Is it possible to control CDK molecular property parameters from KNIME?

KNIME Analytics Platform
1

Hi guys,

I'm using CDK molecular property node in order to calculate some descriptors. I would to know if it would be possible to change the default parameters with which the molecular properties are calculated.

For example let's imagine that I want to calculate the CDK Rotatable Bond Count. This java class take as input the includeTerminals parameter which controls if the terminal bonds have to be considered as rotatable or not. In CDK the default value for this parameter is false, anyway in knime it seems is it implemented as true.

Is there a way to set the includeTerminals parameter dynamically from knime? I sense that this could be done using flow variables but I'm not sure if this is true and so far I didn't found how.

Gio

2

Hi Gio,

there is currently no dynamic way to change the descriptor parameters. It is a good idea though to extend the molecular properties node to allow users to do that.

For now I have added a non-rotatable bonds count descriptor.

Hope that helps.

Stephan

3

Hi Stephan,

Thank you for your quick reply and for adding a non-rotatable bonds count descriptor.

I think it would be nice if in the future all the CDK descriptors options, already available through the descriptor class parameters, could directly be set from KNIME.

Thank you again.

Gio