% --------------------------------------------------------------------------

% the CHEMNUM package

%

% a comprehensive approach for the numbering of chemical compounds

%

% --------------------------------------------------------------------------

% Clemens Niederberger

% --------------------------------------------------------------------------

% https://github.org/cgnieder/chemnum/

% [email protected]

% --------------------------------------------------------------------------

% If you have any ideas, questions, suggestions or bugs to report, please

% feel free to contact me.

% --------------------------------------------------------------------------

% Copyright 2011--2021 Clemens Niederberger

%

% This work may be distributed and/or modified under the

% conditions of the LaTeX Project Public License, either version 1.3c

% 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 1.3c or later is part of all distributions of LaTeX

% version 2008/05/04 or later.

%

% This work has the LPPL maintenance status `maintained'.

%

% The Current Maintainer of this work is Clemens Niederberger.

% --------------------------------------------------------------------------

% !arara: pdflatex: { shell: on , interaction: nonstopmode }

% !arara: pdflatex: { shell: on , interaction: nonstopmode }

% !arara: biber

% arara: pdflatex: { interaction: nonstopmode }

% arara: pdflatex: { interaction: nonstopmode }

\documentclass[load-preamble ,ngerman,british,american]{cnltx-doc}

\usepackage{chemnum}

\setcnltx{

package = chemnum ,

info = numbering of chemical compounds ,

authors = Clemens Niederberger ,

email = [email protected] ,

url = https://github.com/cgnieder/chemnum/ ,

add-cmds = {

chemnumshowdef,

chemnumshowref,

cmpd ,

initcmpd ,

labelcmpd ,

cmpdplain ,

cmpdproperty ,

cmpdref ,

replacecmpd ,

resetcmpd ,

setchemnum ,

cmpdshowdef ,

cmpdshowref ,

newcmpdcounterformat ,

subcmpdplain ,

submaincmpdplain ,

subcmpdproperty ,

subcmpdshowdef ,

subcmpdshowref ,

} ,

add-silent-cmds = {

arrow,

bottomrule,

ch,chemfig,chemname,

CNlabel,CNlabelnoref,CNlabelsub,CNlabelsubnoref,

CNref,CNrefsub,CNsubnoref,

compound,cs,

declarecompound,definesubmol,detokenize,

expandfull,expandtwice,

fcite,

includegraphics,

keyis,

marginnote, midrule,

NewDocumentCommand,

schemestart,schemestop,setchemfig,

theffbibliography, toprule

} ,

index-setup = { othercode=\footnotesize,level=\addsec },

makeindex-setup = { columns=3,columnsep=1em } ,

add-frame = false

}

\usepackage[artemisia]{textgreek}

\activatechemgreekmapping{textgreek}

\usepackage{chemformula}

\setchemformula{format=\libertineLF}

\usepackage{chemfig,relsize}

\setchemfig{

atom sep = 1.78500 em ,

bond style = {line width = 0.06642 em}

}

\renewcommand*\printatom[1]{\textsmaller{\ensuremath{\mathsf{#1}}}}

\usepackage{array,booktabs,csquotes}

\usepackage{graphicx}

\defbibheading{bibliography}[References]{\addsec{#1}}

\usepackage{acro,accsupp}

\acsetup{

format/short = \scshape ,

first-style = short

}

\DeclareAcronym{pdf}{

short = pdf ,

long = portable document format ,

pdfstring = PDF ,

short-acc = PDF

}

\DeclareAcronym{eps}{

short = eps ,

long = encapsulated postscript ,

pdfstring = EPS ,

short-acc = EPS

}

\DeclareAcronym{ps}{

short = ps ,

long = postscript ,

pdfstring = PS ,

short-acc = PS

}

\DeclareAcronym{id}{

short = id ,

long = identification key ,

pdfstring = ID ,

short-acc = ID

}

\begin{document}

\selectlanguage{american}

\section{License and Requirements}\label{sec:license-requirements}

\license

\chemnum\ requires the bundles \bnd{l3kernel}~\cite{bnd:l3kernel} and

\bnd{l3packages}~\cite{bnd:l3packages}. It also requires the

\pkg{translations} package~\cite{pkg:translations},

\pkg{chemgreek}~\cite{pkg:chemgreek} and the \pkg{psfrag}~\cite{pkg:psfrag}

package.

\section{Overview over the Available Commands}\label{sec:overv-over-avail}

This section lists all available commands with a brief description. Commands

marked with \expandablesymbol\ are expandable in an \cs*{edef} like context.

Most of the commands will be explained in a later section in more detail.

\begin{commands}

\command{cmpd}[\sarg\code{ }\oarg{options}\marg{list of \acp{id}}]

The main command for creating and refering to compound labels. This

command is described in detail in section~\ref{sec:deta-comp-labels}. For

many people this will be the only command they need.

\command{refcmpd}[\oarg{options}\marg{\ac{id}}]

This command only refers to an already defined label but does not define a

label itself. This is an alias of \cs{cmpd}\code{ }.

\command{labelcmpd}[\oarg{options}\marg{\ac{id}}]

This command only defines a new label but does not print it. This is an

alias of \cs{cmpd}\sarg.

\expandable\command{cmpdplain}[\marg{\ac{id}}]

Reads a label and writes it expandably without formatting. It is not able

to parse a list. Its sole purpose is usage in \ac{pdf} strings

(\cf\ \cs*{texorpdfstring}\marg{\TeX}\marg{\ac{pdf} string}). This

command is described in section~\ref{sec:deta-comp-labels}.

\expandable\command{subcmpdplain}[\marg{main \ac{id}}\marg{sub \ac{id}}]

Reads a sublabel and writes it expandably without formatting. It is not

able to parse a list. Its sole purpose is usage in pdfstrings

(\cf\ \cs*{texorpdfstring}\marg{\TeX}\marg{\ac{pdf} string}). This

command is described in section~\ref{sec:deta-comp-labels}.

\expandable\command{submaincmpdplain}[\marg{main \ac{id}}\marg{sub \ac{id}}]

Reads a main label and a sublabel and writes them expandably without

formatting. It is not able to parse a list. Its sole purpose is usage in

\ac{pdf} strings (\cf\ \cs*{texorpdfstring}\marg{\TeX}\marg{\ac{pdf}

string}). This command is described in

section~\ref{sec:deta-comp-labels}.

\command{replacecmpd}[\code{ }\oarg{options}\marg{\ac{id}}]

A command for replacing tags in \ac{eps} files, see

section~\ref{sec:replacing-tags-eps-ps} for details.

\command{initcmpd}[\oarg{options}\marg{list of \acp{id}}]

Initiate compound labels. This command can only be used in the preamble.

It is desribed in section~\ref{sec:deta-comp-labels}.

\expandable\command{cmpdproperty}[\marg{\ac{id}}\marg{property}]

Get the associated property \meta{property} of compound

\meta{\ac{id}}. This command is described in

section~\ref{sec:deta-comp-labels}.

\expandable\command{subcmpdproperty}[\marg{main \ac{id}}\marg{sub

\ac{id}}\marg{property}]

Get the associated property \meta{property} of subcompound \meta{sub

\ac{id}} of compound \meta{main \ac{id}}. This command is described

in section~\ref{sec:deta-comp-labels}.

\command{newcmpdcounterformat}[\marg{name}\marg{command}]

Makes the label format \meta{name} known to \chemnum. \meta{command}

needs to be a command that takes an integer number as argument and should

return a formatted version of it. In practice you should not need to use

this command as the most common formats already are defined. This command

is described in section~\ref{sec:change-numbering}.

\command{resetcmpd}[\oarg{integer}]\Default{1}

Reset the numbering for main compound labels to start with \meta{integer}

again. This is the same as

\cs*{setcounter}\Marg{cmpdmain}\Marg{$\text{\meta{integer}}-1$}. The

command is described in section~\ref{sec:reset-numbering}.

\command{cmpdshowdef}[\marg{\ac{id}}]

Internal command used to display \meta{\ac{id}} of a newly defined compound

label when the option \option{show-keys} is used. The command is

described in section~\ref{sec:debugg-inform}.

\command{cmpdshowref}[\marg{\ac{id}}]

Internal command used to display \meta{\ac{id}} of a referencing compound

label when the option \option{show-keys} is used. The command is

described in section~\ref{sec:debugg-inform}.

\command{subcmpdshowdef}[\marg{main \ac{id}}\marg{sub \ac{id}}]

Internal command used to display \meta{main \ac{id}} and \meta{sub

\ac{id}} of a newly defined subcompound label when the option

\option{show-keys} is used. The command is described in

section~\ref{sec:debugg-inform}.

\command{subcmpdshowref}[\marg{main \ac{id}}\marg{sub \ac{id}}]

Internal command used to display \meta{main \ac{id}} and \meta{sub

\ac{id}} of a referencing subcompound label when the option

\option{show-keys} is used. The command is described in

section~\ref{sec:debugg-inform}.

\command{setcmpdproperty}[\marg{property}\marg{main \ac{id}}\marg{value}]

\sinceversion{1.3}Sets property \meta{property} of compound \meta{main

\ac{id}} to \meta{value}.

\command{setcmpdlabel}[\marg{main \ac{id}}\marg{value}]

\sinceversion{1.3}Sets property \code{counter-representation} of compound

\meta{main \ac{id}} to \meta{value}.

\end{commands}

\section{Numbering Compounds}\label{sec:numbering-compounds}

\subsection{Main Command}\label{sec:main-command}\resetcmpd

The main command of this package is this one:

\begin{commands}

\command{cmpd}[\marg{\ac{id}}]

When \meta{\ac{id}} is used the first time, the label is created, saved

(= declared) and printed. Each further use just prints the label.

\end{commands}

\begin{example}

Compounds \cmpd{a} and \cmpd{b} are declared and can be used any time:

\cmpd{a}. No pre-declaring is necessary. Compounds like \cmpd{c} are

numbered in the order they appear in the text.\par

Once again: \cmpd{b}, \cmpd{a}, \cmpd{c}.

\end{example}

If it is necessary to declare a compound without printing the label it is

possible with

\begin{commands}

\command{cmpd}[\sarg\marg{\ac{id}}]

Declare the label \meta{\ac{id}} but don't print anything.

\end{commands}

\begin{example}

The hidden version\cmpd*{d} declares the label but doesn't print anything.

The next \cmpd{e} continues to count with the next number. With \cmpd{d}

the label can be used, of course.

\end{example}

You can pretty much use what you like for a label name except for the

separator symbols (see also section~\ref{sec:chang-input-mark}). Be careful

with blanks though! Leading and trailing spaces are ignored, spaces at other

places are not. It's probably best not to use blanks in label names at all.

\begin{example}[add-sourcecode-options={showspaces=true}]

\cmpd{aa}, \cmpd{aa }, \cmpd{ aa}, and \cmpd{ aa } all have the same label.

Likewise \cmpd{a a}, \cmpd{a a }, \cmpd{ a a}, \cmpd{ a a }, \cmpd{a a},

\cmpd{a a }, \cmpd{ a a}, and \cmpd{ a a }.

\end{example}

\subsection{Sublabels}\label{sec:sublabel}

If you want a label like \cmpd{a.one}, you need to use the following syntax:

\begin{commands}

\command{cmpd}[\Marg{\meta{main \ac{id}}.\meta{sub \ac{id}}}]

\meta{main \ac{id}} is the main name which stays the same, \meta{sub

\ac{id}} varies. This syntax means that the point \code{.}

\emph{cannot} be a part of \meta{main \ac{id}} or \meta{sub \ac{id}}

(except if you enclose the respective \ac{id} in braces). Instead of the

point you also can use another symbol, see

section~\ref{sec:chang-input-mark} for details.

\end{commands}

\begin{example}

\cmpd{f.one} and \cmpd{f.two} are related, as are \cmpd{g.one} and

\cmpd{g.two}. Of course these labels can be used again: \cmpd{g.two} and

\cmpd{f.one}.

\end{example}

This also works if the main name has already been used.

\begin{example}

\cmpd{a} and its variants \cmpd{a.one} and \cmpd{a.two}

\end{example}

The same way the main name of combined labels can be used solely.

\begin{example}[side-by-side]

\cmpd{f} and \cmpd{g}

\end{example}

How you can create a combined label like \cmpd{f.{one,two}} is explained in

section~\ref{sec:lists-rang-subl}.

\subsection{Lists}\label{sec:lists}

There is actually more to the \cs{cmpd} command. It also prints lists of

labels. The right description would be something like:

\begin{commands}

\command{cmpd}[\marg{(possibly comma separated list of) label name(s)}]

Treats each entry of the list as described before.

\end{commands}

This means that with default settings the comma can't be part of the label

name unless hidden in braces. As separator another symbol can be used, too,

see section~\ref{sec:chang-input-mark} for details.

\begin{example}

More than one label can be put inside \cs{cmpd}, separated by commas. Then

a list like \cmpd{a, b, c, e, g.two} is printed.

\end{example}

The Harvard comma (see section~\ref{sec:lang-depend-sett}) in \enquote{\code{, and}}

between \cmpd{e} and \cmpd{g.two} suggests that there are options to customize

the list, see section~\ref{sec:formatting-labels} for more on this.

The option \option{merge} has an effect on lists: if it is set to \code{true}

multiple occurences of a main label with a possibly different set of sublabels

are merged into one label:

\begin{example}

With \keyis{merge}{true} a list like \cmpd{c,g.two,a,g.{one,four}} looks

like \cmpd[merge=true]{c,g.two,a,g.{one,four}}.

\end{example}

\subsection{Lists and Ranges of Sublabels}\label{sec:lists-rang-subl}

Sometimes it can be useful to display a label with a list or a range of

sublabels. Suppose you have compounds

\cmpd{q.one,q.two,q.three,q.four,q.five} which for example differ in their

substituents. It can be useful to refer to them all at once:

The syntax is rather intuitive -- you just input a list of sublabels:

\begin{example}

\setchemnum{compress=false}%

list of labels: \cmpd{q.one, q.two, q.three, q.four, q.five}\par

label with list of sublabels: \cmpd{q.{one,two,three,four,five}}

\end{example}

Since the sublist is input with a comma in the default setting you have to

put them into braces. If you add a list of sublabels to a main label they

will always be printed in the order the sublabels have been declared and not

in the order they're input in the list:

\begin{example}

\setchemnum{compress=false}%

compare \cmpd{q.{one,two,three,four,five}}

with \cmpd{q.{five,four,three,two,one}} and

\cmpd{q.{three,four,one,five,two}}

\end{example}

Using this syntax you also can create ranges of sublabels. For this you

enable the option \option{compress}. Or rather: this is the default setting.

If you don't want compressed sublabels you have to disable the option like in

the previous examples.

\begin{example}[side-by-side]

\cmpd{q.{two,four,three}} \par

\cmpd{q.{five,one,three,four}} \par

\cmpd{q.{one,three,five,two}}

\end{example}

Obviously you can't use a comma as part of a sublabel name. You can change

the input marker, though. See section~\ref{sec:overv-over-avail-1} for

available options.

Sometimes it can be useful to get only the sublabel without the main label.

This is achieved with the option \option{sub-only}:

\begin{example}

% uses packages `chemfig', `chemformula' and `booktabs'

\chemname{\chemfig{*6(=-=-(-R)=-)}}{\cmpd{benzene.{H,Me,OH,NH2}}}

\quad

\begin{tabular}{lll}

\toprule

& \ch{-R} & Name \\

\midrule

\cmpd[sub-only]{benzene.H} & \ch{-H} & Benzene \\

\cmpd[sub-only]{benzene.Me} & \ch{-CH3} & Toluene \\

\cmpd[sub-only]{benzene.OH} & \ch{-OH} & Phenol \\

\cmpd[sub-only]{benzene.NH2} & \ch{-NH2} & Phenylamine (Aniline) \\

\bottomrule

\end{tabular}

\end{example}

\subsection{Usage in Section Headings and Captions}\label{sec:usage-sect-head}

If you use labels in section headings or captions you will want to use either

\cs{refcmpd} or \cs{cmpd}\code{ } (they are completely equivalent). Otherwise

the corresponding labels will be declared when the section headings appear in

the table of contents or maybe the page header. This would mess up the

desired order of the compound numbers.

\section{Details on Compound Labels}\label{sec:deta-comp-labels}

\subsection{How Things Work}\label{sec:how-things-work}

When you call \cs{cmpd} with a new label three things happen:

\begin{itemize}

\item The new label gets initiated. This is nothing more than adding it to

an internal list. The purpose of this is explained in

section~\ref{sec:initiating-labels}.

\item The new label gets declared. This means that a number of internal

commands are defined. Amongst other things they hold a number of

properties associated with the corresponding label. Those properties are

explained in more detail in section~\ref{sec:prop-comp-labels}. The

necessary information of the label are also written to the \code{aux}

file.

\item The label gets printed.

\end{itemize}

Since new labels are declared when \cs{cmpd} is first used using it in section

titles that are written to the table of contents may to lead to wrong

numbering. In order to avoid this compound label information is written to

the \code{aux} file. The command \cs{refcmpd}\oarg{options}\marg{\ac{id}}

only reads those information but does not declare a label. There is also a

command which does the opposite: it declares a label if it hasn't been

declared before but will not print the corresponding label:

\cs{labelcmpd}\oarg{options}\marg{\ac{id}}. Both commands have shortcut

versions: \cs{cmpd}\code{ } is the same as \cs{refcmpd}, \cs{cmpd}\sarg\ is

the same as \cs{labelcmpd}.

Another command available is \cs{cmpdplain}\marg{\ac{id}}. This command is

similar to \cs{refcmpd}. There are a few important differences, though:

\cs{cmpdplain} does \emph{not} take a list of labels as argument. It also is

\emph{not} able to interpret sublabels. \cs{cmpdplain} does not format the

label with whatever format has been declared. And last but not least: it is

expandable. This means it can be used to get labels in \ac{pdf} bookmarks.

It's equivalent \cs{subcmpdplain}\marg{main \ac{id}}\marg{sub \ac{id}} does

the same for sublabels. A third sibling, \cs{submaincmpdplain}\marg{main

\ac{id}}\marg{sub \ac{id}}, writes both the main and the sublabel.

I should also say a few words on lists of labels. A usage like

\verbcode \cmpd{a,b,c,e} will be printed as a \emph{sorted} list. The order

will be in the order \emph{in which the labels have been defined}. The above

usage gives \cmpd{a,b,c,e}. The same thing holds for the order of sublabels

of a compound: the usage \verbcode \cmpd{q.{one,three,four,two,five}} gives

\cmpd{q.{one,three,four,two,five}} or

\cmpd[compress=false]{q.{one,three,four,two,five}} (depending on the

\option{compress} option). Be careful if you have a list with several

occurences of the same main label but with different sublabels: the labels

will not be sorted depending on their sublabels.

\begin{example}[side-by-side]

\cmpd{q.five,q.two} \par

\cmpd{q.two,q.five} \par

\cmpd[merge]{q.five,q.two} \par

\cmpd{q.five,b,r,q.two,a}

\end{example}

A last thing on lists: duplicate entries (\ie, \emph{exact} duplicates) will

be removed.

\subsection{Properties of Compound Labels}\label{sec:prop-comp-labels}

Every label has a number of properties. The first property is of course its

\ac{id} which identifies the label. The other properties are:

\begin{description}

\item[number] An internal unique number.

\item[counter-representation] The counter representation associated with the

label. This is the actual label that get's printed.

\item[pre-label-code] Code to be inserted before the label is printed.

\item[post-label-code] Code to be inserted after the complete label is

printed.

\item[pre-main-label-code] Code to be inserted before the \emph{main} label

is printed.

\item[post-main-label-code] Code to be inserted after the \emph{main} label

is printed.

\item[label-format] Formatting commands for the label. This is most likely

something like \cs*{bfseries}. This is the \emph{default} format. Unlike

the other properties it can be changed locally with the \option{format}

option on a case by case basis.

\end{description}

The properties for a label are set the when a label is declared for the first

time.

\begin{commands}

\expandable\command{cmpdproperty}[\marg{\ac{id}}\marg{property}]

Get the associated property \meta{property} of compound \meta{\ac{id}}. This

command is expandable.

\end{commands}

\begin{example}

\def\expandfull{\romannumeral-`0}%

\def\expandtwice{\detokenize\expandafter\expandafter\expandafter}%

\ttfamily

number: \cmpdproperty{benzene}{number}\par

counter-representation: \cmpdproperty{benzene}{counter-representation}\par

pre-label-code: \cmpdproperty{benzene}{pre-label-code}\par % empty

post-label-code: \cmpdproperty{benzene}{post-label-code}\par % empty

label-format: \expandtwice{\expandfull\cmpdproperty{benzene}{label-format}}

\end{example}

Similarly a sublabel has associated properties. Additionally to the obvious

ones -- its \ac{id} and the \ac{id} the main label it belongs to -- these

are

\begin{description}

\item[number] An internal unique number.

\item[counter-representation] The counter representation associated with the

label. This is the actual label that get's printed.

\end{description}

\begin{commands}

\expandable\command{subcmpdproperty}[\marg{main \ac{id}}\marg{sub

\ac{id}}\marg{property}]

Get the associated property \meta{property} of subcompound \meta{sub

\ac{id}} of compound \meta{main \ac{id}}. This command is

expandable.

\end{commands}

\begin{example}

\ttfamily

main-compound: \subcmpdproperty{benzene}{OH}{main-compound}\par

number: \subcmpdproperty{benzene}{OH}{number}\par

counter-representation: \subcmpdproperty{benzene}{OH}{counter-representation}

\end{example}

If you compile with the \keyis{log}{verbose} all properties of a label are

listed in the log when it is declared. This will typically look like this:

\begin{sourcecode}

.................................................

. chemnum info: defined new compound:

. ID = a

. internal number = 1

. label = A

. pre label code =

. post label code =

. pre main label code =

. post main label code =

. format = \bfseries

.................................................

\end{sourcecode}

\subsection{Initiating Labels}\label{sec:initiating-labels}

Initiating labels is not the same as declaring them although it happens

simultaneously. When a label is \emph{initiated} its \ac{id} is added to an

internal list. When a label is \emph{declared} all of its properties and

associated macros are defined. Initiating can serve two purposes:

\begin{enumerate}

\item It can help in keeping track of defined labels; if you set the option

\option{init} \chemnum\ will either issue a warning or an error (depending

on the actual setting you chose) if a label is used (and hence probably

declared) \emph{that hasn't been initiated}. This can also help in

detecting typos in label names.

\item Since the labels are declared in the preamble you don't need to worry

about a label erroneously being declared in the table of contents. This

means the variants \cs{cmpd}\sarg\ and \cs{cmpd}\code{ } shouldn't be

needed.

\end{enumerate}

Initiating is done via the command \cs{initcmpd}:

\begin{sourcecode}

\initcmpd{a,b,c,d}

\end{sourcecode}

You simply use all \acp{id} you want to use like you would use them in

\cs{cmpd}. \cs{initcmpd} also has an optional argument that allows you to set

options for those labels. Legal options are the same as for \cs{cmpd}.

Remember: \cs{initcmpd} will both initiate the labels \emph{and} declare the

labels!

\section{Overview over the Available Options}\label{sec:overv-over-avail-1}

% Except for the \option{version} option

All of the following options are either

set as options to \cs{cmpd} or \cs{initcmpd} directly or via

\cs{setchemnum}\marg{options}, each time as a comma separated list of

key/value pairs. Options that can only be set via \cs{setchemnum} are marked

with \module{general}, those that only have an effect when used with \cs{cmpd} and

friends are marked with \module{cmpd}. Those marked with \module{both} can

be set either way. The options affecting the compounds are further divided in

two classes: I named them global \module*{(g)} and local \module*{(l)}. Options

from the global class are set when a label is declared the first time and then

are a fixed property of the corresponding label. Options from the local class

can be changed at each instance of a label and will then only be active for

the one instance.

A few of the options only have an effect when used with the \cs{replacecmpd}

command. They are marked with \module{replace}.

\begin{options}

\keyval{counter-within}{counter}\Module{general}

Reset the compound numbers when \meta{counter} is stepped.

\keychoice{counter-format}{arabic,alph,Alph,roman,Roman,greek,Greek}%

\Module{both (g)}\Default{arabic}

The format of the number associated with the main compounds.

\keychoice{sub-counter-format}{arabic,alph,Alph,roman,Roman,greek,Greek}%

\Module{both (g)}\Default{alph}

The format of the number associated with the sub compounds.

\keybool{compress}\Module{both (l)}\Default{true}

If set to true a list of sublabels is compressed, \ie,

\cmpd[compress=false]{q.{one,three,four,five}} becomes

\cmpd{q.{one,three,four,five}}.

\keybool{merge}\Module{both (l)}\Default{false}

If set to true a list of labels is merged, \ie,

``\cmpd{q.five,a,q.two}'' becomes ``\cmpd[merge=true]{q.five,a,q.two}''.

\keyval{pre-label-code}{code}\Module{both (g)}\Default

Code to be inserted before a label.

\keyval{post-label-code}{code}\Module{both (g)}\Default

Code to be inserted after a label.

\keyval{pre-main-label-code}{code}\Module{both (g)}\Default

\sinceversion{1.2a}Code to be inserted before a main label.

\keyval{post-main-label-code}{code}\Module{both (g)}\Default

\sinceversion{1.2a}Code to be inserted after a main label.

\keyval{main-sub-sep}{code}\Module{both (l)}\Default{.}

The separator symbol that is used in \cs{cmpd} to separate the \meta{main

\ac{id}} from a \meta{sub \ac{id}}.

\keyval{format}{formatting commands}\Module{both (l)}\Default{\cs*{bfseries}}

The default format of the labels.

\keyval{list-label-sep}{code}\Module{both (l)}\Default{,}

The separator that is used to separate different \meta{main \acp{id}} in

\cs{cmpd}.

\keyval{sub-list-label-sep}{code}\Module{both (l)}\Default{,}

The marker that is used to split an input list of sublabels.

\keyval{list-sep-two}{code}%

\Module{both (l)}\Default{\visualizespaces{\GetTranslation{chemnum-sep-two}}}

The output separator between labels in a list that contains of two items.

\keyval{list-sep-more}{code}\Module{both (l)}\Default{\visualizespaces{, }}

The output separator between labels in a list that contains of more than

two items.

\keyval{list-sep-last-two}{code}%

\Module{both (l)}\Default{\visualizespaces{\GetTranslation{chemnum-sep-last-two}}}

The output separator between the last two labels in a list that contains

of more than two items.

\keybool{sub-only}\Module{cmpd (l)}\Default{false}

If true the command \cs{cmpd} will only print sublabels but no main

labels.

\keybool{sub-all}\Module{cmpd (l)}\Default{false}

If true the command \cs{cmpd} will print all sublabels belonging to the

corresponding main label.

\keyval{sub-list-sep-two}{code}\Module{both (l)}\Default{,}

The output separator between labels in a sublist that contains of two

items.

\keyval{sub-list-sep-more}{code}\Module{both (l)}\Default{,}

The output separator between labels in a sublist that contains of more

than two items.

\keyval{sub-list-sep-last-two}{code}\Module{both (l)}\Default{,}

The output separator between the last two labels in a sublist that

contains of more than two items.

\keyval{sub-list-sep-range}{code}\Module{both (l)}\Default{--}

The output separator between two labels in a sublist denoting a range.

This is only used when the option \option{compress} is active.

\keybool{replace-auto}\Module{general}\Default{true}

When set to true this adds an incremented integer to the replacement tag.

\keyval{replace-tag}{text}\Module{general}\Default{TMP}

The default replacement tag.

\keyval{replace-tag-nr}{int}\Module{general}\Default{1}

The\sinceversion{1.1} next number used by \cs{replacecmpd} when the

default tag is used.

\keyval{tag}{text}\Module{replace}\Default{TMP\meta{number}}

The local replacement tag. \meta{number} is incremented by one at each

use and starts with \code{1}. The starting number can be changed with the

option \option{replace-tag-nr}. The increment happens locally.

\keyval{replace-style}{code}\Module{general}\Default{\cs*{sffamily}}

Additional \TeX\ code that it placed before the \cs{cmpd} command in the

replacement.

\keyval{style}{code}\Module{replace}\Default{\cs*{sffamily}}

Local additional \TeX\ code that it placed before the \cs{cmpd} command in

the replacement.

\keychoice{replace-pos}{\marg{\TeX\ pos}\marg{\ac{ps}

pos}}\Module{general}\Default{bb}

Options for \pkg{psfrag}'s \cs{psfrag}.

\keychoice{pos}{\marg{\TeX\ pos}\marg{\ac{ps}

pos}}\Module{replace}\Default{bb}

Local options for \pkg{psfrag}'s \cs{psfrag}.

\keychoice{init}{\default{true},main,false,strict,main-strict}%

\Module{general}\Default{false}

Determines how labels have to be initiated. \code{false} means that

labels are initiated when they're used the first time in the text.

\code{true} means that labels should be initiated in the preamble with

\cs{initcmpd}. \code{main} is the same as \code{true} but only for main

labels. \code{strict} means that if an un-initiated label is used an

error is thrown. \code{main-strict} is the same as \code{strict} but only

for main labels.

\keychoice{log}{\default{true},false,silent,verbose}\Module{general}\Default{false}

Determines how the declaration of the labels will be logged. \code{false}

means that no information is written to the \code{.log} file. \code{true}

means that basic information is written to the \code{.log} file when a

label or a sublabel is declared. \code{silent} is an alias of

\code{true}. \code{verbose} means that detailed information is written to

the \code{.log} file when a label or a sublabel is declared.

\keychoice{show-keys}{\default{true},false,def,ref}\Module{general}\Default{false}

This option will write visual hints when a label is defined (choices

\code{true} or \code{def}) or when a label is referenced (choices

\code{true} or \code{ref}).

\keybool{hyperlinks}\Module{general}\Default{false}

\sinceversion{1.2}When package \pkg{hyperref} is loaded and this option is

set to \code{true} then each main label links back to the first time it

has been used (\ie, it has been labelled \emph{and} printed).

\end{options}

\section{The Counter Settings}\label{sec:counter-settings}

The default setting for main labels is arabic numbering which is the most

common use case for compound labels. There are however cases when you might

want a different numbering. The numbering also is not reset in a document. I

have heard of cases where this might be desirable, though. This section will

tell you how you can achieve those things.

\subsection{Change the Numbering}\label{sec:change-numbering}

The counter representation used for the main and the sublabels can be changed

using the following options:

\begin{options}

\keychoice{counter-format}{arabic,alph,Alph,roman,Roman,greek,Greek}%

\Module{general}\Default{arabic}

The format of the number associated with the main compounds.

\keychoice{sub-counter-format}{arabic,alph,Alph,roman,Roman,greek,Greek}%

\Module{general}\Default{alph}

The format of the number associated with the sub compounds.

\end{options}

Those options can be set globally with \cs{setchemnum} or localized for the

single compounds.

\begin{example}[side-by-side]

\cmpd[counter-format=Alph]{Alpha} and

\cmpd[counter-format=greek]{greek}

\end{example}

While it may not be necessary very often to change the default setting one

could image cases where it makes sense, \eg, Greek sublabels for the anomers

of a carbohydrate.

\begin{example}

% this example uses the `chemfig' package

\definesubmol{r}{(-[4]H)(-[0]OH)}

\definesubmol{l}{(-[0]H)(-[4]HO)}

\labelcmpd[sub-counter-format=greek]{glucose.{alpha,beta}}

\labelcmpd{glucose.chain}

\centering

\schemestart

\small\chemfig{

?(-[:-170]HO)

-[:-50](-[:170]HO)

-[:10](-[:-55,0.7]OH)

-[:-10](-[6,0.8]OH)

-[:130]O-[:-170]?(-[:150,0.7]-[2,0.7]OH)

}

\arrow(alpha--chain){<=>}

\small\chemfig{[6]O=^[5]-!r-!l-!r-!r--[7]OH}

\arrow(--beta){<=>}

\small\chemfig{

?(-[:-170]HO)

-[:-50](-[:170]HO)

-[:10](-[:-55,0.7]OH)

-[:-10](-[:10]OH)(-[6,,,,draw=none]\vphantom{OH})

-[:130]O-[:-170]?(-[:150,0.7]-[2,0.7]OH)

}

\arrow(@chain--chainlabel){0}[-90,.2] \cmpd{glucose.chain}

\arrow(@chainlabel--){0}[,2.5] \cmpd{glucose.beta}

\arrow(@chainlabel--){0}[180,2.3] \cmpd{glucose.alpha}

\schemestop

\end{example}

Should it ever be necessary to use another kind of counter representations

than the ones already provided they can be added with this command:

\begin{commands}

\command{newcmpdcounterformat}[\marg{name}\marg{code}]

Makes the label format \meta{name} known to \chemnum. \meta{code}

needs to end with a command that takes an integer number as mandatory

argument and should return a formatted version of it.

\end{commands}

The \code{arabic} and \code{alph} counter settings for example could have been

defined like this:

\begin{sourcecode}

\newcmpdcounterformat{arabic}{\@arabic}

\newcmpdcounterformat{alph} {\@alph}

\end{sourcecode}

This is actually not true: since \chemnum\ is written in expl3 the

corresponding \cs*{int\_to\_\meta{\ldots}} functions have been used.

Although the name of the command suggests otherwise it can be used to

overwrite the default definitions.

\subsection{Reset the Numbering}\label{sec:reset-numbering}

There are cases when it actually might make sense to reset the counting of the

compound labels. For this you can use this command:

\begin{commands}

\command{resetcmpd}[\oarg{integer}]\Default{1}

Reset the numbering for main compound labels to start with \meta{integer}

again. This is the same as

\cs*{setcounter}\Marg{cmpdmain}\Marg{$\text{\meta{integer}}-1$} which

means the change is global!

\end{commands}

Be careful, though. You might end up with the same number for different

compounds:

\begin{example}

\resetcmpd The numbering starts with 1 again: \cmpd{h,i,j}, but:

two compounds with the same label: \cmpd{a,h}

\end{example}

\section{Formatting Labels}\label{sec:formatting-labels}

As you will have noticed by now labels are typeset with a bold face with the

default setting of \chemnum. This can be changed:

\begin{options}

\keyval{format}{formatting commands}\Module{both (l)}\Default{\cs*{bfseries}}

The default format of the labels.

\end{options}

This options works in two ways: it sets the default format that is picked up

by a compound label when it is defined. When you change it later already

defined labels dont change:

\begin{example}[side-by-side]

\setchemnum{format=\itshape}

\cmpd{a,b} and \cmpd{new}

\end{example}

If it is applied directly to the \cs{cmpd} command it changes the formatting

for this usage of the command only, regardless if the label is new or not:

\begin{example}[side-by-side]

\cmpd[format=\itshape]{a,b} vs

\cmpd{a,b}

\end{example}

There is more that you can do. Maybe you want to enclose labels in

parentheses?

\begin{example}

\cmpd[pre-label-code=(,post-label-code=)]{x, y, z.one }

\end{example}

Please note that these options only have an effect for \emph{newly defined}

labels since they belong to a label's properties.

Other options are the customization of the list separators:

\begin{options}

\keyval{list-sep-two}{code}%

\Module{general}\Default{\visualizespaces{\GetTranslation{chemnum-sep-two}}}

The output separator between labels in a list that contains of two items.

\keyval{list-sep-more}{code}\Module{general}\Default{\visualizespaces{, }}

The output separator between labels in a list that contains of more than

two items.

\keyval{list-sep-last-two}{code}%

\Module{general}\Default{\visualizespaces{\GetTranslation{chemnum-sep-last-two}}}

The output separator between the last two labels in a list that contains

of more than two items.

\end{options}

\begin{example}

\setchemnum{list-sep-two=;,list-sep-more=;,list-sep-last-two=;}

\cmpd{a, b, c, d}

\end{example}

In the default settings these separators are language dependent. Setting them

explicitly will overwrite the language sensitivity. If you only want to adapt

the separators to your language have a look at

section~\ref{sec:lang-depend-sett}.

\section{Replacing Tags in \ac{eps} or \ac{ps} Files}\label{sec:replacing-tags-eps-ps}

Although it is quite possible to create reaction schemes within \LaTeX\

directly -- for example with the \pkg{chemfig} package~\cite{pkg:chemfig} --

many people prefer to use a program such as \textsc{ChemDraw} for it. In

order to be able to use the labels with such schemes as well the following

method is usually used:

\begin{itemize}

\item Create the scheme and place temporary tags like \code{TMP1},

\code{TMP2} and so on where you want the compound labels to be.

\item Export the scheme as \ac{eps} or \ac{ps} figure \emph{where you make

sure that the tags are embedded as text strings}. If the tags are not

present as text strings they cannot be replaced. This is a common source

of user problems.

\item Include the \ac{eps} with \cs*{includegraphics}. Right before that

use \cs{replacecmpd} once for every temporary tag.

\end{itemize}

\emph{For the actual replacement please make sure that you compile with

\code{shell-escape} enabled. If you compile with \code{pdflatex} you

probably also need \pkg{auto-pst-pdf}~\cite{pkg:auto-pst-pdf} loaded. In

subsequent runs load it with option \code{off} when you turned off

\code{shell-escape}.}

\begin{commands}

\command{replacecmpd}[\code{ }\oarg{options}\marg{\ac{id}}]

Replaces a tag in the following \ac{eps} file. This command doesn't have

an optional star otherwise the syntax is the same as with \cs{cmpd}.

\end{commands}

Figure~\ref{fig:scheme-tmp-tags} shows a scheme with temporary tags. It is

produced with the following code where the class \cls{standalone} has been

used to get the figure only:

\begin{example}[compile,exe-with={--shell-escape},runs=1,float=htbp,caption={A scheme with

temporary tags.\label{fig:scheme-tmp-tags}}]

% code for figure 1

\documentclass{standalone}

\usepackage{graphicx,auto-pst-pdf}

\begin{document}

\includegraphics{scheme-tmp.ps}

\end{document}

\end{example}

The tags now can be replaced with labels. The result is shown in

figure~\ref{fig:scheme-tmp-tags-replaced}.

\begin{example}[compile,exe-with={--shell-escape},runs=1,float=htbp,caption={A scheme with

temporary tags replaced with labels.\label{fig:scheme-tmp-tags-replaced}}]

% code for figure 2 -- compiled with shell-escape enabled

\documentclass{standalone}

\usepackage{graphicx,auto-pst-pdf,chemnum}

\begin{document}

\replacecmpd{Alc}% replaces TMP1

\replacecmpd{EtherBr}% replaces TMP2

\includegraphics{scheme-tmp.ps}

\end{document}

\end{example}

The replacement is done with the help of the \pkg{psfrag}

package~\cite{pkg:psfrag} and its \cs{psfrag} command. For details on this

package and its command I refer to its documentation.

Although the examples don't do it the usage of \cs{replacecmpd} and the

corresponding graphic file should be placed inside a group (probably a

\env*{figure} or a \env*{scheme} environment) in order to keep the stepping of

the tag number local: this allows to use the same tags \code{TMP1},

\code{TMP2}, \ldots, in the next figure again.

As you can see the labels are printed sans serif. This setting can of course

be changed. The complete list of options is this:

\begin{options}

\keybool{replace-auto}\Module{general}\Default{true}

When set to true this adds an incremented integer to the replacement tag.

\keyval{replace-tag}{text}\Module{general}\Default{TMP}

The default replacement tag.

\keyval{replace-tag-nr}{int}\Module{general}\Default{1}

The\sinceversion{1.1} next number used by \cs{replacecmpd} when the

default tag is used.

\keyval{tag}{text}\Module{replace}\Default{TMP\meta{number}}

The local replacement tag. \meta{number} is incremented by one at each

use and starts with \code{1}. The starting number can be changed with the

option \option{replace-tag-nr}. The increment happens locally.

\keyval{replace-style}{code}\Module{general}\Default{\cs*{sffamily}}

Additional \TeX\ code that it placed before the \cs{cmpd} command in the

replacement.

\keyval{style}{code}\Module{replace}\Default{\cs*{sffamily}}

Local additional \TeX\ code that it placed before the \cs{cmpd} command in

the replacement.

\keychoice{replace-pos}{\marg{\TeX\ pos}\marg{\ac{ps}

pos}}\Module{general}\Default{bb}

Options for \pkg{psfrag}'s \cs{psfrag}.

\keychoice{pos}{\marg{\TeX\ pos}\marg{\ac{ps}

pos}}\Module{replace}\Default{bb}

Local options for \pkg{psfrag}'s \cs{psfrag}.

\end{options}

If you have a scheme with arbitrary tabs like in

figure~\ref{fig:scheme-bla-tags} you can specify the \option{tag} option to

\cs{replacecmpd}. Figure~\ref{fig:scheme-bla-tags-replaced} demonstrates

this. It also demonstrates that you can of course use sublabels in the

\cs{replacecmpd} command.

\begin{example}[compile,exe-with={--shell-escape},runs=1,float=htbp,caption={A scheme with

arbitrary tags.\label{fig:scheme-bla-tags}}]

% code for figure 3

\documentclass{standalone}

\usepackage{graphicx,auto-pst-pdf}

\begin{document}

\includegraphics{scheme-bla.ps}

\end{document}

\end{example}

If you don't want to use \code{TMP\meta{number}} as temporary tags but for

example \code{temp\meta{number}} you can change this with following option:

\begin{sourcecode}

\setchemnum{replace-tag=temp}

\end{sourcecode}

The options \option{pos} and \option{replace-pos} refer to \cs{psfrag}'s

optional arguments which determine the positioning of the \TeX\ box with

respect to the \ac{ps} box that is replaced. This is described in

\pkg{psfrag}'s documentation.

\begin{example}[compile,exe-with={--shell-escape},runs=1,float=htbp,caption={A scheme with

arbitrary tags replaced with labels.\label{fig:scheme-bla-tags-replaced}}]

% code for figure 4 -- compiled with shell-escape enabled

\documentclass{standalone}

\usepackage{graphicx,auto-pst-pdf,chemnum}

\begin{document}

\setchemnum{replace-style=\itshape}

\replacecmpd[tag=blah]{main}% replaces blah

\replacecmpd[tag=blub]{main.sub}% replaces blub

\includegraphics{scheme-bla.ps}

\end{document}

\end{example}

\section{Changing the Input Markers}\label{sec:chang-input-mark}

In \chemnum's labels there are two markers (or three, actually) that can't be

part of a label name: the comma \code{,} and the dot \code{.}. You can change

them with options:

\begin{options}

\keyval{list-label-sep}{token}\Module{general}\Default{,}

The marker that is used to split an input list of main labels.

\keyval{sub-list-label-sep}{token}\Module{general}\Default{,}

The marker that is used to split an input list of sublabels.

\keyval{main-sub-sep}{token}\Module{general}\Default{.}

The marker that divides sublabels from main labels.

\end{options}

\begin{example}[side-by-side]

\setchemnum{

main-sub-sep = ! ,

list-label-sep = ;

}

\cmpd{a; b; c; e; g!two} \par