Re: [Joelib-cvs] Re: Bugfix joelib/io/types/ClearTextFormat.java

[Joerg K. W. <we...@in...>]

Hi Gert,

>>2DCOORD:
>>first line: default length used for the coordinate
> What would be meant with 'default length'? Default z-coordinate maybe?
> Or the default value if a coordinate is missing? It is always '1' in my
> .CTX-files.
I think they mean the multiplication factor for atom coordinates ... for 
more informations we should contact Dr. Ihlenfeldt or one out of the 
Group of Prof Gasteiger, e.g. Achim or Thomas.

>>second line: xmin, xmax, ymin, ymax are the rectangle coordinates
>>including all atom coordi
> I should have figured this out myself.

>>which means a CTX-writer could be also useful
> Sorry, I don't completely understand this deduction. Do you mean that it
> would in any case be useful to implement a CTX-writer, or do you more
> specifically mean that it would be useful to implement the CTX-writer
> because of these rectangle coordinate (seems absurd, but maybe I'm
> missing something)?
1. I think it could be usefull to implement the coordinate ouput more 
correctly to store not only 3D coordinates but also 2D, 3D or both of 
them analogue to CML --> With low priority, in my opinion, because i do 
not really need a CTX writer and the format is not documented really 
well!!! I own only the old 1994 manual in paper form.

2. This requires also taking 2D AND 3D coordinates into account when 
loading molecules, so i recommend the analogue mechanism like the one in
joelib.io.types.cml.MoleculeFileCDO:endObject(String objectType)
which stores 2D informations in
coordinates2Dx
coordinates2Dy
and 3D informations in
coordinates3Dx
coordinates3Dy
coordinates3Dy
Both are simple double 'atom property' descriptors, which allows us also 
to store such kind of informations in all formats which support 
descriptors, e.g. MDL SD

3. Finally the JOELib writer for 2DCOORDS entry can also store the
?
? ? ? ?
options !;-)

So, i think, the writer is really far behind other topics which should 
be implemented ... was just an idea ... i would say forget my last mail !;-)

> Greetings and thanks for the lookup.
> 
> Gert

Regards, Joerg



-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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