Issues with Matched Pair Fragmentation nodes

We are aware of a number of issues with the matched molecular pair fragmentation nodes:

  • The current fragmentation nodes have started giving spurious output for fragmentations, such as *N.*Cl.*Br rather than [1*]N.[2*]Cl.[3*]Br - we have a fix for this which will be released imminently (see separate post when it is released)
  • MMP Molecule Fragment (3rd Gen) and MMP Molecule Multi-cut Fragment (3rd Gen) nodes (deprecated in July 2017) cause KNIME to crash suddenly during node execution, resulting in application completely shutting down unexpectedly without saving etc.
  • Older versions (pre-‘3rd Gen’, deprecated in 2015) appear to lose outputs in the fragmentation table in some circumstances

We are trying to find a solution to the 3rd generation nodes issue, but are not yet able to find a perfect solution.

Due to the age and many other issues with the pre-2015 version, we are unlikely to invest time and effort into fixing these.

The current version of the nodes do not appear to be affected by any of these issues except the first, and we would strongly advise updating workflows to use the latest versions.

We believe the issues are the result of a number of major changes to the RDKit toolkit made in a recent update.


The first of these bugs has been fixed in the nightly build and v3.5 stable build version 1.12.10 released just now (see Update to v1.12.10 (Nightly and v3.5 stable releases) for further details)

An additional behaviour change is that the PMI Align to Inertial Principal Axes node will now modify the chirality in the returned MOL cells as RDKit now automatically percieves chirality from 3D coordinates where none is indicated.


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