Document AFFINose WURCS input contract

README.md

@@ -49,6 +49,8 @@ No Hugging Face token is required for this AFFINose checkpoint now that the repo
 
 Provide one protein-glycan pair or a CSV batch. Glycans should be WURCS strings. Proteins can be provided as IDs linked to precomputed embeddings, or through the companion notebook as raw sequences that are embedded with ESM-C 300M.
 
+Batch CSVs use `sample_id,protein_id,protein_sequence,glycan_wurcs`. Free-text glycan names, common names, SNFG drawings, and IUPAC-condensed strings are not parsed directly by AFFINose. Convert those inputs to WURCS first, then score the protein-glycan pair.
+
 ## Protein Embedding Requirement
 
 AFFINose expects per-residue ESM-C 300M embeddings with shape `[L, 960]`. Do not mean-pool the protein before passing it into AFFINose.
@@ -77,7 +79,7 @@ A scalar protein-glycan interaction score from the trained AFFINose head.
 
 ## Scope
 
-This repository does not perform IUPAC-condensed to WURCS conversion. For now, provide WURCS directly.
+This repository does not perform IUPAC-condensed/name-to-WURCS conversion. For now, provide WURCS directly.
 
 License metadata is currently `other`; update it when the final release license and citation text are chosen.
 

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