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e47b90a
enable user defined restraints in abfe calculations
IAlibay Jun 16, 2026
c5425b9
Merge branch 'abfe_user_defn_restraints' of github.com:OpenFreeEnergy…
IAlibay Jun 16, 2026
82f3c94
Merge branch 'main' into abfe_user_defn_restraints
IAlibay Jun 16, 2026
a453b53
Add something specific to abfe restraints
IAlibay Jun 16, 2026
12c509f
fix some typing
IAlibay Jun 16, 2026
f593327
isolate restraints only for ABFEs for now
IAlibay Jun 16, 2026
505f4b7
Add settings test
IAlibay Jun 16, 2026
6ddcba1
Add test for user defined restraints
IAlibay Jun 17, 2026
801220a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 17, 2026
b3de6fd
Add a news item
IAlibay Jun 17, 2026
487b8ef
Merge branch 'main' into abfe_user_defn_restraints
IAlibay Jun 17, 2026
1fb2991
Add support for smcs as host molecules
IAlibay Jun 17, 2026
f56d0ae
Add news item
IAlibay Jun 17, 2026
3f08aaf
assign None if needed
IAlibay Jun 17, 2026
7dc66d6
Merge branch 'abfe_user_defn_restraints' into smc_hosts_abfe
IAlibay Jun 17, 2026
44931cb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 17, 2026
620f3c0
Merge branch 'abfe_user_defn_restraints' into smc_hosts_abfe
IAlibay Jun 17, 2026
21f9e9b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 17, 2026
0e6c1e0
Add settings to control alchemical ion
IAlibay Jun 17, 2026
da65918
First pass at adding net charge support for ABFEs
IAlibay Jun 17, 2026
db7567d
various bug fixes
IAlibay Jun 17, 2026
543dd7f
some bugfixes
IAlibay Jun 17, 2026
6d2ced5
more bug fixes
IAlibay Jun 17, 2026
fcfe3b1
Add fixes for most tests
IAlibay Jun 17, 2026
5744165
Merge branch 'main' into net_charge_abfe_v2
IAlibay Jun 17, 2026
be5ed1e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 17, 2026
6930b72
add missing imports
IAlibay Jun 17, 2026
98cbc00
Merge branch 'net_charge_abfe_v2' of github.com:OpenFreeEnergy/openfe…
IAlibay Jun 17, 2026
98b8101
fix typo
IAlibay Jun 17, 2026
c059b6c
more missing imports
IAlibay Jun 17, 2026
fdb5679
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 17, 2026
0e7bc94
fix various mypy issues
IAlibay Jun 17, 2026
37ac006
Merge branch 'net_charge_abfe_v2' of github.com:OpenFreeEnergy/openfe…
IAlibay Jun 17, 2026
b2e3ef0
remove unused ignore
IAlibay Jun 17, 2026
977b385
Slightly improve user charge tests
IAlibay Jun 17, 2026
88a014c
Modify validation checks to allow for net charge ligands
IAlibay Jun 17, 2026
b1a788d
small fix
IAlibay Jun 18, 2026
a8987a7
Merge branch 'main' into net_charge_abfe_v2
IAlibay Jun 18, 2026
8d28d96
Some fixes for SepTop tests
IAlibay Jun 18, 2026
234f1ef
Merge branch 'net_charge_abfe_v2' of github.com:OpenFreeEnergy/openfe…
IAlibay Jun 18, 2026
1de4be6
Temporarily disable harmonic bond addition in solvent
IAlibay Jun 22, 2026
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25 changes: 25 additions & 0 deletions news/abfe_host_smc.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
**Added:**

* Add support for SmallMoleculeComponents to act
as host in the ``AbsoluteBindingProtocol``
(`PR 2020 <https://github.com/OpenFreeEnergy/openfe/pull/2020>`_).

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
24 changes: 24 additions & 0 deletions news/abfe_user_dfn_restraints.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
**Added:**

* Added support for user-defined Boresch restraints in the
ABFE Protocol (`PR #2019 <https://github.com/OpenFreeEnergy/openfe/pull/2019>`_).

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
25 changes: 25 additions & 0 deletions news/net_charge_abfe.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
**Added:**

* Add support for transformations involving net
charges in the ABFE Protocol
(`PR #2020 <https://github.com/OpenFreeEnergy/openfe/pull/2020>`_).

**Changed:**

* <news item>

**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
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