[fubin1999]

Summary

• Add parse_smiles() using native R/C++ without an external chemistry runtime.
• Decode atom-order-aware tetrahedral stereochemistry, sugar rings, O-linked glycan trees, supported modifications and reducing-end alditols; retain unknown stereochemistry rather than guessing it.
• Handle equivalent atom traversals and symmetric alditol numbering deterministically. Reject unsupported chemistry rather than dropping atoms.
• Add documentation, provenance, 543 real GlyGen paired fixtures, 230 equivalent-SMILES fixtures, 162 symmetric-alditol regression expressions, and a reproducible full-dataset validation script.

Validation

• Full test suite passed.
• Complete R CMD check: 0 errors, 0 warnings, 0 notes. After a network interruption the final check used installed dependencies and a local empty repository index; remote repository availability was not checked.
• GlyGen 2.12.1: 15,788 same-accession SMILES/WURCS pairs; parse_wurcs() accepts 15,712 and parse_smiles() accepts 15,710 (99.987% of the WURCS-success set).
• 15,708 paired results have equivalent residue graphs, accounting for conventional roots and symmetric alditol numbering. The other two (G20934UH/G71958ED) have an explicit relative anomer in source WURCS but unspecified stereochemistry in source SMILES; tests ensure no anomer is invented.
• Randomized equivalent SMILES across the full dataset preserve acceptance and output.

Deliberate limits

This is a defined glycan subset, not a general-purpose chemical SMILES reader. Charges, isotopes, separate explicit hydrogen atoms, aromatic atoms, disconnected salts, aglycones, unsupported open-chain structures, non-O links, cyclic residue graphs, and unknown modifications are rejected. SMILES is not added to automatic format detection.

Two WURCS-success records remain rejected rather than copied lossily: G27289CV needs non-root alditol state, and G89097YO contains a non-anomeric C2–O–C3 bridge. Correct support needs a representation-model extension. Existing WURCS parsing is unchanged.

Data: GlyGen 2.12.1 GLY_000291/GLY_000292, CC BY 4.0; attribution and source URLs are included with fixtures. No data lookup or external chemistry runtime is required at runtime.

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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🟢 Metrics 289 complexity · 0 duplication

Metric	Results
Complexity	289
Duplication	0

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[fubin1999]

@codex review

[chatgpt-codex-connector]

Codex Review Summary: ✅ Completed

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-11-13T14:43:42.525184Z	50d32f2	Manual request

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[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. More of your lovely PRs please.

Reviewed commit: 50d32f2dac

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