Dear Srikant,
On Tue, Dec 7, 2010 at 4:48 PM, Srikant Verma <srikant.ve...@igib.in> wrote:
> I wanted to find the molecular descriptors of the attached molecule
> "Temp_2.sdf". For that I did these things:
> (1) mols=load.molecules("Temp_2.sdf")
> (2) convert.implicit.to.explicit(mols[[1]])
> At this point I got the following error:
>
> "Error in
> .jcall("org/openscience/cdk/tools/manipulator/AtomContainerManipulator", :
> org.openscience.cdk.exception.CDKException: IAtom is not typed! S"
This error message indicates that the CDK does not know anything about
this atom type.
I have found another example of this charged sulphur in PubChem:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=18982514
and will shortly write a unit test, and add the missing atom type to
the library.
> How can I solve this problem?
Help me with some missing details on this atom type... in particular,
I still need to know if this sulphur has lone pairs (my sulphur
chemistry is really bad), and if it has, how many...
Looking forward to hearing from you,
with kind regards,
Egon
--
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
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
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