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[Bioclipse-users] FPSA-3: value = NaN..

From: Le-Ha Dieu <l.dieu@un...> - 2012-02-15 11:59

To whom it may concern,

I would like to calculate this descriptor: FPSA-3
However, the decriptorValue.xml file showed:

<qsar:descriptorvalue index="11" label="FPSA-3" value="NaN"/>

How can I get the value vor FPSA-3? I entered the molecules using SMILES 
and SDF.

Thanks for your help!

regards,
lea

Re: [Bioclipse-users] FPSA-3: value = NaN..

From: Egon Willighagen <egon.willighagen@gm...> - 2012-02-26 09:14

Dear Le-Ha Dieu,

On Wed, Feb 15, 2012 at 12:59 PM, Le-Ha Dieu <l.dieu@...> wrote:
> I would like to calculate this descriptor: FPSA-3
> However, the decriptorValue.xml file showed:
>
> <qsar:descriptorvalue index="11" label="FPSA-3" value="NaN"/>
>
> How can I get the value vor FPSA-3? I entered the molecules using SMILES
> and SDF.

The CPSADescriptor requires 3D coordinates. If those are missing, it
will return NaNs.

Can you verify that you created 3D coordinates, e.g. with the Balloon
feature in Bioclipse?

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers