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Rule with high product-side symmetry causes BNG to hang while reading in model #214

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lh64 opened this issue Jun 10, 2019 · 0 comments
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lh64 commented Jun 10, 2019

The attached model is a flat import of an SBML model from BioModels. The rule 'R_ENTCS' on line 4072 has a high degree of symmetry, particularly on the product side (9 Hpl and 6 AMP molecules). This is causing BNG to hang while reading in the model. I tracked the issue down to line 2701 of RxnRule.pm:

# Find product graph automorphisms
my @p_auto = $pg->isomorphicToSubgraph($pg);

Is there a way to optimize the subgraph isomorphism algorithm to get around this problem?

oscar-ecoli.bngl.txt

@lh64 lh64 added the Usability label Jun 10, 2019
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