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Feature automated Morse restraints during bond creation#397

Merged
lohedges merged 2 commits intoOpenBioSim:develfrom
akalpokas:feature_alchemical_restraints_2
Feb 3, 2026
Merged

Feature automated Morse restraints during bond creation#397
lohedges merged 2 commits intoOpenBioSim:develfrom
akalpokas:feature_alchemical_restraints_2

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@akalpokas
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Changes proposed in this pull request:

This PR expands on the automated Morse restraint parametrisation to support alchemical contexts where a bond is alchemically being created, for example in a ring-forming case. Specifically it:

  • It updates _restraints.py sire python API to support this, while specifically preventing the user from automatically parametrising a molecule containing multiple bond annihilations or creations simultaneously. We currently don't have a test system which requires such functionality, so therefore I haven't added support for it as of now.
  • Adds an additional test for automatic parametrisation in tests/restraints/test_morse_potential_restraints.py for a propane_cyclopropane.bss system which requires an alchemical bond creation. (I skip the CI in commits to not trigger a sire build without the input file uploaded to test suite, however it should work when uploaded).
  • Updates the Morse restraint tutorial and changelog to reflect the changes.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): y
  • I confirm that I have added a test for any new functionality in this pull request: y
  • I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: y
  • I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): y
  • I confirm that I have permission to release this code under the GPL3 license: y

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@lohedges

…tion when a bond is being alchemically created in addition to annihiliation [ci skip]
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Thanks for this!

@lohedges lohedges merged commit 8846e54 into OpenBioSim:devel Feb 3, 2026
3 of 5 checks passed
@akalpokas akalpokas deleted the feature_alchemical_restraints_2 branch February 3, 2026 11:38
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2 participants