Calculation of McGowan volume.

Groups Cheminformatics
1

Hello,

Is it possible to calculate the McGowan volume from a 2-D or 3-D structure using KNIME?

Thanks and regards,

Tim Ritchie.

2

The PaDEL nodes can do it.

See here for the instructions on the node: http://padel.nus.edu.sg/software/padeldescriptor/index.html

Please note that PaDEL is incompatible with CDK (as they use an older version of the cdk conversion node and still have not separated the namespace) so make sure you do not have CDK nodes installed.

3

Is there any chance of the PaDEL nodes being updated to the new CDK release?

McGowan volume looks at first sight easy enough to calculate, so I'm sure it ought to be possible to either to write a Java Snippet to manually process a mol column, or write a node to do it using the RDKit tools.

Steve

4

The people over at NUS do not seem to put a lot of priority in updating their node, possibly thinking it is fine as it is.

They even did not react to my suggestion simply renaming their CDK 1.4 conversion node to 'Molecule to PaDEL' and giving the in-between structure its own name too, in order to avoid the obvious name-clash.

So the short answer is: dont count on it. (and that is a pitty, it is a powerfull node)