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}} ==

<texcode> \usemodule[This is the built-in version of the previous `chemic]\chemical{HSO_4^{-}}</texcode>` module.

<contextsource="yes"> \usemodule[chemic]

* It You can also be used to typeset chemical ''reactions'':

<texcodecontext source="yes">\usemodule[chemic]

</texcodecontext> == 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>\startchemical \usemodulechemical[chemicSIX,B,C,MOV2,B,C,R234,RZ234,MOV5,MOV6,B,C,R561,RZ561]\startformula \chemical{2H_2 [R,R,+R,O_2R,->R,2H_2O}R]\stopformulastopchemical

An alternative to using the chemistry module or mathmode for typesetting simple formulae are the three ConTeXt commands To draw this structure horizontally:<cmdcontext source="yes">high}}, <cmd>low}} and <cmd>lohi}}. 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).\setupchemical[width=fit]

<texcode>\ss Hdef\lowRotR{2}O also consists of H\high{+} and OH\high{--}.There are two main carbon isotopes: \lohi{6}{12}C and \lohirotate[leftrotation=270]{6\ix R}{13}C.</texcode>

<context>\rotate[rotation=90]{\ss Hstartchemical \low{2}O also consists of Hchemical[SIX,B,C,MOV2,B,C,R234,RZ234,MOV5,MOV6,B,C,R561,RZ561] [\RotR,\high{+} and OHRotR,\high{--}.RotR,\crlfThere are two main carbon isotopes: RotR,\lohi{6}{12}C and RotR,\lohi[leftRotR]{6}{13\stopchemical}C.

Taco's macros implement this approach [http[Image://archivechemistry_example3.contextgarden.net/thread/20060702.084423.a201a280.en.htmlpng]]:

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]<texcodecontext source="yes">\newboxdefinechemical[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]}\chemlowboxstartchemical[scale=big,size=big,left=2600,right=4200,bottom=2800,top=4500]\defbottext{Histidine}\chemlow#chemical[SIX,SB23]\chemical[PB:Z1,SAVE,radical,RESTORE,PE]\chemical[PB:Z2,ONE,SB37,Z03,PE][\SL{C^{\alpha}},H^{\alpha 1%}]\chemical[PB:Z3,SIX,Z5,SB4,Z4,PE][N,H] {\setboxcolor{blue}\chemlowboxchemical[PB:Z4,SIX,Z2,SB2,DB1,Z31,PE][C{\hboxtext{\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}\switchtobodyfontchemical[smallPB:Z2,SIX,Z4,SB34,Z53,PE]#[N{\text{\tiny{+1}}},H{\text{\tiny{+1}}},\SL{CH_3}]}\stopchemical</context> [[Image:histidine.png]]

% An alternative to using the chemistry module or mathmode for "kerning" after F\newif\iffluortypesetting simple formulae are the ConTeXt commands {{cmd|high}}, {{cmd|low}}, {{cmd|lohi}}, and {{cmd|himilo}}. 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).

\unexpanded\def\molecule%<context source="yes"> {\bgroup \catcode`\_=\active \uccode`\~=`\_ ss H\uppercaselow{\let~\chemlow2}% O also consists of H\catcode`\^=\active \uccode`\~=`\^ \uppercasehigh{\let~\chemhigh+}% and OH\dostepwiserecurse high{65--}{90}{1} {\catcode \recurselevel = \active \uccode`\~=.\recurselevelcrlf There are two main carbon isotopes: \uppercaselohi{\edef~6}{\noexpand\finishchem \rawcharacter{\recurselevel}}}12}% \uccode `\~=`C and \F \uppercaselohi[left]{\def~{\finishchem F\fluortrue6}}% \catcode`\-=\active \uccode`\~=`\- \uppercase{\def~{--}13}%C. \loggingall \domolecule }%</context>

\def\domolecule#1% {\expandafter\scantokens\expandafter {\detokenize{#1\finishchem}}\egroup}<Taco’s macros implement this approach [http:/texcode>/archive.contextgarden.net/thread/20060702.084423.a201a280.en.html]:

<contextsource="yes">

{\bsx bs Bold slanted molecules: \molecule{HSO_4^-} and \molecule{SF_6}} 

The main difference with the official chemic module built-in chemistry is that the <code>\modleculemolecule</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 you’re writing dozens of formulas). Hans's module is also more powerful (can do much more trickery than a simple conversion of subscripts and superscripts). See the manuals listed above.

Alternatively one you can setup the <code>style</code> parameter used for chemical formulas manually:

== Chemical structures Old Links == (see also [http://mitglied.lycos.de/ppchtex/00index.html PPCHTeX structure database]) <texcode>\usemodule[chemic]  \starttext \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 \stoptext</texcode> [[Image:Chemistry_example1.png]] <texcode>\usemodule[chemic]\setupchemical[width=fit] \starttext \startchemical \chemical[SIX,B,C,MOV2,B,C,R234,RZ234,MOV5,MOV6,B,C,R561,RZ561] [R,R,R,R,R,R]\stopchemical \stoptext</texcode> [[Image:chemistry_example2.png]] To draw this structure horizontally:<texcode>\usemodule[chemic]\setupchemical[width=fit] \def\RotR{\rotate[rotation=270]{\ix R}} \starttext \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} \stoptext</texcode> [[Image:chemistry_example3.png]]