Re: [cml/ccml-discuss] Some common needed properties in CML

[Peter Murray-R. <pm...@ca...>]

On Mon, May 10, 2010 at 7:26 PM, Konstantin Tokarev <an...@ya...> wrote:
> Hello everyone!
> Some time ago I've asked if there's some agreement on saving these
> properties in CML files:
>

You can store any scalar quantity you like in CML files, using your
own attributes and elements. For example:

<atom xmlns:kt="http://yandex.ru/annulen" kt:color="blue"/>

This will not clash with anyone else - you own the namespace.

Then you should work with the BlueObelisk to see if you can find
otehrs interested in synthesising the approaches. You might then
develop a chemicalColourML which the community feels is worth
adopting. The technology is simple - it's getting general agreement
that is the challenge.


> * Custom label of atom (independent from elementType)
> * Custom color of atom (RGB)
> * Background color of scene (maybe including gradient filling description)
> * Custom atomic radius (in Angstroms)
> * Custom directions of cartesian axes

CML has tools for coordinates and vectors.

>
> AFAIU, such agreemnt doesn't exist. I think it's very important to
> develop agreement or dictionary to make opensource
> chemical software more interoperable.

I agree
>
> Any suggestions?

Create some examples - and software that processes them. See what Jmol
does. Mail on the BO list. Keep trying. It will be hard work but
possible.

P.

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069