br)----)}} + \chemand + \reactant{\ch{HBr}} + \end{rxn} +\end{beispiel} +The optional arguments for \cmd{chemand} and \cmd{reactant} are the same, see +section~\ref{ssec:reactant} for \cmd{reactant}'s options. + +\subsection{\cmd{dummy}}\label{ssec:dummy} +\cmd{dummy} creates an empty node. Up to v1.3 \cmd{arrow} needed to follow after +a node since \cmd{arrow} internally uses \cmd*{tikzchainprevious}. If there was +no node on the chain \emph{before} \cmd{arrow} was used an error was raised. +The same thing happened with \cmd{branch}. By using \cmd{dummy} you could start +a scheme with an arrow anyway. +\begin{beispiel}[code only] + \begin{rxn} + \dummy\arrow{}{} + \end{rxn} +\end{beispiel} +\emph{This is \emph{not} necessary any more}. In some (alignment) cases an empty +node still might be useful so the command still exists. + +\subsection{\cmd{elmove}}\label{ssec:elmove} +\cmd{elmove} just is a wrapper for \paket{chemfig}'s \cmd*{chemmove}. +\begin{beschreibung} + \Befehl{elmove}[<tikz>]{<start>}\ma{<start direction>}\ma{<end>}\ma{<end direction>} +\end{beschreibung} +This is expanding to +\begin{beispiel}[code only] + \chemmove{\draw[<tikz>](<start>).. controls +(<start direction>) and +(<end direction>)..(<end>);} +\end{beispiel} +using \oa{->,red,shorten <=3pt,shorten >=1pt} as default for \code{<tikz>}. How +you use \cmd*{chemmove} is described in the documentation of \chemfig. +\begin{beispiel} + \begin{center} + \setatomsep{1.8em} + \chemfig{*6(=[@{e1}]-=-(-[:120]Br)(-[:60]H)-(-[:-30,.4,,,white]\oplus)-[@{e2}])} + \elmove{e1}{60:4mm}{e2}{0:4mm} + \end{center} +\end{beispiel} +You should use \cmd{elmove} \emph{only inside} of \cmd{anywhere}, \cmd{reactant} +or \cmd{transition}. Otherwise you might get alignment errors. + +\subsection{\cmd{makeinvisible}}\label{ssec:makeinvisible} +\begin{beschreibung} + \Befehl{makeinvisible} +\end{beschreibung} +\cmd{makeinvisible} restores the normal \mychemistry behaviour after \cmd{makevisible} +(see section~\ref{ssec:makevisible}) has been used. \cmd{makeinvisible} only changes +the looks of nodes following after it. + +\subsection{\cmd{makevisible}}\label{ssec:makevisible} +\begin{beschreibung} + \Befehl{makevisible} +\end{beschreibung} +With \cmd{makevisible} you can visualize the nodes within which reactants, arrows +and branches are set. This is useful when you're aligning branches, for example. +You can see an example of the usage of \cmd{makevisible} in section~\ref{ssec:arrow}. +Every kind of nodes is emphasized with a different colour: + +\tikz[baseline=(X.base)]\node[draw=red!60](X){\cmd{reactant}{}};, +\tikz[baseline=(X.base)]\node[draw=green!60](X){\cmd{arrow}{above}};, +\tikz[baseline=(X.base)]\node[draw=blue!60](X){\cmd{arrow}{below}}; +and \tikz[baseline=(X.base)]\node[draw=cyan](X){\cmd{branch}{}};. +Also see section~\ref{ssec:makeinvisible}. + +\cmd{makevisible} only changes the looks of nodes following after it ond only +effects the group whithin which it is used. +\begin{beispiel} + \begin{rxn} + \makevisible + \reactant[,a]{A} + \arrow{a}{b} + \branch[below=of a]{ + \arrow[-90,,,,both]{a}{b} + } + \end{rxn} + \begin{rxn} + {\makevisible + \reactant{\chemfig{[:30]--[::-60]-OH}} + } + \reactant{\chemfig{[:30]--[::-60]-OH}} + \end{rxn} +\end{beispiel} + +\emph{Please beware that \cmd{makevisible} \emph{only} has an effect if the +package option \key{draft} is active}! + +\subsection{\cmd{marrow}}\label{ssec:marrow} +\cmd{marrow} creates a double-headed arrow. +\begin{beschreibung} + \Befehl{marrow}[<direction>] +\end{beschreibung} +It is a shortcut for \cmd{arrow}[<direction>,<->,.5]\ma{}\ma{}. + +\subsection{\cmd{mCsetup}}\label{ssec:mCsetup} +With +\begin{beschreibung} + \Befehl{mCsetup}{<keys>} +\end{beschreibung} +you can fully customize \mychemistry. For each of \mychemistry's commands going +like \cmd{set<command>} except \cmd{setbondshape} there is a key \key{<command>}{<value>}. +Additionally there is the key \key{align}{<value>} with which you can change the +alignment behaviour of both \env{rxn}{} and \env{rxnscheme}{}, and the key +\key{reset} with whith all values are reset to default. +\begin{beispiel} + \mCsetup{ + align=left, + arrowlabel=.7em, + arrowlength=3em, + arrowline=thick, + atomsize=\large, + bondlength=3em, + mergelength=4em, + rcndist=2em + %rxnalign=right, + %schemealign=left + } + \setbondshape{4pt}{2pt}{1pt} + \begin{rxn} + \reactant{A}\arrow{a}{b}\reactant{\chemfig{A-(<[2])(<:[6])-B}} + \end{rxn} + \mCsetup{reset} + \begin{rxn} + \reactant{A}\arrow{a}{b}\reactant{\chemfig{A-(<[2])(<:[6])-B}} + \end{rxn} +\end{beispiel} +\cmd{mCsetup} as well as every other setup command only effects the group whithin +which it is used. + +Here is a complete list of valid keys: +\begin{beschreibung} + \Option{align} + \Option{arrowlabel} + \Option{arrowlength} + \Option{arrowline} + \Option{atomsize} + \Option{bondlength} + \Option{elmove} + \Option{mergelength} + \Option{rcndist} + \Option{reset} + \Option{rxnalign} + \Option{schemealign} +\end{beschreibung} + +\subsection{\cmd{merge}}\label{ssec:merge} +The \cmd{merge} command is used to merge different reaction chains. In order to +do that the reactants that are to be merged must have an anchor name +(\cmd{reactant}[,<anchor>]{}), similar with branches, see sections~\ref{ssec:reactant} +and \ref{ssec:branch}) and be placed \emph{before} \cmd{merge}. +\begin{beschreibung} + \Befehl{merge}[<label>,<direction>,<length>]{<target>}\ma{<start a>}\ma{<start b>} +\end{beschreibung} +\cmd{merge} has three optional and three mandatory arguments. The latter are the +anchor names of the reactants that are to be merged. +\begin{beispiel} + \begin{rxn} + \branch[,first]{ + \reactant[,start_a]{\chemfig{-[:30]-[:-30]OH}} + \reactant[,start_b,xshift=9em]{\chemfig{-[:30]=[:-30]O}} + } + \branch[below=of first,target,yshift=-5em]{ + \reactant{\chemfig{-[:30]-[:-30]O-[:30](-[2]OH)-[:-30]}} + } + \merge[\ch{[OH^-]}]{target}{start_a}{start_b} + \end{rxn} +\end{beispiel} + +The default \code{<direction>} is \code{below}, other possible values are +\code{right}, \code{left} and \code{above}. With \code{<length>} the length of +the arrow from the point of merging to the tip can be changed. The default length +is \SI{3}{em}. The default length can be changed with \cmd{setmergelength} or +\cmd{mCsetup}. +\begin{beispiel} + \begin{rxn} + \reactant[,start_a]{\chemfig{-[:30]-[:-30]OH}} + \branch[below=of start_a,start_b,yshift=-9em]{ + \reactant{\chemfig{-[:30]=[:-30]O}} + } + \branch[right=of start_a,target,xshift=7em,yshift=-6em]{ + \reactant{\chemfig{-[:30]-[:-30]O-[:30](-[2]OH)-[:-30]}} + } + \merge[\ch{[OH^-]},right,5em]{target}{start_a}{start_b} + \end{rxn} +\end{beispiel} +Since you have to place the reactants first it might be useful to know a little +bit about involved lengths. There are three values which influence the needed +distance between start points and the target reactant. There is the \emph{depth} +of the involved reactants, the distance of the ``reaction nodes'' \emph{rcndist} +(see section~\ref{ssec:setrcndist}) and the length of the \cmd{merge} arrow +\emph{mergelength} (also see section~\ref{ssec:setmergelength}). +\begin{rxn} + \node[above](a) at (0,0){A}; + \node[above](b) at (10em,0){B}; + \node[below](c) at (5em,-6em){C}; + \merge{c}{a}{b} + \draw (-8.5em,1em) -- (-8.5em,-9em); + \foreach \x in {-1,0,1,2,3,4,5,6,7,8,9}{ + \draw (-8.5em,-\x em) -- (-8.7em,-\x em); + } + \draw[<->,red] (10em,0)--node[midway,right,xshift=.2em]{rcndist (default: 1em)}(10em,-1em); + \draw[<->,red] (0,0)--(0,-1em); + \draw[<->,red] (5em,-5em)--(5em,-6em); + \draw[<->,blue] (6em,-2em) --node[midway,right,xshift=.2em]{mergelength (default: 3em)} (6em,-5em); + \draw[<->,green] ($(a.base)+(-.5em,0)$)--node[midway,left,xshift=-.2em]{reactant depth}++(0,.5em); +\end{rxn} +At last an example where two chains are merged. +\begin{beispiel} + \begin{rxn} + \setatomsep{1.15em}\footnotesize + % chain 1 + \reactant[,first]{ \chemfig{Cl-[:30,1.5]--[:-30,1.5]O-[:30,1.5]--[:-30,1.5]Cl}{} } + \arrow[,,.5]{}{} + \reactant[,start_above]{ \chemfig{O(-[:-150]**6(-----(-OH)-))-[:90]-[:30]-[:-30]O-[:30]-[:-30]-[:-90]O-[:-30]**6(-(-HO)-----)} } + % chain 2 + \branch[below=of first,start_below,xshift=8em,yshift=-4em]{ + \reactant{ \chemfig{**6((--[6,,,2]HO)-N-(--[6]OH)----)} } + \arrow[,,.5]{}{} + \reactant{ \chemfig{**6((--[6]Br)-N-(--[6]Br)----)} } + } + % target + \branch[right=of start_above,target,xshift=5em,yshift=-4em]{ + \reactant[,c]{ \chemfig{O(-[:-150]**6(-----(-O?)-))-[:90]-[:30]**6(-N-(--[:-90]O-[:-30]**6(-(-O-[6]-[:-150]-[:150]O-[:-150]-[:150]?)-----))----)} } + } + % merging: + \merge[,right]{target}{start_above}{start_below} + \end{rxn} +\end{beispiel} +The usage of \cmd{merge} may require some playing with branches, \code{xshift} +and \code{yshift} until you get the desired result. +\begin{beispiel} + \begin{rxn} + \setatomsep{1.5em} + \reactant[,start_aa]{ \chemname{\chemfig{**6(---(-NH_2)---)}}{Anilin} } + \reactant[below,start_ab,yshift=-3em]{ \chemname{\ch{HNO2}}{salpetrige S\"aure} } + \branch[right=of start_aa,target_a,xshift=6em,yshift=-5em]{ + \reactant{ \chemname{\chemfig{**6(---(-N|_2\fpch)---)}}{Diazoniumion} } + }% = start_ba + \branch[below=of target_a,start_bb,yshift=-3em]{ + \reactant{ \chemname{\chemfig{**6(---(-NH_2)---)}}{Anilin} } + } + \branch[right=of target_a,target_b,xshift=6em,yshift=-5em]{ + \reactant{ \chemname{\chemfig{N(-[:-150]**6(------))=N-[:-30]**6(---(-NH_2)---)}}{\iupac{\para\-Amino\|diazo\|benzol}} } + } + \merge[,right]{target_a}{start_aa}{start_ab} + \merge[,right]{target_b}{target_a}{start_bb} + \end{rxn} +\end{beispiel} + +\subsection{\cmd{mesomeric}}\label{ssec:mesomeric} +The \cmd{mesomeric} command works just like \cmd{branch} (see section~\ref{ssec:branch}) +but places the formul\ae\ into square brackets. +\begin{beschreibung} + \Befehl{mesomeric}[<pos>,<anchor>,<tikz>]{<formula>} +\end{beschreibung} +The resonance formul\ae\ are written into \code{<formula>}. With \cmd{marrow} +(see section~\ref{ssec:marrow}) you can create the resonance arrows. If needed +you can give an anchor (\code{<anchor>}) to \cmd{mesomeric} (also see +section~\ref{ssec:branch}). Alignment is used the same way as with \cmd{reactant}. +\begin{beispiel} + \begin{rxn} + \mesomeric{ + \reactant{ + \chemfig{*6(=[@{e1}]-=-(-[:120]X)(-[:60]H)-(-[:-30,.4,,,white]\fplus)-[@{e2}])} + \elmove{e1}{60:4mm}{e2}{0:4mm} + } + \marrow + \reactant{ + \chemfig{*6(-(-[:90,.4,,,white]\fplus)-[@{e4}]=[@{e3}]-(-[:120]X)(-[:60]H)-=)} + \elmove{e3}{180:4mm}{e4}{150:4mm} + } + \marrow + \reactant{ + \chemfig{*6(-=-(-[:-150,.4,,,white]\fplus)-(-[:120]X)(-[:60]H)-=)} + } + } + \end{rxn} +\end{beispiel} + +Or vertical, too: +\begin{beispiel} + \begin{rxn} + \mesomeric{ + \reactant{ \chemfig{*6(=-=-=-)} } + \marrow[below] + \reactant[below]{ \chemfig{*6(-=-=-=)} } + } + \end{rxn} +\end{beispiel} + +Or maybe a coordination complex? +\begin{beispiel} + \begin{rxn} + \setatomsep{3em} + \mesomeric[,a]{ + \reactant{ \chemfig{H_3\lewis{0,N}-[,1.35,,,dotted]{Cu}(-[2,,,,dotted]\lewis{6,N}H_3)(-[6,,,,dotted]\lewis{2,N}H_3)-[,1.2,,,dotted]\lewis{4,N}H_3} } + } + \node[above right=of a,yshift=-1em] {$2\fplus$}; + \end{rxn} +\end{beispiel} + +\subsection{\cmd{reactant}}\label{ssec:reactant} +\cmd{reactant} is something like the basic command. +\begin{beschreibung} + \Befehl{reactant}[<pos>,<name>,<tikz>]{<formula>} +\end{beschreibung} +Formul\ae\ (\code{<formula>}) are written inside this command and can be named +(\code{<name>}) for other objects to refer to. \code{<pos>} can either be one of +these key words +\begin{enumerate} + \item \code{right}, + \item \code{above right}, + \item \code{above}, + \item \code{above left}, + \item \code{left}, + \item \code{below left}, + \item \code{below}, + \item \code{below right} +\end{enumerate} +or be an angle from the intervall $[\ang{-360};\ang{360}]$. You also can position +it relativ to another object via \code{<anchor>.<angle>}. The default equals +\cmd{reactant}[0]{}. +\begin{beispiel} + below: + \begin{rxn} + \reactant{\ch{Br2}} + \reactant[-90]{\ch{Cl2}} + \end{rxn} + + more than one reactant: + \begin{rxn} + \reactant{\ch{Br2}} + \reactant[-90]{\ch{I2}} + \reactant{\ch{Cl2}} + \end{rxn} + + going down: + \begin{rxn} + \reactant{\ch{Br-Br}} + \arrow[-90,,.5]{$h\nu$}{} + \reactant[-90]{\ch{2 "\Lewis{0.,Br}"}} + \end{rxn} +\end{beispiel} +You can find many more examples in the file \code{examples.tex} or +\code{examples.pdf}, respectively. + +\subsection{rxn (environment)}\label{ssec:rxn} +\env{rxn}{} is a non-floating not numbered environment for reaction schemes. Per +default all schemes are centered. +\begin{beschreibung} + \Umg{rxn}[<alignment>,<scalefactor>]{...} +\end{beschreibung} + +\subsubsection{Options}\label{sssec:rxn_optionen} +\env{rxn}{} has two options which are to be used in the following order, separated +by a comma: +\begin{enumerate} + \item\code{<alignment>}: alignment behaviour of the \env{rxn}{} environment; + default is \code{center}. + \item\code{<scalefactor>}: factor by which the \env{rxn}{} environment is scaled; + default: \code{1.0}. Same behaviour as with \env{rxnscheme}, see + section~\ref{ssec:rxnscheme}. +\end{enumerate} +If you use the \code{<scalefactor>} option you might see strange effects on +\paket{chemfig} formul\ae. + +\begin{beispiel} + \begin{rxn}[,.5] + \reactant{\chemfig{**6(------)}} + \end{rxn} +\end{beispiel} +Scaling does in general not affect the size of \paket{chemfig} formul\ae\ but +does scale the aromaticity ring of benzene and similar molecules. This is not +\mychemistry's fault: +\begin{beispiel} + \chemfig[scale=.5]{**6(------)} +\end{beispiel} +This issue can be solved either by using the \emph{first} optional argument of +\cmd*{chemfig} to undo the scaling or by using the \emph{second} optional argument +to scale the rest of the molecule. +\begin{beispiel} + \begin{rxn}[,.5] + \reactant{\chemfig[scale=2]{**6(------)}} + \reactant{\chemfig[][scale=.5]{**6(------)}} + \end{rxn} + \chemfig[scale=.5][scale=.5]{**6(------)} +\end{beispiel} + +Alignment examples: +\begin{beispiel} + \begin{rxn}[center] + \reactant{center}\arrow{}{}\reactant{centered} + \end{rxn} + \begin{rxn}[right] + \reactant{right}\arrow{}{}\reactant{raggedleft} + \end{rxn} + \begin{rxn}[left] + \reactant{left}\arrow{}{}\reactant{raggedright} + \end{rxn} +\end{beispiel} + +\subsection{rxnscheme (environment)}\label{ssec:rxnscheme} +\env{rxnscheme}{} is a floating environment for reaction schemes. +\begin{beschreibung} + \Umg{rxnscheme}[<label>,<placement>,<alignment>,<scalefactor>,<name>]{\unskip\ma{<caption>} ...} +\end{beschreibung} + +\subsubsection{Options}\label{sssec:rxnscheme_optionen} +\env{rxnscheme}{} has five options which are to be used in the following order, +separated by commas: +\begin{enumerate} + \item\code{<label>}: Like every other floating environment \env{rxnscheme}{} can + be given a label. In order to do that you need to use the option \code{<label>}. + For example if you use +\begin{beispiel}[code only] + \begin{rxnscheme}[rs:schema]{<caption>} + ... + \end{rxnscheme} +\end{beispiel} + you can refer to it by using \cmd*{ref}{rs:schema} as usual. + \item\code{<placement>}: With this option you can change the placement of the + float, \eg with \code{h}. The default value is \code{htp}. + \item\code{<alignment>}: This option changes the alignment of the scheme. You + can choose between \code{left}, \code{center} and \code{right}. + \item\code{<scalefactor>}: \env{rxnscheme}{} has another key with which the + scheme can be scaled. Please keep in mind that it doesn't affect the font size + and the size of \paket{chemfig}'s formul\ae. You can have strange effects on + \paket{chemfig}'s formul\ae\ if you use this key, though. See + section~\ref{sssec:rxn_optionen} for more information. + \item\code{<name>} This option changes the name of the actual scheme from + ``Reaction scheme'' into \code{<name>}. +\begin{beispiel}[code only] + \begin{rxnscheme}[,<placement>]{<caption>} + ... + \end{rxnscheme} +\end{beispiel} +\end{enumerate} + +\begin{beispiel}[code and float] + \begin{rxnscheme}[,,,2]{Big scheme} + \large\setatomsep{3.5em} + \reactant{ \chemfig{=[::30]-[::-60]OH} } + \arrow[,<=>]{}{} + \reactant{ \chemfig{-[::30]=[::-60]O} } + \end{rxnscheme} + \begin{rxnscheme}[,,,.5]{Small scheme} + \setatomsep{1.15em}\footnotesize + \reactant{ \chemfig{=[::30]-[::-60]OH} } + \arrow[,<=>]{}{} + \reactant{ \chemfig{-[::30]=[::-60]O} } + \end{rxnscheme} + \begin{rxnscheme}{center} + \reactant{center}\arrow{}{}\reactant{centered} + \end{rxnscheme} + \begin{rxnscheme}[,,right]{right} + \reactant{right}\arrow{}{}\reactant{raggedleft} + \end{rxnscheme} + \begin{rxnscheme}[,,left]{left} + \reactant{left}\arrow{}{}\reactant{raggedright} + \end{rxnscheme} +\end{beispiel} + +\subsubsection{Customizing rxnscheme} +\paragraph{Style} +If you don't like the style of \env{rxnscheme}{} you can change it by using +\begin{beschreibung} + \Befehl{floatstyle}{<new style>} + \Befehl{rxnfloat} +\end{beschreibung} +There are different possible styles, provided by the \paket{float} package: +\begin{description} + \item[\code{plain}] without any special formatting, the caption is below the object. + \item[\code{plaintop}] like \code{plain} but the caption is placed above the object. + \item[\code{boxed}] the object is boxed, the caption placed below. + \item[\code{ruled}] the caption is placed above the object framed by two rules, + one above and one below, another rule frames the object below; default for + \env{rxnscheme}{}. +\end{description} + +\begin{beispiel}[code and float] + \begin{rxnscheme}{ruled} + \reactant{default style} + \end{rxnscheme} + \floatstyle{boxed} + \restylefloat{rxnfloat} + \begin{rxnscheme}{boxed} + \reactant{framed object} + \end{rxnscheme} + \floatstyle{plain} + \restylefloat{rxnfloat} + \begin{rxnscheme}{plain} + \reactant{without any special formatting} + \end{rxnscheme} +\end{beispiel} +\floatstyle{ruled} +\restylefloat{rxnfloat} + +\paragraph{Placement} +Usually floating environments have an optional argument for their placement. +The default placement is \code{htp}. If you want to change it into \code{H} or +something, you can use +\begin{beschreibung} + \Befehl{floatplacement}{rxnfloat}\ma{<placement>} +\end{beschreibung} + +It's easier, though, loading \mychemistry with the \key{placement} option: +\begin{beispiel}[code only] + \usepackage[placement=<placement>]{mychemistry} +\end{beispiel} + +This will change the default placement behaviour from \code{htp} to \code{<placement>}. +You can also change the placement behaviour of just one \env{rxnscheme}{} by +using the placement option: +\begin{beispiel}[code only] + \begin{rxnscheme}[,<placement>]{<caption>} + ... + \end{rxnscheme} +\end{beispiel} + +\paragraph{Name}\label{par:rxnscheme_name} +If you want to change the name of reaction scheme you can do that with +\begin{beschreibung} + \Befehl{setschemename}{<new name>} +\end{beschreibung} +The default name is ``Reaction scheme'' but can change depending on the language +you've loaded with \paket{babel}. + +\paragraph{Counter} +The counter can be changed just as usual. For example by using +\begin{beispiel}[code only] + \makeatletter + \@addtoreset{rxnfloat}{section} + \makeatletter + \renewcommand*\therxnscheme{\arabic{section}.\arabic{rxnscheme}} +\end{beispiel} +the counter is reset with every new section an looks like \code{section.rxnscheme}. + +\paragraph{List of Schemes} +By writing +\begin{beschreibung} + \Befehl{listof}{rxnfloat}\ma{<title>} +\end{beschreibung} +you can create a list of all schemes created with \env{rxnscheme}{}. +\begin{beispiel} + \listof{rxnfloat}{Reaction schemes} +\end{beispiel} + +\subsection{\cmd{setarrowlabel}}\label{ssec:setarrowlabel} +The distance of arrow labels to the arrow has a default value of \SI{0.2}{em}. +You can change this with +\begin{beschreibung} + \Befehl{setarrowlabel}{<distance>} +\end{beschreibung} +into \code{<distance>}. +\begin{beispiel} + \begin{rxn} + \arrow{a}{b} + \setarrowlabel{.5em} + \arrow{a}{b} + \end{rxn} +\end{beispiel} + +\subsection{\cmd{setarrowlength}}\label{ssec:setarrowlength} +The default length of an reaction arrow is \SI{4}{em}. You can change this value +with +\begin{beschreibung} + \Befehl{setarrowlength}{<length>} +\end{beschreibung} +into \code{<length>}. Mind the fact that you have to use a length unit. If you +leave the argument empty the length is reset to default. + +\subsection{\cmd{setatomsize}}\label{ssec:setatomsize} +With +\begin{beschreibung} + \Befehl{setatomsize}{<font size>} +\end{beschreibung} +you can change the font size of the atom groups. Default value is \cmd*{small}. +If you leave the argument empty the size is reset to default. + +\subsection{\cmd{setbondlength}}\label{ssec:setbondlength} +With +\begin{beschreibung} + \Befehl{setbondlength}{<length>} +\end{beschreibung} +you can change \cmd{setatomsep}{<length>}= for all \paket{chemfig} formul\ae\ +\emph{inside} of the \mychemistry environments. The default value is \SI{1.8}{em}. +If you leave the argument empty the length is reset to default. + +\subsection{\cmd{setarrowline}}\label{ssec:setarrowline} +With the command +\begin{beschreibung} + \Befehl{setarrowline}{<value>} +\end{beschreibung} +the thickness of the arrows can be customized. Possible values are + \begin{flushleft} + \begin{tikzpicture} + \draw[ultra thin] (0,0)--(1,0)node[right]{\ttfamily ultra thin}; + \draw[very thin] (0,-.5)--(1,-.5)node[right]{\ttfamily very thin}; + \draw[thin] (0,-1)--(1,-1)node[right]{\ttfamily thin}; + \draw[semithick] (0,-1.5)--(1,-1.5)node[right]{{\ttfamily semithick} (default)}; + \draw[thick] (0,-2)--(1,-2)node[right]{\ttfamily thick}; + \draw[very thick] (0,-2.5)--(1,-2.5)node[right]{\ttfamily very thick}; + \draw[ultra thick] (0,-3)--(1,-3)node[right]{\ttfamily ultra thick}; + \end{tikzpicture} +\end{flushleft} + +This command also applies to \cmd{merge}. + +\subsection{\cmd{setbondshape}}\label{ssec:setbondshape} +With +\begin{beschreibung} + \Befehl{setbondshape}{<base length>}\ma{<dash thickness>}\ma{<dash spacing>} +\end{beschreibung} +you can change \cmd{setcrambond}{<base length>}\ma{<dash thickness>}\ma{<dash spacing>} +for all \paket{chemfig} formul\ae\ \emph{inside} of the \mychemistry environments. +Default values are (in this order) \SI{3}{pt}, \SI{.5}{pt} and \SI{1}{pt}. If +you leave an argument empty the value is reset to default. + +\subsection{\cmd{setelmove}}\label{ssec:setelmove} +The command +\begin{beschreibung} + \Befehl{setelmove}{<tikz>} +\end{beschreibung} +sets the default style that is used for the lines drawn by \cmd{elmove}. An empty +argument resets to \code{->,red,shorten <=3pt,shorten >=1pt}. + +\subsection{\cmd{setmergelength}}\label{ssec:setmergelength} +With +\begin{beschreibung} + \Befehl{setmergelength}{<length>} +\end{beschreibung} +you can change the length of the \cmd{merge} arrow. More precisely you can change +the length of the arrow from the point of line crossing to the arrow tip (see +section~\ref{ssec:merge}). If you leave the argument empty the value is reset to +default (\SI{3}{em}). + +\subsection{\cmd{setrcndist}}\label{ssec:setrcndist} +The nodes within which the reactants an arrows are set have a certain distance +between them. The default distance is \SI{1}{em}. If you want to change that you +can use +\begin{beschreibung} + \Befehl{setrcndist}{<length>} +\end{beschreibung} +If you leave the argument empty the distance is reset to \SI{1}{em}. +\begin{beispiel} + \setrcndist{2em} + \begin{rxn} + \reactant{A}\arrow{}{} + \end{rxn} + \setrcndist{} + \begin{rxn} + \reactant{A}\arrow{}{} + \end{rxn} +\end{beispiel} + +\subsection{\cmd{setrxnalign}/\cmd{setschemealign}}\label{ssec:setrxnalign}\label{ssec:setschemealign} +With the commands +\begin{beschreibung} + \Befehl{setrxnalign}{<alignment>} + \Befehl{setschemealign}{<alignment>} +\end{beschreibung} +The default alignment behaviour of \env{rxn}{} and \env{rxnscheme}{} (see +sections~\ref{sssec:rxn_optionen} and \ref{sssec:rxnscheme_optionen}) can be set. +You can choose between \code{left}, \code{center} and \code{right}. + +If you leave the argument empty \mychemistry's default behaviour (\code{center}) +is restored. +\begin{beispiel} + \setrxnalign{right} + \begin{rxn} + \reactant{A}\arrow{}{}\reactant{B} + \end{rxn} + \setrxnalign{} + \begin{rxn} + \reactant{A}\arrow{}{}\reactant{B} + \end{rxn} +\end{beispiel} + +\subsection{\cmd{setschemename}}\label{ssec:setschemename} +See page~\pageref{par:rxnscheme_name}. + +\subsection{\cmd{transition}}\label{ssec:transition} +\cmd{transition} works exactly like \cmd{reactant} (see section~\ref{ssec:reactant}). +\begin{beschreibung} + \Befehl{transition}[<pos>,<anchor>,<tikz>]{<formula>} +\end{beschreibung} +\begin{beispiel} + \begin{rxn} + \reactant{ \ch{H2 + I2} } + \arrow[below,<=>,.5]{}{} + \transition[below]{ \chemfig[dotted][]{H?-I-[2]I-[4]H?} } + \arrow[below,<=>,.5]{}{} + \reactant[below]{ \ch{2 HI} } + \end{rxn} +\end{beispiel} + +\appendix +\printindex +\end{document}
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