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ConTeXt comes with the extensive chemistry module [[PPCHTeX ]] which allows the drawing of chemical structures and the typesetting of reactions.
[[PPCHTeX ]] works with plainTeXplain TeX, LaTeX and - of cause course - with ConTeXt.
* [http://www.pragma-ade.com/ppchtex.htm PPCHTeX (general)] by Pragma
* [http://www.pragma-ade.com/document.htm PPCHTeX documenatationdocumentation] by Pragma
* [http://www.ntg.nl/mailman/listinfo/ntg-ppchtex PPCHTeX mailing list]
* [http://www.ntg.nl/pipermail/ntg-ppchtex/ PPCHTeX mailing list archive]
Some other links about chemistry in ConTeXt:
* [[Chromatograms]] macro
* [[manual:xchemml-p.pdf|ChemML]] ([[manual:xchemml-s.pdf|screen]]), [[MathML]] extension for chemistry === Formulae with chemic module === <texcode> \usemodule[chemic]\chemical{HSO_4^{-}}</texcode> <context> \usemodule[chemic]\chemical{HSO_4^{-}}</context> * It can also be used to typeset chemical ''reactions'' <texcode>\usemodule[chemic]\startformula \chemical{2H_2,+,O_2,->,2H_2O}\stopformula</texcode>  <context>\usemodule[chemic]\startformula \chemical{2H_2,+,O_2,->,2H_2O}\stopformula</context> === Simple Formulae in Text Mode === 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 (in titles or slanted fonts, although that might not be desired in all situations). <texcode>\ss H\low{2}O also consists of H\high{+} and OH\high{--}.There are two main carbon isotopes: \lohi{6}{12}C and \lohi[left]{6}{13}C.</texcode> <context>\ss H\low{2}O also consists of H\high{+} and OH\high{--}.\crlfThere are two main carbon isotopes: \lohi{6}{12}C and \lohi[left]{6}{13}C.</context> Taco's macros implement this approach [http://wwwarchive.contextgarden.net/thread/20060702.084423.a201a280.en.html]: <texcode>\newbox\chemlowbox\def\chemlow#1% {\setbox\chemlowbox\hbox{{\switchtobodyfont[small]#1}}} \def\chemhigh#1% {\ifvoid\chemlowbox \high{{\switchtobodyfont[small]#1}}% \else \/\lohi{\box\chemlowbox}{{\switchtobodyfont[small]#1}}\fi } \def\finishchem% {\ifvoid\chemlowbox \else \iffluor \fluorfalse \kern-.pragma1em \fi\low{\box\chemlowbox}\fi} % for "kerning" after F\newif\iffluor \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`\-=\active \uccode`\~=`\- \uppercase{\def~{--}}% \loggingall \domolecule }% \def\domolecule#1% {\expandafter\scantokens\expandafter {\detokenize{#1\finishchem}}\egroup}</texcode> <texcode>\bs Bold slanted molecules: \molecule{HSO_4^-} and \molecule{SF_6}</texcode> <context>\newbox\chemlowbox\def\chemlow#1% {\setbox\chemlowbox\hbox{{\switchtobodyfont[small]#1}}} \def\chemhigh#1% {\ifvoid\chemlowbox \high{{\switchtobodyfont[small]#1}}% \else \/\lohi{\box\chemlowbox}{{\switchtobodyfont[small]#1}}\fi } \def\finishchem% {\ifvoid\chemlowbox \else \iffluor \fluorfalse \kern-ade.com1em \fi\low{\box\chemlowbox}\fi} % for "kerning" after F\newif\iffluor \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`\-=\active \uccode`\~=`\- \uppercase{\def~{--}}% \loggingall \domolecule }% \def\domolecule#1% {\expandafter\scantokens\expandafter {\detokenize{#1\finishchem}}\egroup} {\bsx Bold slanted molecules: \molecule{HSO_4^-} and \molecule{SF_6}} </generalcontext> The main difference with the official chemic module is that the <code>\modlecule</code> from this example uses the same font as the one in surrounding text, while the official module always uses roman font (which is probably the proper way if 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 manualslisted above. Alternatively one can setup the <code>style</code> parameter used for chemical formulas manually: <texcode>\setupchemical[style=\bs]</xchemmltexcode> == Chemical structures == (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,-pRZ1235][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.pdf ChemMLpng]]   An example of an amino acid: Histidine (Ace-His-Nme).The rest of the amino acids are shown in [http://wwwtt4sci.pragma-adewordpress.com/general2009/08/05/manualsdrawing-organic-molecules-in-latex-ii-amino-acids/xchemmlTT4Sci]<texcode>\usepackage{color}\usepackage{m-pictex,m-ch-en} \definechemical[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[scale=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{C^{\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{-s1}}}]}\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</texcode> [[Image:histidine.pdf screenpng]] [[Category:Graphics]][[Category:Chemistry]]), MathML extension for chemistry
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