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diff --git a/Master/texmf-dist/doc/latex/mychemistry/mychemistry_en.tex b/Master/texmf-dist/doc/latex/mychemistry/mychemistry_en.tex deleted file mode 100644 index 269b8fecbfd..00000000000 --- a/Master/texmf-dist/doc/latex/mychemistry/mychemistry_en.tex +++ /dev/null @@ -1,1724 +0,0 @@ -% 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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