Comment out the header line - #12
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Parsers that treat the file as pure data read `Abbreviation<TAB>SMILES` as a row and try to parse "SMILES" as a structure. Prefixing the header with `#` makes it skippable by the usual convention. index.html strips a leading `#` from the header line so the viewer still renders two named columns. lint.py's pandas round-trip and the duplicate check are unaffected.
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What
abbreviations.smiline 1 becomes# Abbreviation<TAB>SMILES.Consumers that treat the file as pure data currently read the header as a row and try to parse the literal string
SMILESas a structure. In BChemXtract that surfaces as aWARN Invalid SMILESwith aCDKExceptionstack trace on every JVM start.#is the comment convention those parsers already skip.Why the second file
index.htmluses line 1 for the DataTables column titles and splits it on whitespace, so a bare#would have produced three columns and misaligned the data. It now strips a leading#from the header line before splitting — the viewer rendersAbbreviation/SMILESexactly as before.Verification
pd.read_csv(sep='\t')→ columns['# Abbreviation', 'SMILES'],to_csv(sep='\t', index=False)round-trip byte-identical, solint.pypasses./scripts/check_duplicates_abbreviations.shpasses;cut -f1 | sort | uniq -dalso cleanindex.htmlparse re-run in node: headers["Abbreviation","SMILES"], 300 data rows, last rowNHMe → [*]NCNo data rows were added, removed, or changed.
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