TeX & chemistry (was: alignment of figures)

TeX & chemistry (was: alignment of figures)

[Mojca Miklavec]

Jörg Hagmann wrote:

> I use "Chemdraw", save as .pict and finish it in Illustrator. I will
> eventually look into PPCHTEX, but at the moment struggling with
> ConTEXt is all I can do. There is a problem with my method: the
> formula saved as .pict look awful (bonds shifted, atoms not aligned
> etc.) and I have to correct everything by hand in Illustrator. I am
> sure PPCHTEX would do a better job. On the other hand, if I switch
> the formulae should look the same (bondlength, thickness, font etc.)
> as the ones I already did (and don't want to do again). I suppose
> that's feasable?

I may be wrong, but I doubt that PPCHTEX would satisfy your needs.
It's a complicated notation which is not flexible enough (I gave up
since there were quite some cases for which I wasn't able to draw what
I wanted to.) XymTeX is more powerful, but not supported by ConTeXt
(although you can still draw single formulas in LaTeX and import them
into ConTeXt as pictures) and still with very complex notation.

(I would say that all you need is a better export from Chemdraw, but
as this is a proprietary software I doubt that there are any
specifications how to write an exporting module. Please correct me if
I'm wrong. I wish I were.)

I'm playing a bit with drawing formulas in metafun, but my question
is: are there any guidelines about how a nice formula should look
like? (Yes, I have problems to decide how thick the lines have to be,
how to draw a triple or a steric bond properly, which size of letters
to use). Knuth did a marvellous job with drawing math formulae in TeX,
there are many books about typography, but I've never seen anything
about chemistry and I haven't found anyone who could answer me this
question.

Mojca

RE: TeX & chemistry (was: alignment of figures)

[Keith McKay]

A quick search on Google found this.  
Keith

http://www.rsc.org/Publishing/ReSourCe/AuthorGuidelines/Illustrations/sect1.
asp
http://pubs.acs.org/books/artwork.shtml

-----Original Message-----
From: ntg-context-bounces@ntg.nl [mailto:ntg-context-bounces@ntg.nl] On
Behalf Of Mojca Miklavec
Sent: 25 October 2005 19:57
To: mailing list for ConTeXt users
Subject: [NTG-context] TeX & chemistry (was: alignment of figures)


Jörg Hagmann wrote:

> I use "Chemdraw", save as .pict and finish it in Illustrator. I will 
> eventually look into PPCHTEX, but at the moment struggling with 
> ConTEXt is all I can do. There is a problem with my method: the 
> formula saved as .pict look awful (bonds shifted, atoms not aligned
> etc.) and I have to correct everything by hand in Illustrator. I am 
> sure PPCHTEX would do a better job. On the other hand, if I switch the 
> formulae should look the same (bondlength, thickness, font etc.) as 
> the ones I already did (and don't want to do again). I suppose that's 
> feasable?

I may be wrong, but I doubt that PPCHTEX would satisfy your needs. It's a
complicated notation which is not flexible enough (I gave up since there
were quite some cases for which I wasn't able to draw what I wanted to.)
XymTeX is more powerful, but not supported by ConTeXt (although you can
still draw single formulas in LaTeX and import them into ConTeXt as
pictures) and still with very complex notation.

(I would say that all you need is a better export from Chemdraw, but as this
is a proprietary software I doubt that there are any specifications how to
write an exporting module. Please correct me if I'm wrong. I wish I were.)

I'm playing a bit with drawing formulas in metafun, but my question
is: are there any guidelines about how a nice formula should look like?
(Yes, I have problems to decide how thick the lines have to be, how to draw
a triple or a steric bond properly, which size of letters to use). Knuth did
a marvellous job with drawing math formulae in TeX, there are many books
about typography, but I've never seen anything about chemistry and I haven't
found anyone who could answer me this question.

Mojca
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Re: TeX & chemistry (was: alignment of figures)

[Tobias Hilbricht]

Am Dienstag, 25. Oktober 2005 20:56 schrieb Mojca Miklavec:
> Jörg Hagmann wrote:

> > I am
> > sure PPCHTEX would do a better job.

If PPCHTeX is capable of drawing your formulas. I tried it, and apart from 
complicated notation it can not draw seven rings, and you need "work arounds" 
for certain bond angles, and there were other things either very complicated 
to code or not at all. There seems to be no big user community of PPCHTeX and 
no development.

> I may be wrong, but I doubt that PPCHTEX would satisfy your needs.
> It's a complicated notation which is not flexible enough

Have a look into the PPCHTEeX-manual and see if it covers all your needs.

> XymTeX is more powerful, but not supported by ConTeXt
>and still with very complex notation.

True, and also XyMTeX lacks a lot of possibilities - apart from seven rings 
many bicyclo-compounds are not possible, if I remember right. Additionally, 
it is not possible to colorize bonds and atoms or to make them bold etc. 
(this is possible with PPCHTeX).

Then there is ochem by Ingo Klöckl, perhaps the most powerful chemistry 
solution in terms of possible compounds - but only for LaTeX, and again with 
a very peculiar notation and a steep learning curve. Colorization of bonds 
only with PostScript-editing.

Finally there is streetex by Igor Strokov - again for LaTeX, more powerful in 
terms of possible compounds than PPCHTeX or XyMTeX and much easier (more 
intuitive) to use. However, as with XyMTeX it is not possible to colorize 
bonds and atoms or to make them bold etc.

> I would say that all you need is a better export from Chemdraw

Recent versions of Cambrigde Soft ChemDraw can produce very nice output in 
various formats. Additionally, ChemDraw has the feature IUPAC name to 
structure - this is very handy, and no TeX-solution has that.

Yours sincerely 

Tobias Hilbricht

Re: TeX & chemistry (was: alignment of figures)

[Jörg Hagmann]

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Many thanks for all the suggestions on incorporating chemical  
formula. PPCHEMTEX now looks like something to play with, but not  
something I will switch to whith a deadline for writing the book  
coming closer.

 From the publisher I got an example of the layout (a book they had  
published), and they have symbols in the inside-margins. The  
"binding" (gluing?) seems to allow that. It's not pretty, but the  
book opens flat  on a table.

And this might interest or amuse the professionals on this site: half  
a year ago, I sent in a "test chapter" as a pdf file, accompanied by  
a tex-file. I expected them (whoever is responsible) to say they  
wanted it in Word (they had told me that based on the test-chapter,  
they would prepare a Word-"mask" for me to fill in text and figures),  
but to my surprise they thought it looked pretty good, and that if I  
could "do just a few minor changes", they could print it as is - but  
that they didn't have anybody who "knows TeX". Now of course I'm a  
bit nervous, not to say afraid, because I'm pretty sure the "minor  
changes" will be way beyond my capabilities...

Cheers, Jörg.

Prof. Dr.med. Jörg Hagmann-Zanolari
Institute of Biochemistry and Genetics
DKBW, University of Basel
Mattenstrasse 28
CH-4058 Basel
Switzerland
Phone +41 (0)61 6953049


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Re: TeX & chemistry (was: alignment of figures)

[Willi Egger]

Hi Jörg,

\relax.

We are still here and I believe that on this list is quite some guru's 
knowledge ... to help in this matter

Willi

Jörg Hagmann wrote:

> Many thanks for all the suggestions on incorporating chemical formula. 
> PPCHEMTEX now looks like something to play with, but not something I 
> will switch to whith a deadline for writing the book coming closer.
>
> From the publisher I got an example of the layout (a book they had 
> published), and they have symbols in the inside-margins. The "binding" 
> (gluing?) seems to allow that. It's not pretty, but the book opens 
> flat  on a table.
>
> And this might interest or amuse the professionals on this site: half 
> a year ago, I sent in a "test chapter" as a pdf file, accompanied by a 
> tex-file. I expected them (whoever is responsible) to say they wanted 
> it in Word (they had told me that based on the test-chapter, they 
> would prepare a Word-"mask" for me to fill in text and figures), but 
> to my surprise they thought it looked pretty good, and that if I could 
> "do just a few minor changes", they could print it as is - but that 
> they didn't have anybody who "knows TeX". Now of course I'm a bit 
> nervous, not to say afraid, because I'm pretty sure the "minor 
> changes" will be way beyond my capabilities...
>
> Cheers, Jörg.
>
> Prof. Dr.med. Jörg Hagmann-Zanolari
>
> Institute of Biochemistry and Genetics
>
> DKBW, University of Basel
>
> Mattenstrasse 28
>
> CH-4058 Basel
>
> Switzerland
>
> Phone +41 (0)61 6953049
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>ntg-context mailing list
>ntg-context@ntg.nl
>http://www.ntg.nl/mailman/listinfo/ntg-context
>  
>

Re: TeX & chemistry (was: alignment of figures)

[Wolfgang Zillig]

Hello,

I absolutely do't have any idea of typesetting formulas but I have a
question on PPCHTeX: is that used in the file eppchtex.pdf which is in
the manuals folder?

Wolfgang

Zitat von Tobias Hilbricht <hilbricht@linopus.de>:

> Am Dienstag, 25. Oktober 2005 20:56 schrieb Mojca Miklavec:
> > Jörg Hagmann wrote:
> 
> > > I am
> > > sure PPCHTEX would do a better job.
> 
> If PPCHTeX is capable of drawing your formulas. I tried it, and apart
> from 
> complicated notation it can not draw seven rings, and you need "work
> arounds" 
> for certain bond angles, and there were other things either very
> complicated 
> to code or not at all. There seems to be no big user community of
> PPCHTeX and 
> no development.
> 
> > I may be wrong, but I doubt that PPCHTEX would satisfy your needs.
> > It's a complicated notation which is not flexible enough
> 
> Have a look into the PPCHTEeX-manual and see if it covers all your
> needs.
> 
> > XymTeX is more powerful, but not supported by ConTeXt
> >and still with very complex notation.
> 
> True, and also XyMTeX lacks a lot of possibilities - apart from seven
> rings 
> many bicyclo-compounds are not possible, if I remember right.
> Additionally, 
> it is not possible to colorize bonds and atoms or to make them bold
> etc. 
> (this is possible with PPCHTeX).
> 
> Then there is ochem by Ingo Klöckl, perhaps the most powerful
> chemistry 
> solution in terms of possible compounds - but only for LaTeX, and
> again with 
> a very peculiar notation and a steep learning curve. Colorization of
> bonds 
> only with PostScript-editing.
> 
> Finally there is streetex by Igor Strokov - again for LaTeX, more
> powerful in 
> terms of possible compounds than PPCHTeX or XyMTeX and much easier
> (more 
> intuitive) to use. However, as with XyMTeX it is not possible to
> colorize 
> bonds and atoms or to make them bold etc.
> 
> > I would say that all you need is a better export from Chemdraw
> 
> Recent versions of Cambrigde Soft ChemDraw can produce very nice
> output in 
> various formats. Additionally, ChemDraw has the feature IUPAC name to
> 
> structure - this is very handy, and no TeX-solution has that.
> 
> Yours sincerely 
> 
> Tobias Hilbricht
> _______________________________________________
> ntg-context mailing list
> ntg-context@ntg.nl
> http://www.ntg.nl/mailman/listinfo/ntg-context
> 
> 

Re: TeX & chemistry (was: alignment of figures)

[Tobias Hilbricht]

Am Mittwoch, 26. Oktober 2005 20:23 schrieb Wolfgang Zillig:
> Hello,
>
> I absolutely do't have any idea of typesetting formulas but I have a
> question on PPCHTeX: is that used in the file eppchtex.pdf which is in
> the manuals folder?

I am not the author of eppchtex.pdf, but that is PPCHTeX, yes.

Yours sincerely

Tobias Hilbricht

Re: TeX & chemistry

[Hans Hagen]

Tobias Hilbricht wrote:

>If PPCHTeX is capable of drawing your formulas. I tried it, and apart from 
>complicated notation it can not draw seven rings, and you need "work arounds" 
>for certain bond angles, and there were other things either very complicated 
>to code or not at all. There seems to be no big user community of PPCHTeX and 
>no development.
>  
>
mostly german users -)

development ... well, demand driven ... also, if you look into the file, 
defining more rings is doable, but ons should do the angle calculations 
once

Hans

Re: TeX & chemistry (was: alignment of figures)

[Mojca Miklavec]

>> I'm playing a bit with drawing formulas in metafun, but my question
>> is: are there any guidelines about how a nice formula should look like?
>> (Yes, I have problems to decide how thick the lines have to be, how to draw
>> a triple or a steric bond properly, which size of letters to use). Knuth did
>> a marvellous job with drawing math formulae in TeX, there are many books
>> about typography, but I've never seen anything about chemistry and I haven't
>> found anyone who could answer me this question.

Keith McKay wrote:

> A quick search on Google found this.
> Keith
>
> http://www.rsc.org/Publishing/ReSourCe/AuthorGuidelines/Illustrations/sect1.
> asp
> http://pubs.acs.org/books/artwork.shtml

(Although a bit late:) thank you very much for the two links above.
The rules don't cover everything, but they represent an important
part. (I didn't have any such list before and data like "space between
bonds has to be 18% of bond length" are pretty useful and exactly part
of those rules that I was looking for.)

Thanks again,
    Mojca