Re: Drawing chemical structures

[Alan Braslau <alan.braslau@cea.fr>]

Indeed, there have been a few changes,
several rationalizations of the syntax:

1. FIVE,FRONT has become FIVEFRONT
2. positions are numbered coherently with FIVE
   (previously they were shifted by one)
3. +R and -R have become LR and RR,
   to be coherent with the non-front structures.
4. Thus, +LSR and -RSR are the asymmetrically shortened
   versions drawing bonds.
5. One can still use dimensional measurements in the thousands,
   but it is preferable to use numbers close to unity, interpreted
   in units of the bond length.
6. The bounding box is by default fit (in ppchtex it was fixed
   4000x4000). Placing labels thus generally requires specifying
   a top or bottom dimension.

Below is your example, corrected.
(For some reason, unicode \alpha currently disappears - a font issue.
This worked early so is indeed a bug.)

A complete new manual has been written. We are currently hung on one or
two minor details that Hans and myself have not yet take care of - just
a question of getting around to it. Indeed, we NEED to release the new
manual...

Alan


\setupbodyfont[11pt]
\starttext

\startchemical[bottom=1.75,size=big,frame=on]
\bottext{\alpha-Glycerophosphate}
\chemical[ONE,SB1357,Z0357][\TL{\alpha}{C},\SL{OPO\lohi{3}{2-}},H,H]
\chemical[MOV1,SB137,Z037][C,\SL{OH},H]
\chemical[MOV1,SB137,Z0137][C,H,\SL{OH},H]
\stopchemical

\definechemical[desoxyribose]
{\chemical[FIVEFRONT,BB123,+SB4,-SB5,Z5][O]
\chemical[FIVEFRONT,+LSR1234,LRZ1234][OH,H,H,\SR{HOH_2C}]
\chemical[FIVEFRONT,+RSR1234,RRZ1234][H,H,OH,H]}

\startchemical[width=3.5,bottom=2,frame=on,axis=on]
\chemical[desoxyribose]
\bottext{Desoxiribosa (dR)}
\stopchemical

\startchemical[width=4,bottom=2,frame=on]
\bottext{$\alpha$-D-Fructofuranose}
\chemical[FIVEFRONT,BB123,+SB4,-SB5,Z5][O]
\chemical[FIVEFRONT,+LSR1234,LRZ1234][CH_2OH,\SR{HO},H,\SR{HOH_2C}]
\chemical[FIVEFRONT,-RSR123,RRZ123][OH,H,\SR{HO},H]
\stopchemical

\startchemical[frame=on]
\chemical [FIVEFRONT,B,+LSR,+RSR]
\chemical [LRZ1..5] [1,2,3,4,5]
\chemical [RRZ1..5] [a,b,c,d,e]
\stopchemical

\stoptext





On Thu, 21 Nov 2013 18:10:45 +0000
DesdeChaves <desdechaves@gmail.com> wrote:

> Dear Sirs,
> 
> I'm trying to run some code from the ppchtex manual, however, the
> chemical structures are not correctly drawn. See the example:
> https://www.dropbox.com/s/w7v8kouc4glndf0/chemicerror.pdf.
> 
> I found this problem en Minimals (last version) and on TexLive 2013.
> 
> 
> \setupbodyfont[11pt]
> \usemodule[chemic]
> \starttext
> 
> 
> \startchemical[width=fit,scale=small,size=big]
> \bottext{α-Glycerophosphate}
> \chemical[ONE,SB1357,Z0357][\TL{α}{C},\SL{OPO\lohi{3}{2-}},H,H]
> \chemical[MOV1,SB137,Z037][C,\SL{OH},H]
> \chemical[MOV1,SB137,Z0137][C,H,\SL{OH},H]
> \stopchemical
> 
> 
> 
> \definechemical[desoxyribose]
> {\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]}
> 
> \startchemical[height=6500,top=2000,bottom=2500,width=4500]
> \chemical[desoxyribose]
> \bottext{Desoxiribosa (dR)}
> \stopchemical
> 
> \startchemical[height=4500,bottom=2500]
> \bottext{$\alpha$-D-Fructofuranose}
> \chemical
> [FIVE,FRONT,BB125,+SB3,-SB4,Z4][O]
> \chemical
> [FIVE,FRONT,+R1235,+RZ1235][\SR{HO},H,\SR{HOH_2C},CH_2OH]
> \chemical
> [FIVE,FRONT,-R1235,-RZ1235][OH,H,\SR{HO},H,CH_2OH]
> \stopchemical
> 
> \startchemical[height=4500,bottom=2500]
> \chemical [FIVE,FRONT,B,R]
> \chemical [+RZ1..5] [1,2,3,4,5]
> \chemical [-RZ1..5] [a,b,c,d,e]
> \stopchemical
> 
> 
> 
> \stoptext


-- 
Alan Braslau
CEA DSM-IRAMIS-SPEC
CNRS URA 2464
Orme des Merisiers
91191 Gif-sur-Yvette cedex FRANCE
tel: +33 1 69 08 73 15
fax: +33 1 69 08 87 86
mailto:alan.braslau@cea.fr
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