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Can you create diagrams of chemical structures in LaTeX?

Example(s) of "chemical structure diagrams":

Example 1

Example 2

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4  
Yes, take a look at the chemfig package. –  Werner Apr 20 '12 at 18:39
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2 Answers

up vote 37 down vote accepted
+500

The answer is: yes. There is actually more than one package to do that:

I have used all but XyMTeX and PPCHTeX myself but nowadays only use chemfig any more.

XyMTeX is in my opinion far from being intuitive so I never bothered learning it. It also is not regularly updated to CTAN and not part of TeX Live. CTAN has v4.06 but the newest version is v5.00.

ochem nearly offers all one needs but 1) is not available from either major free distribution and 2) the work is done by a Perl script that translates formulae and reaction schemes into PostScript, which means it doesn't work with pdflatex.

streeTeX is just too limited in its capabilities besides the fact that it is rather old, is not available from either major free distribution and also doesn't work with pdflatex.

chemfig is a rather new and actively maintained package that not only allows to draw skeletal formulae but also has commands for creating whole reaction schemes. It uses TikZ for the drawing.

PPCHTeX is ConTeXt's chemistry module but it can actually be used with LaTeX, too. I have never used it before and trying to typeset the examples below with it has proven to be more complicated than I thought. That's why I simply copied an example from the conTeXtgarden.

So if you want to draw your formulas and schemes with LaTeX rather than an external program like ChemDraw I can only recommend chemfig.


A chemfig example:

\documentclass{article}
\usepackage{chemfig}
\renewcommand*\printatom[1]{\ensuremath{\mathsf{#1}}}
\begin{document}

\setcrambond{2pt}{}{}
\chemfig{
  HO-[2,.5,2]?<[7,.7](-[2,.5]OH)-[,,,,line width=2.4pt](-[6,.5]OH)>[1,.7]
    (-[:-65,.7]O-[:65,.7]?[b](-[2,.7]CH_2OH)<[:-60,.707](-[6,.5]OH)
      -[,,,,line width=2.4pt](-[2,.5,,2]HO)>[:60,.707](-[6,.5]CH_2OH)-[:162,.9]O?[b])
  -[3,.7]O-[4]?(-[2,.3]-[3,.5]HO)}

\setatomsep{2em}
\chemfig{
  H_3C-[:72]{\color{blue}N}
    *5(-
      *6(-(={\color{red}O})-{\color{blue}N}(-CH_3)-(={\color{red}O})-{\color{blue}N}(-CH_3)-=)
    --{\color{blue}N}=-)}

\end{document}

chemfig demo

An ochem example:

\documentclass{article}
\usepackage{ochem}
\begin{document}

\begin{chemistry}
  set("rLenN",20)
  formula(L,R)
    {
      ring(,,H1=)
        {
          0: bond(r,=C) atom("O") ;
          3: atom("N") bond(r) atom("C",C,R) atom("H$_3$",L) ;
          4: bond(r,=C) atom("O") ;
          5: atom("N") bond(r) atom("CH$_3$",L) ;
          vertex(,1,4,H2=,5)
            {
              1: atom("N") bond(r) atom("C",C,L) atom("H$_3$",R) ;
              3: atom("N") ;
            } ;
        }
    }
\end{chemistry}

\end{document}

ochem demo

A streetex example:

\documentclass{article}
\usepackage{stree}
\begin{document}

\sffamily
\stree{0[2N[0{CH$_3$}]4[=2O]6N[4{CH$_3$}]8[=6O]10]/10N=75N[/7{H$_3$C}]/2}

\end{document}

streetex demo

A XyMTeX example:

\documentclass{article}
\usepackage{xymtex}
\let\substfont\sffamily
\begin{document}

\sixheterovi[{f\fivefusev[d]{1==N;4==N}{1S==CH$_3$}{b}}e]
  {2==N;4==N}
  {1D==O;3D==O;4S==CH$_3$}

\end{document}

XyMTeX demo

A PPCHTeX example

\documentclass{article}
\usepackage{m-pictex}
\usepackage{m-ch-en}% or `m-ch-de' if you like a German interface

\begin{document}

\startchemical
  \chemical[FIVE,FRONT,BB125,+SB3,-SB4,Z4][O]
  \chemical[FIVE,FRONT,+R1235,+RZ1235][H,H,\SR{HOH_2C},OH]
  \chemical[FIVE,FRONT,-R1235,-RZ1235][H,OH,H,H]
\stopchemical

\end{document}

PPCHTeX demo

share|improve this answer
    
xymtex looks (or looked) good, and the author published a pleasing paper in tugboat. the author even uploaded to ctan ... once. when i came to catalogue it, the home page had moved and the uploaded version had been declared obsolete. the package is no doubt a boon for the author's students, but for those he chooses to keep in the dark, chemfig or one of the others i don't know seems the way to go. –  wasteofspace Nov 25 '12 at 15:02
    
The homepage seems to be homepage3.nifty.com/xymtex/fujitas3/xymtex/indexe.html nowadays. What I dislike most about XyMTeX is its documentation, actually. I find it very hard to deduce which commands are available (and what they do) and what options they have (and what they do). Otherwise it seems to be a very capable and complete bundle. –  cgnieder Nov 25 '12 at 15:09
    
Totally agree as a 'jobbing' chemist: chemfig is the only one I'd actually use at all for 'real' work (although I personally do use a graphical tool for most of my work). –  Joseph Wright Aug 17 '13 at 19:31
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For the purpose of rational comparison, more and updated information on XyMTeX would be desirable, because the example shown in the preceding answer has been drawn by the plain mode of XyMTeX (providing slightly poor printing quality within the picture enviroment of LaTeX) and because the comment on the availability of XyMTeX would provide readers with a misleading impression.

The latest version (Version 5.00a) of XyMTeX is available from the XyMTeX homepage (http://xymtex.com/):

http://xymtex.com/fujitas3/xymtex/indexe.html

The two structural formulas shown in the question can be drawn by using the PostScript-compatible mode (as well as the PDF-compatible mode) of XyMTeX.

(1) Disaccharide

\documentclass{article}
\usepackage{xymtexps}%PostScript Mode
%\usepackage{xymtexpdf}%PDF Mode
\begin{document}

\changeunitlength{0.08pt}
\utrigonal{0==O;2==%
\furanose{4==(yl);1Sa==CH$_{2}$OH;2Sb==\lmoiety{HO};%
2Sa==H;3Sb==H;3Sa==OH;4Sb==HOC\rlap{H$_{2}$}};%
3==\pyranose{1==(yl);2Sa==OH;3Sb==OH;4Sa==HO;5Sb==CH$_{2}$OH}}
\hskip4cm
\utrigonal{0==O;2==%
\fivesugarh{5==O;%
1s==\WedgeAsSubst(0,0)(-3,-5){120};%
4s==\WedgeAsSubst(0,0)(3,-5){120};%
3s==\PutBondLine(-15,0)(305,0){3.2pt}%
}{4==(yl);1Sa==CH$_{2}$OH;2Sb==\lmoiety{HO};2Sa==H;%
3Sb==H;3Sa==OH;4Sb==HOC\rlap{H$_{2}$}}[abc];%
3==\sixsugarh{6==O;1s==\WedgeAsSubst(0,0)(-3,-5){120};%
4s==\WedgeAsSubst(0,0)(3,-5){120};%
3s==\PutBondLine(-15,0)(305,0){3.2pt}%
}{1==(yl);2Sa==OH;3Sb==OH;4Sa==HO;5Sb==CH$_{2}$OH}[abc]}

\end{document}

enter image description here

(2) Caffeine

\documentclass{article}
\usepackage{xymtexps}%PostScript Mode
%\usepackage{xymtexpdf}%PDF Mode
\usepackage{graphicx}
%\pagestyle{empty}
\begin{document}

\changeunitlength{0.08pt}
\sixheterov[e{e\fivefusev[d]{1==\bluex{N};4==\bluex{N}}{1==CH$_{3}$}{b}}]
{1==\bluex{N};3==\bluex{N}}
{1==CH$_{3}$;3==CH$_{3}$;2D==\redx{O};4D==\redx{O}}
\\ \vskip0.5cm
{%
\let\substfont=\sffamily
\purinev[aj]{3==CH$_{3}$;%
4D==\addbscolor{\green}{\redx{O}};5==CH$_{3}$;%
6D==\addbscolor{\green}{\redx{O}};7==CH$_{3}$}
\quad
\def\grayx#1{\xymcolor{gray}{#1}}
\nonaheterov[aj]{1==\bluex{N};3==\bluex{N};5==\bluex{N};7==\bluex{N}}%
{3==\addbscolor{\red}{\grayx{CH$_{3}$}};%
4D==\addbscolor{\green}{\redx{O}};5==\addbscolor{\red}{\grayx{CH$_{3}$}};%
6D==\addbscolor{\green}{\redx{O}};7==\addbscolor{\red}{\grayx{CH$_{3}$}}}
}

\end{document}

enter image description here

For further information, please see XyMTeX-tips in the XyMTeX homepage (http://xymtex.com/):

http://xymtex.com/fujitas3/xymtex-tips/indexe.html

The present topic has been deposited as 130208a-ps.pdf, 130208b-ps.pdf etc.

As for a tool for publishing a book on organic chemistry, the combination of XyMTeX-LaTeX has been used to publish the following book:

S. Fujita, "Organic Chemistry of Photography", Springer-Verlag (2004),

in which all of the structural formulas (among 480 illustrations) have been drawn by using XyMTeX.

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3  
Are you going to upload version 5 of XyMTeX on CTAN? –  egreg Feb 10 '13 at 0:02
    
I am heavily engaged in writing another book on enumeration of organic compounds now (for a previous publication, cf. S. Fujita, "Symmetry and Combinatorial Enumeration in Chemistry", springer.com/chemistry/organic+chemistry/book/978-3-540-54126-4 Springer-Verlage 1991). And so, sorry to say that it is hard to support two WEB pages simultaneously. –  Fujita Feb 10 '13 at 7:22
    
@Fujita If the code is usable, I don't see why it can't go to CTAN: I send stuff there almost every week :-) –  Joseph Wright Feb 10 '13 at 11:10
1  
@fujita: if you upload to ctan, all you need do is provide a short outline of changes (e.g., "this is v5.0, large number of changes since v4.xx"). we (ctan) look after the web page(s) for you, and provide searching tools specific to the subject matter; in short, we try to make life as easy as possible for the uploader. mail ctan@dante.de if you have queries of detail. –  wasteofspace Feb 11 '13 at 10:17
2  
@wasteofspace, Thanks. The deadline of the book I am now writing is the beginning of April. I hope to improve the documentation of XyMTeX after that deadline in order to meet the comment of cgnieder on the documentation. Would you please wait for a while. –  Fujita Feb 11 '13 at 11:57
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