Re: [Cdk-devel] valid cml file?

[E.L. W. <eg...@sc...>]

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On Friday 21 May 2004 00:36, Miguel wrote:
> I have several questions about this CML file:

<snipped CML file />

> Ola generated it using CDK:
>
> I have included the file inline:
>
> Problem/Question:
>
> I realize that these are 2D coordinates, but I expected the coordinates to
> be in angstroms ... perhaps shortened or stretched to fit in a flat world.
>
> Either these units are not angstroms or something is wrong ... the carbons
> are 36.0 units apart.
>
> Q: What units are used for 2D coordinates?

This is one of the problems with 2D coordinates: it often uses a screen pix=
el=20
coordinate system.

> Regarding the bonds:
>
> Q: Are these bonds defined in acceptable CML2 format? With the order
> defined as a part of a scalar tag rather than as an attribute of the bond
> tag?

The order attribute of the bond tag is for integers... CDK uses fractional=
=20
(double) bond orders... so those can not be put into the attribute...
But, and I will fix this today, it should check wether the bond order match=
es=20
BOND_ORDER_SINGLE (as in CDKConstants) and then it *should* use the order=20
attribute...

> Q: I assume that order=3D=3D1.5 means aromatic ... please confirm.

Yes, see CDKConstants.

Egon

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eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

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