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Add new monomer set to bring us to v1.1.0 - #4
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The default 2D layout overlaps the bridge atoms of
2-azaBCH2223S-3-CO2H ((3S)-2-azabicyclo[2.2.2]octane-3-carboxylic
acid), so RDKit cannot interpret the wedge at C3 when the SDF is read
back ("ambiguous stereochemistry - overlapping neighbors"). The
molecule then loses its alpha-carbon stereocentre and verify.py fails
with "SDF molecule 122 does not match its JSON SMILES".
Ring templates give caged systems a standard, non-overlapping layout.
All 4719 records now round-trip; 87 get new 2D coordinates, with no
change to any structure, stereo, or the JSON/CSV/TSV outputs.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
jerics83
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Sep 30, 2026
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Reviewed and fixes the issue. The change in code correct some names and structures.
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This PR brings the number of monomers in the dataset from 2,488 to 4,719.