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Fix issue #166 #167

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merged 22 commits into from
Feb 22, 2024
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509c637
Use SYBL atom type to infer the element. [closes #166] [ci skip]
lohedges Feb 22, 2024
e9ebfa8
Update CHANGELOG. [ci skip]
lohedges Feb 22, 2024
02ee306
Can now detect when the AmberPrm file changes the atom order because of
chryswoods Feb 22, 2024
ee8d025
Added a progress bar and unit test for the amber topology renumbering…
chryswoods Feb 21, 2024
949b36e
Improve flexibility of boresch function
Jan 21, 2024
e9c6ade
Clear up import and type errors in _restraints.py
Jan 21, 2024
0df0c02
Fix bug in boresch return value
Feb 11, 2024
c2c99aa
Add tests for boresch plus minor tweaks to boresch
Feb 11, 2024
281b56d
Add Boresch analytical correction and test
Feb 11, 2024
3b79038
Improve formatting of examples in boresch and get_standard_state_corr…
Feb 11, 2024
ac13459
Fix typo in name of sphinx-issues in development guide
Feb 11, 2024
29d8192
Add missing space in boresch example
Feb 11, 2024
5244875
Allow boresch arguments to be passed using a map
Feb 11, 2024
7f6dd3c
Tiny tweak to how default temperature is specified
Feb 11, 2024
1f6666e
Add Boresch restraints to the tutorial
Feb 11, 2024
a370190
Update changelog
Feb 11, 2024
751a0f3
Autoformatting changes [ci skip]
Feb 20, 2024
469cc23
Can now detect when the AmberPrm file changes the atom order because of
chryswoods Feb 20, 2024
3c8dcc7
Added in the SDF scoring fix, and also added the update to Cursor so …
chryswoods Feb 21, 2024
59afb3a
Added map support for the perturbable molecules written by Gro87
chryswoods Feb 22, 2024
62dc361
Update CHANGELOG. [ci skip]
chryswoods Feb 22, 2024
90b81cd
Merge branch 'devel' into fix_166
chryswoods Feb 22, 2024
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Update changelog
finlayclark authored and chryswoods committed Feb 22, 2024
commit a370190e1b541f95600393684f1760782962a6c1
7 changes: 7 additions & 0 deletions doc/source/changelog.rst
Original file line number Diff line number Diff line change
@@ -141,6 +141,13 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.

* Please add an item to this changelog when you create your PR

* Added more support for Boresch restraints. Specifically, :func:`sire.restraints.boresch`
now supports the specification of equilibrium values, uses different default force
constants, and warns the user if the restraints are likely to be unstable.
:func:`sire.restraints.get_standard_state_correction` was implemented for Boresch
restraints. Tests were added for restraint creation and for the standard state
correction. Boresch restraints were added to :doc:`tutorial <tutorial/part06/03_restraints>`.

`2023.5.1 <https://github.com/openbiosim/sire/compare/2023.5.0...2023.5.1>`__ - January 2024
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