fingerprints not working

fingerprint generation stopped working after last community nightly update on knime 2.7.4 , linux 64 bit. Please check all fp as also other nodes like properties and bcut descriptors as there have been similar issues earlier.

Hi,

I have tested the plug-in on Linux Mint 64 bit with KNIME 2.7.4. I could not reproduce your error.

Can you please send me an example workflow with data? 

 

Many thanks,

Stephan

Hmm probably some problem in my knime install or fedora.. Its working now.

I have latest nightly updates. Unable to use a cast SMILES column  with CDK fingerprint node after mol to cdk conversion. Converting to sdf using marvin molconvertor does not help either.The rename node confirms that the cast node does change it to smiles and not stringcell.

 

error : Fingerprints     Configure failed (IllegalArgumentException): No converter for type StringCell exists
 

After a while , clikcing any node gives : 10 elements (21), looks like we are leaking contexts somewhere.

 

moltocdk, Fingerprint nodes work fine with sdf input

Hi,

I'm currently away on holiday with limited internet connection. I will take a look at it on Monday.

Best regards,

Stephan

I have updated the nightly build. Changes should take effect tomorrow.

 

I believe the problem was due to a faulty auto-configure method. The auto-configuration works fine now on cells of type Smiles. Could you be more specific with regard to the issue of "leaking contexts"? I couldn't reproduce that error.

 

Many thanks,

Stephan

 

Updated nightly build. CDK fp still not working., with/without cast .Please see screenshot.

 

Leaking context happens with both cdk non-cdk nodes (like csv reader) when i click the node configure menu more than once after it does not respond and open upon clicking the 1st time. After restarting nodes-> configure dialog opens and leaking context error does not occur.

Seems to think the CDK column is string. Have you tried deleting fingerprint node and inserting a fresh one from node repository and reconfiguring it to the CDK column.

Simon.

The "leaking context" message does indeed come from you double-clicking the node too often before the dialog opens. Just be a bit more patient ;-) It's not critical, but we have it on the list for 2.8.1.

Tried to reproduce the error by following your example but without success. 2.7 and 2.8 work with the nightly build with and without the Molecule to CDK node in between.

 

Please follow richards99's suggestion and make sure you have updated KNIME-CDK and the chemistry base types. If it still doesn't work, please send me an email with the zipped workflow, best with some example data.

 

Kind regards,

Stephan

Thanks Simon and Stephan.

I fully removed and reinstalled cdk on 2 diff computers with different OS's, to no avail. In both cases I had upgraded to 2.8 from 2.7. Problem persists, workflow with data attached. This weekend I will check whether a new 2.8 install does the trick.

Hi,

thanks for sharing the workflow. That helped me to find and fix the error. There was a problem with the "configure" method of the Fingerprint node. It wouldn't cofigure properly for chemistry columns above position 0.

The fixed nightly version should be available tomorrow (Monday).

Thanks for reporting the bug.

Stephan

Hi,

thanks for sharing the workflow. That helped me to find and fix the error. There was a problem with the "configure" method of the Fingerprint node. It wouldn't cofigure properly for chemistry columns above position 0.

The fixed nightly version should be available tomorrow (Monday).

Thanks for reporting the bug.

Stephan

Thanks for posting the workflow. That helped to find and fix the bug.

There was a problem with the "configure" method that did not allow correct column configuration for any index greater zero.

I have updated the nightly build. It's already available from the repo.

 

Thanks again

Stephan

yep. fixed. thanks a lot