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* [[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{--}.\crlf
There are two main carbon isotopes: \lohi{6}{12}C and \lohi[left]{6}{13}C.
</context>
Taco's macros implement this approach [http://archive.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-.1em \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-.1em \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}}
</context>
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 manuals listed above.
Alternatively one can setup the <code>style</code> parameter used for chemical formulas manually:
<texcode>
\setupchemical[style=\bs]
</texcode>
== 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,-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]]
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]
<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{-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
</texcode>
[[Image:histidine.png]]
[[Category:Graphics]]
[[Category:Chemistry]]
