Covalent bonds - #397
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peter-s-obi wants to merge 4 commits into
Open
Covalent bonds#397peter-s-obi wants to merge 4 commits into
peter-s-obi wants to merge 4 commits into
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Summary
Adds query-level covalent bonds for inference. A user can specify connections between named atoms, and OpenFold-3 (OF3) will include them through its existing structure assembly, tokenization, and bond features.
Changes
covalent_bondsquery field using[chain_id, residue_id, atom_name]endpoints, with one-based residue IDs.Related Issues
Related to #219 — Support covalently bound ligands in inference.
Testing
All tests pass