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@SimonBoothroyd SimonBoothroyd released this 19 May 18:16
0.1.0
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Learn about vigilant mode.

This release marks the first in which the OpenEye toolkit is no longer required to use this package. From this release onwards either the OpenEye toolkit or a combination of RDKit and AmberTools can be used to power the fragmentation.

The use of open source and freely available backends has been made possible through a re-write of the framework to be based around the openff-toolkit. While every care has been taken to ensure that this release after the re-write produces fragments which are similar to those generated by previous releases, there will likely be differences due to how newer versions of OpenEye and how AmberTools both generate conformers and compute the Wiberg Bond orders.

Possible Behaviour Changes

  • While the OpenFF toolkit should give very similar WBOs to the pure OE approach previously used this may not be guaranteed in all cases - it seems that the older versions of OE will produce slightly different WBOs for the same input conformer when computing them using a newer OE version but the same input conformer. See #80 for details.

  • The number of conformers used to compute the average WBO may be less after the refactor. It seems that setting omega.SetCanonOrder(True) (old behaviour) will lead to more conformers than setting it to false (OpenFF toolkit behaviour). See #80 for this change.

  • Ortho groups are now detected using SMARTS matching approach (see #83). The fixes the issues found in older version where non-ortho groups would be falsely flagged and retained.

  • When expanding fragments to include the functional groups an atom is in all functional groups the atom appears in are now considered. Previously only the last group an atom was assigned to would be considered. See #84, #88 and #91.

  • The OE code which extracts the fragment molecule from the parent based on a set of atom and bond indices was modified to include hydrogens which are bound to atoms to include in the substructure search. This is so that those in the final fragment will retain their map indices which should be more helpful and will also more closely match of the output of the RDKit implementation. See #89.

  • The indexing of some rings may change after #90 when using OpenEye due to differences in how the OpenFF toolkit canonically orders OE molecules.

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