Re: [Cdk-devel] MDLV2000Writer ouputs query molecule features

[<ma...@eb...>]

commit c20a0ea691211c55cd45e28bb079cbe3d029d41d
Author: Stefan Kuhn <Ste...@eb...>
Date:   Wed Mar 31 10:37:59 2010 +0100
    MDL reading and writing valency

Looks like a patch for Jchempaint, it's not mine so I don't know the
details. But the only implication would probably be a visual one. I don't
think undoing it should break anything. But then to be consistent, the
reader should not read valency either (unless it produces a query
molecule?)

Mark

> Hi, it seems that the MDLV2000Writer includes some properties, that as
> far as I can see, are specific to query molecules.
>
> For example, on reading a molecule and performing atom typing, the
> valency of each atom is specified. On writing the molecule, the
> valency gets written out in the hydrogen count field of the atom block
> lines. The query seems to indicate that this field is just for query
> molecules. When such output is viewed in say MarvinView, each atom
> gets labeled with a V(n)
>
> Example code is at https://gist.github.com/835128
>
> I had thought that the MDLV2000Writer was not meant to be writing
> query molecules, but Egon pointed out that the patch to include this
> feature in the writer cam from the EBI. So, is this feature used at
> the EBI? And if so, it would be nice to have a way to avoid writing a
> query molecule if desired.