drugs.csv: drug-derived entities per pathway (deltasignal specs/032) - #98
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…th any drug component; set whose every member is one) beside cofactors.csv, for a consumer modelling a cell without the drug (deltasignal specs/032). Network output unchanged. Also: stale +228 comment -> +197. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…iled drug query no longer costs containment.csv); class+name from the structure query (the unlabelled MATCH scanned every node, ~30 s a pathway; whole catalog now 0.8 s); list each node's exact id, a set_variant judged by its parent or chosen members; tests: candidate-only set (dropping hasCandidate now caught), the Cypher+cache path, variant ids. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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….csv (#99) * drugs.csv: ship the pathway's drug-derived entities (Drug; complex with any drug component; set whose every member is one) beside cofactors.csv, for a consumer modelling a cell without the drug (deltasignal specs/032). Network output unchanged. Also: stale +228 comment -> +197. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * Review of #98: drugs.csv in its own try block after containment (a failed drug query no longer costs containment.csv); class+name from the structure query (the unlabelled MATCH scanned every node, ~30 s a pathway; whole catalog now 0.8 s); list each node's exact id, a set_variant judged by its parent or chosen members; tests: candidate-only set (dropping hasCandidate now caught), the Cypher+cache path, variant ids. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * LNG_SET_POOL (deltasignal specs/033, default off): a bare EntitySet catalyst/regulator becomes one pool node (the set) fed by set_member edges, feeding each reaction copy once, instead of every member wired onto every copy as a separate AND (catalyst/pos) or OR (neg) term. Reachability unchanged. nodes.csv kind set_pool. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * Review of set-pool: a pooled catalyst no longer depletes its own member (the stId guards compared the SET's id; 4 E3-ligase sets would have closed member->pool-|member cycles); pooling only under complex-as-node; pool->reaction keeps the role flag under LNG_SET_MEMBERS_OR. Tests: depletion self-skip (mutation-checked), complex-as-node guard, SET_MEMBERS_OR, export_nodes set_pool kind. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * LNG_SET_POOL default on (trial, specs/033: held-out +6, tuning +10, exp +3); legacy regulator tests pinned to LNG_SET_POOL=0; test that pooling is the default Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * WIP LNG_CAP_POOLS (deltasignal specs/036, default off): a set input that resolves to several nodes in one virtual reaction (alternatives bundled by the variant cap) is emitted as a set pool feeding the reaction once. RAF's scaffold binding reaction: 28 inputs -> its 4 curated components. Tests to follow. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * tests for LNG_CAP_POOLS: bundled alternatives pooled, single chosen member not, flag off, no leak between pathways, modifier sets excluded Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * Review of combined-037: cap pools only in reactions the variant cap bundled (CAPPED_IDS; an uncapped copy's chosen complex alternative resolves to co-required subunits -- miR-93 RISC in PIP3 was averaged); leaves grouped by alternative, a complex alternative is an AND unit (leaves -assembly-> alternative -set_member-> pool); a leaf another input also maps to stays direct; curated set stoichiometry on the pool edge; depletion onto a pool goes to its members. Phase 3 input emission factored into _emit_vr_inputs and tested; gate mutation-checked. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Superseded by #99, which includes this change (drugs.csv export plus its review fixes) and was merged. Closing without merging. |
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drugs.csvbesidecofactors.csv, listing the entities in each pathway that are drug-derived.Drugcounts; a complex with any drug component counts; a set counts only if every member does.🤖 Generated with Claude Code