In the last few weeks (including this evening) we have released a series of updates to our Matched Molecular Pairs nodes, resulting in significant further performance improvements, and some changes to canonicalisation, along with a number of bug fixes. Currently only in the nightly build - please do give the updates a try and let us know if there are any further problems with them.
Full details from the changelog:
17-Feb-2016 - v1.6.3 (Nightly Only)
- Moved filtering of fragmentations forwards in process, resulting in significant performance improvements for filtered fragmentations (Unchanging HAC and Changing/Unchanging HAC ratio)
- Improvements to H-removal algorithm
- Moved all H-removal handling to fragmentation factory, and removed subsequent duplicate calls to H-removal (further performance improvement)
- Added check for presence of unassigned double bonds before trying to do any assignment (upto 25% performance improvement)
- Filter/Splitter nodes no longer pass multicomponent structures
- Fragmentor nodes no longer fail with multicomponent structures
- Fixed bug in which certain double bond geometries to near-symmetrical aromatic rings became corrupted causing crashes
- Fixed bug causing multi-fragment node to only perform two cuts to a bond ([2*]-[1*] value) when the maximum number of cuts was 2
- Improved garbage collector class to remove possible references to deleted native objexts
12-Feb-2016 - v1.6.2 (Nightly only)
- Fixed loss of stereointegrity issue in MMP fragmentation
- Fixed canonicalisation issue resulting from above fix (NB 'Values' will not be differently canonicalised to previously)
- Fixed graceless failures for some salted forms and apparent successful failures of other salted forms
02-Feb-2016 - v1.6.1 (Nightly only)
- RCSB PDB Loader nodes make 5 attempts to load each file before failing if unable to load (previously only a single attempt was made, resulting in a missing value in the output)
- Local PDB Loader now makes 5 attempts to load each, but continues with a WARN to the console and a missing value cell if it fails to load a file
- Bug fixes to MMP nodes which resulted in loss of double bond geometry (Change in RDKit toolkit behaviour), scrambling of attachment point labels and node failures in certain circumstances
- Nodes transferred to the KNIME core product (Wait for time, Wait to time, Flow variable Case switch) deprecated