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leaf_refs.csv: modifications column (deltasignal specs/107 amendment 1) - #129
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…, so a consumer can tell a compartment copy from a modified form (deltasignal specs/107 amendment 1: SMAD2 and p-SMAD2 share a reference entity) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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leaf_refs.csv(LNG #128) gains a third column,modifications. It holds each leaf's modified residues, sorted and joined by;, and is empty when the leaf has none.The column lets deltasignal's specs/107 rule 3b join copies of one protein only when they differ by compartment. Under rule 3, SMAD2 and p-S465,S467-SMAD2 share a reference entity, so their phosphorylation cycle was read as a closed carrier loop (held-out −50).
get_leaf_modificationsinsrc/neo4j_connector.py(hasModifiedResiduedisplay names).export_leaf_refswrites the new column; the test covers a compartment copy and a modified form.Nothing in the network files changes.
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