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Merged
IAlibay merged 129 commits into from
Jul 4, 2025
Merged

Restraints API #1043

IAlibay merged 129 commits into from
Jul 4, 2025

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@IAlibay IAlibay commented Dec 9, 2024 •
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github-actions bot commented Dec 9, 2024

🚨 API breaking changes detected! 🚨

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codecov bot commented Dec 9, 2024 •
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Codecov Report

❌ Patch coverage is 98.80869% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.20%. Comparing base (ccf856a) to head (27447b3).
⚠️ Report is 226 commits behind head on main.

Files with missing lines Patch % Lines
...protocols/restraint_utils/openmm/omm_restraints.py 92.18% 10 Missing ⚠️
openfe/protocols/restraint_utils/geometry/utils.py 96.55% 7 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #1043      +/-   ##
==========================================
- Coverage   94.63%   93.20%   -1.44%     
==========================================
  Files         143      165      +22     
  Lines       10962    12389    +1427     
==========================================
+ Hits        10374    11547    +1173     
- Misses        588      842     +254
Flag Coverage Δ
fast-tests 93.20% <98.80%> (?)
slow-tests ?

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github-actions bot commented Dec 9, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 9, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 11, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

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github-actions bot commented Dec 12, 2024

🚨 API breaking changes detected! 🚨

hannahbaumann
hannahbaumann reviewed Jun 18, 2025
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@IAlibay IAlibay changed the title [WIP] Restraints API Restraints API Jul 4, 2025
IAlibay
IAlibay commented Jul 4, 2025
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IAlibay
IAlibay commented Jul 4, 2025
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openfe/protocols/restraint_utils/geometry/boresch/host.py
)
atom_finder.run()

if not atom_finder.results.host_idxs.any():
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@IAlibay IAlibay Jul 4, 2025

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Issue #1418

IAlibay
IAlibay commented Jul 4, 2025
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openfe/protocols/restraint_utils/geometry/utils.py
v2 = positions[atoms[i + 2], :] - positions[atoms[i + 1], :]
if dimensions is not None:
v1 = minimize_vectors(v1, box=dimensions)
v2 = minimize_vectors(v2, box=dimensions)
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@IAlibay IAlibay Jul 4, 2025

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Needs tests see #1419

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github-actions bot commented Jul 4, 2025

No API break detected ✅

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IAlibay commented Jul 4, 2025

Dismissing @hannahbaumann's review as most things have either been addressed or will be addressed in a future PR.

@IAlibay IAlibay dismissed hannahbaumann’s stale review July 4, 2025 15:57

Has been addressed or will be addressed elsewhere.

@IAlibay IAlibay merged commit 04387d7 into main Jul 4, 2025
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@IAlibay IAlibay deleted the omm-restraints branch July 4, 2025 16:14
@Kamecs Kamecs mentioned this pull request Jul 27, 2025
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Boresch host search tests Boresch guest search tests DSSP filtering tests Restraint geometry utils tests

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