Changes

ConTeXt comes always came with the extensive chemistry module [[PPCHTeX]] which allows the support including drawing of chemical structures and the typesetting of reactions.

[[In MkII this was called PPCHTeX]] , which works also with plain TeX, and LaTeX and - of course - with ConTeXt.

* [http://wwwThere doesn’t seem to be any current documentation (all previous links were long dead), while chemistry support is still part of the distribution, but currently broken.pragma(2023-10-ade01: part of the math upgrade, please wait until it becomes stable.com/ppchtex.htm PPCHTeX (general)] by Pragma* There are a few working examples in the [[httpmanual://www.pragmamkiv-adepublications.com/document.htm PPCHTeX documentationpdf|publications] by Pragma* [http://www.ntg.nl/mailman/listinfo/ntg-ppchtex PPCHTeX mailing list]* [http://wwwmanual (chapter 10.ntg2), i.nl/pipermail/ntg-ppchtex/ PPCHTeX mailing list archive] Some other PPCHTeX links:* [http://mitgliede.lycos.de/ppchtex/00index.html PPCHTeX structure database]* in the file [httphttps://wwwsource.mitcontextgarden.edu/afs/athena/contrib/tex-contrib/Chem2/ppchtexnet/doc/fh-ch-en.htm PPCHTeX FAQ] and [http:/context/www.pragma-ade.comsources/general/faqs/ PPCHTeX FAQ in PDF](rather old)* [http:manuals/publications/wwwC6H6O.tugbib C6H6O.org/TUGboat/Articles/tb17-1/tb50hage.pdf TUG Boat article on PPCHTeXbib] by Hans Hagen and A.F Otten

* [[manual:xchemml-p.pdf|ChemML]] ([[manual:xchemml-s.pdf|screen]]), [[MathML]] extension for chemistry.

=== Formulae with chemic module =Using {{cmd|chemical}} ==

This is the built-in version of the previous `chemic` module. <texcodecontext source="yes">\usemodule[chemic]

</texcodecontext> You can also typeset chemical ''reactions'': <context source="yes"> \startformula \chemical{2H_2,+,O_2,->,2H_2O}\stopformula</context> == Chemical structures == (The “good” images are old; the broken ones are the result of the current code.) <context source="yes"> \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</context> [[Image:Chemistry_example1.png]] <context source="yes"> \setupchemical[width=fit] \startchemical \chemical[SIX,B,C,MOV2,B,C,R234,RZ234,MOV5,MOV6,B,C,R561,RZ561] [R,R,R,R,R,R]\stopchemical</context> [[Image:chemistry_example2.png]] To draw this structure horizontally:<context source="yes"> \setupchemical[width=fit] \def\RotR{\rotate[rotation=270]{\ix R}} \rotate[rotation=90]{\startchemical \chemical[SIX,B,C,MOV2,B,C,R234,RZ234,MOV5,MOV6,B,C,R561,RZ561] [\RotR,\RotR,\RotR,\RotR,\RotR,\RotR]\stopchemical}</context> [[Image:chemistry_example3.png]]

An example of an amino acid: Histidine (Ace-His-Nme).The rest of the amino acids are shown in [http://tt4sci.wordpress.com/2009/08/05/drawing-organic-molecules-in-latex-ii-amino-acids/ TT4Sci]<contextsource="yes">\usemoduledefinechemical[radical]{\chemical[SAVE,ONE,SB768,Z068][C,H,H]\chemical[MOV7,ONE,Z0][C]\chemical[MOV7,FIVE,ROT4,SB12345,EB42,Z1235,SR125,RZ125,RESTORE][N,C,N,C,H,H,H]}\startchemical[chemicscale=big,size=big,left=2600,right=4200,bottom=2800,top=4500]\bottext{Histidine}\chemical[SIX,SB23]\chemical[PB:Z1,SAVE,radical,RESTORE,PE]\chemical[PB:Z2,ONE,SB37,Z03,PE][\SL{HSO_4C^{\alpha}},H^{\alpha 1}]\chemical[PB:Z3,SIX,Z5,SB4,Z4,PE][N,H]{\color{blue}\chemical[PB:Z4,SIX,Z2,SB2,DB1,Z31,PE][C{\text{\tiny{-1}}},\SR{H_3C},O{\text{\tiny{-1}}}]}\chemical[SIX,MOV1,SB23]\chemical[PB:Z3,SIX,Z5,DB4,Z4,PE][C,O]{\color{red}\chemical[PB:Z2,SIX,Z4,SB34,Z53,PE][N{\text{\tiny{+1}}},H{\text{\tiny{+1}}},\SL{CH_3}]}\stopchemical

=== Simple Formulae in Text Mode ===[[Image:histidine.png]] 

An alternative to using the chemistry module or mathmode for typesetting simple formulae are the three ConTeXt commands <cmd>high</cmd>, <cmd>low</cmd> and <cmd>lohi</cmd>. This might be useful if you want to typset the formula with the same font as the surrounding text (== Simple Formulae in titles or slanted fonts, although that might not be desired in all situations).Text Mode ==

<texcode>\ss H\lowAn alternative to using the chemistry module or mathmode for typesetting simple formulae are the ConTeXt commands {{2cmd|high}O also consists of H\high}, {{+cmd|low} and OH\high}, {{--}.There are two main carbon isotopes: \cmd|lohi{6}{12}C , and \lohi[left]{6{cmd|himilo}{13}C.</texcode>This might be useful if you want to typset the formula with the same font as the surrounding text (in titles or slanted fonts, although that might not be desired in all situations).

<contextsource="yes">

Taco's Taco’s macros implement this approach [http://archive.contextgarden.net/thread/20060702.084423.a201a280.en.html]: '''This is broken code from 2006!'''

<texcodecontext source="yes">

</texcodecontext>

The main difference with the built-in chemistry is that the <contextcode>\newbox\chemlowbox\def\chemlow#1% {\setbox\chemlowbox\hbox{{\switchtobodyfont[small]#1}}}molecule</code> from this example uses the same font as the one in surrounding text, while the official module always uses the (mostly roman) math font (which is probably the proper way if you’re writing dozens of formulas).

\def\chemhigh#1% {\ifvoid\chemlowbox \high{{\switchtobodyfont[small]#1}}% \else \Alternatively you can setup the <code>style</\lohi{\box\chemlowbox}{{\switchtobodyfont[small]#1}}\fi }code> parameter used for chemical formulas manually:

\def\finishchem%<texcode> {\ifvoid\chemlowbox setupchemical[style=\elsebs] \iffluor \fluorfalse \kern-.1em \fi\low{\box\chemlowbox}\fi}</texcode>

\unexpanded\def\molecule% {\bgroup \catcode`\_=\active \uccode`\~=`\_ \uppercase{\let~\chemlow}% \catcode`\^=\active \uccode`\~=`\^ \uppercase{\let~\chemhigh}% \dostepwiserecurse {65}{90}{1} {\catcode \recurselevel = \active \uccode`\~=\recurselevel \uppercase{\edef~{\noexpand\finishchem \rawcharacter{\recurselevel}}}}% \uccode `\~=`\F \uppercase{\def~{\finishchem F\fluortrue}}% \catcode`\* [http://www.mit.edu/afs/athena/contrib/tex-=\active \uccode`\~=`\contrib/Chem2/ppchtex/doc/fh- \uppercase{\def~{ch--}}% \loggingall \domolecule }% \def\domolecule#1% {\expandafter\scantokens\expandafter {\detokenize{#1\finishchem}}\egroup}en.htm PPCHTeX FAQ] (1997){\bsx Bold slanted molecules* [http: \molecule{HSO_4^//www.tug.org/TUGboat/Articles/tb17-} 1/tb50hage.pdf TUG Boat article on PPCHTeX] by Hans Hagen and \molecule{SF_6}} </context>A.F. Otten 1996

[[Category:Graphics]][[Category:ChemistrySciences]]