Re: [NTG-context] ppchTeX

[Henri Menke]

Dear Alan,

thanks a lot for fixed code.  Could you point out where to find the
updated manual for MkIV?

Cheers,
Henri

On 07/07/2016 08:26 PM, Alan BRASLAU wrote:
> On Wed, 6 Jul 2016 18:23:57 +0200
> Henri Menke  wrote:
> 
>> Dear list,
>>
>> I just wanted to check whether chemical structures typeset in ConTeXt
>> can be exported as XML.  Therefore I wanted to setup a simple example
>> with ppchTeX.  I copied example 3.1 from the manual [1]
>>
>>> \usemodule[chemic]
>>> \starttext
>>>
>>> \startchemical[height=4500,bottom=2500]
>>>   \bottext{$\beta$-D-Fructopyranose}
>>>   \chemical[SIX,FRONT,BB1236,+SB4,-SB5,Z5][O]
>>>   \chemical[SIX,FRONT,+R12346,+RZ12346][\SR{HO},H,H,H,OH]
>>>   \chemical[SIX,FRONT,-R12346,-RZ12346][H,OH,\SR{HO},H,CH_2OH]
>>> \stopchemical
>>>
>>> \stoptext  
>>
>> Unfortunately, typesetting with MkIV distributed with TL 2016 produces
>> something really weird (see attached).
>>
>> Is the module `chemic` compatible with MkIV or am I doing something
>> wrong?
>>
>> Cheers,
>> Henri
>>
>> [1] http://www.pragma-ade.nl/general/manuals/mp-ch-en.pdf
> 
> 
> \usemodule[chemic] is MKII. It has been replace with core MKIV commands.
> 
> The syntax has been somewhat rationalized and many bugs corrected.
> 
> The example can be reproduced as follows:
> 
> 
> \starttext
> 
> \startchemical [height=4500,bottom=2500]
>   \bottext{$\beta$-D-Fructopyranose}
>   \chemical[SIXFRONT,BB123,B4,+SB5,-SB6,Z6] [O]
>   \chemical[+LR12345,LRZ12345] [OH,\SR{HO},H,H,H]
>   \chemical[+RR12345,RRZ12345] [CH_2OH,H,\SL{OH},\SR{HO},H]
> \stopchemical
> 
> \stoptext 
> 
> 
> 
> Unfortunately, the revised manual still has some errors that I need to
> fix...
> 
> Alan
> 

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Re: [NTG-context] ppchTeX

[Alan BRASLAU]

On Wed, 6 Jul 2016 18:23:57 +0200
Henri Menke  wrote:

> Dear list,
> 
> I just wanted to check whether chemical structures typeset in ConTeXt
> can be exported as XML.  Therefore I wanted to setup a simple example
> with ppchTeX.  I copied example 3.1 from the manual [1]
> 
> > \usemodule[chemic]
> > \starttext
> > 
> > \startchemical[height=4500,bottom=2500]
> >   \bottext{$\beta$-D-Fructopyranose}
> >   \chemical[SIX,FRONT,BB1236,+SB4,-SB5,Z5][O]
> >   \chemical[SIX,FRONT,+R12346,+RZ12346][\SR{HO},H,H,H,OH]
> >   \chemical[SIX,FRONT,-R12346,-RZ12346][H,OH,\SR{HO},H,CH_2OH]
> > \stopchemical
> > 
> > \stoptext  
> 
> Unfortunately, typesetting with MkIV distributed with TL 2016 produces
> something really weird (see attached).
> 
> Is the module `chemic` compatible with MkIV or am I doing something
> wrong?
> 
> Cheers,
> Henri
> 
> [1] http://www.pragma-ade.nl/general/manuals/mp-ch-en.pdf


\usemodule[chemic] is MKII. It has been replace with core MKIV commands.

The syntax has been somewhat rationalized and many bugs corrected.

The example can be reproduced as follows:


\starttext

\startchemical [height=4500,bottom=2500]
  \bottext{$\beta$-D-Fructopyranose}
  \chemical[SIXFRONT,BB123,B4,+SB5,-SB6,Z6] [O]
  \chemical[+LR12345,LRZ12345] [OH,\SR{HO},H,H,H]
  \chemical[+RR12345,RRZ12345] [CH_2OH,H,\SL{OH},\SR{HO},H]
\stopchemical

\stoptext 



Unfortunately, the revised manual still has some errors that I need to
fix...

Alan
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Re: [NTG-context] PPCHTEX: bonds overlaps the radicals groups

[Alan BRASLAU]

On Mon, 28 Sep 2015 15:37:27 +0100
DesdeChaves  wrote:

> I try inserting several \chemical[ONE, .2MOV1] statements in some key
> places, but without success. Can you provide me a very simple example?

The idea is to draw the bond, then move, then the atom:

\chemical [ONE,SB5,Z5,.2MOV1,Z0,.2MOV1,SB1,1.2MOV1,Z0] [H_3C,CH_2,CH_2]

a bit sloppy, perhaps, but such is the syntax.
On the other hand, one can make multiple calls to \chemical, thus
making the code more readable.

Alternately, one can shorten the bond segments which are defined as
[.25,.75] of the bond length, but this turns out to be less aesthetic
than adding small moves.

One could imagine also to draw the text inside a framed box using a
white background, as in
\framed[frame=off,background=color,backgroundcolor=white]{\chemical{CH_2}}
but I do not like this solution at all.


I suppose that we could modify the underlying MP code to avoid
extending any bond over the text box, but this would impose that the
user draw the nodes before the bonds and would surely fail as one
builds molecules in segments (unless the user be fully aware of the
drawing process). We decided that this would be worse.

Alan
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Re: [NTG-context] PPCHTEX: bonds overlaps the radicals groups

[Alan BRASLAU]

On Sun, 27 Sep 2015 18:00:23 +0100
DesdeChaves  wrote:

> Some time ago I wrote the code attached to create random branched
> organic molecules. However, with recent versions of Context the
> carbon-carbon bonds overwrites the radicals. How can I fix this?

The mkiv chemistry module (replacing the mkii PPCHTEX code) uses
tighter spacing around the nodes, which looks nicer with single atomic
symbols. You are placing CH and CH_2 groups so it is necessary to
increasing the spacing at these spots. One trick could be:
  \chemical [ONE,.2MOV1]
which moves .2 bond lengths in the x-direction.

You also need to pay attention to the automatic alignment of symbols,
in particular when using ONE. For Z0 is centered, Z1 is right adjusted,
Z5 is left adjusted... One can explicitly fix the alignment using:
  \chemical [ONE,simalign=lft,Z1]
(MetaPost alignment keys) but it is much easier to leave simalign=auto
and to choose appropriate nodes (using [ONE,MOV1,Z0] rather than
[ONE,Z1] for example).


> Another question: is there a way to change the bonds color? I would
> like to blank some radicals and bonds and ask the students to draw it.

\chemical [rulecolor=red,ONE,B]

Of course, it is a "global" so you will need to use multiple calls in
order to color particular bonds.

Alan
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Re: [NTG-context] ppchtex, color and mkiv

[Alan BRASLAU]

On Friday 19 November 2010 09:52:47 Jörg Hagmann wrote:
  From a thread on this list (May 2009:
 http://archive.contextgarden.net/message/20090512.132914.5c29b5f4.en.html)
 I gather that whereas colouring a whole molecule works fine, colouring
 groups within a chemical structure is not yet fully implemented in mkiv.
   Is that still correct?
 
 Putting colour on atoms works with {\blue C} etc. or \defineprocessor
 ... etc. chemred-C etc.. However, I couldn't find a way to colour the
 bonds belonging to the group. Is there one?

The only way that I managed to do this is to draw the chemical twice and to 
use overlays (or to trick the bounding box using left=,right=,top=,bottom=). 
It would be nice to be able to draw colored bonds, perhaps with the syntax:
\chemical[SIX,rulecolor=blue,SB1,rulecolor=black,SB2..6][]

The problem is that we usually don't mix single tokens with token=val.
(but Hans has broken this rule with an experimental feature: Z1=C, currently 
broken as it converts C to lowercase...)

For now, rulecolor= can only be specified in \startchemical or \setupchemical.

Maybe we can discuss this with Hans off-list?

Alan
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Re: [NTG-context] ppchtex questions

[Jörg Hagmann]

Hi Alan,

Thanks for the explanations.


Try style=sans. We also have color= and rulecolor=.


syle=sans works, but not for aligned atoms, e.g. \SL{OH}; a bug? For the 
time being, I can use \SL{\ss OH}.



There are some problems still in mkiv, notably with CARBON, NEWMANSTAGGER,
NEWMANECLIPSE, and CHAIR. Hans (and I) intend to work on this but it is not
too high of a priority for the moment. Let me know if you have other problems
in using ppchtex.


I'm sure there will be more questions!

I'm using context version 2010.09.05 13.23, have there been any 
improvements since then?


Thanks, Jörg
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Re: [NTG-context] ppchtex questions

[Alan BRASLAU]

On Thursday 18 November 2010 10:54:23 Jörg Hagmann wrote:
 
 syle=sans works, but not for aligned atoms, e.g. \SL{OH}; a bug? For the
 time being, I can use \SL{\ss OH}.
 

There are indeed bugs in the use of \SL{} under mkiv.  For example, one 
currently needs to use \SL{\small CH$_2$} rather than \SL{CH_2} as one would 
expect (use of both \small and explicit math mode). The same is true for any 
text macro, i.e. \rotate[rotation=+30]{\small N$|$NH}.

Hans is on copy as he can probably find the bug rapidly, that is once he can 
find the time to look into this.

Alan
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Re: [NTG-context] ppchtex questions

[Alan BRASLAU]

On Wednesday 17 November 2010 12:37:34 Jörg Hagmann wrote:
 I just started using (and liking) ppchtex, and I have a few questions:
 
 1. Is there a way to define a frame offset (there is fit and there are
 dimensions, but an offset would be more convenient)?

[left=,top=]

I'll look into your other questions a little later today.

Are you using mkii (texexec) or mkiv (context) or LaTeX?

Alan
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Re: [NTG-context] ppchtex questions

[Jörg Hagmann]

Thanks, Alan.

On 11/17/10 2:13 PM, Alan BRASLAU wrote:

1. Is there a way to define a frame offset (there is fit and there are
dimensions, but an offset would be more convenient)?


[left=,top=]


This gives absolute values. I would prefer something giving me fit + 
dimension


I'll look into your other questions a little later today.


When playing with top, bottom etc again I discovered that increasing the 
bottom dimension also moves \bottext down.  So there only remains 
question number 3: I would like the atom labels (but not the bodyfont of 
the document) as \ss -- without including \ss for every single atom.



Are you using mkii (texexec) or mkiv (context) or LaTeX?


I am using mkiv (of course!)...

Thanks again, Jörg
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Re: [NTG-context] ppchtex questions

[Alan BRASLAU]

On Wednesday 17 November 2010 16:21:49 Jörg Hagmann wrote:
 Thanks, Alan.
 
 On 11/17/10 2:13 PM, Alan BRASLAU wrote:
  1. Is there a way to define a frame offset (there is fit and there are
  dimensions, but an offset would be more convenient)?
  
  [left=,top=]
 
 This gives absolute values. I would prefer something giving me fit +
 dimension

width=,left=,right=,height=,top=,bottom= (of course, only two of width, left, 
and right are to be used at a time, as well as two of height, top, and bottom) 
define the bounding box of the drawing. This is given in units of 4000 per 
standard bond length. To visualize this, try,

\startchemical [frame=on,axis=on,width=4000,height=4000]
\chemical [ONE,SB,Z0] [O]
\chemical [THREE,B]
\chemical [FOUR,B]
\chemical [FIVE,B]
\chemical [SIX,B,R,RZ] [1,2,3,4,5,6]
\chemical [EIGHT,B]
\stopchemical

For fit+offset, I suggest positioning the chemical drawing inside a 
\framed[frame=off]{} box using offsets, or some other variant (I particularly 
like using collectors).

 When playing with top, bottom etc again I discovered that increasing the
 bottom dimension also moves \bottext down.  So there only remains
 question number 3: I would like the atom labels (but not the bodyfont of
 the document) as \ss -- without including \ss for every single atom.

Try style=sans. We also have color= and rulecolor=.

  Are you using mkii (texexec) or mkiv (context) or LaTeX?
 
 I am using mkiv (of course!)...

There are some problems still in mkiv, notably with CARBON, NEWMANSTAGGER, 
NEWMANECLIPSE, and CHAIR. Hans (and I) intend to work on this but it is not 
too high of a priority for the moment. Let me know if you have other problems 
in using ppchtex.

Alan
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Re: [NTG-context] PPCHTEX with PSTricks option

[Helge Kruse]

Am 07.05.2010 20:38, schrieb Marius:

http://wiki.contextgarden.net/ConTeXt_Minimals#Installation_and_use_on_Windows


I downloaded context-setup-mswin.zip, unzipped it to
  C:\Program Files(x86)\context
and ran first-setup.bat --context=current. Now I have a Directory 
C:\Program\context. In the command prompt window I can see a lot of 
error messages like


  rsync: change_dir 
/cygdrive/c/Program/texmf-context/scripts/context/lua failed: No such 
file or directory (2)


  rsync: change_dir /current/context/=current (in minimals) failed: 
No such file or directory (2)


I also created a shortcut to a command prompt as described in the wiki. 
The command prompt opens but context fails to start:


  C:\Users\Helge\Documents\TeX\contextcontext
  'context' is not recognized as an internal or external command,
  operable program or batch file.

  C:\Users\Helge\Documents\TeX\context

I found in the wiki:
  It is recommended that you choose a directory that does not have a
  space in its full path.

Ok. This recommendation should be a least a warning. But currently I 
have some new questions:

- How do I uninstall context?
- Which directories have been modified by the installer? Where do I have 
to repair my system?


Best regards,
Helge
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Re: [NTG-context] PPCHTEX with PSTricks option

[Hans Hagen]

On 7-5-2010 9:12, Alan BRASLAU wrote:


ppchtex has been rewritten for conTeXt using luatex
and line drawing has been considerably improved.
However, I do not believe that this version will (ever)
be adapted for use with LaTeX. Perhaps Hans can give
you a better answer.


indeed the mkiv reimplementation will not be backported to latex as it 
involved a combination of tex, lua and mp now and is integrated into the 
context kernel (we have math in the kernel so why not chemistry)



I tried your example, with decent results (see test.pdf)
with the latest texlive version of pdflatex.
Yet trying the pstricks driver gives an error:

! Undefined control sequence.
recently read  \...@lor@t...@ps


looks like a pstricks is not loadec completely

i cannot test it here as pstricks with ppchtex in mkii does not work 
that well because i need to support latex and using the context pstricks 
layer would then complicat ethe code (in mkii we use metapost instead 
anyway)


Hans

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Re: [NTG-context] PPCHTEX with PSTricks option

[Alan BRASLAU]

On Friday 07 May 2010 10:23:20 Hans Hagen wrote:
 On 7-5-2010 9:12, Alan BRASLAU wrote:
  ppchtex has been rewritten for conTeXt using luatex
  and line drawing has been considerably improved.
  However, I do not believe that this version will (ever)
  be adapted for use with LaTeX. Perhaps Hans can give
  you a better answer.
 
 indeed the mkiv reimplementation will not be backported to latex as it
 involved a combination of tex, lua and mp now and is integrated into the
 context kernel (we have math in the kernel so why not chemistry)
 
  I tried your example, with decent results (see test.pdf)
  with the latest texlive version of pdflatex.
  Yet trying the pstricks driver gives an error:
  
  ! Undefined control sequence.
  recently read  \...@lor@t...@ps
 
 looks like a pstricks is not loadec completely
 
 i cannot test it here as pstricks with ppchtex in mkii does not work
 that well because i need to support latex and using the context pstricks
 layer would then complicat ethe code (in mkii we use metapost instead
 anyway)
 
 Hans

Indeed, the problem is that I tried to run the pstricks option
under pdflatex, which, of course, does not work!
As I (almost) never use LaTeX anymore (and certainly never dvips)
I had forgotten about this.

I guess that I have become far too accustomed to ConTeXt and,
in particular, mkiv.

As to the original post, it yields acceptable results. The new ppchtex
in mkiv core is an improvement and, as Hans confirms, will not be backported
to laTeX. This could be one of many good reasons to switch from LaTeX to
ConTeXt!

Alan
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Re: [NTG-context] PPCHTEX with PSTricks option

[Hans Hagen]

On 7-5-2010 8:12, Helge Kruse wrote:

Am 07.05.2010 13:04, schrieb Alan BRASLAU:

On Friday 07 May 2010 10:23:20 Hans Hagen wrote:

On 7-5-2010 9:12, Alan BRASLAU wrote:
indeed the mkiv reimplementation will not be backported to latex as it
involved a combination of tex, lua and mp now and is integrated into the
context kernel (we have math in the kernel so why not chemistry)


So PPCHTEX is frozen for LaTeX?


apart from bug fixes (and/or if someone submits more drawing definitions)

in fact, as we move on to luatex, the context version for pdftex / xetex 
is frozen as well



Indeed, the problem is that I tried to run the pstricks option
under pdflatex, which, of course, does not work!

The pictex output is not convincing, so I hoped the PSTricks output
would gave better result. In general it works, but the diagonal bonds
are too long. I Hoped that this could be fixed.


if we kno wwhere the problem sits it will of course be solved, however 
as i don't run latex i cannot see what goes wrong



Skimming the ppchtex.noc I found that metapost is one possible output
driver. I also found a documentation for metapost. But I don't see how
I can make PPCHTEX work with metapost in LaTeX. I even don't know if
metapost can be used in LaTeX as in ConTeXt.


in context mkii metapost support has been integrated for quite some time 
and in context mkiv it can be processed without noticing so there 
ppchtex uses even more metapost (which is why there are also some extras)



As I (almost) never use LaTeX anymore (and certainly never dvips)
I had forgotten about this.

I guess that I have become far too accustomed to ConTeXt and,
in particular, mkiv.

As to the original post, it yields acceptable results. The new ppchtex
in mkiv core is an improvement and, as Hans confirms, will not be
backported
to laTeX. This could be one of many good reasons to switch from LaTeX to
ConTeXt!

Well I am curious and I would evaluate ConTeXt. I think that
http://www.pragma-ade.com/ will be a good starting point to do that.
Unfortunately I did not found How to install ConTeXt. Can this be done
by adding some packages in MiKTeX 2.8? Probably a silly question...


best start with installing the so called minimals (from 
contextgarden.net) which will give you an independent tree that does not 
interfere with anything else


btw, an easy test is:

\starttext

\startTEXpage

... some chemical ...

\stopTEXpage

\stoptext

which will give you a graphic that you then can include in a latex doc

Hans

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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Hans Hagen]

On 23-4-2010 7:37, Denis Bitouzé wrote:

Le jeudi 22/04/10 à 23h32,
Hans Hagenpra...@wxs.nl  a écrit :


btw, in mkiv ppchtex is reimplemented; it still has some flaws but it
has more room for extensions and is now part of the context mkiv
kernel


As I'm not using ConTeXt for the moment (but it may change! :), what
are the consequences of this for a LaTeX user?


we have context mkii and context mkiv; the new ppchtex module is for 
mkiv and uses a combination of lua, tex and mp; as context and latex are 
quite different (and even more when you consider mkiv) the new ppchtex 
code targets at context


Hans


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le vendredi 23/04/10 à 09h34,
Hans Hagen pra...@wxs.nl a écrit :

 we have context mkii and context mkiv; the new ppchtex module is for 
 mkiv and uses a combination of lua, tex and mp; as context and latex
 are quite different (and even more when you consider mkiv) the new
 ppchtex code targets at context

Too bad... but I can understand...

Thanks!
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le dimanche 18/04/10 à 23h23,
Hans Hagen pra...@wxs.nl a écrit :

 can you check if your ppchtex.noc file has
 
 \input supp-mis.mkii \let\writestatus\undefined
 \input syst-gen.mkii
 \input syst-fnt.mkii
 
 i.e loads the mkii files?

Yes, those lines are present in the file ppchtex.noc:

[bito...@drums ~]$ kpsewhich ppchtex.noc
/usr/local/texlive/2009/texmf-dist/tex/generic/context/ppchtex.noc
[bito...@drums ~]$
cd /usr/local/texlive/2009/texmf-dist/tex/generic/context/
[bito...@drums context]$ more ppchtex.noc | grep mkii
\input supp-mis.mkii \let\writestatus\undefined
\input syst-gen.mkii
\input syst-fnt.mkii
\input ppchtex.mkii
[bito...@drums context]$

Thanks for any further idea! ;)
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 13h41,
Hans Hagen pra...@wxs.nl a écrit :

 can you download the cont-tmf.zip file and unzip it in the texmd-dist
 root?

It works! Well almost: no compilation trouble, but an empty page with
the following MCE:

\documentclass{article}
\usepackage{etex,m-pictex,m-ch-en}
\begin{document}
\startchemical
\chemical{2H_2,PLUS,O_2,GIVES,2H_2O}
\stopchemical
\end{document}

Thanks!
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 15h21,
Denis Bitouzé dbito...@wanadoo.fr a écrit :

 no compilation trouble

Sorry, no error but the following message in the .log file:

ppchtex: the {}{}-alternative is not permitted here
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Hans Hagen]

On 22-4-2010 3:30, Denis Bitouzé wrote:

Le jeudi 22/04/10 à 15h21,
Denis Bitouzédbito...@wanadoo.fr  a écrit :


no compilation trouble


Sorry, no error but the following message in the .log file:

ppchtex: the {}{}-alternative is not permitted here


so use the [][] variant instead ({}{} is for inline)
--

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 | www.pragma-pod.nl
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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 16h42,
Hans Hagen pra...@wxs.nl a écrit :

 so use the [][] variant instead ({}{} is for inline)

OK, that's better :) But the following MCE:

\documentclass{article}
\usepackage{etex,m-pictex,m-ch-en}
\begin{document}
\startchemical
\chemical[2H_2,PLUS,O_2,GIVES,2H_2O]
\stopchemical
\end{document}

leads to the messages:

ppchtex: unknown chemical definition 2H_2
ppchtex: unknown chemical definition O_2
ppchtex: unknown chemical definition 2H_2O

and, indeed, only the + sign and the arrow are printed.

Thanks.
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 16h51,
Denis Bitouzé dbito...@wanadoo.fr a écrit :

 But the following MCE:
 
 \documentclass{article}
 \usepackage{etex,m-pictex,m-ch-en}
 \begin{document}
 \startchemical
 \chemical[2H_2,PLUS,O_2,GIVES,2H_2O]
 \stopchemical
 \end{document}
 
 leads to the messages:
 [...]

Well, the following one:

\documentclass{article}
\usepackage{etex,m-pictex,m-ch-en}
\begin{document}
\chemical{2H_2,PLUS,O_2,GIVES,2H_2O}
\end{document}

is actually OK!

What is strange is that ppchtex \chemical formulas used to be inserted
between \startchemical and \stopchemical... Moreover, the following:

\documentclass{article}
\usepackage{etex,m-pictex,m-ch-en}
\begin{document}
\startchemical
  \chemical[SIX,B,R,RZ][1,2,3,4,5,6]
\stopchemical
\end{document}

works only with \startchemical and \stopchemical.

Are those changes: 

  1. {}{} rather than [][],

  2. pair \startchemical, \stopchemical or not,

  3. etc.

documented somewhere?

Thanks.
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Hans Hagen]

On 22-4-2010 7:09, Denis Bitouzé wrote:


Are those changes:

   1. {}{} rather than [][],

   2. pair \startchemical, \stopchemical or not,

   3. etc.

documented somewhere?


sure, in the ppchtex manual; indeed {}{} is used inline (in math mode or 
not) and [][] between start/stop pairs


Hans

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 | www.pragma-pod.nl
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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Hans Hagen]

On 22-4-2010 7:09, Denis Bitouzé wrote:


Are those changes:

   1. {}{} rather than [][],

   2. pair \startchemical, \stopchemical or not,

   3. etc.


btw, in mkiv ppchtex is reimplemented; it still has some flaws but it 
has more room for extensions and is now part of the context mkiv kernel


Hans

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 | www.pragma-pod.nl
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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 23h32,
Hans Hagen pra...@wxs.nl a écrit :

 btw, in mkiv ppchtex is reimplemented; it still has some flaws but it 
 has more room for extensions and is now part of the context mkiv
 kernel

As I'm not using ConTeXt for the moment (but it may change! :), what
are the consequences of this for a LaTeX user?

Thanks!
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Denis Bitouzé]

Le jeudi 22/04/10 à 23h30,
Hans Hagen pra...@wxs.nl a écrit :

 sure, in the ppchtex manual; indeed {}{} is used inline (in math mode
 or not) and [][] between start/stop pairs

Well, sorry for my misreading...
-- 
Denis


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Re: [NTG-context] [ppchtex] \normalifx: Undefined control sequence

[Hans Hagen]

On 17-4-2010 11:10, Denis Bitouzé wrote:

Hello,

thanks to contributors of this list I was able to use ppchtex with
LaTeX when I encountered a \writestatus: Undefined control sequence
problem:

http://www.ntg.nl/pipermail/ntg-context/2009/044672.html

Everything went well (though I have a little use of ppchtex) but, as I
tried it some days ago, I was facing another trouble pointed out by the
following MCE:

\listfiles{}
\documentclass{article}
\usepackage{etex,m-pictex,m-ch-en}
\begin{document}
\startchemical
\chemical{2H_2,PLUS,O_2,GIVES,2H_2O}
\stopchemical
\end{document}

The error is:

! Undefined control sequence.
\dodogetgroupargument -\normalifx


can you check if your ppchtex.noc file has

\input supp-mis.mkii \let\writestatus\undefined
\input syst-gen.mkii
\input syst-fnt.mkii

i.e loads the mkii files?

i font, get the cont-tmf.zip file from our website and unzip it in your 
tex tree (and run mktexlsr afterwards)


Hans

-
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 | www.pragma-pod.nl
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[luigi scarso]

On Wed, Nov 4, 2009 at 8:12 AM, Denis Bitouzé dbito...@wanadoo.fr wrote:
 Hello everybody,

 with a fresh TeX Live 2009 distribution, I cannot compile old files
 because of \writestatus which seems to be undefined.

 For instance:

 \listfiles
 \documentclass{article}
 \usepackage[utf8]{inputenc}
 \usepackage[T1]{fontenc}
 \usepackage{etex}
 \usepackage{m-pictex,m-ch-en}
 \begin{document}
 Hello World!
 \end{document}
Sorry,
this is ConTeXt mailing list, not LaTeX  mailing list .
-- 
luigi
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Denis Bitouzé]

Le mercredi 04/11/09 à 09h25,
luigi scarso luigi.sca...@gmail.com a écrit :

 Sorry,
 this is ConTeXt mailing list, not LaTeX  mailing list .

OK, but it seems to be a related to ConTeXt problem:

[bito...@drums ~]$ kpsewhich m-pictex.sty
/usr/local/texlive/2009/texmf-dist/tex/latex/context/m-pictex.sty
[bito...@drums ~]$ kpsewhich m-ch-en.sty
/usr/local/texlive/2009/texmf-dist/tex/latex/context/m-ch-en.sty
-- 
Denis


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[luigi scarso]

On Wed, Nov 4, 2009 at 9:54 AM, Denis Bitouzé dbito...@wanadoo.fr wrote:
 Le mercredi 04/11/09 à 09h25,
 luigi scarso luigi.sca...@gmail.com a écrit :

 Sorry,
 this is ConTeXt mailing list, not LaTeX  mailing list .

 OK, but it seems to be a related to ConTeXt problem:

 [bito...@drums ~]$ kpsewhich m-pictex.sty
 /usr/local/texlive/2009/texmf-dist/tex/latex/context/m-pictex.sty
 [bito...@drums ~]$ kpsewhich m-ch-en.sty
 /usr/local/texlive/2009/texmf-dist/tex/latex/context/m-ch-en.sty
yes, it can be.
Can you post a small example with context mkii ?




-- 
luigi
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Denis Bitouzé]

Le mercredi 04/11/09 à 10h01,
luigi scarso luigi.sca...@gmail.com a écrit :

 Can you post a small example with context mkii ?

Well, maybe the problem comes from TeX Live 2009, since:

$ tlmgr list | grep context
i collection-context: ConTeXt format
i context: The ConTeXt macro package.
i context-account: A simple accounting package.
i context-algorithmic: Algorithm handling.
i context-bnf: A BNF module for Context.
i context-chromato: ConTeXt macros for chromatograms.
i context-construction-plan: Construction plans in ConTeXt.
i context-degrade: Degrading JPEG images in ConTeXt.
i context-fixme: Make editorial marks on a document.
i context-french: Support for writing French in ConTeXt.
i context-games: (shortdesc missing)
i context-gnuplot: Inclusion of Gnuplot graphs in ConTeXt.
i context-letter: Context package for writing letters.
i context-lettrine: A ConTeXt implementation of lettrines.
i context-lilypond: Lilypond code in ConTeXt.
i context-mathsets: Set notation in ConTeXt.
i context-notes-zh-cn: Notes on using ConTeXt MkIV.
i context-simplefonts: Simplified font usage for ConTeXt.
i context-simpleslides: A module for preparing presentations.
i context-top-ten: The top ten ConTeXt commands.
i context-typearea: Something like Koma-Script typearea.
i context-typescripts: Small modules to load various fonts for use in
  ConTeXt.
i context-vim: Generate Context syntax highlighting code from
  vim.
  context.alpha-linux: alpha-linux files of context
  context.i386-cygwin: i386-cygwin files of context
i context.i386-linux: i386-linux files of context
  context.i386-netbsd: i386-netbsd files of context
  context.i386-solaris: i386-solaris files of context
  context.mips-irix: mips-irix files of context
  context.powerpc-aix: powerpc-aix files of context
  context.powerpc-linux: powerpc-linux files of context
  context.sparc-linux: sparc-linux files of context
  context.sparc-solaris: sparc-solaris files of context
  context.universal-darwin: universal-darwin files of context
  context.win32: win32 files of context
  context.x86_64-linux: x86_64-linux files of context
i maybemath: Make math bold or italic according to context.
i scheme-context: ConTeXt scheme

but, with:

$ more test-context.tex
\starttext
Hello World!
\stoptext

I get:

$ context test-context
MTXrun | unknown script 'context.lua' or 'mtx-context.lua'
-- 
Denis


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[luigi scarso]

On Wed, Nov 4, 2009 at 10:16 AM, Denis Bitouzé dbito...@wanadoo.fr wrote:
 Le mercredi 04/11/09 à 10h01,
 luigi scarso luigi.sca...@gmail.com a écrit :

 Can you post a small example with context mkii ?

 with:

 $ more test-context.tex
 \starttext
 Hello World!
 \stoptext

 I get:

 $ context test-context
 MTXrun | unknown script 'context.lua' or 'mtx-context.lua'

OK mkiv seems  not ok.
What about mkii, ie
$ texexec  test-context

-- 
luigi
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Denis Bitouzé]

Le mercredi 04/11/09 à 10h20,
luigi scarso luigi.sca...@gmail.com a écrit :

 $ texexec  test-context

It is OK for the MCE Hello world I gave earlier, except the following
warning:

pdfTeX warning: pdftex: no GlyphToUnicode entry has been inserted yet!

The same occurs with chemical formulas.

So this seems to definitively be a TeX Live related problem: I will post
on the relevant mailing list.

Thanks.
-- 
Denis


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[luigi scarso]

On Wed, Nov 4, 2009 at 10:52 AM, Denis Bitouzé dbito...@wanadoo.fr wrote:
 Le mercredi 04/11/09 à 10h20,
 luigi scarso luigi.sca...@gmail.com a écrit :

 $ texexec  test-context

 It is OK for the MCE Hello world I gave earlier, except the following
 warning:

 pdfTeX warning: pdftex: no GlyphToUnicode entry has been inserted yet!

 The same occurs with chemical formulas.

 So this seems to definitively be a TeX Live related problem: I will post
 on the relevant mailing list.
Can you also  post a small example with
with chemical formulas so
I can check  it with latest mkiv minimals ?

-- 
luigi
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Taco Hoekwater]

Denis Bitouzé wrote:
 Le mercredi 04/11/09 à 10h20,
 luigi scarso luigi.sca...@gmail.com a écrit :
 
 $ texexec  test-context
 
 It is OK for the MCE Hello world I gave earlier, except the following
 warning:
 
 pdfTeX warning: pdftex: no GlyphToUnicode entry has been inserted yet!

This (luatex) warning can be ignored, and I will remove it from the next
release.

Best wishes,
Taco
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Taco Hoekwater]

Taco Hoekwater wrote:
 
 Denis Bitouzé wrote:
 Le mercredi 04/11/09 à 10h20,
 luigi scarso luigi.sca...@gmail.com a écrit :

 $ texexec  test-context
 It is OK for the MCE Hello world I gave earlier, except the following
 warning:

 pdfTeX warning: pdftex: no GlyphToUnicode entry has been inserted yet!
 
 This (luatex) warning can be ignored, and I will remove it from the next
 release.

Sorry, that was more than a bit confusing. What I meant to say was:

This pdftex warning can be ignored. It used to be present in luatex as
well, but it was removed in version 0.37.0.

Best wishes,
Taco


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[luigi scarso]

On Wed, Nov 4, 2009 at 11:06 AM, Taco Hoekwater t...@elvenkind.com wrote:


 Taco Hoekwater wrote:

 Denis Bitouzé wrote:
 Le mercredi 04/11/09 à 10h20,
 luigi scarso luigi.sca...@gmail.com a écrit :

 $ texexec  test-context
 It is OK for the MCE Hello world I gave earlier, except the following
 warning:

 pdfTeX warning: pdftex: no GlyphToUnicode entry has been inserted yet!

 This (luatex) warning can be ignored, and I will remove it from the next
 release.

 Sorry, that was more than a bit confusing. What I meant to say was:

 This pdftex warning can be ignored. It used to be present in luatex as
 well, but it was removed in version 0.37.0.
OK -- but what does it means ?
-- 
luigi
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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Denis Bitouzé]

Le mercredi 04/11/09 à 10h55,
luigi scarso luigi.sca...@gmail.com a écrit :

 Can you also  post a small example with
 with chemical formulas so
 I can check  it with latest mkiv minimals ?

Here it is:

\usemodule[pictex,chemic]
\starttext
\startchemical
  \chemical[SIX,B,R,RZ][1,2,3,4,5,6]
\stopchemical
\stoptext
-- 
Denis


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Taco Hoekwater]

Hi,

luigi scarso wrote:
 This pdftex warning can be ignored. It used to be present in luatex as
 well, but it was removed in version 0.37.0.
 OK -- but what does it means ?

To the best of my knowledge, it only means that no ToUnicode values
have been set up using \pdfglyphtounicode yet at the moment that pdftex
(or luatex for an 8-bit font) is writing some ToUnicode values for some
font to the pdf disk file. (in mkiv, such values can be set up via
pdfr-def.mkii)

The warning is not pointless per se, but special ToUnicode entries are
usually not needed at all for latin scripts (AR is smart enough to
solve common cases itself). That makes the warning a bit over the top,
and so I removed it in luatex to avoid confusing users.

Best wishes,
Taco



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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Hans Hagen]

Denis Bitouzé wrote:


loading : ConTeXt Support Macros / Miscellaneous (2004.10.26) )
(/usr/local/texlive/2009/texmf-dist/tex/context/base/syst-gen.mkii !
Undefined control sequence. l.4441


what happens if in syst-gen.mkii you change around line 4438

\let\writestatus\normalwritestatus

into:

\ifx\normalwritestatus\undefined
% for use within latex
\ifx\writestatus\undefined
\def\writestatus#1#2{\immediate\write16{#1 : #2}}
\fi
\else
\let\writestatus\normalwritestatus
\fi

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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Hans Hagen]

Denis Bitouzé wrote:

Le mercredi 04/11/09 à 09h25,
luigi scarso luigi.sca...@gmail.com a écrit :


Sorry,
this is ConTeXt mailing list, not LaTeX  mailing list .


OK, but it seems to be a related to ConTeXt problem:


sure, an dit involves some generic context modules that are used in 
ppchtex when used in latex; however as i never test if they work in 
latex only latex users can figure out problems


Hans


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Re: [NTG-context] [ppchtex] \writestatus: Undefined control sequence

[Hans Hagen]

Denis Bitouzé wrote:

Le mercredi 04/11/09 à 10h55,
luigi scarso luigi.sca...@gmail.com a écrit :


Can you also  post a small example with
with chemical formulas so
I can check  it with latest mkiv minimals ?


Here it is:

\usemodule[pictex,chemic]
\starttext
\startchemical
  \chemical[SIX,B,R,RZ][1,2,3,4,5,6]
\stopchemical
\stoptext


for context mkiv there is no need to load the modules. in mkiv ppchtex 
is rewritten (and is now a mix of lua, mp and tex)


Hans


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Re: [NTG-context] ppchtex experience

[Alan BRASLAU]

On Monday 20 April 2009 17:27:42 Helge Kruse wrote:
 Hello,

 I need to write some chemical strucutures in LaTeX and dont know, what is
 the best tools to do it. The structures are crown ether and cryptands. Yes,
 and I am unexperienced.

 1) What would be the way to write a [18]crown-6
 (http://en.wikipedia.org/wiki/Crown_ether) structure formula with PPCHTEX?
 2) Is there any kind of repository, where I can take common structures
 and/or adapt these to the required structures?

 Regards,
 Helge

I just came across your message from over a month ago...
Here is my solution (ConTeXt):

\usemodule[chemic]
\starttext
% 18-Crown-6
\startchemical[width=fit,height=fit]
\chemical[SIX,B5,-SB4,+SB6,Z4,MOV1][O]
\chemical[SIX,B6,-SB5,+SB1,Z5,MOV2][O]
\chemical[SIX,B1,-SB6,+SB2,Z6,MOV3][O]
\chemical[SIX,B2,-SB1,+SB3,Z1,MOV4][O]
\chemical[SIX,B3,-SB2,+SB4,Z2,MOV5][O]
\chemical[SIX,B4,-SB3,+SB5,Z3][O]
\stopchemical

% my discotic mesogene...
\startchemical[width=6500,height=8000,top=2500,left=2500]
\chemical[SIX,B5,-SB4,+SB6,PB:Z4,ONE,SB6,Z06,PE,MOV1][N,R]
\chemical[SIX,B6,-SB5,+SB1,PB:Z5,ONE,SB7,Z07,PE,MOV2][N,R]
\chemical[SIX,B1,-SB6,+SB2,PB:Z6,ONE,SB8,Z08,PE,MOV3][N,R]
\chemical[SIX,B2,-SB1,+SB3,PB:Z1,ONE,SB2,Z02,PE,MOV4][N,R]
\chemical[SIX,B3,-SB2,+SB4,PB:Z2,ONE,SB3,Z03,PE,MOV5][N,R]
\chemical[SIX,B4,-SB3,+SB5,PB:Z3,ONE,SB4,Z04,PE][N,R]
\stopchemical

\stoptext

Alan

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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

i split ppchtex in mkii/mkiv (and included the fixes) so we can improve
things eventually

can you check if it still runs ok (beta zip on website)

Hans


Works correctly (bonds in red, atoms in black):

\usemodule[chemic]
\setupchemical[rulecolor=red]
\starttext
\startchemical
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext


However, the following variant does not work.

\usemodule[chemic]
\starttext
\startchemical[rulecolor=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext

I don't understand, as my (quick) look at the source code
indicates that the parameters should be handled identically.


no, that was actually the problem ... local vs global ... for the moment 
set it up local (per formula) as i need to make an inheritance chain


now that i've split in mkii/mkiv that's easier since we no longer have 
to keep things working in latex (which means that we can use more core 
helper code)


just remind me occasionally

Hans


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Re: [NTG-context] ppchtex color

[Alan BRASLAU]

On Wednesday 13 May 2009 10:33:18 Hans Hagen wrote:
 Alan BRASLAU wrote:
  Works correctly (bonds in red, atoms in black):
 
  \usemodule[chemic]
  \setupchemical[rulecolor=red]
  \starttext
  \startchemical
  \chemical[ONE,SB,Z0][C]
  \stopchemical
  \stoptext
 
 
  However, the following variant does not work.
 
  \usemodule[chemic]
  \starttext
  \startchemical[rulecolor=red]
  \chemical[ONE,SB,Z0][C]
  \stopchemical
  \stoptext
 
  I don't understand, as my (quick) look at the source code
  indicates that the parameters should be handled identically.

 no, that was actually the problem ... local vs global ... for the moment
 set it up local (per formula) as i need to make an inheritance chain

 now that i've split in mkii/mkiv that's easier since we no longer have
 to keep things working in latex (which means that we can use more core
 helper code)

 just remind me occasionally

OK. The following extension would also be useful:

\usemodule[chemic]
\starttext
\startchemical
\chemical[SIX,B,rulecolor=red,AU][]
\stopchemical
\stoptext

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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

On Wednesday 13 May 2009 10:33:18 Hans Hagen wrote:

Alan BRASLAU wrote:

Works correctly (bonds in red, atoms in black):

\usemodule[chemic]
\setupchemical[rulecolor=red]
\starttext
\startchemical
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext


However, the following variant does not work.

\usemodule[chemic]
\starttext
\startchemical[rulecolor=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext

I don't understand, as my (quick) look at the source code
indicates that the parameters should be handled identically.

no, that was actually the problem ... local vs global ... for the moment
set it up local (per formula) as i need to make an inheritance chain

now that i've split in mkii/mkiv that's easier since we no longer have
to keep things working in latex (which means that we can use more core
helper code)

just remind me occasionally


OK. The following extension would also be useful:

\usemodule[chemic]
\starttext
\startchemical
\chemical[SIX,B,rulecolor=red,AU][]
\stopchemical
\stoptext


in mkiv syntax that is:

\defineprocessor[chemred][color=red]

\startchemical
\chemical[SIX,SB,C135,R,Z][chemred-A,chemred-C,chemred-C]
\stopchemical

we can rewrite ppchtex a bit but it depends on how much time you want to 
spend on filling in the holes that i will create (i can make the framework)



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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:


\startchemical
\color[red]{\chemical[ONE,SB,Z0][C]}
\stopchemical
% text C is offset...


add a % after the } (maybe we should ignore endofline, i.e. make a mkiv 
variant and extend/maintain that)



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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

No, ppchtex is not dead...

I would like to use color.

1. color= and rulecolor= does not appear to be implemented (mkiv)...
2. how can one change the color of the bonds?
3. using \color[red]{} causes the text to be offset.

minimal example:

\setupcolors[state=start]
\usemodule[chemic]
\starttext

\startchemical
\chemical[ONE,SB,Z0][C]
\stopchemical

\startchemical
\color[red]{\chemical[ONE,SB,Z0][C]}
\stopchemical
% text C is offset...

\startchemical
\chemical[ONE,SB,Z0][{\red C}]
\stopchemical
% OK, but I would like to draw the bonds as well in red.

\startchemical[color=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
% C is red in mkii, black in mkiv


has to do with different color mechanism ..

path line 1171:

\setbox2=\hbox{\@@dochemicalcolor$\@@dochemicalstyle{\@@localchemicalformat 
\chemicaltext}$}%




\startchemical[rulecolor=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
% bonds are black, C is red in mkii, black in mkiv

\stoptext

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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

No, ppchtex is not dead...

I would like to use color.

1. color= and rulecolor= does not appear to be implemented (mkiv)...
2. how can one change the color of the bonds?
3. using \color[red]{} causes the text to be offset.

minimal example:

\setupcolors[state=start]
\usemodule[chemic]
\starttext

\startchemical
\chemical[ONE,SB,Z0][C]
\stopchemical

\startchemical
\color[red]{\chemical[ONE,SB,Z0][C]}
\stopchemical
% text C is offset...

\startchemical
\chemical[ONE,SB,Z0][{\red C}]
\stopchemical
% OK, but I would like to draw the bonds as well in red.

\startchemical[color=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
% C is red in mkii, black in mkiv

\startchemical[rulecolor=red]
\chemical[ONE,SB,Z0][C]
\stopchemical


setting happened at the outer level (ok, that's broken now but we can 
fix that later); so now, each formula must have the settings; when i 
have time i'll make a mkiv variant so that we can upgrade (i don't want 
interference with mkii since that version is also used in latex and we 
don't need to upgrade that)


\def\setchemicalattributes
  {\scratchdimen\@@chemicalrulethickness
   \def\chemicalattributes
 {withpen pencircle scaled \the\scratchdimen\space
  withcolor }%
   \doifelsenothing\@@chemicalrulecolor
 {\edef\chemicalattributes{\chemicalattributes black}}
 {\edef\chemicalattributes{\chemicalattributes 
\MPcolor{\@@chemicalrulecolor}}}%

   \startMPdrawing
 drawoptions (\chemicalattributes) ;
   \stopMPdrawing}


-
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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

No, ppchtex is not dead...


i split ppchtex in mkii/mkiv (and included the fixes) so we can improve 
things eventually


can you check if it still runs ok (beta zip on website)

Hans

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Re: [NTG-context] ppchtex color

[Alan BRASLAU]

 i split ppchtex in mkii/mkiv (and included the fixes) so we can improve
 things eventually
 
 can you check if it still runs ok (beta zip on website)
 
 Hans

Unzipped cont-tmf.zip on top of my minimals installation and ran context on my 
current working documents:

system  : module chemic loaded
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-chemic.tex 
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-chemic.mkiv
system  : module pictex loaded
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-pictex.tex 
(/usr/local/context.new/tex/texmf-context/tex/context/base/thrd-pic.tex
warning : \dimen \linethickness is already defined (\relax it first)
)) (/usr/local/context.new/tex/texmf-context/tex/context/base/ppchtex.mkiv
ppchtex : using PiCTeX and MetaPost
)))

It appears to work as before...
(I will now look into your color suggestions.)

Alan



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Re: [NTG-context] ppchtex color

[Alan BRASLAU]

 i split ppchtex in mkii/mkiv (and included the fixes) so we can improve
 things eventually
 
 can you check if it still runs ok (beta zip on website)
 
 Hans

Works correctly (bonds in red, atoms in black):

\usemodule[chemic]
\setupchemical[rulecolor=red]
\starttext
\startchemical
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext


However, the following variant does not work.

\usemodule[chemic]
\starttext
\startchemical[rulecolor=red]
\chemical[ONE,SB,Z0][C]
\stopchemical
\stoptext

I don't understand, as my (quick) look at the source code
indicates that the parameters should be handled identically.

Alan

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Re: [NTG-context] ppchtex color

[Hans Hagen]

Alan BRASLAU wrote:

i split ppchtex in mkii/mkiv (and included the fixes) so we can improve
things eventually

can you check if it still runs ok (beta zip on website)

Hans


Unzipped cont-tmf.zip on top of my minimals installation and ran context on my 
current working documents:


system  : module chemic loaded
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-chemic.tex 
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-chemic.mkiv

system  : module pictex loaded
(/usr/local/context.new/tex/texmf-context/tex/context/base/m-pictex.tex 
(/usr/local/context.new/tex/texmf-context/tex/context/base/thrd-pic.tex

warning : \dimen \linethickness is already defined (\relax it first)
)) (/usr/local/context.new/tex/texmf-context/tex/context/base/ppchtex.mkiv
ppchtex : using PiCTeX and MetaPost
)))

It appears to work as before...
(I will now look into your color suggestions.)


color should work ok (that is: color=red, and rulecolor=red)


-
  Hans Hagen | PRAGMA ADE
  Ridderstraat 27 | 8061 GH Hasselt | The Netherlands
 tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com
 | www.pragma-pod.nl
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Re: [NTG-context] ppchtex experience

[Henning Hraban Ramm]

2009/4/20 Helge Kruse helge.kruse-nos...@gmx.net:
 I need to write some chemical strucutures in LaTeX and dont know, what is
 the best tools to do it. The structures are crown ether and cryptands. Yes,
 and I am unexperienced.

 1) What would be the way to write a [18]crown-6
 (http://en.wikipedia.org/wiki/Crown_ether) structure formula with PPCHTEX?
 2) Is there any kind of repository, where I can take common structures
 and/or adapt these to the required structures?

see http://wiki.contextgarden.net/Chemistry
and http://mitglied.lycos.de/ppchtex/00index.html

Sorry, can't help you further.


Greetlings, Hraban
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Re: [NTG-context] PPCHTEX and LaTeX

[Wolfgang Schuster]

Hi Helge,

Thanks for your kind reply. I have a MikTeX system installed on  
Windows XP. The context is part of the installation.




Although I think that all packages mentioned below are installed I  
get some error messages in the log. The dvi output is generated, but  
the errors are strange. Is this a kind of incompatibility described  
in a FAQ?



! Missing { inserted.
to be read again
  \def
l.659 \unexpanded\def
\complexstartchemical[#1]%


This problem was mentioned once 2007 and Hans fixed it
and I don't get it with TeXLive 2008.

Can you send use the file ppchtex.noc from your system,
it's possible MikTeX includes a old version of the file
without the patch.

Wolfgang

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Re: [NTG-context] PPCHTEX: Reaction troubles

[Taco Hoekwater]

per.maier wrote:
 
 Hi,
 
 I already sent this message to the ppchtex mailing list, but apparently 
 it's dead since a few years, so I hope you can help me with my problem.

When  I run this through context the output looks ok, but that
may not mean much as context no longer uses pictex for chemics,
I believe. Someone with a good latex setup should have a look.

Best wishes,
Taco

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Re: [NTG-context] ppchtex german language compiling problems

[Wolfgang Schuster]

On Sun, 30 Dec 2007 20:51:27 +0100
Martin Scholz [EMAIL PROTECTED] wrote:

 Hi there,
 
 I'm new to ConTeXt and found out how nice it is to construct coverpages. 

It's even better for the whole document.

 So it would be nice to have an opportunity to include the whole 
 procedure into an LaTeXe environment. As far as I already read up to now 
 there is now possibility.

You could try to write the ConTeXt code into a external file and
process this file on the fly with write18.

 But today I think I found a bug in the german 
 version of ppchtex. I used the following little script to set an example 
 formula.
 The used code is the following:
 
 \verwendemodule[pictex,chemie]
 
 
 \starttext
 
 \stellechemieein[breite=passend,oben=1500,unten=3500]
 \startchemie
 \chemie[ONE,Z0,DB1,SB3,SB7,Z3,Z7,MOV1,Z0,SB1,SB3,Z3,MOV1,Z0,DB1,SB3,Z3,MO
 V1,Z0,SB3,SB7,Z3,Z7][C,H,H,C,H,C,H,C,H,H]
 \textunter{1,3-Butadieen}
 \stopchemie
 
 \stoptext
 
 with the following commands I got the same errormessages.

[...]

 ConTeXt  ver: 2007.01.12 15:56 MKII  fmt: 2007.12.29  int: german/german

This is a ancient version, I tried your example with the last release
and it works for me.

[...]

 
 Would be nice if somebody has an idea how to solve the problem or where 
 something went wrong in the code.
 
 Another question is how I could get ppchtex to work in a 
 LaTeXe-environment. Would be nice if there also would be the possibility 
 to load the german version.

\usepackage[pictex]{m-ch-de}

or

\usepackage[pstricks]{m-ch-de}

 Thanks to all for there help and have a happy new year everybody.
 
 Martin

Wolfgang
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Re: [NTG-context] ppchtex

[Hans Hagen]

Johannes Werner wrote:
Hans Hagen wrote:
Johannes Werner wrote:
hi everyone,
i want to use PPCHTEX. when i process my .tex-file with texexec i get 
the message:
   .
   specials : fdf loaded
   )
   specials : fdf,tpd loaded
   \openout6 = `chemie-mpgraph.mp'.
   Randomizer initialized to 1275417501. [MP to PDF] 
(./chemie-mpgraph.4000))
   *

and the program stops and waits for a command. when i type \end  it 
continues. this happens again and then i have my target file.
what wants the system tell me? why does it stop?. it's irksome, to 
type in a command for nothing. when i process with latex everything 
is ok.

how does your smallest test file that does thsi look like?
Hans

the testfile was:
   \enableregime[utf]
   \usemodule[pictex,chemie]
   \setupoutput[pdf]
   %\setupchemical[axis=on, frames=on]
   \par Substituent A
   \startchemical
   \chemical[ONE,SB4,SB6,Z0][O]
   \stopchemical
with a file, which is a little bit bigger i get the following (an no 
output is generated):

Randomizer initialized to 1431757445. [MP chemie-bigger-mpgraph.4000]
   [MP chemie-bigger-mpgraph.3999] [MP chemie-bigger-mpgraph.3998]
   [MP chemie-bigger-mpgraph.3997] [MP chemie-bigger-mpgraph.3996]
   [MP chemie-bigger-mpgraph.3995])
   *
how about adding \starttext ...\stoptext around it?
Hans
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 tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com
 | www.pragma-pod.nl
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Re: [NTG-context] ppchtex

[Hans Hagen]

Johannes Werner wrote:
hi everyone,
i want to use PPCHTEX. when i process my .tex-file with texexec i get 
the message:
   .
   specials : fdf loaded
   )
   specials : fdf,tpd loaded
   \openout6 = `chemie-mpgraph.mp'.
   Randomizer initialized to 1275417501. [MP to PDF] 
(./chemie-mpgraph.4000))
   *

and the program stops and waits for a command. when i type \end  it 
continues. this happens again and then i have my target file.
what wants the system tell me? why does it stop?. it's irksome, to type 
in a command for nothing. when i process with latex everything is ok.
how does your smallest test file that does thsi look like?
Hans
-
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  Ridderstraat 27 | 8061 GH Hasselt | The Netherlands
 tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com
 | www.pragma-pod.nl
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Re: [NTG-context] ppchtex

[Johannes Werner]

Hans Hagen wrote:
Johannes Werner wrote:
hi everyone,
i want to use PPCHTEX. when i process my .tex-file with texexec i get 
the message:
   .
   specials : fdf loaded
   )
   specials : fdf,tpd loaded
   \openout6 = `chemie-mpgraph.mp'.
   Randomizer initialized to 1275417501. [MP to PDF] 
(./chemie-mpgraph.4000))
   *

and the program stops and waits for a command. when i type \end  it 
continues. this happens again and then i have my target file.
what wants the system tell me? why does it stop?. it's irksome, to 
type in a command for nothing. when i process with latex everything 
is ok.

how does your smallest test file that does thsi look like?
Hans
the testfile was:
   \enableregime[utf]
   \usemodule[pictex,chemie]
   \setupoutput[pdf]
   %\setupchemical[axis=on, frames=on]
   \par Substituent A
   \startchemical
   \chemical[ONE,SB4,SB6,Z0][O]
   \stopchemical
with a file, which is a little bit bigger i get the following (an no 
output is generated):

Randomizer initialized to 1431757445. [MP chemie-bigger-mpgraph.4000]
   [MP chemie-bigger-mpgraph.3999] [MP chemie-bigger-mpgraph.3998]
   [MP chemie-bigger-mpgraph.3997] [MP chemie-bigger-mpgraph.3996]
   [MP chemie-bigger-mpgraph.3995])
   *



chemie-bigger.tex
Description: TeX document
This is pdfeTeX, Version 3.14159-1.10b-2.1 (Web2C 7.4.5) (format=cont-en 
2005.2.23)  15 MAR 2005 20:22
entering extended mode
**cont-en chemie-bigger.tex
(./chemie-bigger.tex{/usr/share/texmf/pdftex/config/pdftex.cfg
Warning: pdfetex (file /usr/share/texmf/pdftex/config/pdftex.cfg): expected num
ber in ^^J returning 10
}

ConTeXt  ver: 2003.1.31  fmt: 2005.2.23  int: english  mes: english

language   : language en is active
protectionstate 0
system : cont-new loaded
(/usr/share/texmf/tex/context/base/cont-new.tex
systems: beware: some patches loaded from cont-new.tex!
system (E-TEX) : [line 726] \ifcsname 
)
system : cont-old loaded
(/usr/share/texmf/tex/context/base/cont-old.tex
loading: Context Old Macros
)
system : cont-fil loaded
(/usr/share/texmf/tex/context/base/cont-fil.tex
loading: Context File Synonyms
)
system : cont-sys loaded
(/usr/share/texmf/tex/context/base/cont-sys.tex
symbols: loading symbolset nav
(/usr/share/texmf/tex/context/base/symb-nav.tex
pdftex : needs map file: original-context-symbol.map
pdftex : needs map file: pl0-ams-cmr.map
pdftex : needs map file: original-vogel-symbol.map
)
symbols: loading symbolset mvs
(/usr/share/texmf/tex/context/base/symb-mvs.tex
encoding   : coding default
))
bodyfont   : 12pt rm is loaded
language   : patterns 2:2-en-2 3:2-uk-2 4:2-de-2 5:2-fr-2 6:2-es-2 7:2-it-2
 8:2-nl-2 loaded
specials   : tex,postscript,rokicki loaded
\openout2 = `chemie-bigger.tui'.

system : chemie-bigger.top loaded
(./chemie-bigger.top)
\openout0 = `chemie-bigger-mpgraph.mp'.

\openout0 = `chemie-bigger-mprun.mp'.

\openout0 = `mpgraph.mp'.

\openout0 = `mprun.mp'.


system : no macros found in module pictes
system : macros of module chemie loaded
(/usr/share/texmf/tex/context/base/m-chemic.tex
(/usr/share/texmf/tex/generic/pictex/pictex.tex)
(/usr/share/texmf/tex/context/base/ppchtex.tex
ppchtex: using PiCTeX and MetaPost
))
specials   : loading definition file tpd
(/usr/share/texmf/tex/context/base/spec-tpd.tex
specials   : loading definition file fdf
(/usr/share/texmf/tex/context/base/spec-fdf.tex unprotect 3
system (E-TEX) : [line 1815] \ifcsname 
unprotect 4 protect 4 protect 3)
specials   : fdf loaded
)
specials   : fdf,tpd loaded
\openout6 = `chemie-bigger-mpgraph.mp'.

Randomizer initialized to 1431757445. [MP chemie-bigger-mpgraph.4000]
[MP chemie-bigger-mpgraph.3999] [MP chemie-bigger-mpgraph.3998]
[MP chemie-bigger-mpgraph.3997] [MP chemie-bigger-mpgraph.3996]
[MP chemie-bigger-mpgraph.3995])
*\end
systems: end file chemie-bigger at line 0
[flush and process chemie-bigger-mpgraph.mp afterwards]
! You can't use `\end' in internal vertical mode.
recently read \normalend 
   
* \end

? \end
Type return to proceed, S to scroll future error messages,
R to run without stopping, Q to run quietly,
I to insert something, 
1 or ... or 9 to ignore the next 1 to 9 tokens of input,
H for help, X to quit.
? X
 
Here is how much of TeX's memory you used:
 1864 strings out of 68091
 26130 string characters out of 753759
 4452029 words of memory out of 5567915
 31601 multiletter control sequences out of 1+5
 10565 words of font info for 35 fonts, out of 50 for 1000
 62 hyphenation exceptions out of 1000
 29i,11n,48p,275b,658s stack positions out of 1500i,500n,5000p,20b,5000s
 0 PDF objects out of 30
 0 named destinations out of 131072
 0 words of extra memory for PDF output out of 65536
No pages of output.
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Re: [NTG-context] ppchtex

[Willi Egger]

Hi Johannes,
I looked at your coding.
The use module line has two typo's It should be \usemodule[pictex,chemic]
The statements are not complete i.e. you forgot  the \stopcombination. 
Further when starting a combination one needs to give the number of rows 
and columns e.g. [2*3]. with only [6] all of the structures are placed 
inline, but only 4 of them fit in one row  so ...
In order to produce output you need to enclose the code between 
\starttext ... \stoptext.

Please see the attached file
Kind regards
Willi
Johannes Werner wrote:
Hans Hagen wrote:
Johannes Werner wrote:
hi everyone,
i want to use PPCHTEX. when i process my .tex-file with texexec i get 
the message:
   .
   specials : fdf loaded
   )
   specials : fdf,tpd loaded
   \openout6 = `chemie-mpgraph.mp'.
   Randomizer initialized to 1275417501. [MP to PDF] 
(./chemie-mpgraph.4000))
   *

and the program stops and waits for a command. when i type \end  it 
continues. this happens again and then i have my target file.
what wants the system tell me? why does it stop?. it's irksome, to 
type in a command for nothing. when i process with latex everything 
is ok.

how does your smallest test file that does thsi look like?
Hans

the testfile was:
   \enableregime[utf]
   \usemodule[pictex,chemie]
   \setupoutput[pdf]
   %\setupchemical[axis=on, frames=on]
   \par Substituent A
   \startchemical
   \chemical[ONE,SB4,SB6,Z0][O]
   \stopchemical
with a file, which is a little bit bigger i get the following (an no 
output is generated):

Randomizer initialized to 1431757445. [MP chemie-bigger-mpgraph.4000]
   [MP chemie-bigger-mpgraph.3999] [MP chemie-bigger-mpgraph.3998]
   [MP chemie-bigger-mpgraph.3997] [MP chemie-bigger-mpgraph.3996]
   [MP chemie-bigger-mpgraph.3995])
   *


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% CHmeical structures
% Johannes Werner
% CONTEXT file
% filename:

\enableregime[utf]
\usemodule[pictex,chemic]%pstricks
\setupoutput[pdf]

%\setupchemical[axis=on, frames=on]

\starttext
\par A
\placefigure[force]{none}
{\startcombination[2*3]
{\startchemical \chemical[ONE,SB4,SB6,Z0][O] \stopchemical}{}
{\startchemical \chemical[ONE,SB4,SB6,Z0][S] \stopchemical}{}
{\startchemical \chemical[ONE,SB4,SB6,Z0][NH] \stopchemical}{}
{\startchemical \chemical[ONE,DB1,SB4,SB6,Z01][C,O] \stopchemical}{}
{\startchemical \chemical[ONE,DB1,SB4,SB6,Z01][C,NR] \stopchemical}{}
{\startchemical \chemical[ONE,DB1,SB4,SB6,Z01][C,CR_2] \stopchemical}{}
\stopcombination}
\stoptext
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Re: [NTG-context] PPCHTeX Bug?

[Tobias Hilbricht]

Am Mi, den 29.09.2004 schrieb Mojca Miklavec um 00:40:
  (there's no way to make such a trivial thing 
 as a thetraedral or trigonal angle - 109.5 and 120 degrees).

Well, it is possible by abusing the basal structures ONE and SIX. As
an example for a 120 degree angle using SIX see the sample some messages
before in this thread.
However, you are right, there are things which are not present, such as
certain bonds etc.

Yours sincerely

Tobias Hilbricht

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Re: [NTG-context] PPCHTeX Bug?

[Mojca Miklavec]

In my opinion - it's not only its complexity preventing the users from 
using it, but also it's insufficient flexibility. As long as I 
understood the manual (and tried to draw some formulas), it is possible 
to create a certain subset of images, which covers the most needs, but 
certainly not all of them (there's no way to make such a trivial thing 
as a thetraedral or trigonal angle - 109.5 and 120 degrees).

see: http://www.ntg.nl/pipermail/ntg-ppchtex/2002/02.html
Even the ones with lots of experience gave up.
Perhaps chemistry is too complex to be applied easily without some help 
of graphical tools. SMILES 
(http://www.daylight.com/dayhtml/smiles/ssmiles.html) could be a 
solution, say

   \startSSMILES
   CC(=O)O
   \stopSSMILES
producing a nice picture of acetic acid (using metafun), but perhaps 
still not serving all the puposes a chemist needs.

Mojca
Taco Hoekwater wrote:
Hi Thomas,
I believe your problem is that ppchtex is a very specialistic package
and there are not that many people using it to it's full capacity. As a 
result of that, there isn't that much expert knowledge available. Personally,
I don't understand any of it. Luckily, the only chemical stuff I have ever had 
to typeset could be done by cutpaste and making trivial changes to the 
examples in the manual.

Greetings, Taco
On Sun, 26 Sep 2004 07:47:18 +0200, Thomas wrote:
Hi to all,
One week is gone and I got no answer, no comment to my problems!
What's going wrong!
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Re: [NTG-context] PPCHTeX Bug?

[Henning Hraban Ramm]

Am 14.09.2004 um 11:17 schrieb Hans Hagen:
On TeX-D-L (german ML) was last week a dicussion about a PPCHTeX bug
(at least with LaTeX), it seems that the file ppchtex.tex lost its 
tail (ca. 3kB).
I told the user to ask at the PPCHTeX Mailing list, but he only got a 
message,
that the list was moderated.
what tail?
Sorry, I don't like to moderate between TeX-D-L and here (and will be 
off from tomorrow to end of September)...
CC to Thomas Meyer: Please care for yourself now.

Thomas Meyer wrote, some PPCHTeX code wouldn't work, the error message 
was:
ppchtex.tex:3390: undefined control sequence
He uses an actual MikTeX (again, only problems with this, we should 
mark it red in the wiki...)
His file ppchtex.tex ends like:

\def\cpos#1#2%
  {\iftrialtypesetting
 #2%
   \else
 \bgroup
 \globalpushmacro\dowithchemical
3390
 
\gdef\dowithchemical##1{\hpos{#1}{##1}\globalpopmacro\dowithchemical}%
 #2%
 \egroup
  \fi}

\fi
\protect \endinput
Tobias Hilbricht answered, the code would work with his ppchtex.tex 
version from TeX Live 2003,
there line 3390 (second line from the end) had only a lonely \fi, but 
the file is 3kB bigger,
but both show the same date of 1997-03-19 (I guess this date is only 
the creation date and not
altered at changes, isn't it?)

With Tobias' file it worked at Thomas.
Thomas downloaded the file from pragma-ade.nl, and it doesn't work 
again.

I told him to ask at the PPCHTeX list, see above.
Further Thomas wanted to draw seven-rings, and that seems not supported 
by PPCHTeX.

Grüßlis vom Hraban!
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Re: [NTG-context] PPCHTeX broken

[Hans Hagen]

Peter Münster wrote:
On Mon, 2 Aug 2004, Tobias Burnus wrote:
 

If I do a dvips -Ppdf test.dvi I get the following warning:
dvips: Could not find figure file ./test-mpgraph.4000; continuing
dvips: Could not find figure file ./test-mpgraph.3999; continuing
dvips: Could not find figure file ./test-mpgraph.3998; continuing
I don't see from the log whether you have them, but in any case a DVI 
file doesn't carry enough information, you need a Post Script or PDF file.
   

Oh, excuse me, I didn't see, that the dvi depends on other files...
Now I send a pdf file.
 

With 2004.4.9 this works - well, the bonds are a bit randomly 
distributed but otherwise. Can you state a bit more clearly what should 
be different from the result you get?
   

The result should be as in example 5.9 on page 1-18 of the manual
(http://www.pragma-ade.com/general/manuals/mp-ch-en.pdf).
I complied the same TeX-file with an older version (2003.1.31) and the
result is ok (also attached as pdf).
Now, temporally working with the old ConTeXt version, I try to substitute
Atoms in a chair structure. Is this possible?
The following example shows the situation a little bit clearer:
\usemodule[pictex,chemic]
\starttext
\startchemical
\chemical [SIX,B,Z] [a,b,c,d,e,f]
\stopchemical
\startchemical
\chemical [CHAIR,B,Z] [a,b,c,d,e,f] % Z seems to be without effect here...
\stopchemical
\stoptext
Cheers, Peter
 

looks like there is some interference with pdf inclusion (quite hard to 
find reasonable compromised in handling offsets and bboxes); i'll look 
into it

Hans
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Re: [NTG-context] PPCHTeX broken

[Tobias Burnus]

Hello,
Peter Münster wrote:
PPCHTeX seems to be broken in the latest ConTeXt beta version.
Here an example (copied from the manual):
 

If I do a dvips -Ppdf test.dvi I get the following warning:
dvips: Could not find figure file ./test-mpgraph.4000; continuing
dvips: Could not find figure file ./test-mpgraph.3999; continuing
dvips: Could not find figure file ./test-mpgraph.3998; continuing
I don't see from the log whether you have them, but in any case a DVI 
file doesn't carry enough information, you need a Post Script or PDF file.

\usemodule[pictex,chemic]
\starttext
\startchemical[scale=small,width=6000,height=6000,frame=on]
 \chemical[SIX,SB2356,DB14,Z2346,SR36,RZ36] [C,N,C,C,H,H_2]
 \chemical[PB:Z1,ONE,Z0,DIR8,Z0,SB24,DB7,Z27,PE] [C,C,CH_3,O]
 \chemical[PB:Z5,ONE,Z0,DIR6,Z0,SB24,DB7,Z47,PE] [C,C,H_3C,O]
 \chemical[SR24,RZ24] [CH_3,H_3C]
\stopchemical
\stoptext
 

With 2004.4.9 this works - well, the bonds are a bit randomly 
distributed but otherwise. Can you state a bit more clearly what should 
be different from the result you get?

Tobias
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