Konstantin Tokarev wrote:
> There are some parameters, which are not part of CML, but could be
useful for both 2D and 3D chemical structures:
Peter can probably answer better than me, but some of these things you
suggest can already be done in CML.
> 1. Custom label of atom (independent from elementType)
The elementType attribute is strictly for representing chemical elements
(with a couple of exceptions - 'Du', 'R'), but atoms can have child
atomType and label elements. Different atom types and labels can be
distinguished by dictRefs
<atom elementType="O">
<atomType dictRef="cml:mol2">O.co2</atomType>
<atomType dictRef="cml:mmff94">O=CO</atomType>
</atom>
<atom elementType="C">
<label dictRef="pdb:name" value="CA" />
</atom>
> 2. Custom color of atom
> 1. Custom atomic radius (in Angstroms)
Similarly, child property elements can be used to associate other values
to atoms (or other CML elements):
<atom>
<property dictRef="gfx:color">
<scalar type="xsd:string">#ff0000</scalar>
</property>
<property dictRef="cml:radius">
<scalar type="xsd:float" units="units:angstrom">1.2</scalar>
</property>
</atom>
> 2. Custom directions of cartesian axes
The x3,y3,z3 axis is defined as right-handed in the schema.
What's needed is agreement on which dictRefs to use, and publically
available definitions of the terms. We're planning to put considerable
effort into this in the near future, and any help is welcome!
As part of Chem4Word we are looking into some of these issues (e.g.
colouring, radius, default bond angles, functional group
representations) and are investigating the possibility of a chemical
'CSS' equivalent.
Regards,
Sam
--
Unilever Centre for Molecular Science Informatics
Cambridge University Chemical Laboratories Tel: 01223 763073
Lensfield Road email: [email protected]
Cambridge CB2 1EW
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