pools: orient by the active form (specs/039 amendments 6+7; made_from default) - #102
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phi0 is the share of the ACTIVE form at rest, so orientation now asks which state acts downstream: a state is active if, at node level, it has a catalyst edge or a positive regulator edge into a reaction node that is not one of the pool's own steps (any copy). With exactly one active state the base is the other state (two states) or the non-active state furthest from it in the state graph (more states; a tie falls back). Otherwise the residue / donor / component rule of amendment 1 decides, as before. Counted as oriented_by_activity and activity_fallbacks; ties are counted only among the fallbacks. On build 20260928-0320_6815dfd_pools039e: 1 of 37 pools is oriented by activity and no base flips. CCNA:CDK2 <-> CCNA:p-Y15-CDK2 (R-HSA-69242) does not flip: in R97 neither form catalyses anything; the kinase that acts is CCNA:p-T160-CDK2, reached from CCNA:CDK2 by CAK phosphorylation (an input edge, which the rule does not count). RAS keeps base GDP (RAS:GTP binds RAF as an input, so it is not active by the rule; the donor rule decides). tests/test_pools.py: 24 tests. New: an inhibitory phosphorylation (the unmodified state catalyses downstream) makes the modified state the base; a positive regulator edge counts and a negative one does not; an activating phosphorylation keeps the unmodified base; both or neither active falls back; a state's own step (RAS:GTP's intrinsic hydrolysis) does not make it active; three states take the non-active state furthest from the active one, and a tie falls back. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…de (amendment 6 census clarification) Since specs/033 a member of a set-valued catalyst or regulator reaches the reaction through the set's pool node, by a set_member edge. For the active state test that node's catalyst and positive regulator edges are therefore the member's: a state with a set_member edge into a set-pool node that acts on a reaction outside the pool's own steps is active. This is the case of the lipin pools (R-HSA-68875 pools 2-4, LPIN1/2/3 <-> p-S106-LPINn), whose unphosphorylated states catalyse PA dephosphorylation only through the "lipins" set-pool node; the earlier census wrongly reported no lipin pool. tests/test_pools.py: 25 tests; the new one has a state that is a member of a catalysing set-pool node (base flips to the modified state) and the same node acting on nothing outside the pool (fallback). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…ehind a flag) Amendment 7: a state is also active if an input edge from it enters a reaction that is not a pool step and, within two reactions, that route reaches a catalyst or positive regulator of another non-step reaction (the regulator reached directly or through a set-pool node). CCNA:CDK2 is made into the catalytic CCNA:p-T160-CDK2 by CAK, one reaction outside its pool. The flag lets both arms build from one commit: - LNG_POOL_ACTIVE_VIA=direct (default): amendment 6 plus the set-pool clarification, unchanged; - LNG_POOL_ACTIVE_VIA=made_from: the direct test first, then the made-from test for the states it did not mark; exactly-one-active and the fallbacks are as in amendment 6. Any other value raises at startup (_reject_removed_env, which bin/create-pathways.py runs before any work) and in find_pools. The flag is in pathway_generator's fingerprinted env, so fingerprint.json and the catalog's BUILD.json record it like LNG_SET_POOL and LNG_CAP_POOLS. tests/test_pools.py: 28 tests. New: the CDK2 shape flips under made_from, not under direct or the default, and through a set-pool node too; the RAS shape (RAS:GTP binds RAF as an input, the complex catalyses nothing within two reactions) does not flip; an unknown value is an error. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
…39 amendment 7 adopted, 2026-09-28) Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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deltasignal specs/039 amendments 6 and 7: orient each pool by its active form. φ₀ (the share of a pool at rest in its minority form) now refers to the active form, as Adam decided on 2026-09-28. Until now it referred to the modified form, and for an inhibitory modification (CDK2 p-Y15, lipin p-S106) the two are opposite.
A state is active when it acts downstream of the pool:
LNG_POOL_ACTIVE_VIA=made_from, the default): or it is the form the catalytic form is made from, within 2 reactions. For example, CCNA:CDK2 is made into the catalytic CCNA:p-T160-CDK2 by CAK.The other state becomes the base (resting) form. Otherwise orientation falls back to the previous rule.
directkeeps amendment 6 only.Census on 37 pools:
Result in deltasignal (
balance, same build, against the rule off):balanceas its default in a companion PR.Tests:
tests/test_pools.pyhas 28 tests.ruffandmypyare clean. The one full-suite failure is the known MHC ratio test, which is local-output dependent and green in CI.Implemented by a Fable 5.1 subagent.
🤖 Generated with Claude Code