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Add proper torsion-bend coupling#86

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fjclark wants to merge 1 commit intomainfrom
feature-torsion-bend-coupling
Open

Add proper torsion-bend coupling#86
fjclark wants to merge 1 commit intomainfrom
feature-torsion-bend-coupling

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@fjclark
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@fjclark fjclark commented Oct 8, 2025

Description

Add terms which couple proper torsions and bond angles. From the ProperTorsionBendHandler docstring:

    A custom SMIRNOFF handler for Proper Torsion-Bend coupling interactions.
    The functional form is as given in eqn. 10 in Nevins, N.; Chen, K.;
    Allinger, N. L. Molecular Mechanics (MM4) Calculations on Alkenes.
    J. Comput. Chem. 1996, 17 (5–6), 669–694.
    https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6%253C669::AID-JCC7%253E3.0.CO;2-S.
    Each line in the OFFXML file specifies the term corresponding to a single bond angle-proper
    torsion combination, hence two lines are needed to specify the whole of eqn. 10. The angle
    is specified by the first 3 labels in the SMIRKS e.g. i,j,k in i,j,k,l. Hence, the order of
    the labels in the SMIRKS matters, and i,j,k,l is not equivalent to l,k,j,i if the type is not
    symmetrical.

Status

Please hang off reviewing until we decide whether or not to tweak the functional form.

  • Ready to go

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codecov-commenter commented Oct 8, 2025

Codecov Report

❌ Patch coverage is 87.64045% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.63%. Comparing base (9c92d50) to head (372ebf1).

Files with missing lines Patch % Lines
smirnoff_plugins/handlers/valence.py 68.18% 7 Missing ⚠️
smirnoff_plugins/collections/valence.py 94.02% 4 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #86      +/-   ##
==========================================
+ Coverage   86.58%   86.63%   +0.05%     
==========================================
  Files           9        9              
  Lines         693      778      +85     
==========================================
+ Hits          600      674      +74     
- Misses         93      104      +11     
Flag Coverage Δ
unittests 86.63% <87.64%> (+0.05%) ⬆️

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@j-wags
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j-wags commented Oct 20, 2025

Hi @fjclark - We saw you checked "ready to go" on this. Would you like this reviewed in preparation to merge, or do you plan to continue making changes to this branch?

@fjclark
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fjclark commented Oct 21, 2025

Hi @j-wags thanks for following up. Please hang off for the moment in case we decide a different functional form is better (I think this is ready to go if not). I'll comment again when we're sure this is final.

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4 participants