ppchtex questions

ppchtex questions

[Jörg Hagmann]

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)?

2. Is it possible to move the "\bottext" further down?  It gets too 
close to the formula, especially with larger fontsize and smaller 
formula structures, see example)?

\starttext
\usemodule[chemic]
\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
\stoptext

By the way: X_subscript and X^superscript don't work within \SL{...}.

3. How can I get \ss for *all* the atoms in the formulae and in the 
bottom text (I tried a few things within \setupchemical)?

Thanks, Jörg
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Re: 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: 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: 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: 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: 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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