Drawing chemical structures
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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
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Hello,
We have completely rewritten the chemical macros from ppchtex, taking
some liberty with some details of the syntax. I will look into your
examples to see what is going wrong.
Alan
On Thu, 21 Nov 2013 18:10:45 +0000
DesdeChaves
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
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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
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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On Thu, 21 Nov 2013 15:55:09 -0500
Aditya Mahajan
Unicode alpha gets translated to \greekalpha, so you need a font (like dejavu) that includes those glyphs
Yes, thanks for this clarification. When I tested this earlier, I was indeed using dejavu... In the chemistry macros, we are using a particular version of mathematics mode (subscripts, superscripts, ...) but in normal font, so greek characters, etc. will work if the font includes them. Alan
participants (3)
-
Aditya Mahajan
-
Alan Braslau
-
DesdeChaves