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readYAMLmodel: fix position-dependent metCharges/metComps defaults #709

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Merged
edkerk merged 1 commit into from
Aug 28, 2026
Merged

readYAMLmodel: fix position-dependent metCharges/metComps defaults #709

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12 changes: 10 additions & 2 deletions io/readYAMLmodel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -668,6 +668,14 @@
[~, model.metComps] = ismember(model.metComps, model.comps);
[~, model.geneComps] = ismember(model.geneComps, model.comps);
[~, model.rxnComps] = ismember(model.rxnComps, model.comps);
% A metabolite with no explicit compartment is still ismember'd above (it
% parses as ''), so it resolves to 0 -- not the "assume first compartment"
% default the emptyOrFill call further down intends -- unless it happens
% to be the trailing metabolite in the file, the only case emptyOrFill
% actually reaches (it only extends a too-short array, and ismember has
% already made this one full-length). Catch every 0 here so the default
% applies regardless of position, not just at the end of the list.
model.metComps(model.metComps==0) = 1;

% Fill S-matrix
rxnIdx = cellfun('isempty', equations(:,1));
Expand Down Expand Up @@ -725,10 +733,10 @@
for i={'metNames','inchis','metFormulas','metMiriams','metFrom','metSmiles','metNotes'} % Empty strings
model = emptyOrFill(model,i{1},{''},'mets');
end
for i={'metCharges','unconstrained'} % Zeros
for i={'unconstrained'} % Zeros
model = emptyOrFill(model,i{1},0,'mets');
end
for i={'metDeltaG'} % % NaNs
for i={'metCharges','metDeltaG'} % NaNs
model = emptyOrFill(model,i{1},NaN,'mets');
end
for i={'metComps'} % Ones, assume first compartment
Expand Down