Inconsistencies with KNIME-CDK “Lipinski's rule of five” descriptor

Hi KNIME&CDK lovers,

I'm using the knime-cdk molecular property node in order to calculate molecular descriptors and I'm facing some inconsistencies related to the “Lipinski's rule of five” descriptor. In principle this descriptor just counts the number of Lipinski's rules that a certain molecule is violating. Anyway I found that this number in certain molecules is not consistent with the calculated singular descriptors.

I attach an example workflow with a molecule having a molecular weight > 500 but a Lipinski's rule of five = 0 (while it should be 1). Why this is happening? Please, can anybody comment on this?

Thanks in advance,

Gio

Hi Gio,

thanks for reporting this bug and attaching a workflow to reproduce the error.

You are absolutely right, the rule violation should result in a score of 1. This bug has been fixed in the nightly build of the plugin. Please update your plugin to the nightly (http://tech.knime.org/community) and try again.

Kind regards,

Stephan

Hi Stephan,

Thanks for your reply and I'm sorry to be late. I tried to update from the nightly build (latest available version: 1.5.1.201408051308) but it gives me the following error:

Cannot complete the request. See the error log for details.

"KNIME-CDK" will be ignored because a newer version is already installed.

Indeed the current version installed in my system seems to be newer: 1.5.1.201409032225.

Do you know why this happens? Is it possible that a "commit & push" to the nightly repo is missing?

Thanks in advance,

Gio

Hi Gio,

that's strange. I am on the same version. The node should be up to date and working correctly. I'm attaching the executed workflow from my 1.5.1.2... installation.

I installed the CDK plug-in via the nightly repository, so the changes are commited.

Stephan

OK Stephan,

The automatic updating from the nighly build repo didn't work for me, as explained above. Anyway finally I downloaded the update manually and then I substituted the whole cdk dir inside KNIME plugins dir. Finally I tested the Lipinski node bug and now it works!

Congrats and thanks a lot!

Gio