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The policy drop removes each complex that has a subunit without an ortholog and removes the reaction when no complex remains. It removed the reaction as soon as one subunit had no ortholog.
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Function test results539 tests 529 ✅ 2m 50s ⏱️ For more details on these errors, see this check. Results for commit a037baa. |
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getModelFromHomologywithcomplexPolicydropremoves each complex that has a subunit without an ortholog, and removes the reaction only when no complex remains. For the rule(A and B) or (C and D)without an ortholog ofB, the draft has the orthologs ofCandD. Before, the reaction was removed as soon as one subunit had no ortholog.The step that removes the placeholder genes of isozymes reads the rule as a tree, in which
andbinds tighter thanor. For the rule(A or B and C) and Dwithout an ortholog ofB, the draft rule is(nA or (OLD_T_B and nC)) and nDunderflag,(nA or nC) and nDunderkeepandnA and nDunderdrop. The result differs from before only for rules with unbracketedandandoror with nestedorgroups.The same policy is implemented in raven-toolbox#199.