I've noticed some (I think) erroneous behaviour in the MCS node. It seems that under certain circumstances it will break open rings even when told not to.
I've attached a zipped up KNIME workflow to demonstrate the problem. It shows how mining a fuzzy MCS (in terms of element type) from a set of results in a SMARTS pattern containing aromatic bonds that no longer describe a ring. This is the SMARTS I'm getting:
The input SMILES strings are:
The node configuration is as follows:
Ring matches ring only: checked
Complete rings only: checked
Match valences: unchecked
Atom comparisons: "Compare Any"
Bond comparisons: "Compare Order"
The node doesn't time out, but I've seen this behaviour more often when it does.
I think this behaviour is a bug and is definitely undesired for me, since I'm using this node to identify scaffolds with complete rings. Instead of breaking bonds, I would instead expect the node to produce a SMARTS pattern that just doesn't include the ring atoms.