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Fix disulfide bond detection for split cysteines with altlocs - #94
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find_disulfide_links paired SG atoms by distance and residue alone, so with both cysteines of a bridge split into altlocs, conformer A of one was bonded to conformer B of the other as well. An SG with an altloc now pairs only with the same altloc or a blank one, matching the rule the disulfide angles and torsions already follow. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016Kt1r7DAxHJxaawQ7HogvG
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Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016Kt1r7DAxHJxaawQ7HogvG
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Summary
Disulfide bond detection now correctly handles alternative conformations (altlocs) by ensuring that an SG atom in conformer A only bonds with an SG in conformer A or one without an altloc designation. This prevents incorrect cross-conformer bonds (e.g., A to B) that would artificially pull different conformers together.
Key Changes
find_disulfide_links()function: Added optionalaltlocparameter to filter disulfide pairs based on conformer labels. When both atoms have altloc assignments, they must match to form a bond.build_topology_with_values()function: Updated to pass thealtloccolumn data tofind_disulfide_links().test_disulfide_bonds_stay_within_one_conformer()that verifies:_split_cys21()to generate test PDB with split cysteinesImplementation Details
The fix modifies the disulfide pair filtering logic to check altloc compatibility:
The changelog has been updated to document this fix.
https://claude.ai/code/session_016Kt1r7DAxHJxaawQ7HogvG