From mboxrd@z Thu Jan 1 00:00:00 1970 X-Msuck: nntp://news.gmane.io/gmane.comp.tex.context/85368 Path: news.gmane.org!not-for-mail From: DesdeChaves Newsgroups: gmane.comp.tex.context Subject: Drawing chemical structures Date: Thu, 21 Nov 2013 18:10:45 +0000 Message-ID: Reply-To: mailing list for ConTeXt users NNTP-Posting-Host: plane.gmane.org Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="===============0145568723==" X-Trace: ger.gmane.org 1385057446 11525 80.91.229.3 (21 Nov 2013 18:10:46 GMT) X-Complaints-To: usenet@ger.gmane.org NNTP-Posting-Date: Thu, 21 Nov 2013 18:10:46 +0000 (UTC) To: ntg-context@ntg.nl Original-X-From: ntg-context-bounces@ntg.nl Thu Nov 21 19:10:52 2013 Return-path: Envelope-to: gctc-ntg-context-518@m.gmane.org Original-Received: from balder.ntg.nl ([5.39.185.229]) by plane.gmane.org with esmtp (Exim 4.69) (envelope-from ) id 1VjYiK-0000iQ-KK for gctc-ntg-context-518@m.gmane.org; Thu, 21 Nov 2013 19:10:52 +0100 Original-Received: from localhost (localhost [127.0.0.1]) by balder.ntg.nl (Postfix) with ESMTP id DD39110219; Thu, 21 Nov 2013 19:10:51 +0100 (CET) X-Virus-Scanned: Debian amavisd-new at balder.ntg.nl Original-Received: from balder.ntg.nl ([127.0.0.1]) by localhost (balder.ntg.nl [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 9N8U7cO2j4BS; Thu, 21 Nov 2013 19:10:50 +0100 (CET) Original-Received: from balder.ntg.nl (localhost [IPv6:::1]) by balder.ntg.nl (Postfix) with ESMTP id E9B40101F7; Thu, 21 Nov 2013 19:10:49 +0100 (CET) Original-Received: from localhost (localhost [127.0.0.1]) by balder.ntg.nl (Postfix) with ESMTP id 3E6B6101F7 for ; Thu, 21 Nov 2013 19:10:48 +0100 (CET) X-Virus-Scanned: Debian amavisd-new at balder.ntg.nl Original-Received: from balder.ntg.nl ([127.0.0.1]) by localhost (balder.ntg.nl [127.0.0.1]) (amavisd-new, port 10024) with LMTP id YKxOjMmEGRQf for ; Thu, 21 Nov 2013 19:10:46 +0100 (CET) Original-Received: from filter4-ams.mf.surf.net (filter4-ams.mf.surf.net [192.87.102.72]) by balder.ntg.nl (Postfix) with ESMTP id D7091101F6 for ; Thu, 21 Nov 2013 19:10:46 +0100 (CET) Original-Received: from mail-oa0-x22c.google.com (mail-oa0-x22c.google.com [IPv6:2607:f8b0:4003:c02::22c]) by filter4-ams.mf.surf.net (8.14.3/8.14.3/Debian-9.4) with ESMTP id rALIIGO8016418 for ; Thu, 21 Nov 2013 19:18:16 +0100 Original-Received: by mail-oa0-f44.google.com with SMTP id m1so126469oag.31 for ; Thu, 21 Nov 2013 10:10:45 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:date:message-id:subject:from:to:content-type; bh=e0tTWM22E8P09/7YlpSrRdasOPFSjCSk7PkqWoYLYzw=; b=cY4e5tS+Arc/LFu5oYTWFTjdvg+OF/3KjJShHb4zPA/QfVfzc5WUqHO15nNdgP0UId /rl5eR36XvoNVq+3e7YUFZ0In4ZDpd+yXosE039uCdJCow5CdsHc0C3MHqsWWCVyuq2m VAlIZ1FKJkhC+NB3ekXYfn7WknbHa+71CiNYa6xtz9u2eOtWHOpBKwNvWfjoD7yMwqLP T+1OYJRiZewYKZEhTMk+sTw1l5XcOCxu+6V4Jn5R58BZQKcuzTX91DaT2SzHxpKJnnta QIAlfVhAitwmeEyxeWpLSrSzTfNXiDjVjbTSIe5mFd6rBXyhyhI1uyCcB2reKv9gSnpG sxsw== X-Received: by 10.60.47.228 with SMTP id g4mr6655087oen.10.1385057445274; Thu, 21 Nov 2013 10:10:45 -0800 (PST) Original-Received: by 10.60.93.131 with HTTP; Thu, 21 Nov 2013 10:10:45 -0800 (PST) X-Bayes-Prob: 0.0012 (Score 0, tokens from: @@RPTN) X-CanIt-Geo: ip=2607:f8b0:4003:c02::22c; country=US X-CanItPRO-Stream: uu:ntg-context@ntg.nl (inherits from uu:default, base:default) X-Canit-Stats-ID: 01KQiigqa - 645bf60b3ca9 - 20131121 X-Scanned-By: CanIt (www . roaringpenguin . com) X-BeenThere: ntg-context@ntg.nl X-Mailman-Version: 2.1.14 Precedence: list List-Id: mailing list for ConTeXt users List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: ntg-context-bounces@ntg.nl Original-Sender: ntg-context-bounces@ntg.nl Xref: news.gmane.org gmane.comp.tex.context:85368 Archived-At: --===============0145568723== Content-Type: multipart/alternative; boundary=001a11c2fcf604eae804ebb3d102 --001a11c2fcf604eae804ebb3d102 Content-Type: text/plain; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable 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=3Dfit,scale=3Dsmall,size=3Dbig] \bottext{=E1-Glycerophosphate} \chemical[ONE,SB1357,Z0357][\TL{=E1}{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=3D6500,top=3D2000,bottom=3D2500,width=3D4500] \chemical[desoxyribose] \bottext{Desoxiribosa (dR)} \stopchemical \startchemical[height=3D4500,bottom=3D2500] \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=3D4500,bottom=3D2500] \chemical [FIVE,FRONT,B,R] \chemical [+RZ1..5] [1,2,3,4,5] \chemical [-RZ1..5] [a,b,c,d,e] \stopchemical \stoptext --001a11c2fcf604eae804ebb3d102 Content-Type: text/html; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable
Dear Sirs,

I'm trying to run = some code from the ppchtex manual, however, the chemical structures are not= correctly drawn. See the example:=A0https://www.dropbox.com/s/w7v8kouc4glndf0/c= hemicerror.pdf.

I found this problem en Minimals (last vers= ion) and on TexLive 2013.


\setupbodyfont[11pt]
\usemodule[chemic]
\starttext


\startchemical[width=3Df= it,scale=3Dsmall,size=3Dbig]
\bottext{=E1-Glycerophosphate}
=
\chemical[ONE,SB1357,Z0357][\TL{=E1}{C},\SL{OPO\lohi{3}{2-}},H,H]
\chemical[MOV1,SB137,Z037][C,\SL{OH},H]
\chemical[MOV1,SB137,Z013= 7][C,H,\SL{OH},H]
\stopchemical



\definechemical[desoxyribose]
{\chemical[FI= VE,FRONT,BB125,+SB3,-SB4,Z4][O]
\chemical[FIVE,FRONT,+R1235,+RZ1235][H,H,\SR{HOH_2C},OH]
\ch= emical[FIVE,FRONT,-R1235,-RZ1235][H,OH,H,H]}

\star= tchemical[height=3D6500,top=3D2000,bottom=3D2500,width=3D4500]
\c= hemical[desoxyribose]
\bottext{Desoxiribosa (dR)}
\stopchemical

\startchemical[height=3D4500,bottom=3D2500]
\bottext{$\alp= ha$-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

\startchemic= al[height=3D4500,bottom=3D2500]
\chemical [FIVE,FRONT,B,R]
\chemical [+RZ1..5] [1,2,3,4,5]
\chemical [-RZ1..5] [a,b,c,d,e]
\stopchemical
=


\stoptext
--001a11c2fcf604eae804ebb3d102-- --===============0145568723== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline ___________________________________________________________________________________ If your question is of interest to others as well, please add an entry to the Wiki! maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context webpage : http://www.pragma-ade.nl / http://tex.aanhet.net archive : http://foundry.supelec.fr/projects/contextrev/ wiki : http://contextgarden.net ___________________________________________________________________________________ --===============0145568723==--