%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ------------------------------------------------------------------------------------- %
% - myChemistry - mychemistry_en.tex -------------------------------------------------- %
% - Create reaction schemes with LaTeX and ChemFig ------------------------------------ %
% ------------------------------------------------------------------------------------- %
% - Clemens Niederberger -------------------------------------------------------------- %
% - 2011/04/27 ------------------------------------------------------------------------ %
% ------------------------------------------------------------------------------------- %
% - http://www.niederberger-berlin.net/2011/02/latex-mychemistry/ --------------------- %
% - kontakt@niederberger-berlin.net --------------------------------------------------- %
% ------------------------------------------------------------------------------------- %
% - If you have any ideas, questions, suggestions or bugs to report, please feel free - %
% - to contact me. -------------------------------------------------------------------- %
% ------------------------------------------------------------------------------------- %
% - Copyright 2011 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 mychemistry.sty, mychemistry_de.tex,              - %
% - mychemistry_en.tex, examples.tex                                                  - %
% ------------------------------------------------------------------------------------- %
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\documentclass[DIV10,titlepage,toc=index]{scrartcl}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Pakete ---------------------------------------------------------------------------- %
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\usepackage{etoolbox}
\usepackage{scrhack}                             % verbessert KOMAs Zusammenspiel mit floats
\usepackage{emerald}                             % Schriftarten
\usepackage[utf8]{inputenx}                      % Zeichenkodierung: Eingabe
\usepackage[T1]{fontenc}                         % Text-Ausgabe-Codierung
\usepackage{textcomp,mathcomp}
\usepackage[makeindex]{splitidx}                 % Index; Kompilieren: makeindex -sl index.ist *.idx
\usepackage[english]{babel}                      % Sprache
\usepackage{xspace,paralist}                     % xspace und Listen
\usepackage{siunitx,booktabs}
  \DeclareSIUnit{\emlength}{em}
  \DeclareSIUnit{\pt}{pt}
  \sisetup{separate-uncertainty = true,
           exponent-product     = \cdot,
           per-mode             = symbol}
\usepackage{listings,fancyvrb}                   % wortwörtliche Anzeige
  \newcommand{\vitem}[1][]{\SaveVerb[aftersave={\item[\textnormal{\UseVerb[#1]{vsave}}]}]{vsave}}
\usepackage[perpage,multiple]{footmisc}          % Fußnoten
\usepackage[ngerman]{varioref}                   % flexibles Referenzieren
  \labelformat{section}{section #1}
  \labelformat{subsection}{section #1}
  \labelformat{subsubsection}{section #1}
  \labelformat{table}{table #1}
\usepackage[dvipsnames]{xcolor}                  % Farbe
  \colorlet{code}{RawSienna}
  \xdefinecolor{MyDarkRed}{rgb}{0.4392,0.0627,0.0627}
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% - Anzeige des Inhaltsverzeichnisses ------------------------------------------------- %
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\usepackage{titletoc}
\titlecontents{section} [6.5pc]                                      % SECTION-ANZEIGE
   {\renewcommand\familydefault{ppl}\addvspace{2pc}\bfseries
    \color{MyDarkRed}\titlerule[2pt]\filright\normalcolor\nobreak}     % davor
   {\contentslabel
      [\textsc{Section}\
       \thecontentslabel]{6.5pc}}                                    % nummerierter Eintrag
   {\hspace{-6.5pc}\scshape\thecontentslabel}                        % unnummerierter Eintrag
   {\hfill\contentspage}
   [\addvspace{3pt}\renewcommand\familydefault{ppl}]                 % danach
%%
\newcommand{\xquad}{\hspace{1em plus.4em minus.4em}}
\titlecontents*{subsubsection}[6pc]                                  % SUBSUBSECTION-ANZEIGE
   {\footnotesize\itshape}
   {}
   {}
   {,~\thecontentspage}
   [\xquad\textbullet\xquad]
   {}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Hyperlinks ------------------------------------------------------------------------ %
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\usepackage{hyperref}
  \hypersetup{colorlinks=true,                   % Setup der Hyperlinks und des pdf
              linkcolor=MyDarkRed!20!red,
              urlcolor=blue!70,
              plainpages=false,
              bookmarksopen=true,
              bookmarksopenlevel=2,
              bookmarksnumbered=true,
              pdfstartview=FitH,
              pdfauthor={Clemens Niederberger},
              pdftitle={myChemistry - english documentation},
              pdfsubject={Create reaction schemes with LaTeX and ChemFig},
              pdfkeywords={myChemistry},
              pdfcreator={LaTeX}
  }
\usepackage[english,color=MyDarkRed]{mychemistry} % myChemistry
  \renewcommand\thebeispiel{\arabic{beispiel}}   % chemexec angepasst
  \labelformat{beispiel}{example #1}
  \labelformat{rxnfloat}{scheme #1}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Listings anpassen ----------------------------------------------------------------- %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\fvset{numbers=left,numbersep=3pt,xleftmargin=20pt,gobble=0,numberblanklines=true}
\lstset{literate={ä}{{\"a}}1 {ö}{{\"o}}1 {ü}{{\"u}}1 {Ä}{{\"A}}1 {Ö}{{\"O}}1 {Ü}{{\"U}}1 {ß}{{\ss}}1}
\lstset{
   language=[LaTeX]TeX,
   basicstyle={\ttfamily},                       % Grundstil
   extendedchars=true,
   numbers=left,                                 % Zeilennummern
   numberstyle=\tiny,                            % Größe des Zeilennummern
   numberblanklines=true,                        % Leerzeilen nummerieren
   gobble=0,                                     % das erste Leerzeichen abschneiden
   xleftmargin=20pt,                             % Einrückung links
   breaklines=true,                              % Zeilenumbruch
   moredelim=[is][\color{red!25!purple}]{!!}{!!},% Hervorhebung
   commentstyle={\color[named]{Gray}},
   emph={begin,end},                             % Umgebungen hervorheben
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   fancyvrb=true
   }

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Kopf- und Fußzeile ---------------------------------------------------------------- %
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\usepackage{scrpage2}
\pagestyle{scrheadings}
\setheadwidth{textwithmarginpar}
\automark{section}
\ihead{\mC v\mCversion}
\ohead{Manual}
\ifoot{\small\color{gray}-~page~\thepage~-}
\cfoot{}
\ofoot{}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - Komascript ------------------------------------------------------------------------ %
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\setkomafont{disposition}{\rmfamily\bfseries}    % Gewicht fett und Schriftart roman

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% - neue Befehle ---------------------------------------------------------------------- %
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% - Hyperlinks in Listings ------------------------------------------------------------ %
% - auf Basis von Code usenet: comp.text.tex ------------------------------------------ %
\makeatletter
\AtBeginEnvironment{VerbatimOut}{\let\lsthk@OutputBox\lsthk@OutputBox@H@@k\let\lstbasicfont\footnotesize}
\AtBeginEnvironment{Verbatim}{\let\lsthk@OutputBox\lsthk@OutputBox@H@@k\let\lstbasicfont\footnotesize}
\AtBeginEnvironment{SideBySideExample}{\let\lsthk@OutputBox\lsthk@OutputBox@H@@k\let\lstbasicfont\footnotesize}
\AtBeginDocument{\preto\FV@VerbatimBegin{\let\lsthk@OutputBox\lsthk@OutputBox@H@@k\let\lstbasicfont\footnotesize}}
\AtBeginDocument{\preto\FV@VerbatimBegin{\let\lsthk@OutputBox\lsthk@OutputBox@H@@k\let\lstbasicfont\footnotesize}}
\providerobustcmd*\ifrefundefined [1]{%
  \begingroup%
    \csname @safe@activestrue\endcsname%
    \expandafter\endgroup\csname @\ifcsname r@#1\endcsname second\else first\fi oftwo\endcsname
}% \ifrefundefined
\def\lsthk@OutputBox@H@@k{%
    \begingroup%
      \let\lst@UM\@empty%
      \edef\@tempc{ssec:\detokenize\expandafter{\the\lst@token }}%\edef
      \ifrefundefined{\@tempc}%
    \endgroup%
    \sethyperlistings%
}% \lsthk@OutputBox@fcltxH@@k
\def\sethyperlistings {\global\let \hyperlistingsreference =\@tempc
     \endgroup \aftergroup \dohyperlistings }% after \hbox
\def\dohyperlistings {\def\lst@alloverstyle ##1{\hyperlistings ##1}}
\def\hyperlistings{%
    \setbox\@tempboxa\hbox%
    \bgroup%
      \rlap{\hypersetup {linkcolor=.}\relax\fboxrule\z@%
      \hyperref[\hyperlistingsreference]{\boxframe{\wd\@tempboxa}{\ht\@tempboxa}{\dp\@tempboxa}}}%
      \unhbox\@tempboxa%
    \egroup%
}% \hyperlistings
\let\lsthk@OutputBox\lsthk@OutputBox@H@@k
% - Beispiele ------------------------------------------------------------------------- %
% - auf Basis der Beispiele in der fancyvrb-Dokumentation ----------------------------- %
\newcommand{\BeginExample}{%
 \VerbatimEnvironment
 \begin{VerbatimOut}[gobble=1]{\jobname.tmp}}

 \newcommand{\BelowExample}[1]{%
 \VerbatimInput[numbersep=3pt,fontsize=\footnotesize,
                  numbers=left,xleftmargin=5mm,xrightmargin=0pt]{\jobname.tmp}
#1}
% - Code, Ergebnis rechts ------------------------------------------------------------- %
\newcommand{\SideBySide@Example}[1]{%
\setlength{\parindent}{0pt}%
\begin{minipage}[c]{.48\textwidth}
 \VerbatimInput[numbersep=3pt,fontsize=\footnotesize,
                numbers=left,xleftmargin=5mm,xrightmargin=0pt]{\jobname.tmp}
\end{minipage}%
\hspace*{2mm}
\begin{minipage}[c]{.48\textwidth}
 #1
\end{minipage}
}

\def\SideBySideExample{%
 \catcode`\^^M=\active
 \@ifnextchar[{\catcode`\^^M=5\beispiel\vspace*{1mm}\SideBySideExample@}%
              {\catcode`\^^M=5\beispiel\vspace*{1mm}\SideBySideExample@@}}
\def\SideBySideExample@[#1]{#1\SideBySideExample@@}
\def\SideBySideExample@@{\BeginExample}
\def\endSideBySideExample{%
 \end{VerbatimOut}%
 \SideBySide@Example{\input{\jobname.tmp}}\vspace*{1mm}\endbeispiel}
% - Code, Ergebnis danach ------------------------------------------------------------- %
\newcommand{\@Example}[1]{%
\setlength{\parindent}{0pt}%
\begin{minipage}{\textwidth}
 \VerbatimInput[numbersep=3pt,fontsize=\footnotesize,
                numbers=left,xleftmargin=5mm,xrightmargin=0pt]{\jobname.tmp}
\end{minipage}%

\smallskip
\begin{minipage}{\textwidth}
 #1
\end{minipage}
}

\def\Example{%
 \catcode`\^^M=\active
 \@ifnextchar[{\catcode`\^^M=5\beispiel\vspace*{1mm}\Example@}%
              {\catcode`\^^M=5\beispiel\vspace*{1mm}\Example@@}}
\def\Example@[#1]{#1\Example@@}
\def\Example@@{\BeginExample}
\def\endExample{%
 \end{VerbatimOut}%
 \@Example{\input{\jobname.tmp}}\vspace*{1mm}\endbeispiel}
\makeatother

% - weitere Makros -------------------------------------------------------------------- %
\newcommand{\mC}{{\color{MyDarkRed}\ECFJD my\-Che\-mis\-try}\xspace} % Paketname
\newcommand{\CF}{{\ECFAugie ChemFig}\xspace}     % ChemFig in der originalen Schrift
\newcommand{\eg}{\mbox{e.\,g.}\xspace}
\newcommand{\TikZ}{\mbox{Ti{\bfseries\itshape k}Z}\xspace}
\newcommand\NEU[1][0pt]{\leavevmode\llap{\footnotesize\ECFTeenSpirit\color{red}New\kern\dimexpr20pt+#1\relax}}
\newlength{\tmplength}
% - für Beispiele --------------------------------------------------------------------- %
\newcommand{\abovearrow}{\tikz\node[draw,minimum width=3em,minimum height=1.5em,blue]{\footnotesize above};}
\newcommand{\belowarrow}{\tikz\node[draw,minimum width=3em,minimum height=1.5em,red]{\footnotesize below};}
\newcommand{\substance}{\tikz\node[draw,minimum width=5em,minimum height=3em]{};}

\begin{document}
\begin{titlepage}
  % inspired by the titlepage of chemfig's documentation
  \begin{tikzpicture}[remember picture,overlay]
    \shade [color=MyDarkRed,right color=white](current page.south west) rectangle ([yshift=3cm,xshift=-3cm]current page.center);
    \shade[top color=black,bottom color=MyDarkRed]([yshift=7cm]current page.east)rectangle([yshift=2.5cm]current page.west);
    \node[text width=\textwidth,opacity=.15,yshift=-5.3cm] at (current page.center) {%
\begin{verbatim}
 \begin{rxn}[,.7]
   \setatomsep{1.5em}\footnotesize
   \reactant[,a]{
     \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3)
       (-[6]OH)-CH_3}
   }
   \arrow[a.20]{}{}
   \reactant[20]{
     \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[@{e1}6,,,2]H_2@{e2}
       \chembelow{O}{\oplus})-C(-[2]CH_3)(-[6]OH)-CH_3}\elmove{e1}
       {10:4mm}{e2}{-10:4mm}
   }
   \arrow[,,1.42]{$-\ce{H2O}$}{}
   \reactant{
     \chemfig{\chembelow{C}{\oplus}(-[4]*6(=-=-=-))(-[2]
     *6(=-=-=-))-C(-[2]CH_3)(-[6]OH)-CH_3}
   }
   \arrow[a.-20,-|>]{}{}
   \reactant[-20]{
     \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3)
       (-[@{e3}6]@{e4}\chembelow{O}{\oplus}H_2)-CH_3}\elmove{e3}
       {170:4mm}{e4}{-170:4mm}
   }
   \arrow[,,1.42]{$-\ce{H2O}$}{}
   \reactant{
     \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-
       \chembelow{C}{\oplus}(-[2]CH_3)-CH_3}
   }
 \end{rxn}
\end{verbatim}%
};
  \end{tikzpicture}
  \begin{center}
    \scalebox{4}{\mC}\par
    \Large v\mCversion\par\bigskip
    \footnotesize\mCdate{en}\par
    \normalsize Clemens Niederberger\par\vskip1.5cm
    \color{white}\huge Creating reaction schemes with \LaTeX\ and \CF%
  \end{center}
  \vskip3cm
\begin{rxn}[,.7]
  \setatomsep{1.5em}\footnotesize
  \reactant[,a]{ \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3)(-[6]OH)-CH_3} }
    \arrow[a.20]{}{}
    \reactant[20]{ \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[@{e1}6,,,2]H_2@{e2}\chembelow{O}{\oplus})-C(-[2]CH_3)(-[6]OH)-CH_3}\elmove{e1}{10:4mm}{e2}{-10:4mm} }
    \arrow[,,1.42]{$-\ce{H2O}$}{}
    \reactant{ \chemfig{\chembelow{C}{\oplus}(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))-C(-[2]CH_3)(-[6]OH)-CH_3} }{}
    \arrow[a.-20,-|>]{}{}
    \reactant[-20]{ \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3)(-[@{e3}6]@{e4}\chembelow{O}{\oplus}H_2)-CH_3}\elmove{e3}{170:4mm}{e4}{-170:4mm} }
    \arrow[,,1.42]{$-\ce{H2O}$}{}
    \reactant{ \chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-\chembelow{C}{\oplus}(-[2]CH_3)-CH_3} }
\end{rxn}
\end{titlepage}

\tableofcontents

\section{About}
\subsection{Changes}
The most recent changes are marked with {\ECFTeenSpirit\color{red}New}.

\subsubsection{Version 1.2}
Since v1.2 there are some new features. The main part plays behind the scenes: the wrong arrow- and branch-alignments have been corrected. \textbf{Due to these changes \mC now needs Version 2.10 of \TikZ (or pgf, actually}, see \ref{ssec:voraussetzungen}).

There are some new "frontend" features as well. For one thing there are some new package options (see \ref{ssec:paketoptionen}). Additionally the arrows have got two new keys (see \ref{ssec:arrow}).

The environments have gained a few features, with which they can be customized, too (see \ref{sssec:rxn_optionen}, \ref{sssec:rxnscheme_optionen} and \ref{ssec:setrcndist}).

Last but not least since v1.2 \mC underlies LPPL version 1.3 or later.

\subsubsection{Version 1.3}
The commands \lstinline+\branch+, \lstinline+\mesomeric+, \lstinline+\reactant+ and \lstinline+\transition+ now cannot only accept alignment as optional argument but \TikZ keys as well. Also the second mandatory Argument \lstinline+<anchor>+ now is an optional one. So the first argument still is alignment, the second is the anchor name and in the third you can use arbitrary \TikZ keys.
\begin{lstlisting}
 \command[<pos>,<anchor>,<tikz>]{}
\end{lstlisting}
Version 1.2 explicitly needed a given alignment, if one wanted to use \TikZ keys, even with default alignment. Since v\mCversion\ this isn't required any more.
\begin{lstlisting}
  % up to version 1.2:
  \reactant{\ce{Br2}}{}\arrow{$h\nu$}{}\reactant!![right,draw,inner sep=5pt]!!{\ce{2 \lewis{0.,Br}}}{}
  % since version 1.3:
  \reactant{\ce{Br2}}\arrow{$h\nu$}{}\reactant!![,,draw,inner sep=5pt]!!{\ce{2 \lewis{0.,Br}}}
\end{lstlisting}
The commands to customize \mC have been renamed and the command\linebreak\lstinline+\mCsetup+ has been added. Now you can customize \mC using only one command. See \ref{ssec:setarrowlength}, \ref{ssec:setatomsize}, \ref{ssec:setbondlength}, \ref{ssec:setbondshape} and \ref{ssec:mCsetup}.

There is the new command \lstinline+\chemand+, which produces a $+$, see \ref{ssec:chemand}.

And you might find this one nice: every \mC command in a listing in this do\-cu\-mentation is a hyperlink referring to the corresponding entry in the command reference.

\subsubsection{Version 1.4}
The command \lstinline+\merge+ has been rewritten. Now the arrow can be labeled.

The main purpose of the command \lstinline+\dummy+ now is obsolete. The command still exists, though.

Both environments \lstinline+rxn+ and \lstinline+rxnscheme+ have changed regarding the usage of their options, see \ref{sssec:rxn_optionen} and \ref{sssec:rxnscheme_optionen}.

The keys of the \lstinline+\arrow+ command now are options, so the syntax of the command now is consistent with the syntax of the other commands. Then there are three new arrow types, see \ref{ssec:arrow}. Also new is the appearance of the arrows and the possibility of customizing the line thickness of the arrows, see \ref{ssec:setarrowline}.

There is another new command \lstinline+\anywhere+ (\ref{ssec:anywhere}), with which text or formul\ae\ can be placed off the chain.

\subsubsection{Version \mCversion}
\NEU%
Much happened in the background. This also provides some new features in the foreground. Most importantly is a new handling of the positioning of objects. All objects (reactants, arrows, branches \ldots) now cannot only be positioned with key words like \lstinline+right below+ but by using an actual angle.

There are the new arrow types \lstinline+<=>>+ and \lstinline+<<=>+ which indicate an imbalanced equilibrium.

The default placement identifier of \lstinline+rxnscheme+ has been changed from \lstinline+H+ to \lstinline+htp+.

The example section has been moved from this manual to the file \texttt{examples.tex} or \texttt{examples.pdf}, resp.

The commands \lstinline+\arrow+, \lstinline+\reactant+, \lstinline+\mesomeric+, \lstinline+\transition+, \lstinline+\anywhere+, \lstinline+\dummy+, \lstinline+\branch+ and \lstinline+\chemand+ are only defined inside the \lstinline+rxn+ and \lstinline+rxnscheme+ environments.

\subsection{Licence}
\mC v\mCversion\ underlies the The \LaTeX\ project public license\\(\url{http://www.latex-project.org/lppl.txt}).

\subsection{Requirements}\label{ssec:voraussetzungen}\index{requirements|(}
In order to function properly \mC needs some packages to be available.
\begin{description}
 \item[\CF]\index{requirements!ChemFig@\CF} without it why would you use \mC?
 \item[ifthen]\index{requirements!ifthen} for internal queries;
 \item[calc]\index{requirements!calc} for internal calculations;
 \item[xkeyval]\index{requirements!xkeyval} package options and command keys are created with this package;
 \item[float]\index{requirements!float} the \lstinline=rxnscheme= environment is defined with this package;
 \item[pgf/\TikZ]\index{requirements!pgf}\index{requirements!TikZ@\TikZ} pgf actually isn't just one package but a whole bundle. They are the basis layer for \TikZ. \mC needs at least the version from 09/08/2010\footnote{\url{http://sourceforge.net/projects/pgf/files/}}. More precisely: the command \lstinline=\pgfpositionnodelater= must exist. Even more precisely: only the \lstinline+\arrow+ key \lstinline+both+ (see \ref{ssec:arrow}) needs \lstinline=\pgfpositionnodelater=. If you don't use this option, \mC should work nicely with pgf v2.00. Older versions have not been tested.
\end{description}
\index{requirements|)}

\subsection{The Idea}
Since \CF was published August 2010, there is a flexible solution for creating organic structures. With \CF and `mhchem' one is able to create nearly all structural and molecular formulars that a chemist needs. There is one thing, though, in which `ochem' still beats \CF: creating reaction mechanisms. This is where \mC comes in.

\mC loads the packages
\begin{itemize}
 \item \CF\footnote{by Christian Tellechea, \url{http://www.ctan.org/tex-archive/macros/generic/chemfig/}}\index{ChemFig@\CF},
 \item `mhchem'\footnote{by Martin Hensel, \url{http://www.ctan.org/tex-archive/macros/latex/contrib/mhchem/}}\index{mhchem} in version 3, when ist exists,
 \item `chemexec'\footnote{by me, \url{http://www.ctan.org/tex-archive/macros/latex/contrib/chemexec/}}\index{chemexec}, when it exists, and
 \item `chemcompounds'\footnote{by Stephan Schenk, \url{http://www.ctan.org/tex-archive/macros/latex/contrib/chemcompounds/}}\index{chemcompounds}, when ist exists.
\end{itemize}
How these packages work, you can read in their documentations. Commands provided by these packages are for example
\begin{itemize}
 \item \lstinline=\ce{}= (mhchem)\index{mhchem}
 \item \lstinline=\ox{}{}=, \lstinline=\om[]=, \lstinline=\op[]=, \lstinline=\Hyd=, \lstinline=\Hpl= (chemexec)\index{chemexec}
 \item \lstinline=\chemfig[][]{}=, \lstinline=\chemrel[]{}=, \lstinline=\chemsign[]{}=, \lstinline=\lewis{}= (\CF)\index{ChemFig@\CF}
 \item \lstinline=\declarecompound[]{}=, \lstinline=\compound{}= (chemcompounds)\index{chemcompounds}.
\end{itemize}
Some of these commands are used in the examples of this documentation \textit{without being mentioned explicitly}.

Above all, \mC provides commands for creating reaction mechanisms.

\section{Usage}
\subsection{Background}
\mC provides two environments within which the mechanisms are created. Both environments basically are \lstinline+tikzpicture+ environments. One might ask oneself: why? You can do loads of stuff with \CF already. And \TikZ provides all the possibilities one could ask for. But since I'm a lazy guy I wrote several macros providing \TikZ commands, I often used. They got so many and got more and more possibilities to adjust, that I bundled them into this package. Of course you can still use \TikZ and stay more flexible with it, if you like.

\subsection{Basic Principle}
Within the \lstinline+tikzpicture+ reactants and arrows are placed as nodes on a \lstinline+chain+\footnote{Provided by the tikzlibrary `chains'}.
\begin{SideBySideExample}
 \begin{tikzpicture}[start chain]
 \node [on chain] {A};
 \node [on chain] {B};
 \node [on chain] {C};
 \end{tikzpicture}
\end{SideBySideExample}
This way there are several possibilities to place the nodes relative to the others.
\begin{SideBySideExample}
 \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{SideBySideExample}
Above all \mC uses the possibility of creating branches to the chain.
\begin{SideBySideExample}
 \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{SideBySideExample}
You don't have to understand that mechanism in detail, but you should remember the placement commands in the last example, because \mC uses them in the same way.

In some of the examples in this documentation the nodes are boxed with a coloured frame (see \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 three basic commands:\index{reactant}\index{rxn}\index{arrow}
\begin{lstlisting}
 \begin{rxn}[<alignment>,<scale factor>]
  \reactant[<pos>,<name>,<tikz>]{<formula>}
  \arrow[<pos>,<type>,<length factor>,<name>,both,<tikz>]{<above>}{<below>}
 \end{rxn}
\end{lstlisting}
Schemes are created within the \lstinline+rxn+ environment. There you place reactants and arrows.
\begin{SideBySideExample}
 \begin{rxn}
  \reactant{ \chemfig{-[::30]-[::-60]OH} }
  \arrow{Ox.}{}
  \reactant{ \chemfig{-[::30]=_[::-60]O} }
 \end{rxn}
\end{SideBySideExample}
When you don't use options reactants and arrows always are put to the right of the last object. With the option \lstinline+<pos>+ you can change this behaviour.
\begin{SideBySideExample}
  % 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{SideBySideExample}
\begin{table}
 \centering
 \begin{tabular}{>{\tt}lSS}
  \toprule
  {\normalfont key word} & {pos. angle} & {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 \ref{tab:keywords}) like \lstinline+below+ or by using the angle relative to the horizontal line. Every angle from the interval $[\ang{-360};\ang{360}]$. \ang{0} corresponds to \lstinline+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{SideBySideExample}
 \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{SideBySideExample}

\subsubsection{Positioning}
Reactants and arrows cannot only be positioned through key words and angles. They can refer to another reactant or arrow.
\begin{Example}
 \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{Example}
In the last example the first reactant got the \lstinline+<name>+ \lstinline+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
\begin{lstlisting}
 <anchor>.<angle>
\end{lstlisting}
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{SideBySideExample}
 \begin{rxn}
  \reactant{\chemfig{[:60]-(-[::60])=[::-60](-[::-60])-}}
  \arrow[,,,arrow]{}{}
  \reactant[arrow.90]{\ce{H2O}}
 \end{rxn}
\end{SideBySideExample}
Using this kind of positioning does \emph{not} break the chain.
\begin{lstlisting}
 \begin{rxn}
  \reactant[,a]{A}
  \arrow{}{}
  \reactant{B}
  \arrow[a.-90]{}{}
  \reactant[-90]{C}
  \arrow[a.180]{}{}
  \reactant[180]{D}
 \end{rxn}
\end{lstlisting}
All seven objects of this example are logically speaking part of the same chain. The next obect 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\index{branch}
\begin{lstlisting}
 \branch[<pos>,<name>,<tikz>]{<formulae>}
\end{lstlisting}
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{lstlisting}
 <angle>              % on the chain
 <key>                % on the chain
 <anchor>.<angle>     % not on the chain
 on chain=going <key> % on the chain
 <key>=of <anchor>    % not on the chain
\end{lstlisting}
As \lstinline+<key>+ you again use the values from \ref{tab:keywords}.
\begin{Example}
 \begin{rxn}
  \reactant{ \chemfig{-[::30]-[::-60]OH} }
  \arrow{}{}
  \reactant[,carbonyl]{ \chemfig{-[::30]=_[::-60]O} }
  \branch[carbonyl.-90]{
    \arrow[-90,<=>]{\ce{NH2R}}{}
    \reactant[-90]{ \chemfig{-[::30]=_[::-60]N(-[6]H)-[::60]R} }
  }
  \arrow{}{}
  \reactant{ \chemfig{-[::30](-[::60]OH)=_[::-60]O} }
 \end{rxn}
\end{Example}
Please note that in the last example the arrow and the reactant placed after branch continue the original chain.
\begin{lstlisting}
 \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{lstlisting}
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}}
 \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 \lstinline+\branch+ allows to create schemes with several branches:
\begin{Example}
 \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]{\ce{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{$-\ce{H2O}$}{}
  \reactant{ \chemfig{-[::30]=[::-60]-[::60]=[::60]O} }
 \end{rxn}
\end{Example}

\subsubsection{Numbered Schemes}
There is another environment to create schemes.\index{rxnscheme}
\begin{lstlisting}
 \begin{rxnscheme}[<label>,<placement>,<alignment>,<skale factor>,<title>]{<caption>}
  ...
 \end{rxnscheme}
\end{lstlisting}
This is a floating environment for schemes, which can be given a \lstinline+<caption>+, a \lstinline+<label>+ and the common placement identifiers like \lstinline+htp+ (default).
\begin{Example}
  \begin{rxnscheme}[,H]{Keto-Enol-tautomerism}
  \reactant{ \chemfig{=[::30]-[::-60]OH} }
  \arrow[,<=>]{}{}
  \reactant{ \chemfig{-[::30]=[::-60]O} }
 \end{rxnscheme}
\end{Example}

\subsection{Predefined Values}\index{default 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 \CF-formul\ae\ \emph{inside of \mC environments} some values are predefined as follows:
\begin{lstlisting}
 \setatomsep{1.8em}
 \setcrambond{3pt}{0.5pt}{1pt}
\end{lstlisting}
Outside the \mC environments the defaults of \CF still are set.
\begin{SideBySideExample}
 \begin{rxn}
  \reactant{\chemfig{**6(------)}}
 \end{rxn}
 \chemfig{**6(------)}
\end{SideBySideExample}
\mC's defaults can be changed with these commands:\index{setbondlength}\index{setbondshape}\index{setatomsize}
\begin{lstlisting}
 \setbondlength{<length>}
 \setbondshape{<base length>}{<dash thickness>}{<dash spacing>}
 \setatomsize{<font size>}
\end{lstlisting}
With these commands, the parameters are changed \emph{for all following} \mC environments. If you leave the arguments empty, default values are restored. Default for  \lstinline=\setatomsize= is  \lstinline=\small=.
\begin{Example}
 \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{Example}
If you only want to change the parameters of a single environment you can use \CF's commands and \LaTeX's fontsize commands \emph{inside the environment}.
\begin{Example}
 \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{Example}
The default length of reaction arrows is \SI{4}{\emlength}, the default line width is \lstinline+semithick+ and the default label distance is \SI{0.2}{\emlength}. You can change these default values with the commands\index{setarrowlength}\index{setarrowline}\index{setarrowlabel}
\begin{lstlisting}
 \setarrowlength{<length>}
 \setarrowline{<line width>}
 \setarrowlabel{<label distance>}
\end{lstlisting}
or with\index{mCsetup}
\begin{lstlisting}
 \mCsetup{arrowlength=<length>,
          arrowline=<line width>,
          arrowlabel=<label distance>}
\end{lstlisting}
\index{default values|)}

\subsection{Package options}\label{ssec:paketoptionen}\index{options|(}
\mC has a number of package options.
\begin{description}
 \vitem+chemstyle+\index{options!chemstyle}load the `chemstyle' package, without conflicts with \mC.
 \vitem+color=<colour>+\index{options!color} This loads `chemexec' with the options \lstinline=color<colour>= \&\ \lstinline+shade=true+.
 \vitem+english+\index{options!english} With this option, \mC loads the english version of `chemexec', if the package isn't loaded separately before. The name of the \lstinline=rxnscheme= environment (see \ref{ssec:rxnscheme}) is changed into "Reaction scheme".
 \vitem+nochemexec+\index{options!nochemexec} prevent \mC from loading `chemexec'.
 \vitem+nocolor+\index{options!nocolor} `chemexec' is loaded without colour and with the option \lstinline+shade=false+ (default behaviour of \mC).
 \vitem+nocompounds+\index{options!nocompounds}prevent \mC from loading `chemcompounds'.
 \vitem+nomhchem+\index{options!nomhchem}prevent \mC from loading `mhchem' lädt, if `chemexec' isn't loaded either.
 \vitem+nopackages+\index{options!nopackages}prevent \mC from loading \emph{any} package (except \CF)\footnote{apart from the ones \mC needs to function (like \TikZ etc.).}.
 \vitem+placement=<position>+\index{options!placement} The default placement behaviour of the \lstinline=rxnscheme= environment is changed to \lstinline=<position>=.
 \vitem+shade+\index{options!shade} loads `chemexec' with the \lstinline+shade=true+ option.
\end{description}
\index{options|)}

\section{Advanced Usage, Usage with \TikZ}
The biggest problem with \mC usually is the correct positioning of reactants and arrows. \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 \lstinline+\node+ inside a \lstinline+tikzpicture+. If a node is placed with \lstinline+\node[<tikz>](<placement>){<anything>};+, then \lstinline+<tikz>+ is about the same in \eg \lstinline+\reactant[,,<tikz>]{}+\index{reactant!tikz}. With this you can customize your scheme in many ways.

\subsection{The Alignment Question}\label{ssec:ausrichtungsfrage}\index{alignment|(}
Since reactants, arrows and branches are aligned centered to the referred object, the default alignment not always produces nice results.
\begin{Example}
 \makevisible
 \begin{rxn}
  \reactant{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \compound{benzene}} }
  \arrow{}{}
  \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \compound{bromobenzene}} }
 \end{rxn}
\end{Example}
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{Example}
 \makevisible
 \begin{rxn}
  \reactant[,,yshift=-1em]{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \compound{benzene}} }
  \arrow{}{}
  \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \compound{bromobenzene}} }
 \end{rxn}
\end{Example}
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 at all. The following arrow always is centered to the object before.
\begin{SideBySideExample}
 \makevisible
 \begin{rxn}
  \reactant{A}
  \chemand
  \reactant[,,yshift=1em]{B}
  \arrow{}{}
 \end{rxn}
\end{SideBySideExample}
Since there is no possibility to change the alignment of the arrow itself (yet), what you can do is put it inside a branch.
\begin{Example}
 \makevisible
 \begin{rxn}
  \reactant{A}
  \chemand
  \reactant[,,yshift=1em]{B}
  \branch[,,yshift=-1em]{\arrow{}{}}
 \end{rxn}
 \begin{rxn}
  \reactant{ \chemname{\chemfig{*6(-=-=-=)}}{benzene \compound{benzene}} }
  \branch[,,yshift=1em]{\arrow{}{}}
  \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \compound{bromobenzene}} }
 \end{rxn}
\end{Example}
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{Example}
 \makevisible
 \begin{rxn}
  \reactant{ \chemname{\chemfig{*6(-=-=(-[,,,,draw=none]\phantom{Br})-=)}}{benzene \compound{benzene}} }
  \arrow{}{}
  \reactant{ \chemname{\chemfig{*6(-=-=(-Br)-=)}}{bromobenzene \compound{bromobenzene}} }
 \end{rxn}
\end{Example}
In other cases, too, an invisible substituent should be preferred over \TikZ code, since it's easier and more precise:
\begin{Example}
 \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{Example}
I'm afraid that in many other cases you'll have to play with \lstinline+xshift+\index{xshift} and \lstinline+yshift+\index{yshift}, though, until the scheme looks the way you want. Maybe further versions of \mC will provide a more user friendly alignment syntax.
\index{alignment|)}

\subsection{Using \TikZ to Achieve Other Results}
You could, just for fun?, change the looks of a molecule with \TikZ.
\begin{SideBySideExample}
 \begin{rxn}
  \reactant[,,->,green!45!blue!55]{ \chemfig{*6(---(-)---)} }
 \end{rxn}
 \chemfig[->,green!45!blue!55]{*6(---(-)---)}
\end{SideBySideExample}
The last example is not very good, of course, since you can achieve the same result using \CF's own possibilities. But other cases are imaginable: for example one could define a style with which reactants are shown:
\begin{Example}
 \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{Example}
This way certain parts of a scheme could be emphasized:
\begin{Example}
 \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]\oplus)-[:-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}{\oplus}(-[@{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}{\oplus}(-[:-30]H)-[:-150]H)-[:-30]O-[:30]-[:-30]R^2}}
  \arrow[,<=>,2]{\ce{- \Hpl - 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{Example}
\newpage

\section{Alphabetical Command Reference}
In the following section every command is explained.

\subsection{anywhere}\label{ssec:anywhere}\index{anywhere|(}\index{commands!anywhere}
\NEU%
Sometimes it might be useful to be able to place a reactant or anything else off the chain.
\begin{lstlisting}
 \anywhere{<pos>,<name>,<tikz>}{<something>}
\end{lstlisting}
For this case there's \lstinline+\anywhere+. It is positioned with \lstinline+<pos>+ similar to \lstinline+\branch+.
\begin{lstlisting}
 <anchor>.<angle>     % not on the chain
 on chain=going <key> % on the chain
 <key>=of <anchor>    % not on the chain
\end{lstlisting}
\textbf{Please be aware that \lstinline+<pos>+ cannot be left empty.}
\begin{SideBySideExample}
 \begin{rxn}
  \reactant[,carbonyl_A]{\chemfig{R_2C=O}}
  \anywhere{above=of carbonyl_A}{\chemfig{H-[:-30]O-[:30]H}};
 \end{rxn}
\end{SideBySideExample}
You can use this command \eg for placing labels naxt to reactants.
\begin{Example}
 \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}{$+$\color{blue}\Hyd}
  \arrow[,<=>]{\tiny slow}{}
  \mesomeric[,mesomer]{
    \reactant[,carbanion]{\chemfig{H_2|\chemabove[3pt]{\lewis{2,C}}{\scriptstyle\ominus}-C(=[:60]\lewis{02,O})-[:-60]C|H_3}}
    \marrow
    \reactant[,enolate]{\chemfig{H_2C=C(-[:60]\chemabove{\lewis{024,O}}{\hspace*{5mm}\scriptstyle\ominus})-[:-60]C|H_3}}
  }
  \anywhere{above=of enolate}{\tiny enolate ion}
  \anywhere{above=of carbanion}{\tiny carbanion}
  \anywhere{below=of mesomer}{$+$\color{blue}\ce{H2O}}
 \end{rxn}
\end{Example}
You can find many further examples for the usage of \lstinline+\anywhere+ in \texttt{examples.tex} or \texttt{examples.pdf}, resp.
\index{anywhere|)}

\subsection{arrow}\label{ssec:arrow}\index{arrow|(}\index{commands!arrow}
Reaction arrows are created with \lstinline=\arrow=.
\begin{lstlisting}
 \arrow[<pos>,<type>,<length factor>,<name>,both,<tikz>]{<above>}{<below>}
\end{lstlisting}
\subsubsection{Options}\index{arrow!options|(}
There are a number of options to customize the arrows. The options must be used in the right order, seperated with commas.
\begin{enumerate}
\item\lstinline+<pos>+\index{arrow!options!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]{above right = \ang{45}}}
  \branch[above=of a]{\arrow[above]{}{}\reactant[above]{above = \ang{90}}}
  \branch[above left=of a]{\arrow[above left]{}{}\reactant[above left]{above left = \ang{135}}}
  \branch[left=of a]{\arrow[left]{}{}\reactant[left]{left = \ang{180} = \ang{-180}}}
  \branch[below left=of a]{\arrow[below left]{}{}\reactant[below left]{below left = \ang{225} = \ang{-135}}}
  \branch[below=of a]{\arrow[below]{}{}\reactant[below]{below = \ang{270} = \ang{-90}}}
  \branch[below right=of a]{\arrow[below right]{}{}\reactant[below right]{below right = \ang{315} = \ang{-45}}}
 \end{rxn}
 \NEU%
 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 \lstinline+<name>+: \lstinline+<name>.<angle>+. This means the arrow is placed in an angle of \lstinline+<angle>+ next to \lstinline+<name>+. You can find lots of examples in \texttt{examples.tex} or\texttt{examples.pdf}, resp.
\item\lstinline+<type>+\index{arrow!options!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\lstinline+<length factor>+\index{arrow!options!length} -- this factor multiplies with the arrow length (\SI{4}{\emlength} with factor = $1.0$, default) \item\lstinline+<name>+\index{arrow!options!name} -- can be used to give the arrow an anchor, to which another object can refer.
\item\lstinline+both+\index{arrow!options!both}-- this gives both nodes within which the labels are written the same size.
\item\lstinline+<tikz>+\index{arrow!options!tikz} -- you can modify the arrow with \TikZ keys. Not every \TikZ keys have an effect, though. You can't shift arrows with \lstinline+shift=<coord>+, for example.
\end{enumerate}
\begin{Example}
  \begin{rxn}
  \arrow[,,.25]{M}{}\arrow[,,.5]{MM}{}\arrow[,,.75]{MMM}{}\arrow{MMMM}{}\arrow[,,1.125]{MMMMM}{}\arrow[,,1.25]{MMMMM}{}
 \end{rxn}
\end{Example}
Please note, that the labels \lstinline+<above>+ and \lstinline+<below>+ are rotated with the arrow. At an angle of \ang{180} \lstinline+<above>+ actually is \emph{below} the arrow.
\begin{SideBySideExample}
 \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{SideBySideExample}
\NEU%
You need to be aware of one or two points, when using the arrow type \lstinline"-+>": if you leave the labels empty, the arrow is the same as \lstinline"->".
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.\index{arrow!options!type}
\begin{SideBySideExample}
 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{SideBySideExample}
\NEU%
You can change the appearance of an arrow with \TikZ keys:\index{arrow!options!tikz}
\begin{Example}
 \begin{rxn}
  \mCsetup{arrowlabel=.7em,arrowlength=6em}
  \reactant{A}
  \arrow[20,,,,,decorate,decoration=snake,blue]{a}{b}
  \reactant[20]{A$^*$}
 \end{rxn}
\end{Example}
\index{arrow!options|)}

\subsubsection{Alignment}\index{arrow!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{SideBySideExample}
 \makevisible
 \begin{rxn}
  \reactant[,a]{A}
  \arrow{}{}
  \branch[below=of a]{
    \arrow[-90]{\chemfig{-[::30]-[::-60]OH}}{}
  }
 \end{rxn}
 \makeinvisible
\end{SideBySideExample}
By using the option \lstinline=both=\index{arrow!options!both} both nodes get the same size. This can correct the alignment.
\begin{SideBySideExample}
 \makevisible
 \begin{rxn}
  \reactant[,a]{A}
  \arrow{}{}
  \branch[below=of a]{
   \arrow[-90,,,,both]{\chemfig{-[::30]-[::-60]OH}}{}
  }
 \end{rxn}
 \makeinvisible
\end{SideBySideExample}
There's more to the question of alignment in \ref{sssec:branch_ausrichtung}.
\index{arrow!alignment|)}

\subsubsection{Appearance}\index{arrow!appearance}
You can change the general appearance of arrows with \lstinline+\setarrowlength+ (\ref{ssec:setarrowlength}) and \lstinline+\setarrowline+ (\ref{ssec:setarrowline}).
\index{arrow|)}

\subsection{branch}\label{ssec:branch}\index{branch|(}\index{commands!branch}
\lstinline=\branch= is used to, well, create a branch to a reaction.
\begin{lstlisting}
 \branch[<pos>,<anchor>,<tikz>]{<branch code>}
\end{lstlisting}
For \lstinline=\branch= positioning an anchor is important. Let's take a look at an example:
\begin{Example}
 \begin{rxn}
  \reactant[,start]{\chemfig{-[::30]=_[::-60](-[::-60])-[::60]}}
  \arrow[,,.75]{\ce{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]{\ce{H2O}}{}
    \reactant[-45]{\chemfig{-[::30]-[::-60](-[::120]OH)(-[::-60])-[::60]}}
    \chemand
    \reactant{\chemfig{-[::30](-[::60]OH)-[::-60](-[::-60])-[::60]}}
  }
 \end{rxn}
\end{Example}
The first reactant got the anchor \lstinline+start+ (line 2, also see \ref{ssec:reactant}).
\begin{lstlisting}[firstnumber=2]
 \reactant[,!!start!!]{ ... }
\end{lstlisting}
\lstinline=\branch= now refers to it in its alignment (line 7):
\begin{lstlisting}[firstnumber=7]
 \branch[below right!!=of start!!]{ ... }
\end{lstlisting}
If you don't use the alignment reference to an anchor, you automatically refer to the last \lstinline=\reactant= or \lstinline=\arrow=. If you don't use alignment at all, then the branch is aligned to the right of the last \lstinline=\reactant= or \lstinline=\arrow=.
\begin{SideBySideExample}
 \begin{rxn}
  \reactant{ \chemfig{CH_2=CH-OH} }
  \arrow[,<=>,.5]{}{}
  \branch{ \reactant{ \chemfig{CH_3-CH=O} } }
 \end{rxn}
\end{SideBySideExample}

\subsubsection{Positioning}\label{sssec:branch_positionierung}\index{branch!positioning|(}
There are several ways to position a branch. It can either be part of the chain or be a real branch.
\begin{lstlisting}
 <angle>              % on the chain
 <key>                % on the chain
 <anchor>.<angle>     % not on the chain
 on chain=going <key> % on the chain
 <key>=of <anchor>    % not on the chain
\end{lstlisting}
Default behaviour is equal to \lstinline+\branch[0]{}+. In different situations different ways can be favoured. For example if you want to use \lstinline+\branch+ to shift an arrow, it can still be part of the chain.
\begin{SideBySideExample}
 \begin{rxn}
  \reactant{A}
  \branch[,,yshift=1em]{\arrow{}{}}
  \reactant[,,yshift=-1em]{B}
 \end{rxn}
\end{SideBySideExample}
If you like to start a real branch, it \emph{does} matter, which way you use.
\begin{SideBySideExample}
 \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{SideBySideExample}
If a reactant isn't squared or circled \ang{-45} does not mean the same as "below right".
\begin{SideBySideExample}
 \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{SideBySideExample}
\index{branch!positioning|)}

\subsubsection{Alignment problems}\label{sssec:branch_ausrichtung}\index{branch!alignment|(}
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 \lstinline=\arrow= key \lstinline=both= isn't a solution, since the smaller argument then is not placed next to the arrow but is centered in its node.
\begin{SideBySideExample}
 \makevisible
 \begin{rxn}
  \reactant[,a]{A}
  \arrow{}{}
  \branch[below=of a]{
   \arrow[below,,,,both]{\chemfig{-[::30]-[::-60]OH}}{\Hpl}
  }
 \end{rxn}
 \makeinvisible
\end{SideBySideExample}
What you have to do is shift the branch using the \TikZ keys \lstinline+xshift+\index{xshift} and \lstinline+yshift+\index{yshift}.
\begin{SideBySideExample}
 \makevisible
 \begin{rxn}
  \reactant[,a]{A}
  \arrow{}{}
  \branch[below=of a,,xshift=-1.35em]{
   \arrow[below]{\chemfig{-[::30]-[::-60]OH}}{\Hpl}
  }
 \end{rxn}
 \makeinvisible
\end{SideBySideExample}
\index{branch!alignment|)}\index{branch|)}

\subsection{chemand}\label{ssec:chemand}\index{chemand|(}\index{commands!chemand}
The command
\begin{lstlisting}
 \chemand[<alignment>,<anchor>,<tikz>]
\end{lstlisting}
produces and places a $+$ in the same way \lstinline+\reactant+ places arbitrary text.
\begin{Example}
 \begin{rxn}
  \reactant{\chemfig{*6(------)}}
  \chemand
  \reactant{\ce{Br2}}
  \arrow{$h\nu$}{}
  \reactant{\chemfig{*6(--(-Br)----)}}
  \chemand
  \reactant{\ce{HBr}}
 \end{rxn}
\end{Example}
The optional arguments for \lstinline+\chemand+ and \lstinline+\reactant+ are the same, see \ref{ssec:reactant} for \lstinline+\reactant+'s options.
\index{chemand|)}

\subsection{dummy}\label{ssec:dummy}\index{dummy|(}\index{commands!dummy}
\NEU\lstinline=\dummy= creates an empty node. Up to v1.3 \lstinline=\arrow= needed to follow after a node, because \lstinline=\arrow= internally uses \lstinline=\tikzchainprevious=. If there was no node on the chain \emph{before} \lstinline=\arrow= was used, it caused an error. With \lstinline+\branch+ it was similar. By using \lstinline=\dummy= you could start a scheme with an arrow anyway.
\begin{lstlisting}
 \begin{rxn}
  \dummy\arrow{}{}
 \end{rxn}
\end{lstlisting}
\textbf{This is \emph{not} necessary any more}. In some (alignment) cases, an empty node still might be useful, so the command still exists.
\index{dummy|)}

\subsection{elmove}\label{ssec:elmove}\index{elmove|(}\index{commands!elmove}
\lstinline=\elmove= just is a shortcut for \CF's \lstinline=\chemmove=.
\begin{lstlisting}
 \elmove[<tikz>]{<start>}{<start direction>}{<end>}{<end direction>}
\end{lstlisting}
This is expanding the command
\begin{lstlisting}
 \chemmove{\draw[!!<tikz>!!](!!<start>!!).. controls +(!!<start direction>!!) and +(!!<end direction>!!)..(!!<end>!!);}
\end{lstlisting}
using \lstinline?[->,red,shorten <=3pt,shorten >=1pt]? as default for \lstinline=<tikz>=. How you use \lstinline+\chemmove+ is described in the documentation for \CF.
\begin{Example}
 \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{Example}
You should use \lstinline+\elmove+ \emph{only inside} of \lstinline+\anywhere+, \lstinline+\reactant+ or \lstinline+\transition+. Otherwise, you might get alignment errors.
\index{elmove|)}

\subsection{makeinvisible}\label{ssec:makeinvisible}\index{makeinvisible|(}\index{commands!makeinvisible}
\lstinline=\makeinvisible= restores the normal \mC behaviour after \lstinline=\makevisible= (see \ref{ssec:makevisible}) has been used. \lstinline=\makeinvisible= only changes the looks of nodes following after it.
\index{makeinvisible|)}

\subsection{makevisible}\label{ssec:makevisible}\index{makevisible|(}\index{commands!makevisible}
With \lstinline=\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 for \lstinline=\makevisible= in \ref{ssec:arrow}. Every kind of nodes is emphasized with a different colour: 

\tikz[baseline=(X.base)]\node[draw=red!60](X){\texttt{\textbackslash reactant\{\}}};, \tikz[baseline=(X.base)]\node[draw=green!60](X){\texttt{\textbackslash arrow\{above\}\{\}}};, \tikz[baseline=(X.base)]\node[draw=blue!60](X){\texttt{\textbackslash arrow\{\}\{below\}}}; und \tikz[baseline=(X.base)]\node[draw=cyan](X){\texttt{\textbackslash branch\{\}}};. Also see \ref{ssec:makeinvisible}.

 \lstinline=\makevisible= only changes the looks of nodes following after it ond only effects the group whithin which it is used.
\begin{SideBySideExample}
 \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{SideBySideExample}
\index{makevisible|)}

\subsection{marrow}\label{ssec:marrow}\index{marrow|(}\index{commands!marrow}
\lstinline=\marrow= creates a double-headed arrow.
\begin{lstlisting}
 \marrow[<direction>]
\end{lstlisting}
It is a shortcut for \lstinline+\arrow[<direction>,<->,.5]{}{}+.
\index{marrow|)}

\subsection{mCsetup}\label{ssec:mCsetup}\index{mCsetup|(}\index{commands!mCsetup}
With
\begin{lstlisting}
 \mCsetup{<keys>}
\end{lstlisting}
you can fully customize \mC. For each of \mC's commands going like \lstinline+\set<command>+ except \lstinline+\setbondshape+ there is a key \lstinline+<command>=<value>+. Additionally there is the key \lstinline+align=<value>+, with which you can change the alignment behaviour of both \lstinline+rxn+ and \lstinline+rxnscheme+, and the key \lstinline+reset+, with whith all values are reset to default.\index{mCsetup!align}\index{mCsetup!arrowlength}\index{mCsetup!atomsize}\index{mCsetup!bondlength}\index{mCsetup!mergelength}\index{mCsetup!rcndist}\index{mCsetup!rxnalign}\index{mCsetup!schemealign}\index{mCsetup!reset}
\begin{Example}
 \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{Example}
\lstinline+\mCsetup+ \textbf{as well as for every other setup command only effects the group whithin which it is used.}
\index{mCsetup|)}

\subsection{merge}\label{ssec:merge}\index{merge|(}\index{commands!merge}
\NEU%
The \lstinline+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 (\lstinline+\reactant[,<anchor>]{}+, similar with branches, see \ref{ssec:reactant} and \ref{ssec:branch}) and be placed \emph{before} \lstinline+\merge+.
\begin{lstlisting}
 \merge[<label>,<direction>,<length>]{<target>}{<start a>}{<start b>}
\end{lstlisting}
\lstinline+\merge+ has three optional and three mandatory arguments. The latter are the anchor names of the reactants, that are to be merged.
\begin{Example}
 \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[\ce{[\Hyd]}]{target}{start_a}{start_b}
 \end{rxn}
\end{Example}
The default \lstinline+<direction>+ is \lstinline+below+, other possible values are \lstinline+right+, \lstinline+left+ or \lstinline+above+. With \lstinline+<length>+ the length of the arrow from the point of merging to the tip can be changed. The default length is \SI{3}{\emlength}. The default length can be changed with \lstinline+\setmergelength+\index{setmergelength} or \lstinline+\mCsetup+\index{mCsetup}.
\begin{Example}
 \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[\ce{[\Hyd]},right,5em]{target}{start_a}{start_b}
 \end{rxn}
\end{Example}
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 {\color{green}depth} of the involved reactants, the distance of the "reaction nodes" {\color{red}rcndist} (see \ref{ssec:setrcndist}) and the length of the \lstinline+\merge+ arrow {\color{blue}mergelength} (also see \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{Example}
 \begin{rxn}
  \setatomsep{1em}\tiny
  % 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{Example}
The usage of \lstinline=\merge= may require some playing with branches, \lstinline+xshift+\index{xshift} and \lstinline+yshift+\index{yshift}, until you get the desired result.
\begin{Example}
 \begin{rxn}
  \setatomsep{1.5em}
  \reactant[,start_aa]{ \chemname{\chemfig{**6(---(-NH_2)---)}}{Anilin} }
  \reactant[below,start_ab,yshift=-3em]{ \chemname{\ce{HNO2}}{salpetrige S"aure} }
  \branch[right=of start_aa,target_a,xshift=6em,yshift=-5em]{
    \reactant{ \chemname{\chemfig{**6(---(-N|_2\op)---)}}{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)---)}}{p-Aminodiazobenzol} }
  }
  \merge[,right]{target_a}{start_aa}{start_ab}
  \merge[,right]{target_b}{target_a}{start_bb}
 \end{rxn}
\end{Example}
\index{merge|)}

\subsection{mesomeric}\label{ssec:mesomeric}\index{mesomeric|(}\index{commands!mesomeric}
The \lstinline=\mesomeric= command works just like \lstinline=\branch= (see \ref{ssec:branch}) but places the formul\ae\ into square brackets.
\begin{lstlisting}
 \mesomeric[<pos>,<anchor>,<tikz>]{<formula>}
\end{lstlisting}
The resonance formul\ae\ are written into \lstinline=<formula>=. With \lstinline=\marrow= (see \ref{ssec:marrow}) you create the resonance arrows. If needed you can give an anchor (\lstinline=<anchor>=) to \lstinline=\mesomeric= (also see \ref{ssec:branch}). Alignment is used the same way as with \lstinline=\reactant=.
\begin{Example}
 \begin{rxn}
  \mesomeric{
    \reactant{
      \chemfig{*6(=[@{e1}]-=-(-[:120]X)(-[:60]H)-(-[:-30,.4,,,white]\oplus)-[@{e2}])}
      \elmove{e1}{60:4mm}{e2}{0:4mm}
    }
    \marrow
    \reactant{
      \chemfig{*6(-(-[:90,.4,,,white]\oplus)-[@{e4}]=[@{e3}]-(-[:120]X)(-[:60]H)-=)}
      \elmove{e3}{180:4mm}{e4}{150:4mm}
    }
    \marrow
    \reactant{
      \chemfig{*6(-=-(-[:-150,.4,,,white]\oplus)-(-[:120]X)(-[:60]H)-=)}
    }
   }
 \end{rxn}
\end{Example}
Or vertical, too:
\begin{SideBySideExample}
 \begin{rxn}
  \mesomeric{
    \reactant{ \chemfig{*6(=-=-=-)} }
    \marrow[below]
    \reactant[below]{ \chemfig{*6(-=-=-=)} }
  }
 \end{rxn}
\end{SideBySideExample}
Or maybe a coordination complex?
\begin{Example}
 \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] {$2\oplus$};
 \end{rxn}
\end{Example}
\index{mesomeric|)}

\subsection{reactant}\label{ssec:reactant}\index{reactant|(}\index{commands!reactant}
\lstinline=\reactant=\footnote{In earlier versions it was called \texttt{\textbackslash reactand}. You can still use it.} is something like the basic command.
\begin{lstlisting}
 \reactant[<pos>,<name>,<tikz>]{<formula>}
\end{lstlisting}
Formul\ae\ (\lstinline=<formula>=) are written inside this command and can be named (\lstinline=<name>=) for other objects to refer to. \lstinline+<pos>+ can either be one of these key words
\begin{alphlist}
 \item \lstinline+right+,
 \item \lstinline+above right+,
 \item \lstinline+above+,
 \item \lstinline+above left+,
 \item \lstinline+left+,
 \item \lstinline+below left+,
 \item \lstinline+below+,
 \item \lstinline+below right+
\end{alphlist}
\NEU%
or be an angle from the intervall $[\ang{-360};\ang{360}]$. You also can position it relativ to another object via \lstinline+<anchor>.<angle>+. The default equals \lstinline+\reactant[0]{}+.
\begin{SideBySideExample}
 below:
 \begin{rxn}
   \reactant{\ce{Br2}}
   \reactant[-90]{\ce{Cl2}}
 \end{rxn}

 more than one reactant:
 \begin{rxn}
   \reactant{\ce{Br2}}
   \reactant[-90]{\ce{I2}}
   \reactant{\ce{Cl2}}
 \end{rxn}

 going down:
 \begin{rxn}
  \reactant{\ce{Br-Br}}
  \arrow[-90,,.5]{$h\nu$}{}
  \reactant[-90]{\ce{2 ~\lewis{0.,Br}}}
 \end{rxn}
\end{SideBySideExample}
You can find many more examples in the file \texttt{examples.tex} or \texttt{examples.pdf}, resp.
\index{reactant|)}

\subsection{rxn (environment)}\label{ssec:rxn}\index{rxn|(}\index{commands!rxn|see{rxn}}\index{environment!rxn|see{rxn}}
\lstinline=rxn= is a non-floating not numbered environment for reaction schemes. Per default all schemes are centered.
\begin{lstlisting}
 \begin{rxn}[<alignment>,<scalefactor>]
  ...
 \end{rxn}
\end{lstlisting}

\subsubsection{Options}\label{sssec:rxn_optionen}\index{rxn!options|(}
\NEU\lstinline=rxn= has two options, which are to be used in the following order, separated by a comma:
\begin{enumerate}
 \item\lstinline+<alignment>+\index{rxn!options!alignment} alignment behaviour of the \lstinline=rxn= environment; default is `center'.
 \item\lstinline+<scalefactor>+\index{rxn!options!scale} factor by which the \lstinline=rxn= environment is scaled; default: `1.0'. Same behaviour as with \lstinline+rxnscheme+, see \ref{ssec:rxnscheme}.
\end{enumerate}
If you use the \lstinline+scalefactor+ option, you might see strange effects on \CF formul\ae.
\begin{SideBySideExample}
 \begin{rxn}[,.5]
  \reactant{\chemfig{**6(------)}}
 \end{rxn}
\end{SideBySideExample}
Scaling does in general not affect the size of \CF formul\ae, but does scale the aromaticity ring of benzene and similar molecules. This is due to a possible bug in \CF itself.
\begin{SideBySideExample}
 \chemfig[scale=.5]{**6(------)}
\end{SideBySideExample}
This can be solved either by using the \emph{first} optional argument of \lstinline+\chemfig+ to undo the scaling or by using the \emph{second} optional argument to scale the rest of the molecule.
\begin{Example}
 \begin{rxn}[,.5]
  \reactant{\chemfig[scale=2]{**6(------)}}
  \reactant{\chemfig[][scale=.5]{**6(------)}}
 \end{rxn}
 \chemfig[scale=.5][scale=.5]{**6(------)}
\end{Example}
Alignment examples:
\begin{Example}
 \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{Example}
\index{rxn!options|)}\index{rxn|)}

\subsection{rxnscheme (environment)}\label{ssec:rxnscheme}\index{rxnscheme|(}\index{commands!rxnscheme|see{rxnscheme}}\index{environment!rxnscheme|see{rxnscheme}}
\lstinline+rxnscheme+ is a floating environment for reaction schemes.
\begin{lstlisting}
 \begin{rxnscheme}[<label>,<placement>,<alignment>,<scalefactor>,<name>]{<caption>}
  ...
 \end{rxnscheme}
\end{lstlisting}

\subsubsection{Options}\label{sssec:rxnscheme_optionen}\index{rxnscheme!options|(}
\NEU\lstinline=rxnscheme= has five options, which are to be used in the following order, separated by commas:
\begin{enumerate}
 \item\lstinline+<label>+\index{rxnscheme!options!label} Like every other floating environment \lstinline+rxnscheme+ can be given a label. To do that, you need to use the option \lstinline+<label>+. For example if you use
\begin{lstlisting}
 \begin{rxnscheme}[rs:schema]{<caption>}
  ...
 \end{rxnscheme}
\end{lstlisting}
 you can refer to it by using \lstinline=\ref{rs:schema}= as usual.
 \item\lstinline+<placement>+\index{rxnscheme!options!placement} With this option you can change the placement of the float, \eg with \lstinline+htp+. The default value is \lstinline+htp+.
 \item\lstinline+<alignment>+\index{rxnscheme!options!alignment}This option changes the alignment of the scheme. You can choose between \lstinline=left=, \lstinline=center= and \lstinline=right=.
 \item\lstinline+<scalefactor>+\index{rxnscheme!options!scale} \lstinline+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 \CF formul\ae. You can have strange effects on \CF formul\ae\ if you use this key, though. See \ref{sssec:rxn_optionen} for more information.
 \item\lstinline+<name>+\index{rxnscheme!options!name} This option changes the name of the actual scheme from "Reaktionschema" or "Reaction scheme" into \lstinline+<name>+.
\begin{lstlisting}
 \begin{rxnscheme}[,<placement>]{<caption>}
  ...
 \end{rxnscheme}
\end{lstlisting}
\end{enumerate}
\begin{Example}
 \begin{rxnscheme}[,H,,2]{Big scheme}
  \large\setatomsep{3.5em}
  \reactant{ \chemfig{=[::30]-[::-60]OH} }
  \arrow[,<=>]{}{}
  \reactant{ \chemfig{-[::30]=[::-60]O} }
 \end{rxnscheme}
 \begin{rxnscheme}[,H,,.5]{Small scheme}
  \tiny\setatomsep{1em}
  \reactant{ \chemfig{=[::30]-[::-60]OH} }
  \arrow[,<=>]{}{}
  \reactant{ \chemfig{-[::30]=[::-60]O} }
 \end{rxnscheme}
 \begin{rxnscheme}[,H]{center}
  \reactant{center}\arrow{}{}\reactant{centered}
 \end{rxnscheme}
 \begin{rxnscheme}[,H,right]{right}
  \reactant{right}\arrow{}{}\reactant{raggedleft}
 \end{rxnscheme}
 \begin{rxnscheme}[,H,left]{left}
  \reactant{left}\arrow{}{}\reactant{raggedright}
 \end{rxnscheme}
\end{Example}
\index{rxnscheme!options|)}

\subsubsection{Customizing rxnscheme}\index{rxnscheme!customize|(}
\paragraph{Style}\index{rxnscheme!customize!style}
If you don't like the style of \lstinline+rxnscheme+ you can change it by using
\begin{lstlisting}
 \floatstyle{<new style>}
 \restylefloat{rxnfloat}
\end{lstlisting}
There are different possible styles, privided by the `float' package:
\begin{description}
 \vitem=plain= without any special formatting, the caption is below the object
 \vitem=plaintop= like \lstinline=plain=, but the caption is placed above the object
 \vitem=boxed= the object is boxed, the caption placed below
 \vitem=ruled= the caption is placed above the object framed by to rules, one above and one below, another rule frames the object below; default for \lstinline+rxnscheme+
\end{description}
\begin{Example}
 \begin{rxnscheme}[,H]{ruled}
  \reactant{default style}
 \end{rxnscheme}
 \floatstyle{boxed}
 \restylefloat{rxnfloat}
 \begin{rxnscheme}[,H]{boxed}
  \reactant{framed object}
 \end{rxnscheme}
 \floatstyle{plain}
 \restylefloat{rxnfloat}
 \begin{rxnscheme}[,H]{plain}
  \reactant{without any special formatting}
 \end{rxnscheme}
\end{Example}
\floatstyle{ruled}
\restylefloat{rxnfloat}
\paragraph{Placement}\index{rxnscheme!customize!placement}
Usually floating environments have an optional argument for their placement. \lstinline=rxnscheme='s default placement is \lstinline=H= which means, it is placed \emph{exactly here}. If you want to change it into \lstinline=htp= or something, you can use
\begin{lstlisting}
 \floatplacement{rxnfloat}{<placement>}
\end{lstlisting}
It's easier, though, loading \mC with the `placement' option:
\begin{lstlisting}
 \usepackage[placement=<placement>]{mychemistry}
\end{lstlisting}
This will change the default placement behaviour from \lstinline=H= to \lstinline=<placement>=. You can also change the placement behaviour of just one \lstinline+rxnscheme+ environment by using the placement option:
\begin{lstlisting}
 \begin{rxnscheme}[,<placement>]{<caption>}
  ...
 \end{rxnscheme}
\end{lstlisting}

\paragraph{Name}\label{par:rxnscheme_name}\index{rxnscheme!customize!name}
If you want to change the name of reaction scheme\footnote{You probably do. You reading the English documention means probably, that you're not German.}, you can do that with
\begin{lstlisting}
 \setschemename{<new name>}
\end{lstlisting}
The default name is "Reaktionschema" or, with package option `english', "Reaction scheme".
\paragraph{Counter}\index{rxnscheme!customize!counter}
The counter can be changed just as usual. For example by using
\begin{lstlisting}
 \makeatletter
 \@addtoreset{rxnfloat}{section}
 \makeatletter
 \renewcommand{\therxnscheme}{\arabic{section}.\arabic{rxnscheme}}
\end{lstlisting}
the counter is reset with every new section an looks like \lstinline+section.rxnscheme+. Please be aware, that you have to write \lstinline=\@addtoreset= between \lstinline=\makeatletter= and \lstinline=\makeatother= because of the {@}.
\paragraph{List of schemes}\index{rxnscheme!customize!list}
By writing
\begin{lstlisting}
 \listof{rxnfloat}{<title>}
\end{lstlisting}
you can create a list of all schemes created with \lstinline+rxnscheme+.
\begin{SideBySideExample}
 \listof{rxnfloat}{Reaction schemes}
\end{SideBySideExample}
\index{rxnscheme!customize|)}\index{rxnscheme|)}

\subsection{setarrowlabel}\label{ssec:setarrowlabel}\index{setarrowlabel|(}\index{commands!setarrowlabel}
\NEU%
The distance of arrow labels to the arrow has a default value of \SI{0.2}{\emlength}. You can change this with
\begin{lstlisting}
 \setarrowlabel{<distance>}
\end{lstlisting}
into \lstinline+<distance>+.
\begin{SideBySideExample}
 \begin{rxn}
  \arrow{a}{b}
  \setarrowlabel{.5em}
  \arrow{a}{b}
 \end{rxn}
\end{SideBySideExample}
\index{setarrowlabel|)}

\subsection{setarrowlength}\label{ssec:setarrowlength}\index{setarrowlength|(}\index{commands!setarrowlength}
The default length of an reaction arrow is \SI{4}{\emlength}. You can change this value with
\begin{lstlisting}
 \setarrowlength{<length>}
\end{lstlisting}
into \lstinline+<length>+. Mind the fact that you have to use a length unit. If you leave the argument empty, the length is reset to default.
\index{setarrowlength|)}

\subsection{setatomsize}\label{ssec:setatomsize}\index{setatomsize|(}\index{commands!setatomsize}
With
\begin{lstlisting}
 \setatomsize{<font size>}
\end{lstlisting}
you can change the font size of the atom groups. Default value is \lstinline=\small=. If you leave the argument empty, the size is reset to default.
\index{setatomsize|)}

\subsection{setbondlength}\label{ssec:setbondlength}\index{setbondlength|(}\index{commands!setbondlength}
With
\begin{lstlisting}
 \setbondlength{<length>}
\end{lstlisting}
you can change \lstinline=\setatomsep{<length>}= for all \CF formul\ae\ \emph{inside} of the \mC environments. Default value is \SI{1.8}{\emlength}. If you leave the argument empty, the length is reset to default.
\index{setbondlength|)}

\subsection{setarrowline}\label{ssec:setarrowline}\index{setarrowline|(}\index{Befehle!setarrowline}
\NEU%
With the command
\begin{lstlisting}
 \setarrowline{<value>}
\end{lstlisting}
the thickness of the arrows can be customized. Possible values are
 \begin{flushleft}
 \begin{tikzpicture}
   \draw[ultra thin] (0,0)--(1,0)node[right]{\tt ultra thin};
   \draw[very thin] (0,-.5)--(1,-.5)node[right]{\tt very thin};
   \draw[thin] (0,-1)--(1,-1)node[right]{\tt thin};
   \draw[semithick] (0,-1.5)--(1,-1.5)node[right]{{\tt semithick} (default)};
   \draw[thick] (0,-2)--(1,-2)node[right]{\tt thick};
   \draw[very thick] (0,-2.5)--(1,-2.5)node[right]{\tt very thick};
   \draw[ultra thick] (0,-3)--(1,-3)node[right]{\tt ultra thick};
 \end{tikzpicture}
\end{flushleft}
The values \lstinline+very thick+ and \lstinline+ultra thick+ should not be used.

This command also applies to \lstinline+\merge+\index{merge}.
\index{setarrowline|)}

\subsection{setbondshape}\label{ssec:setbondshape}\index{setbondshape|(}\index{commands!setbondshape}
With
\begin{lstlisting}
 \setbondshape{<base length>}{<dash thickness>}{<dash spacing>}
\end{lstlisting}
you can change \lstinline=\setcrambond{<base length>}{<dash thickness>}{<dash spacing>}= for all \CF formul\ae\ \emph{inside} of the \mC 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.
\index{setbondshape|)}

\subsection{setmergelength}\label{ssec:setmergelength}\index{setmergelength|(}\index{commands!setmergelength}
\NEU%
With
\begin{lstlisting}
 \setmergelength{<länge>}
\end{lstlisting}
you can change the length of the \lstinline+\merge+ arrow. More precisely you can change the length of the arrow from the point of line crossing to the arrow tip (see \ref{ssec:merge}). If you leave an argument empty, the value is reset to default (\SI{3}{\emlength}).
\index{setmergelength|)}

\subsection{setrcndist}\label{ssec:setrcndist}\index{setrcndist|(}\index{commands!setrcndist}
The nodes within which the reactants an arrows are set have a certain distance between them. The default distance is \SI{1}{\emlength}. If you want to change that, you can use
\begin{lstlisting}
 \setrcndist{<länge>}
\end{lstlisting}
If you leave the argument empty, the distance is reset to \SI{1}{\emlength}.
\begin{SideBySideExample}
 \setrcndist{2em}
 \begin{rxn}
  \reactant{A}\arrow{}{}
 \end{rxn}
 \setrcndist{}
 \begin{rxn}
  \reactant{A}\arrow{}{}
 \end{rxn}
\end{SideBySideExample}
\index{setrcndist|)}

\subsection{setrxnalign/setschemealign}\label{ssec:setrxnalign}\label{ssec:setschemealign}\index{setrxnalign|(}\index{commands!setrxnalign}\index{setschemealign|(}\index{commands!setschemealign}
With the commands
\begin{lstlisting}
 \setrxnalign{<alignment>}
 \setschemealign{<alignment>}
\end{lstlisting}
The default alignment behaviour of \lstinline+rxn+ and \lstinline+rxnscheme+ (see \ref{sssec:rxn_optionen} \&\ \ref{sssec:rxnscheme_optionen}) can be set. You can choose between \lstinline=left=, \lstinline=center= and \lstinline=right=.

If you leave the argument empty, \mC's default behaviour (\lstinline=center=) is restored.
\begin{Example}
 \setrxnalign{right}
 \begin{rxn}
  \reactant{A}\arrow{}{}\reactant{B}
 \end{rxn}
 \setrxnalign{}
 \begin{rxn}
  \reactant{A}\arrow{}{}\reactant{B}
 \end{rxn}
\end{Example}
\index{setrxnalign|)}\index{setschemealign|)}

\subsection{setschemename}\label{ssec:setschemename}\index{setschemename|(}\index{commands!setschemename}
See \ref{par:rxnscheme_name}.
\index{setschemename|)}

\subsection{transition}\label{ssec:transition}\index{transition|(}\index{commands!transition}
\lstinline=\transition= works exactly like \lstinline=\reactant= (see \ref{ssec:reactant}).
\begin{lstlisting}
 \transition[<pos>,<anchor>,<tikz>]{<formula>}
\end{lstlisting}
\begin{SideBySideExample}
 \begin{rxn}
  \reactant{ \ce{H2 + I2} }
  \arrow[below,<=>,.5]{}{}
  \transition[below]{ \chemfig[dotted][]{H?-I-[2]I-[4]H?} }
  \arrow[below,<=>,.5]{}{}
  \reactant[below]{ \ce{2 HI} }
 \end{rxn}
\end{SideBySideExample}
\index{transition|)}

\section{Epilogue}
\mC is still very new. This means there are probably a number of bugs I haven't discovered yet. There also might be missing one or two features, that would be useful. Since I only can test and work on \mC in my spare time, I'd be very glad about \emph{every} kind of feedback. If you like \mC, why don't you help me improve it by telling me your experiences?

I tried using real chemical reactions but I didn't make sure, that they all make sense chemically. So you shouldn't trust the examples in respect to chemistry but rather take a look into a real chemistry teaching book.

I apologize for any bad or wrong English. I hope you understood the documention anyway.

Have fun with \mC!

\par\vspace{.5cm}\hspace{.5cm}Clemens Niederberger, Berlin, \mCdate{en}

\section{Thanks}
I owe thanks for bug reports and suggestions to:

F.\,Chervet, Ferghun, V.\,Garibal and C.\,Tellechea (who pointed out some essential issues).

\printindex
\end{document}