New CDK plugin

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1

Thanks to Stephan Beisken from EBI we now have a new version for the CDK plugin which uses  CDK 1.3 instead of 1.0 which the plugin on the standard update site still does. The new plugin is currently only available via the nightly update site of the community contributions, since there are still some internal changes to make which may break workflows saved with data. As soon as everything is resolved we will make a stable release. Feel free to try it out and report problems and wishes.

2

Seems to be missing the Substructure Search and ChemSpider nodes. Really need that first one to test workflows.

So far, have yet to see any timeouts using the Molecule to CDK node, wheras the old node would produce errors for 10-20% of a given data set.

(the other) Simon

 

[edited: 'old node' for 'old set']

3

Yes, you are right, they were missing. They are available with the next nightly build tomorrow.

4

Thanks.

 

One last request: could we please have the 'query' for the Substructure Search node available as a flow variable or optional input-port? I hate the thought of having to draw out hundreds of sub-structure searches.

 

(the other) Simon

5

dear

 

I tried to calculate MACSS fingerprint with the new cdk plugin and to do a fingerprint similarity with both erlwood node and indigo node but i find this error

ERROR Fingerprint Similarity Execute failed: org.knime.core.data.DataType$MissingCell cannot be cast to org.knime.core.data.vector.bitvector.BitVectorValue

6

This indicates that both similarity nodes do not handle missing values correctly. But it's also a good question why CDK creates a missing value. Is it possible to get the molecule for which no MACSS fingerprint could be generated?

7

Has anyone checked the CDK structure checker node? I get this error

ERROR     Structure Sketcher     Configure failed (NoClassDefFoundError): org/openscience/cdk/exception/CDKException
ERROR     OpenDialogAction     The dialog pane for node 'Structure Sketcher 0:2:4' has thrown a 'NoClassDefFoundError'. That is most likely an implementation error.
ERROR     OpenDialogAction     The dialog pane for node 'Structure Sketcher 0:2:4' has thrown a 'NoClassDefFoundError'. That is most likely an implementation error.
 

8

BUMP.

Hi thor,

Just wanted to remind you of my request to have the 'query' for the Substructure Search node available as a flow variable or optional input-port.

Thanks,

(the other) Simon