diff options
| -rw-r--r-- | Master/texmf-dist/doc/latex/carbohydrates/README | 33 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.pdf | bin | 0 -> 478777 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.tex | 375 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/latex/carbohydrates/test.tex | 143 | ||||
| -rw-r--r-- | Master/texmf-dist/tex/latex/carbohydrates/carbohydrates.sty | 874 | ||||
| -rwxr-xr-x | Master/tlpkg/bin/tlpkg-ctan-check | 2 | ||||
| -rw-r--r-- | Master/tlpkg/tlpsrc/carbohydrates.tlpsrc | 0 | ||||
| -rw-r--r-- | Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc | 1 |
8 files changed, 1427 insertions, 1 deletions
diff --git a/Master/texmf-dist/doc/latex/carbohydrates/README b/Master/texmf-dist/doc/latex/carbohydrates/README new file mode 100644 index 00000000000..9d9c162a3af --- /dev/null +++ b/Master/texmf-dist/doc/latex/carbohydrates/README @@ -0,0 +1,33 @@ +-------------------------------------------------------------------------- +the CARBOHYDRATES package v0.1 2015/12/01 + + ready drawn carbohydrates with chemfig + +-------------------------------------------------------------------------- +Clemens Niederberger +Web: https://github.com/cgnieder/carbohydrates/ +E-Mail: contact@mychemistry.eu +-------------------------------------------------------------------------- +Copyright 2014-2015 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. +-------------------------------------------------------------------------- +The carbohydrates package consists of the files + - carbohydrates.sty + - carbohydrates_en.tex, carbohydrates_en.pdf + - README +-------------------------------------------------------------------------- +If you have any ideas, questions, suggestions or bugs to report, please +feel free to contact me. +-------------------------------------------------------------------------- + diff --git a/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.pdf b/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.pdf Binary files differnew file mode 100644 index 00000000000..317bd283ed6 --- /dev/null +++ b/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.pdf diff --git a/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.tex b/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.tex new file mode 100644 index 00000000000..4da1156d2a9 --- /dev/null +++ b/Master/texmf-dist/doc/latex/carbohydrates/carbohydrates_en.tex @@ -0,0 +1,375 @@ +% arara: pdflatex +% arara: biber +% arara: pdflatex +% arara: pdflatex +\documentclass[load-preamble+]{cnltx-doc} +\usepackage[utf8]{inputenc} +\usepackage{carbohydrates} + +\setcnltx{ + package = {carbohydrates} , + authors = Clemens Niederberger , + email = contact@mychemistry.eu , + info = {carbohydrate molecules with \pkg*{chemfig}} , + url = https://github.com/cgnieder/carbohydrates/ , + abstract = {% + \carbohydrates\ offers macros for making exercise sheets when teaching + carbohydrate chemistry a lot less tedious. It uses \pkg{chemfig} for + drawing the formulas. + } , + add-cmds = { + allose , altrose , arabinose , + carbohydrate , + desoxyribose , + erythrose , + galactose , glucose , glycerinaldehyde , gulose , + idose , + lyxose , + mannose , + newaldose , + ribose , + setcarbohydrates , setcarbohydratedefaults , + talose , threose , + xylose + } , + add-silent-cmds = { + arrow , + bondboldwidth , bondhashlength , bondwidth , + D , + chemfig , chemname , chemnameinit , + definesubmol , + iupac , + printatom , + schemestart , schemestop , setatomsep , setbondoffset , setbondstyle , + setcrambond , setdoublesep + } , + index-setup = { othercode = \footnotesize , level = \addsec } , + makeindex-setup = { columns = 3 , columnsep = 1em } +} + +\defbibheading{bibliography}[References]{\addsec{#1}} +\addbibresource{\jobname.bib} + +\usepackage{filecontents} +\begin{filecontents*}{\jobname.bib} +@online{texdev, + url = {http://www.texdev.net/} , + urldate = {2014-04-25} , + author = {Joseph Wright} +} +\end{filecontents*} + +\usepackage{varioref} + +\usepackage{chemmacros} +\chemsetup{greek=newtx} +\newcommand*{\bondwidth}{0.06642 em} +\newcommand*{\bondboldwidth}{0.22832 em} +\newcommand*{\bondhashlength}{0.25737 em} +\setdoublesep{0.35700 em} +\setatomsep{1.78500 em} +\setbondoffset{0.18265 em} +\setbondstyle{line width = \bondwidth} +\setcrambond + {\dimexpr\bondwidth*2 + \bondboldwidth\relax} + {\bondwidth} + {\bondhashlength} +\renewcommand*\printatom[1]{{\small\ensuremath{\mathsf{#1}}}} + +\usepackage{rotating,array,tabu,booktabs} + +\defabbr\vs{\cnltxlatin{vs}} + +\begin{document} + +\section{Licence and Requirements} +\license + +\carbohydrates\ loads the packages \pkg{chemfig}~\cite{pkg:chemfig}, +\pkg{etoolbox}~\cite{pkg:etoolbox} and \pkg{xcolor}~\cite{pkg:xcolor}. + +\section{The Idea} +When teaching chemistry -- and in the case of this package: carbohydrate +chemistry -- you have to show many examples of the basic aldoses and you have +to explain the Fischer and the Haworth representation as well. This means you +may have nearly the same \pkg{chemfig}~\cite{pkg:chemfig} formulas over and +over in your documents. \carbohydrates\ aims to ease this task. + +The following example will give a short impression of what the package does: +\begin{example} + \glucose + \glucose[model={fischer=skeleton}] + \setatomsep{2.5em} + \glucose[model=haworth,ring] + \glucose[model=haworth,ring=furanose] +\end{example} + +\section{Usage} +\subsection{The Base Macro} +\begin{commands} + \command{carbohydrate}[\oarg{options}\marg{spec}] + A generic macro for typesetting carbohydrates. +\end{commands} +We will talk about the options in a bit. First lets see what \meta{spec} +means. This argument is a series of the tokens \code{r}, \code{l} and +\code{0} denoting an hydroxy group placed to the right or the left in the +Fischer projection of the carbohydrate. A \code{0} means that the hydroxy +group is to be left out. The series of tokens is meant to describe the +hydroxy groups at the chiral centers. The aldehyde group\footnote{Also the + keto group once ketoses will be implemented.} and the hydroxy group at the +end of the chain will be set automatically. Unless specified otherwise the +command expects a hexose which means a series of \emph{four} tokens. + +\begin{example} + \chemname{\carbohydrate{llrr}}{\iupac{\D-Mannose}} + \chemname{\carbohydrate[model={fischer=skeleton}]{llrr}}{\iupac{\D-Mannose}} + \setatomsep{2.5em}\chemnameinit{} + \chemname{\carbohydrate[model=chair]{llrr}}{\iupac{\D-Mannose}} + \chemname{\carbohydrate[model=haworth]{llrr}}{\iupac{\D-Mannose}} +\end{example} + +Adding the option \option{pentose} means that now only \emph{three} tokens +need to be specified. + +\begin{example} + \chemname{\carbohydrate[pentose]{rlr}}{\iupac{\D-Xylose}} + \chemname{\carbohydrate[pentose,model={fischer=skeleton}]{rlr}}{\iupac{\D-Xylose}} + \setatomsep{2.5em}\chemnameinit{} + \chemname{\carbohydrate[pentose,model=haworth,ring]{rlr}}{\iupac{\D-Xylose}} + \chemname{\carbohydrate[pentose,model=haworth,ring=pyranose]{rlr}}{\iupac{\D-Xylose}} +\end{example} + +\subsection{Available Options} +As you have already seen in the pevious examples \cs{carbohydrate} has an +optional argument that takes different options. Here is a complete list: +\begin{options} + % model/fischer/skeleton/.code = \def\cbhdr@model{fischer@skeleton} , + % model/fischer/full/.code = \def\cbhdr@model{fischer} , + \keychoice{model}{fischer,haworth,chair}\Default{fischer} + The model to be used to draw the molecule. The choice \option{fischer} + is itself an option with two choices: \keyis{fischer}{skeleton} and + \keyis{fischer}{full}. Leaving the choice out will use \code{full} as + default choice. + \opt{chain} + Draw the open chain isomer. + \keychoice{ring}{\default{true},pyranose,furanose} + Draw a ring isomer. If you don't specify what ring type should be drawn + (\ie, if you choose \code{true}) the default depends on the length of the + carbohydrate. For example for hexoses the default ring type is + \code{pyranose}. + \keychoice{anomer}{alpha,beta,undetermined}\Default{alpha} + The ring anomer. + \keychoice{length}{6,5,4,3}\Default{6} + The length of the carbohydrate. \keyis{length}{6} draws a hexose, + \keyis{length}{3} draws a triose. + \opt{hexose} + An alias for \keyis{length}{6}. + \opt{pentose} + An alias for \keyis{length}{5}. + \opt{tetrose} + An alias for \keyis{length}{4}. + \opt{triose} + An alias for \keyis{length}{3}. + \keybool{3d}\Default{false} + Draw some of the bonds of the rings in the \code{haworth} and \code{chair} + models in a way that indicates the three dimensional structure of the + molecules. + \keylit-{color}{\marg{name}\marg{color}} + This option takes two arguments: \meta{name} specifies which part of the + molecule is to be colored, \meta{color} specifies the color to be used, + also see table~\vref{tab:color} and section~\ref{sec:colors}. +\end{options} + +\begin{table}[htb] + \centering + \caption{Available names for the \option*{color} option.}\label{tab:color} + \begin{tabular}{>{\ttfamily}ll} + \toprule + \rmfamily\bfseries Name & \bfseries Function \\ + \midrule + C1 & carbon 1 \\ + C2 & carbon 2 \\ + O-C2 & oxygen of the hydroxy group at carbon 2 \\ + H-C2 & hydrogen of the hydroxy group at carbon 2 \\ + C3 & carbon 3 \\ + O-C3 & oxygen of the hydroxy group at carbon 3 \\ + H-C3 & hydrogen of the hydroxy group at carbon 3 \\ + C4 & carbon 4 \\ + O-C4 & oxygen of the hydroxy group at carbon 4 \\ + H-C4 & hydrogen of the hydroxy group at carbon 4 \\ + C5 & carbon 5 \\ + O-C5 & oxygen of the hydroxy group at carbon 5 \\ + H-C5 & hydrogen of the hydroxy group at carbon 5 \\ + C6 & carbon 6 \\ + O-C6 & oxygen of the hydroxy group at carbon 6 \\ + H-C6 & hydrogen of the hydroxy group at carbon 6 \\ + anomerO & oxygen of the anomeric hydroxy group\slash aldehyde oxygen \\ + anomerH & hydrogen of the anomeric hydroxy group \\ + ringO & oxygen in the ring \\ + \bottomrule + \end{tabular} +\end{table} + +\subsection{Defining Shortcuts}\label{sec:defining-shortcuts} + +\carbohydrates\ allows to define shortcuts for aldoses: + +\begin{commands} + \command{newaldose}[\marg{cs}\oarg{options}\marg{spec}] + This defines the macro \meta{cs} with preset options \meta{options}. + \meta{spec} has the same meaning as for \cs{carbohydrate}. + \command{renewaldose}[\marg{cs}\oarg{options}\marg{spec}] + The same command but redefines an existing macro. +\end{commands} + +In fact, \carbohydrates\ already defines macros for the common aldoses. They +are listed in table~\ref{tab:predefined-aldoses} on +page~\pageref{tab:predefined-aldoses}. They don't have any predefined options +(except for \option{hexose}, \option{pentose} \etc). + +\begin{sidewaystable} + \setcarbohydrates{model={fischer=skeleton}} + \caption{Overview over the predefined aldoses.} + \label{tab:predefined-aldoses} + \begin{tabu}{*{8}{X[c]<{\strut}}} + \toprule + \allose & \altrose & \glucose & \mannose & + \gulose & \idose & \galactose & \talose \\ + \cs{allose} & \cs{altrose} & \cs{glucose} & \cs{mannose} & + \cs{gulose} & \cs{idose} & \cs{galactose} & \cs{talose} \\ + \iupac{\D-Allose} & \iupac{\D-Altrose} & + \iupac{\D-Glucose} & \iupac{\D-Mannose} & + \iupac{\D-Gulose} & \iupac{\D-Idose} & + \iupac{\D-Galactose} & \iupac{\D-Talose} \\ + \midrule + \ribose & \arabinose & \xylose & \lyxose & \desoxyribose \\ + \cs{ribose} & \cs{arabinose} & \cs{xylose} & \cs{lyxose} & + \multicolumn{2}{l}{\cs{desoxyribose}} \\ + \iupac{\D-Ribose} & \iupac{\D-Arabinose} & + \iupac{\D-Xylose} & \iupac{\D-Lyxose} & + \iupac{\D-Desoxy|ribose} \\ + \midrule + \erythrose & \threose & \glycerinaldehyde \\ + \cs{erythrose} & \cs{threose} & \multicolumn{2}{l}{\cs{glycerinaldehyde}} \\ + \iupac{\D-Erythrose} & \iupac{\D-Threose} & + \iupac{\D-Glycerin|aldehyde} \\ + \bottomrule + \end{tabu} +\end{sidewaystable} + +\subsection{Available Models}\label{sec:available-models} + +\carbohydrates\ implements different models for drawing carbohydrates: +\begin{itemize} + \item Fischer -- skeleton: the Fischer representation with only a skeleton + formula. + \item Fischer -- full: the Fischer representation including all C and H + atoms. + \item Haworth: the Haworth representation. + \item Chair: the chair conformation. +\end{itemize} + +While the Fischer model is implemented for all carbohydrates both Haworth and +chair are not. The chair model is only implemented for aldohexoses, Haworth +is implemented for aldotetroses, -pentoses and -hexoses. + +\begin{example} + \glucose[model={fischer=skeleton}] + \glucose[model={fischer=full}] + \setatomsep{2.5em} + \glucose[model=haworth] + \glucose[model=chair] +\end{example} + +\subsection{Chain \vs\ Ring Forms} + +While the chain forms are available in all models the ring forms obviously +aren't. There are two ring forms for hexoses and pentoses: pyranoses and +furanoses. For tetroses only the furanose rings are available as there don't +exist pyranose ring forms (for obvious reasons). It is also clear that +neither pyranose nor furanose forms of trioses exist. + +\begin{example} + \setatomsep{2.5em} + \glucose[model=haworth,ring] + \ribose[model=haworth,ring] + \threose[model=haworth,ring] +\end{example} + +\textbf{Actually the above is not true: the chain forms are not available in all +models for all aldoses. As said in section~\ref{sec:available-models} the +chair model is only implemented for aldohexoses. Also chains are not +implemented for tetroses and trioses in the Haworth model.} + +\subsection{Default Settings} +\begin{commands} + \command{setcarbohydrate}[\marg{options}] + Set package options for all carbohydrates within the current scope. + \command{setcarbohydratedefaults}[\marg{csname}\marg{options}] + Set options for a predefined carbohydrate within the current scope. The + first argument \meta{csname} is the macro name of the shortcut (see + section~\ref{sec:defining-shortcuts}). +\end{commands} + +\begin{example} + \setatomsep{2.5em} + \setcarbohydratedefaults\glucose{ring,model=haworth,anomer=undetermined} + \glucose\ + \mannose +\end{example} + +\subsection{Colors}\label{sec:colors} +For educating purposes it may be useful to be able to color certain atoms. The +\option{color} option allows this. +\begin{example} + \setcarbohydrates{model=chair} + \setatomsep{2.5em} + \schemestart + \glucose[color={anomerO}{red},color={O-C5}{green},color={H-C5}{blue}] + \arrow{<=>} + \glucose[ring,color={anomerO}{red},color={ringO}{green},color={anomerH}{blue}] + \schemestop +\end{example} + +\section{\texorpdfstring{\textsc{todo}}{TODO}s} +There are still quite a number of missing features that I'd like to implement +some day such as +\begin{itemize} + \item ring forms for \laevus-carbohydrates, + \item support for both chair conformations and the boat conformation, + \item support for ketoses, + \item support for oxidized and reduzed forms, and + \item disaccharides. +\end{itemize} +There is \emph{no} time table, though -- wether these features will be implemented +any time soon or at all is undecided. + +\section{About the Examples in this Manual} +All macros used in the examples either belong to \carbohydrates\ and are +described in this manual or they belong to either +\pkg{chemfig}~\cite{pkg:chemfig}, \pkg{chemmacros}~\cite{pkg:chemmacros}, +\pkg{chemformula}~\cite{pkg:chemformula}, or are standard \LaTeX\ macros. I +encourage you to take a look at the packages for typesetting chemistry +documents. + +The \pkg{chemfig} settings have been adjusted for the examples in this +manual. Specifically the preamble of this document makes these settings: + +\begin{sourcecode} + \newcommand*{\bondwidth}{0.06642 em} + \newcommand*{\bondboldwidth}{0.22832 em} + \newcommand*{\bondhashlength}{0.25737 em} + \setdoublesep{0.35700 em} + \setatomsep{1.78500 em} + \setbondoffset{0.18265 em} + \setbondstyle{line width = \bondwidth} + \setcrambond + {\dimexpr\bondwidth*2 + \bondboldwidth\relax} + {\bondwidth} + {\bondhashlength} + \renewcommand*\printatom[1]{{\small\ensuremath{\mathsf{#1}}}} +\end{sourcecode} +These settings are taken from~\cite{texdev}. Search the page for +\code{chemfig} and you should be able to find them there. + +\end{document} diff --git a/Master/texmf-dist/doc/latex/carbohydrates/test.tex b/Master/texmf-dist/doc/latex/carbohydrates/test.tex new file mode 100644 index 00000000000..a5bd6041f57 --- /dev/null +++ b/Master/texmf-dist/doc/latex/carbohydrates/test.tex @@ -0,0 +1,143 @@ +\documentclass{scrartcl} +\usepackage{carbohydrates} +% \setcarbohydrates{ +% color={anomerO}{red} , +% color={anomerH}{blue} , +% color={ringO}{green} , +% color={C2}{yellow} , +% color={O-C2}{yellow} , +% color={H-C2}{yellow} , +% color={C5}{purple} , +% color={O-C5}{purple} , +% color={H-C5}{purple} , +% color={C6}{orange} , +% color={O-C6}{orange} , +% color={H-C6}{orange} +% } + +\begin{document} + +\setcarbohydrates{model=chair} +\schemestart + \glucose[color={anomerO}{red},color={O-C5}{green},color={H-C5}{blue}] + \arrow{<=>} + \glucose[ring,color={anomerO}{red},color={ringO}{green},color={anomerH}{blue}] +\schemestop + +\end{document} + +\documentclass{scrartcl} + +\usepackage{carbohydrates} +\colorlet{cbhdr@anomerO}{green} +\colorlet{anomerH}{blue} +\colorlet{cbhdr@ringO}{red} +\colorlet{cbhdr@O-C5}{orange} +\colorlet{cbhdr@H-C5}{yellow} + +\begin{document} + +\glucose[model=haworth,chain] + +\ribose[model=haworth,chain] + +\ribose[model=haworth,ring] + +\end{document} + +\glucose[model={fischer=skeleton}] +\quad +\glucose[model={fischer=skeleton},ring] + +\bigskip + +\threose[model={fischer=skeleton}] +\quad +\threose[ring,model=haworth] + +% \glycerinaldehyde[ring] + +\bigskip + +\ribose[ring=pyranose] +\quad +\ribose[model=haworth,ring] +\quad +\ribose[model=haworth,ring=pyranose] + +\bigskip + +\carbohydrate[model=haworth,ring=furanose,]{l0ll} + +\end{document} +% \makeatletter + +\glucose +\quad +\glucose[ring] +\quad +\glucose[ring,anomer=beta] + +\bigskip + +\glucose[ring=furanose] +\quad +\glucose[ring=furanose,model=haworth] +\quad +\galactose[ring=furanose,model=haworth] + +\end{document} + +\bigskip + +\glucose[model={fischer=skeleton}] +\quad +\glucose[model={fischer=skeleton},ring] +\quad +\glucose[model={fischer=skeleton},ring,anomer=beta] + +\bigskip + +\glucose[model=haworth] +\quad +\glucose[model=haworth,ring] +\quad +\glucose[model=haworth,ring,anomer=beta] + +\bigskip + +\glucose[model=chair] +\quad +\glucose[model=chair,ring] +\quad +\glucose[model=chair,ring,anomer=beta] + +\glucose[model=haworth,ring,anomer=undetermined] + +\bigskip + +\idose[model=haworth] +\quad +\idose[model=haworth,ring] +\quad +\idose[model=haworth,ring,anomer=beta] + +\bigskip + +\idose[model=chair] +\quad +\idose[model=chair,ring] +\quad +\idose[model=chair,ring,anomer=beta] + +\bigskip + +\ribose +\quad +\desoxyribose +\quad +\desoxyribose[model={fischer=skeleton},ring] + + +\end{document} + diff --git a/Master/texmf-dist/tex/latex/carbohydrates/carbohydrates.sty b/Master/texmf-dist/tex/latex/carbohydrates/carbohydrates.sty new file mode 100644 index 00000000000..2e1814bab76 --- /dev/null +++ b/Master/texmf-dist/tex/latex/carbohydrates/carbohydrates.sty @@ -0,0 +1,874 @@ +% -------------------------------------------------------------------------- +% the CARBOHYDRATES package +% +% ready drawn carbohydrates with chemfig +% +% -------------------------------------------------------------------------- +% Clemens Niederberger +% Web: https://github.com/cgnieder/carbohydrates +% E-Mail: contact@mychemistry.eu +% -------------------------------------------------------------------------- +% Copyright 2014-2015 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. +% -------------------------------------------------------------------------- +% If you have any ideas, questions, suggestions or bugs to report, please +% feel free to contact me. +% -------------------------------------------------------------------------- +\def\cbhdr@date{2015/12/01} +\def\cbhdr@version{v0.1} +\def\cbhdr@info{carbohydrate molecules with chemfig} + +\ProvidesPackage{carbohydrates}[% + \cbhdr@date\space + \cbhdr@version\space + \cbhdr@info\space (CN)] + +\RequirePackage{etoolbox} +\RequirePackage{chemfig,xcolor} + +% ========================================================================== +% message handling +% generic help message: +\newrobustcmd\cbhdr@create@message[2]{% + \ifstrequal{#1}{Error} + {% + \lowercase{\csdef{cbhdr@#1}}##1{% + \csuse{Package#1}{carbohydrates}{##1}{#2}}% + }{% + \lowercase{\csdef{cbhdr@#1}}##1{% + \csuse{Package#1}{carbohydrates}{##1}}% + }} + +\newcommand*\cbhdr@error@message{% + For details have a look at the `carbohydrates' manual.% +} + +% create message macros: +\cbhdr@create@message{Error}{\cbhdr@error@message} +\cbhdr@create@message{Warning}{} +\cbhdr@create@message{WarningNoLine}{} +\cbhdr@create@message{Info}{} + +\newcommand*\cbhdr@ring@error[2]{% + \cbhdr@error{#1 can't form #2 rings}% +} + +\newcommand*\cbhdr@define@ring@error[3]{% + \protected\csdef{cbhdr@aldo#2@#1@ring@#3}{\cbhdr@ring@error{#2s}{#3}}% +} + +\newcommand*\cbhdr@define@chain@error[2]{% + \protected\csdef{cbhdr@aldo#2@#1@chain}{% + \cbhdr@error{The chain is not implemented for #2s in the #1 model}% + }% +} + +\newcommand*\cbhdr@chair@error[1]{% + \cbhdr@error{The chair model is not implemented for #1}% +} + +\newcommand*\cbhdr@define@chair@errors[1]{% + \protected\csdef{cbhdr@aldo#1@chair@chain}{\cbhdr@chair@error{#1s}}% + \protected\csdef{cbhdr@aldo#1@chair@ring@pyranose}{\cbhdr@chair@error{#1s}}% + \protected\csdef{cbhdr@aldo#1@chair@ring@furanose}{\cbhdr@chair@error{#1s}}% +} + +\newrobustcmd\cbhdr@expand@x[2]{% + \begingroup\edef\cbhdr@expand@tmp{\endgroup\unexpanded{#1}{#2}}% + \cbhdr@expand@tmp +} +\newrobustcmd\cbhdr@expand@nx[3]{% + \begingroup\edef\cbhdr@expand@tmp{\endgroup\unexpanded{#1{#2}}{#3}}% + \cbhdr@expand@tmp +} + +\newcommand*\cbhdr@stripbs{\expandafter\@gobble\string} + +% ========================================================================== +% colors +\newrobustcmd*\cbhdr@defcolor[2]{\colorlet{cbhdr@#1}{#2}} + +\cbhdr@defcolor{C1}{black} +\cbhdr@defcolor{C6}{black} +\cbhdr@defcolor{O-C6}{black} +\cbhdr@defcolor{H-C6}{black} +\cbhdr@defcolor{anomerO}{black} +\cbhdr@defcolor{anomerH}{black} +\cbhdr@defcolor{ringO}{black} + +\newcommand*\cbhdr@atom@color[2]{\unexpanded{\textcolor{cbhdr@#1}{#2}}} + +% ========================================================================== +% wavy bonds: +\usetikzlibrary{decorations.pathmorphing} +\pgfdeclaredecoration{cbhdr wave}{initial}{ + \state{initial}[ + width = +0pt , + next state = sine, + persistent precomputation = { + \pgfmathsetmacro\matchinglength{ + \pgfdecoratedinputsegmentlength / + int(\pgfdecoratedinputsegmentlength/\pgfdecorationsegmentlength) + } + \setlength{\pgfdecorationsegmentlength}{\matchinglength pt} + } + ]{} + \state{sine}[width=\pgfdecorationsegmentlength]{ + \pgfpathsine{ + \pgfpoint + {0.25\pgfdecorationsegmentlength} + {0.5\pgfdecorationsegmentamplitude} + } + \pgfpathcosine{ + \pgfpoint + {0.25\pgfdecorationsegmentlength} + {-0.5\pgfdecorationsegmentamplitude} + } + \pgfpathsine{ + \pgfpoint + {0.25\pgfdecorationsegmentlength} + {-0.5\pgfdecorationsegmentamplitude} + } + \pgfpathcosine{ + \pgfpoint + {0.25\pgfdecorationsegmentlength} + {0.5\pgfdecorationsegmentamplitude} + } + } + \state{final}{} +} + +\tikzset{ + cbhdr/wavy bond/.style = + { + decorate, + decoration = + { + amplitude = 0.23*\CF@atom@sep/3 , + post length = 0 pt, + pre length = 0 pt, + % Use the atom spacing: saved + segment length = \CF@atom@sep/5 , + cbhdr wave + } + } +} + +% ========================================================================== +% sub molecules for all the modular building of the molecules later +\newcommand*\cbhdr@C[1]{\cbhdr@atom@color{C#1}{C}} + +\newcommand*\cbhdr@OH[1]{% + \cbhdr@atom@color{O-C#1}{O}|% + \cbhdr@atom@color{H-C#1}{H}% +} +\newcommand*\cbhdr@HO[1]{% + \cbhdr@atom@color{H-C#1}{H}|% + \cbhdr@atom@color{O-C#1}{O}% +} +\newcommand*\cbhdr@ring@O{\cbhdr@atom@color{ringO}{O}} +\newcommand*\cbhdr@anomer@O{\cbhdr@atom@color{anomerO}{O}} +\newcommand*\cbhdr@anomer@OH{% + \cbhdr@atom@color{anomerO}{O}|% + \cbhdr@atom@color{anomerH}{H}% +} +\newcommand*\cbhdr@anomer@HO{% + \cbhdr@atom@color{anomerH}{H}|% + \cbhdr@atom@color{anomerO}{O}% +} + +\newrobustcmd*\cbhdr@definesubmol@expand{\cbhdr@expand@nx\definesubmol} +\newrobustcmd*\cbhdr@chemfig@expand{\cbhdr@expand@x\chemfig} + +\newrobustcmd\cbhdr@define@Csubmols[1]{% + \cbhdr@defcolor{O-C#1}{black}% + \cbhdr@defcolor{H-C#1}{black}% + \cbhdr@defcolor{C#1}{black}% + % aldohexoses: + % fischer: + % skeletons + \cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@C#1@OHr}{(-[:0]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@C#1@OHl}{(-[:180]\cbhdr@HO{#1})}% + \cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@C#1@OH0}{}% + % with C and H + \cbhdr@definesubmol@expand{cbhdr@fischer@C#1@OHr}{(-[:0]\cbhdr@OH{#1})(-[:180]H)}% + \cbhdr@definesubmol@expand{cbhdr@fischer@C#1@OHl}{(-[:180]\cbhdr@HO{#1})(-[:0]H)}% + \cbhdr@definesubmol@expand{cbhdr@fischer@C#1@OH0}{(-[:180]H)(-[:0]H)}% + % haworth: + \ifnum#1=5\relax + \cbhdr@definesubmol@expand{cbhdr@haworth@C#1@OHr}{(-[:0]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@haworth@C#1@OHl}{(-[:180,.5]\cbhdr@HO{#1})}% + \else + \cbhdr@definesubmol@expand{cbhdr@haworth@C#1@OHr}{(-[:-90,.5,,1]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@haworth@C#1@OHl}{(-[:90,.5,,1]\cbhdr@OH{#1})}% + \fi + \definesubmol{cbhdr@haworth@C#1@OH0}{}% + % chair: + \ifcase#1 + \or % 1 + \or % 2 + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHr}{(-[:-55,.75,,1]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHl}{(-[:90,.5,,1]\cbhdr@OH{#1})}% + \or % 3 + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHr}{(-[:-90,.5,,1]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHl}{(-[:170,.75,,2]\cbhdr@HO{#1})}% + \or % 4 + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHr}{(-[:190,.75,,2]\cbhdr@HO{#1})}% + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHl}{(-[:90,.5,,1]\cbhdr@OH{#1})}% + \or % 5 + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHr}{(-[:10,.75,,1]\cbhdr@OH{#1})}% + \cbhdr@definesubmol@expand{cbhdr@chair@C#1@OHl}{(-[:-90,.5,,1]\cbhdr@OH{#1})}% + \fi + \definesubmol{cbhdr@chair@C#1@OH0}{}% +} +\cbhdr@define@Csubmols{2} +\cbhdr@define@Csubmols{3} +\cbhdr@define@Csubmols{4} +\cbhdr@define@Csubmols{5} + +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C2@OHr}{(-[:-90,.5]\cbhdr@OH{2})} +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C2@OHl}{(-[:90,.5,,2]\cbhdr@HO{2})} +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C2@OH0}{} + +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C3@OHr}{(-[:-90,.5]\cbhdr@OH{3})} +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C3@OHl}{(-[:90,.5]\cbhdr@OH{3})} +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C3@OH0}{} + +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHr}{(-[:20]\cbhdr@OH{4})} +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OH0}{} + +% 4=r, 5=r +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHr@C5@OHr}{( + -[:90,.5](<[:30,.5]\cbhdr@OH{5}) + -[:120,.5] + -[:-180,.5,,2]HO +)} +% 4=l, 5=r +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHl@C5@OHr}{( + -[:-90,.5](<:[:150,.5]\cbhdr@HO{5}) + -[:-120,.5] + -[:180,.5,,2]HO +)} + +% 4=r, 5=l +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHr@C5@OHl}{( + -[:90,.5](<:[:30,.5]\cbhdr@OH{5}) + -[:120,.5] + -[:-180,.5,,2]HO +)} +% 4=l, 5=l +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHl@C5@OHl}{( + -[:-90,.5](<[:150,.5]\cbhdr@HO{5}) + -[:-120,.5] + -[:180,.5,,2]HO +)} + +% 4=r, 5=0 +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHr@C5@OH0}{( + -[:90,.5] + -[:120,.5] + -[:-180,.5]HO +)} +% 4=l, 5=0 +\cbhdr@definesubmol@expand{cbhdr@haworth@furanose@C4@OHl@C5@OH0}{( + -[:-90,.5] + -[:-120,.5] + -[:180,.5]HO +)} +% 4=0 wouldn't make sense since then the furanose ring cannot be formed + +% fischer +\cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@aldehyde}{(=_[:30]\cbhdr@anomer@O)} +\cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@OHalpha}{(-[:0]\cbhdr@anomer@OH)} +\cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@OHbeta}{(-[:180]\cbhdr@anomer@HO)} +\cbhdr@definesubmol@expand{cbhdr@fischer@skeleton@OHundetermined}{(-[:0]\cbhdr@anomer@OH)} + +\cbhdr@definesubmol@expand{cbhdr@fischer@aldehyde}{(=[:30]\cbhdr@anomer@O)(-[:150]H)} +\cbhdr@definesubmol@expand{cbhdr@fischer@OHalpha}{(-[:0]\cbhdr@anomer@OH)(-[:180]H)} +\cbhdr@definesubmol@expand{cbhdr@fischer@OHbeta}{(-[:180]\cbhdr@anomer@HO)(-[:0]H)} +\cbhdr@definesubmol@expand{cbhdr@fischer@OHundetermined}{(-[:0]\cbhdr@anomer@HO)(-[:180]H)} + +% haworth +\cbhdr@definesubmol@expand{cbhdr@haworth@OHalpha}{(-[:-90,.5,,1]\cbhdr@anomer@OH)} +\cbhdr@definesubmol@expand{cbhdr@haworth@OHbeta}{(-[:90,.5,,1]\cbhdr@anomer@OH)} +\cbhdr@definesubmol@expand{cbhdr@haworth@OHundetermined} + {(-[:0,.75,,1,cbhdr/wavy bond]\cbhdr@anomer@OH)} + +% chair: +\cbhdr@definesubmol@expand{cbhdr@chair@OHalpha}{(-[:-90,.5,,1]\cbhdr@anomer@OH)} +\cbhdr@definesubmol@expand{cbhdr@chair@OHbeta}{(-[:10,.75,,1]\cbhdr@anomer@OH)} +\cbhdr@definesubmol@expand{cbhdr@chair@OHundetermined} + {(-[:0,.75,,1,cbhdr/wavy bond]\cbhdr@anomer@OH)} + +% ========================================================================== +% commands to define the chain and ring molecules avoiding code duplication: + +% the arguments of a chain refer to r and l for the chiral centers. A hexose +% needs four arguments: \cbhdr@newchain\hexose#1#2#3#4{<code>} + +% \cbhdr@newchain<macro><arguments>{<chemfig code>} + +\protected\def\cbhdr@newchain#1{\cbhdr@newchain@aux@i{#1}} +\protected\def\cbhdr@newchain@aux@i#1#2#{\cbhdr@newchain@aux@ii{#1}{#2}} +\protected\def\cbhdr@newchain@aux@ii#1#2#3{% + \protected\csdef{\cbhdr@stripbs#1@aux}#2\q@stop{\cbhdr@chemfig@expand{#3}}% + \newrobustcmd*#1[1]{\csuse{\cbhdr@stripbs#1@aux}##1\q@stop}% +} + +% the first argument of a ring always is alpha/beta, the following arguments +% refer to r and l for the chiral centers. A hexose needs five arguments: +% \cbhdr@newring\hexose#1#2#3#4#5{<code>} + +% \cbhdr@newring<macro><arguments>{<chemfig code>} + +\protected\def\cbhdr@newring#1{\cbhdr@newring@aux@i{#1}} +\protected\def\cbhdr@newring@aux@i#1#2#{\cbhdr@newring@aux@ii{#1}{#2}} +\protected\def\cbhdr@newring@aux@ii#1#2#3{% + \protected\csdef{\cbhdr@stripbs#1@aux}#2\q@stop{\cbhdr@chemfig@expand{#3}}% + \newrobustcmd*#1[1]{\csuse{\cbhdr@stripbs#1@aux}{\cbhdr@anomer}##1\q@stop}% +} + +% ========================================================================== +% now let's build the molecules using the submolecules from above. They're +% all named using the following naming scheme: +% +% \<module>@<model>@<chain>/<ring>(@<ringtype>) +% +% -------------------------------------------------------------------------- +% Fischer - skeleton formulas + +%%% +% hexoses +% chain +\cbhdr@newchain\cbhdr@aldohexose@fischer@skeleton@chain#1#2#3#4{ + !{cbhdr@fischer@skeleton@aldehyde} + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#1} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C4@OH#3} + -[:-90]!{cbhdr@fischer@skeleton@C5@OH#4} + -[:-90](-[:0]\cbhdr@OH{6}) +} + +% pyranoses +\cbhdr@newring\cbhdr@aldohexose@fischer@skeleton@ring@pyranose#1#2#3#4#5{% + !{cbhdr@fischer@skeleton@OH#1}(-[:90]-[:0]-?) + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#3} + -[:-90]!{cbhdr@fischer@skeleton@C4@OH#4} + -[:-90](-[:0]\cbhdr@ring@O-?) + -[:-90](-[:0]\cbhdr@OH{6}) +} + +% furanoses +\cbhdr@newring\cbhdr@aldohexose@fischer@skeleton@ring@furanose#1#2#3#4#5{% + !{cbhdr@fischer@skeleton@OH#1}(-[:90]-[:0]-?) + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#3} + -[:-90](-[:0]\cbhdr@ring@O-?) + -[:-90]!{cbhdr@fischer@skeleton@C5@OH#5} + -[:-90](-[:0]\cbhdr@OH{6}) +} + +%%% +% pentoses +% chain +\cbhdr@newchain\cbhdr@aldopentose@fischer@skeleton@chain#1#2#3{% + !{cbhdr@fischer@skeleton@aldehyde} + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#1} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C4@OH#3} + -[:-90](-[:0]\cbhdr@OH{5}) +} + +% pyranoses +\cbhdr@newring\cbhdr@aldopentose@fischer@skeleton@ring@pyranose#1#2#3#4{% + !{cbhdr@fischer@skeleton@OH#1}(-[:90]-[:0]-?) + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#3} + -[:-90]!{cbhdr@fischer@skeleton@C4@OH#4} + -[:-90](-[:0]\cbhdr@ring@O-?) +} + +% furanoses +\cbhdr@newring\cbhdr@aldopentose@fischer@skeleton@ring@furanose#1#2#3#4{% + !{cbhdr@fischer@skeleton@OH#1}(-[:90]-[:0]-?) + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#3} + -[:-90](-[:0]\cbhdr@ring@O-?) + -[:-90](-[:0]\cbhdr@OH{5}) +} + +%%% +% tetroses +% chain +\cbhdr@newchain\cbhdr@aldotetrose@fischer@skeleton@chain#1#2{% + !{cbhdr@fischer@skeleton@aldehyde} + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#1} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#2} + -[:-90](-[:0]\cbhdr@OH{4}) +} + +% pyranoses +\cbhdr@define@ring@error{fischer@skeleton}{tetrose}{pyranose} + +% furanoses +\cbhdr@newring\cbhdr@aldotetrose@fischer@skeleton@ring@furanose#1#2#3{% + !{cbhdr@fischer@skeleton@OH#1}(-[:90]-[:0]-?) + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#2} + -[:-90]!{cbhdr@fischer@skeleton@C3@OH#3} + -[:-90](-[:0]\cbhdr@ring@O-?) +} + +%%% +% trioses +% chain +\cbhdr@newchain\cbhdr@aldotriose@fischer@skeleton@chain#1{% + !{cbhdr@fischer@skeleton@aldehyde} + -[:-90]!{cbhdr@fischer@skeleton@C2@OH#1} + -[:-90](-[:0]\cbhdr@OH{3}) +} + +% pyranoses +\cbhdr@define@ring@error{fischer@skeleton}{triose}{pyranose} + +% furanoses +\cbhdr@define@ring@error{fischer@skeleton}{triose}{furanose} + +% -------------------------------------------------------------------------- +% Fischer - with C and H + +%%% +% hexoses +% chain +\cbhdr@newchain\cbhdr@aldohexose@fischer@chain#1#2#3#4{% + \cbhdr@C{1}!{cbhdr@fischer@aldehyde} + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#1} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#2} + -[:-90]\cbhdr@C{4}!{cbhdr@fischer@C4@OH#3} + -[:-90]\cbhdr@C{5}!{cbhdr@fischer@C5@OH#4} + -[:-90]\cbhdr@C{6}(-[:0]\cbhdr@OH{6})(-[:180]H) + -[:-90]H +} + +% pyranoses +\cbhdr@newring\cbhdr@aldohexose@fischer@ring@pyranose#1#2#3#4#5{% + \cbhdr@C{1}!{cbhdr@fischer@OH#1}(-[:90]-[:0]-?) + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#2} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#3} + -[:-90]\cbhdr@C{4}!{cbhdr@fischer@C4@OH#4} + -[:-90]\cbhdr@C{5}(-[:0]\cbhdr@ring@O-?)(-[:180]H) + -[:-90]\cbhdr@C{6}(-[:0]\cbhdr@OH{6})(-[:180]H) + -[:-90]H +} + +% furanoses +\cbhdr@newring\cbhdr@aldohexose@fischer@ring@furanose#1#2#3#4#5{% + \cbhdr@C{1}!{cbhdr@fischer@OH#1}(-[:90]-[:0]-?) + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#2} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#3} + -[:-90]\cbhdr@C{4}(-[:0]\cbhdr@ring@O-?)(-[:180]H) + -[:-90]\cbhdr@C{5}!{cbhdr@fischer@C5@OH#5} + -[:-90]\cbhdr@C{6}(-[:0]\cbhdr@OH{6})(-[:180]H) + -[:-90]H +} + +%%% +% pentoses +% chain +\cbhdr@newchain\cbhdr@aldopentose@fischer@chain#1#2#3{% + \cbhdr@C{1}!{cbhdr@fischer@aldehyde} + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#1} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#2} + -[:-90]\cbhdr@C{4}!{cbhdr@fischer@C4@OH#3} + -[:-90]\cbhdr@C{5}(-[:0]\cbhdr@OH{5})(-[:180]H) + -[:-90]H +} + +% pyranoses +\cbhdr@newring\cbhdr@aldopentose@fischer@ring@pyranose#1#2#3#4{% + \cbhdr@C{1}!{cbhdr@fischer@OH#1}(-[:90]-[:0]-?) + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#2} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#3} + -[:-90]\cbhdr@C{4}!{cbhdr@fischer@C4@OH#4} + -[:-90]\cbhdr@C{5}(-[:0]\cbhdr@ring@O-?)(-[:180]H) + -[:-90]H +} + +% furanoses +\cbhdr@newring\cbhdr@aldopentose@fischer@ring@furanose#1#2#3#4{% + \cbhdr@C{1}!{cbhdr@fischer@OH#1}(-[:90]-[:0]-?) + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#2} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#3} + -[:-90]\cbhdr@C{4}(-[:0]\cbhdr@ring@O-?)(-[:180]H) + -[:-90]\cbhdr@C{5}(-[:0]\cbhdr@OH{5})(-[:180]H) + -[:-90]H +} + +%%% +% tetroses +% chain +\cbhdr@newchain\cbhdr@aldotetrose@fischer@chain#1#2{% + \cbhdr@C{1}!{cbhdr@fischer@aldehyde} + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#1} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#2} + -[:-90]\cbhdr@C{4}(-[:0]\cbhdr@OH{4})(-[:180]H) + -[:-90]H +} + +% pyranoses +\cbhdr@define@ring@error{fischer}{tetrose}{pyranose} + +% furanoses +\cbhdr@newring\cbhdr@aldotetrose@fischer@ring@furanose#1#2#3{% + \cbhdr@C{1}!{cbhdr@fischer@OH#1}(-[:90]-[:0]-?) + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#2} + -[:-90]\cbhdr@C{3}!{cbhdr@fischer@C3@OH#3} + -[:-90]\cbhdr@C{4}(-[:0]\cbhdr@ring@O-?)(-[:180]H) + -[:-90]H +} + +%%% +% trioses +% chain +\cbhdr@newchain\cbhdr@aldotriose@fischer@chain#1{% + \cbhdr@C{1}!{cbhdr@fischer@aldehyde} + -[:-90]\cbhdr@C{2}!{cbhdr@fischer@C2@OH#1} + -[:-90]\cbhdr@C{3}(-[:0]\cbhdr@OH{3})(-[:180]H) + -[:-90]H +} + +% pyranoses +\cbhdr@define@ring@error{fischer}{triose}{pyranose} + +% furanoses +\cbhdr@define@ring@error{fischer}{triose}{furanose} + +% -------------------------------------------------------------------------- +% Haworth +\newcommand*\cbhdr@decr{-} % > +\newcommand*\cbhdr@thick{} % line width=3pt +\newcommand*\cbhdr@incr{-} % < + +%%% +% hexoses +% chain +\cbhdr@newchain\cbhdr@aldohexose@haworth@chain#1#2#3#4{% + -[:30] + ?(-[:90,.5]-[:150,.5]\cbhdr@HO{6})!{cbhdr@haworth@C5@OH#4}-[,,,,draw=none] + -[:-30,,1,,draw=none](=_[:0]\cbhdr@anomer@O) + \cbhdr@incr[:-150]!{cbhdr@haworth@C2@OH#1} + -[:-180,,,,\cbhdr@thick]!{cbhdr@haworth@C3@OH#2} + \cbhdr@decr[:150]?!{cbhdr@haworth@C4@OH#3} +} + +% pyranoses +\cbhdr@newring\cbhdr@aldohexose@haworth@ring@pyranose#1#2#3#4#5{% + -[:30] + ?(-[:90,.5]-[:150,.5]\cbhdr@HO{6})-\cbhdr@ring@O + -[:-30]!{cbhdr@haworth@OH#1} + \cbhdr@incr[:-150]!{cbhdr@haworth@C2@OH#2} + -[:-180,,,,\cbhdr@thick]!{cbhdr@haworth@C3@OH#3} + \cbhdr@decr[:150]?!{cbhdr@haworth@C4@OH#4} +} + +% furanoses +\cbhdr@newring\cbhdr@aldohexose@haworth@ring@furanose#1#2#3#4#5{% + \cbhdr@ring@O?-[:-20]!{cbhdr@haworth@OH#1} + -[:-110]!{cbhdr@haworth@furanose@C2@OH#2} + -[:180,1.1954]!{cbhdr@haworth@furanose@C3@OH#3} + -[:110]?!{cbhdr@haworth@furanose@C4@OH#4@C5@OH#5} +} + +%%% +% pentoses +% chain +\cbhdr@newchain\cbhdr@aldopentose@haworth@chain#1#2#3{% + ?-[:-20,,,,draw=none](=_[:0]\cbhdr@anomer@O) + -[:-110]!{cbhdr@haworth@furanose@C2@OH#1} + -[:180,1.1954]!{cbhdr@haworth@furanose@C3@OH#2} + -[:110]?[,,{draw=none}](-[:90,.5]-[:150,.5]\cbhdr@HO{5}) + !{cbhdr@haworth@furanose@C4@OH#3} +} + +% pyranoses +\cbhdr@newring\cbhdr@aldopentose@haworth@ring@pyranose#1#2#3#4{% + -[:30] + ?-\cbhdr@ring@O + -[:-30]!{cbhdr@haworth@OH#1} + \cbhdr@incr[:-150]!{cbhdr@haworth@C2@OH#2} + -[:-180,,,,\cbhdr@thick]!{cbhdr@haworth@C3@OH#3} + \cbhdr@decr[:150]?!{cbhdr@haworth@C4@OH#4} +} + +% furanoses +\cbhdr@newring\cbhdr@aldopentose@haworth@ring@furanose#1#2#3#4{% + \cbhdr@ring@O?-[:-20]!{cbhdr@haworth@OH#1} + -[:-110]!{cbhdr@haworth@furanose@C2@OH#2} + -[:180,1.1954]!{cbhdr@haworth@furanose@C3@OH#3} + -[:110]?(-[:90,.5]-[:150,.5]\cbhdr@HO{5}) +} + +%%% +% tetroses +% chain +\cbhdr@define@chain@error{haworth}{tetrose} + +% pyranoses +\cbhdr@define@ring@error{haworth}{tetrose}{pyranose} + +% furanoses +\cbhdr@newring\cbhdr@aldotetrose@haworth@ring@furanose#1#2#3{% + \cbhdr@ring@O?-[:-20]!{cbhdr@haworth@OH#1} + -[:-110]!{cbhdr@haworth@furanose@C2@OH#2} + -[:180,1.1954]!{cbhdr@haworth@furanose@C3@OH#3} + -[:110]? +} + +%%% +% trioses +% chain +\cbhdr@define@chain@error{haworth}{triose} + +% pyranoses +\cbhdr@define@ring@error{haworth}{triose}{pyranose} + +% furanoses +\cbhdr@define@ring@error{haworth}{triose}{furanose} + +% -------------------------------------------------------------------------- +% Chair + +%%% +% hexoses +% chain +\cbhdr@newchain\cbhdr@aldohexose@chair@chain#1#2#3#4{% + -[:-10] + ?(-[:150,.75]-[:90,.5,,1]\cbhdr@OH{6})!{cbhdr@chair@C5@OH#4}-[:10,,,,draw=none] + -[:-50,,1,,draw=none](=_[:70]\cbhdr@anomer@O) + \cbhdr@incr[:-170]!{cbhdr@chair@C2@OH#1} + -[:-190,,,,\cbhdr@thick]!{cbhdr@chair@C3@OH#2} + \cbhdr@decr[:130]?!{cbhdr@chair@C4@OH#3} +} + +% pyranoses +\cbhdr@newring\cbhdr@aldohexose@chair@ring@pyranose#1#2#3#4#5{% + -[:-10] + ?(-[:150,.75]-[:90,.5,,1]\cbhdr@OH{6})-[:10]\cbhdr@ring@O + -[:-50]!{cbhdr@chair@OH#1} + \cbhdr@incr[:170]!{cbhdr@chair@C2@OH#2} + -[:190,,,,\cbhdr@thick]!{cbhdr@chair@C3@OH#3} + \cbhdr@decr[:130]?!{cbhdr@chair@C4@OH#4} +} + +% furanoses +\newrobustcmd*\cbhdr@aldohexose@chair@ring@furanose{% + \cbhdr@chair@error{furanose rings}% +} + +%%% +% pentoses +\cbhdr@define@chair@errors{pentose} + +%%% +% tetroses +\cbhdr@define@chair@errors{tetrose} + +%%% +% trioses +\cbhdr@define@chair@errors{triose} + + +% ========================================================================== +% the user commands - built from the commands above using the already +% mentioned naming scheme +% +% <module>@<model>@<chain>/<ring>(@<ringtype>) + +\newcommand*\cbhdr@model{} % fischer/haworth/chair +\newcommand*\cbhdr@fischer{} % @skeleton +\newcommand*\cbhdr@form{} % chain/ring +\newcommand*\cbhdr@chain{chain} +\newcommand*\cbhdr@ring{ring@\cbhdr@ringtype} +\newcommand*\cbhdr@ringtype{} % pyranose/furanose +\newcommand*\cbhdr@ringtype@default{} + +% -------------------------------------------------------------------------- +% options for the user command: +\pgfkeys{ + cbhdr/.cd, + model/.is choice , + model/fischer/.is choice , + model/fischer/skeleton/.code = \def\cbhdr@model{fischer@skeleton} , + model/fischer/full/.code = \def\cbhdr@model{fischer} , + model/fischer/.default = full , + model/haworth/.code = \def\cbhdr@model{haworth} , + model/chair/.code = \def\cbhdr@model{chair} , + chain/.code = \def\cbhdr@constitution{chain} , + ring/.is choice , + ring/true/.code = \def\cbhdr@constitution{ring@\cbhdr@ringtype@default} , + ring/pyranose/.code = \def\cbhdr@constitution{ring@pyranose} , + ring/furanose/.code = \def\cbhdr@constitution{ring@furanose} , + ring/.default = true , + anomer/.is choice , + anomer/alpha/.code = \def\cbhdr@anomer{alpha} , + anomer/beta/.code = \def\cbhdr@anomer{beta} , + anomer/undetermined/.code = \def\cbhdr@anomer{undetermined} , + length/.is choice , + length/6/.code = + \def\cbhdr@ringtype@default{pyranose} + \def\cbhdr@length{aldohexose} , + length/5/.code = + \def\cbhdr@ringtype@default{furanose} + \def\cbhdr@length{aldopentose} , + length/4/.code = + \def\cbhdr@ringtype@default{furanose} + \def\cbhdr@length{aldotetrose} , + length/3/.code = + % doesn't matter: will cause an error anyway + \def\cbhdr@ringtype@default{pyranose} + \def\cbhdr@length{aldotriose} , + hexose/.style = { length=6 } , + pentose/.style = { length=5 } , + tetrose/.style = { length=4 } , + triose/.style = { length=3 } , + 3d/.is choice , + 3d/true/.code = + \def\cbhdr@decr{>} + \def\cbhdr@thick{line width=3pt} + \def\cbhdr@incr{<} , + 3d/false/.code = + \def\cbhdr@decr{-} + \def\cbhdr@thick{} + \def\cbhdr@incr{-} , + 3d/.default = true , + defaults/.style = { + model = fischer , + chain , + anomer = alpha , + length = 6 + } , + color/.code 2 args = \cbhdr@defcolor{#1}{#2} +} +\pgfqkeys{/cbhdr}{defaults} + +% -------------------------------------------------------------------------- +% the user command: +\newrobustcmd*\cbhdr@carbohydrate[2]{% + \begingroup + \pgfqkeys{/cbhdr}{defaults,#1}% + \csuse{cbhdr@\cbhdr@length @\cbhdr@model @\cbhdr@constitution}{#2}% + \endgroup +} + +\newrobustcmd*\carbohydrate[2][]{\cbhdr@carbohydrate{#1}{#2}} + +% ========================================================================== +% a command to define ready made carbohydrates + +\newrobustcmd*\newaldose[1]{% + \@ifnextchar[ % ] + {\cbhdr@newaldose{#1}} + {\cbhdr@newaldose{#1}[]}% +} + +\protected\def\cbhdr@newaldose#1[#2]#3{% + \cbhdr@expand@x + \pgfkeys{ + cbhdr/.cd, + \cbhdr@stripbs#1-defaults/.style={\unexpanded{#2}} + }% + \newrobustcmd*#1[1][]{% + \expandafter\cbhdr@carbohydrate\expandafter{\cbhdr@stripbs#1-defaults,##1}{#3}% + }% +} + +\newrobustcmd*\renewaldose[1]{% + \@ifnextchar[ % ] + {\cbhdr@renewaldose{#1}} + {\cbhdr@renewaldose{#1}[]}% +} + +\protected\def\cbhdr@renewaldose#1[#2]#3{% + \cbhdr@expand@x + \pgfkeys{ + cbhdr/.cd, + \cbhdr@stripbs#1-defaults/.style={\unexpanded{#2}} + }% + \renewrobustcmd*#1[1][]{% + \expandafter\cbhdr@carbohydrate\expandafter{\cbhdr@stripbs#1-defaults,##1}{#3}% + }% +} + +% ========================================================================== +% predefined carbohydrates: +% aldohexoses: +\newaldose \allose [hexose]{rrrr} +\newaldose \altrose [hexose]{lrrr} +\newaldose \glucose [hexose]{rlrr} +\newaldose \gulose [hexose]{rrlr} +\newaldose \mannose [hexose]{llrr} +\newaldose \idose [hexose]{lrlr} +\newaldose \galactose[hexose]{rllr} +\newaldose \talose [hexose]{lllr} + +% aldopentoses: +\newaldose \ribose [pentose]{rrr} +\newaldose \arabinose[pentose]{lrr} +\newaldose \xylose [pentose]{rlr} +\newaldose \lyxose [pentose]{llr} + +\newaldose \desoxyribose[pentose]{0rr} + +% aldotetroses: +\newaldose \erythrose[tetrose]{rr} +\newaldose \threose [tetrose]{lr} + +% aldotrioses: +\newaldose \glycerinaldehyde[triose]{r} + +% ========================================================================== +% setup commands +% general defaults: +\newrobustcmd*\setcarbohydrates[1]{% + \pgfkeys{ + cbhdr/.cd , + defaults/.style = {#1} , + defaults + }% +} + +% defaults for particular carbohydrate defined with \newaldose: +\newrobustcmd*\setcarbohydratedefaults[2]{% + \edef\cbhdr@tmpa{\cbhdr@stripbs#1}% + \pgfkeys{ + cbhdr/.cd , + \cbhdr@tmpa-defaults/.style = { #2 } , + \cbhdr@tmpa-defaults + }% +} + +\endinput +% ========================================================================== +% HISTORY: + +% ========================================================================== +% TODO: +- Ringe fuer L-Saccharide +- Ketten für Tri- Tetr- und Pentosen +- Optionen für Farben + +- Ketosen - viell. nur Fructose + +- Optionen für oxidierte u reduzierte Formen? + diff --git a/Master/tlpkg/bin/tlpkg-ctan-check b/Master/tlpkg/bin/tlpkg-ctan-check index f2e8ccb4589..003201ea81a 100755 --- a/Master/tlpkg/bin/tlpkg-ctan-check +++ b/Master/tlpkg/bin/tlpkg-ctan-check @@ -113,7 +113,7 @@ my @TLP_working = qw( c90 c-pascal cabin cachepic caladea calcage calctab calculation calculator calligra calligra-type1 calrsfs cals calxxxx-yyyy cancel canoniclayout cantarell - capt-of captcont captdef caption carlisle carlito carolmin-ps + capt-of captcont captdef caption carbohydrates carlisle carlito carolmin-ps cascadilla cases casyl catchfilebetweentags catcodes catechis catoptions cbcoptic cbfonts cbfonts-fd diff --git a/Master/tlpkg/tlpsrc/carbohydrates.tlpsrc b/Master/tlpkg/tlpsrc/carbohydrates.tlpsrc new file mode 100644 index 00000000000..e69de29bb2d --- /dev/null +++ b/Master/tlpkg/tlpsrc/carbohydrates.tlpsrc diff --git a/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc b/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc index 959873bc324..71f77b22023 100644 --- a/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc +++ b/Master/tlpkg/tlpsrc/collection-latexextra.tlpsrc @@ -107,6 +107,7 @@ depend canoniclayout depend capt-of depend captcont depend captdef +depend carbohydrates depend cases depend casyl depend catchfilebetweentags |