Keep Largest Fragment?

Community Extensions CDK
#1

Hi,

 

I've noticed that in all of the KNIME chemoinformatics stuff, the only thing that exists that removes fragments is the RDKit Salt Stripper.  Whilst I've found this useful, it does require you to define salts when the pre-defined ones are not wanted.

 

A simple node that removes the smallest fragment (or keeps the largest fragment) in a "molecule" would be great.  I'm somewhat surprised this hasn't been implemented in one of the APIs before (though I post this in the CDK library as I rely on CDK slightly more than the other 2).

 

Thanks in advance,
Ed.

#2

Hi Ed,

does the "ConnectivityChecker" suit your purposes? It has an option to keep only the largest fragment. Otherwise we simply add what you need. :)

Cheers,

Stephan

#3

Ther are the indigo nodes as well which will split out the fragments to leave the largest. Without the need to give a predefined list.

thanks,

simon.

#4

Hi, sorry for long reply, I only just noticed there were replies!

 

richards99 - Are you referring to the Component Separator node?

Stephan - Ah right, I didn't notice that node before!  Thanks, I'll check that out.

#5

Yes I am, the Component Separator node.

Simon.