_emit_substrate_depletion_edges is called at src/logic_network_generator.py:1925; _emit_boundary_decomposition_edges at :1937. The latter computes root_uuids = sources - targets.
A depletion edge adds catalyst -> input, which makes that input a target. So a root-input complex that a depletion edge points at stops being a root and loses its assembly expansion — its subunits never get member->complex edges, so the individual proteins are no longer addressable for perturbation at that node.
Verified: 13 root-input complex occurrences catalog-wide lose their assembly expansion this way — Signaling_by_PDGF 3, Signaling_by_EGFR 2, Semaphorin 2, ROBO 2, and 4 singletons.
Small, but it is an emission-order artifact rather than a modelling decision: whether a complex's subunits are addressable should not depend on whether a phosphatase happens to deplete it. Computing root_uuids before the depletion pass (or excluding depletion edges from the targets set) would fix it.
Worth a DeltaSignal before/after like any connectivity change, though the expected effect is small — the perturbed-gene coverage of 13 complexes across the catalog.
_emit_substrate_depletion_edgesis called atsrc/logic_network_generator.py:1925;_emit_boundary_decomposition_edgesat:1937. The latter computesroot_uuids = sources - targets.A depletion edge adds
catalyst -> input, which makes that input a target. So a root-input complex that a depletion edge points at stops being a root and loses its assembly expansion — its subunits never get member->complex edges, so the individual proteins are no longer addressable for perturbation at that node.Verified: 13 root-input complex occurrences catalog-wide lose their assembly expansion this way — Signaling_by_PDGF 3, Signaling_by_EGFR 2, Semaphorin 2, ROBO 2, and 4 singletons.
Small, but it is an emission-order artifact rather than a modelling decision: whether a complex's subunits are addressable should not depend on whether a phosphatase happens to deplete it. Computing
root_uuidsbefore the depletion pass (or excludingdepletionedges from thetargetsset) would fix it.Worth a DeltaSignal before/after like any connectivity change, though the expected effect is small — the perturbed-gene coverage of 13 complexes across the catalog.