pools: a multi-step path must regenerate its enzyme (specs/039 amendment 5) - #101
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…amendment 5) A multi-step path is an enzyme cycle only if every non-R entity a step of it consumes is output again by a step of the same path (the enzyme comes back out). Consumed = the step's non-small inputs other than its R-containing source; small molecules (SimpleEntity, now ``small`` in the form profile) are exempt as cofactors (ATP in, ADP out is the modification, not a partner lost), and ubiquitin is a donor as elsewhere. Entities are compared by id, so a released copy the uuids separated still counts. Failing paths are dropped and counted (nonregenerating_paths); single-step paths are unaffected. The states that remain must reach one another through the kept paths: the pool keeps its largest strongly connected set of states and is dropped, counted under no_path_pools, when that has fewer than two (a pool with no path in one direction goes too). On build 20260928-0115_bdaed8e_pools039d: 11 multi-step paths dropped (HDR p-RPA machine; EGFR pool1 Beta-Pix:CDC42:GTP; Insulin pool1 the ligand; ERBB2 x4, PLCG1 and PTK6 leave phosphorylated; TGF-beta SMAD2/3 x2; the ERBB2 side of the PTK6 cycle x2), 7 pools dropped, 37 pools remain with 4 multi-step (BAD:14-3-3, RAS:GAP, SHC1:INSR, and PTK6 <-> p-Y342-PTK6 through p-ERBB2 heterodimers:PTK6 and PTPN1, which the shared-node rule used to remove). tests/test_pools.py: 19 tests. New: the kinase ring regenerates; a machine path whose co-input leaves transformed is dropped and the pool with it; an HDR-like growing machine is not a pool; small molecules are exempt; mutual modification inside a complex is a cycle for neither protein. The shared-node fixture is rebuilt with single-step side branches, since the old shape now fails regeneration first. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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deltasignal specs/039 amendment 5. A multi-step path counts as an enzyme cycle only if every non-R entity its steps consume is released again by the same path. In other words, the enzyme is regenerated.
nonregenerating_paths.no_path_pools).What it removes: machine-like "pools" whose exit step is driven by the pool's own product. In HDR, the resection machine's exit depends on p-CHEK1, which comes from the pool's own intermediates.
Census on build
20260928-0320_6815dfd_pools039e:Effect in DeltaSignal (
DS_CYCLE_MODE=balanceonly; the default stays off):Tests:
tests/test_pools.pyhas 19 tests.ruffandmypyare clean. Implemented by a Fable 5.1 subagent.🤖 Generated with Claude Code