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fix: metabolite names starting with a number, and a spurious addRxns warning #682

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Merged
edkerk merged 1 commit into from
Jul 17, 2026
Merged

fix: metabolite names starting with a number, and a spurious addRxns warning #682

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6 changes: 4 additions & 2 deletions manipulation/addRxns.m
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Original file line number Diff line number Diff line change
Expand Up @@ -252,8 +252,10 @@
%Parse the equations. This is done at this early stage since I need the
%reversibility info
[S, mets, badRxns, reversible]=constructS(rxnsToAdd.equations);
EM='The following equations have one or more metabolites both as substrate and product. Only the net equations will be added:';
warning('RAVEN:warning', '%s', ravenList(EM, rxnsToAdd.rxns(badRxns)));
if any(badRxns)
EM='The following equations have one or more metabolites both as substrate and product. Only the net equations will be added:';
warning('RAVEN:warning', '%s', ravenList(EM, rxnsToAdd.rxns(badRxns)));
end

newModel.rev=[newModel.rev;reversible];
newModel.rxns=[newModel.rxns;rxnsToAdd.rxns(:)];
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9 changes: 9 additions & 0 deletions queries/constructS.m
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Expand Up @@ -65,6 +65,10 @@
equations=strtrim(equations);
equations=fixEquations(equations);

%A supplied list is authoritative, so an entry in it can be matched in full
%before the leading number of "2 oxoglutarate" is read as a coefficient. A
%list derived from the equations cannot disambiguate that.
metsSupplied=~isempty(mets);
if isempty(mets)
mets=parseRxnEqu(equations);
end
Expand Down Expand Up @@ -125,6 +129,11 @@
%No coefficient
coeff=1;
name=metabolites{j};
elseif metsSupplied && any(strcmp(strtrim(metabolites{j}),mets))
%The whole entry is a known metabolite, so its leading number is
%part of its name ("2 oxoglutarate") rather than a coefficient
coeff=1;
name=strtrim(metabolites{j});
else
coeff=str2double(metabolites{j}(1:space(1)));

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10 changes: 10 additions & 0 deletions testing/function_tests/tManipulation.m
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Expand Up @@ -85,6 +85,16 @@ function addTransportAddsRxn(testCase)
testCase.verifyGreaterThan(numel(m2.rxns), numel(testCase.model.rxns));
end

function addRxnsCleanEquationDoesNotWarn(testCase)
% The "metabolite on both sides" warning must only fire for the
% equations it names, not on every call.
rxnsToAdd.rxns = {'newRxn'};
rxnsToAdd.equations = {[testCase.model.mets{1} ' => ' testCase.model.mets{2}]};
lastwarn('');
evalc('addRxns(testCase.model, rxnsToAdd, 1);');
testCase.verifyEmpty(strfind(lastwarn, 'both as substrate and product')); %#ok<STRIFY>
end

function changeGrRulesUpdatesRule(testCase)
m2 = changeGrRules(testCase.model, 'ACKr', 'b2296 and b1849', true);
idx = strcmp(m2.rxns, 'ACKr');
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18 changes: 18 additions & 0 deletions testing/function_tests/tQueries.m
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Expand Up @@ -45,6 +45,24 @@ function constructSSimple(testCase)
testCase.verifyEqual(full(S), [-1;-1;1]);
end

function constructSLeadingNumberIsPartOfName(testCase)
% A metabolite whose name starts with a number must not have that
% number read as a stoichiometric coefficient when the metabolite
% list says the whole entry is a metabolite.
mets = {'2 oxoglutarate';'succinate'};
[S, outMets] = constructS({'2 oxoglutarate => succinate'}, 'mets', mets);
testCase.verifyEqual(outMets, mets);
testCase.verifyEqual(full(S), [-1;1]);
end

function constructSLeadingNumberStillReadsCoefficient(testCase)
% With no such metabolite, the leading number is a coefficient.
mets = {'oxoglutarate';'succinate'};
[S, outMets] = constructS({'2 oxoglutarate => succinate'}, 'mets', mets);
testCase.verifyEqual(outMets, mets);
testCase.verifyEqual(full(S), [-2;1]);
end

function getAllRxnsFromGenesType(testCase)
% Use a reaction that has a gene association.
withGpr = testCase.model.rxns(find(~cellfun(@isempty, ...
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