Re: [Cdk-user] viewing a SMILES string

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

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On Wednesday 21 January 2004 04:28, Rajarshi Guha wrote:
>   I'm playing around with CDK and have installed it on a Fedora Linux
> system. The installation appears to have succeeded and I can run
> programs like cdk-fingerprinter and cdk-fileconvert.

Good to hear that it compiles on that platform too... which version did you=
=20
use? The one that was released yesterday?

> I'm having a problem with cdk-view. I have a Hyperchem HIN file which I
> converted to SMILES format with babel. But when I do the command
>
> bin/cdk-viewer --smiles "c1cccn(c1)CC"
>
> I get the following error:
>
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/openscience/cdk/applications/Viewer$AppCloser
>         at org.openscience.cdk.applications.Viewer.view(Viewer.java:147)
>         at org.openscience.cdk.applications.Viewer.view(Viewer.java:154)
>         at
> org.openscience.cdk.applications.Viewer.viewSMILES(Viewer.java:178)
>         at org.openscience.cdk.applications.Viewer.main(Viewer.java:261)

That's a bug. I'll try to reproduce it and will file it on the SourceForge=
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website...

> I'm not too familiar with the setup of Java programs and I'm not sure
> whether the problem is with CDK or my Java setup.
>
> Does anybody know what might be going wrong and if so how to fix it?
> (I'm runnign Fedora Core 1 and Blackdown Java 1.4.2)

It seems that something is wrong with the jar that is generated... the erro=
r=20
suggests that an internal class is missing...

> I also converted my HIN file to an XYZ file with babel and used
> cdk-fileconvert to convert it to SMILES. But when I do
>
> bin/cdk-viewer --smiles
> "C.C.N.C.C.C.[H].[H].[H].[H].[H].C.C.[H].[H].[H].[H].[H]"

Ah... first of all, the XYZ file does not have bonds, which is why all the=
=20
dots are in the string... which means that each atom is *one* molecule...

> I get
>
> Problem parsing SMILES:
> org.openscience.cdk.exception.InvalidSmilesException: Expected element
> symbol, found null!

That's a bug again... I'll try to reproduce it and report then...

> I would have expected it to be able to read SMILES strings that it
> generates itself - am I doing something wrong?

You're not doing anything wrong... you're just doing things we have not don=
e=20
yet...=20

Thank you very much for reporting these problems. I'll get back to you when=
 I=20
have confirmed these bugs.

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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