bug: simplifyModel with irreversible backwards-only reactions

[edkerk]

Description of the issue:

Reactions that are defined backwards-only (so lb<0 and ub=0) could arguably have their rev field as 0. But this raises a problem when simplifyModel is run with deleteInaccessible is set as true. In this line:

RAVEN/core/simplifyModel.m

Line 129 in e296b5d

revS=[reducedModel.S,reducedModel.S(:,reducedModel.rev~=0)*-1 I(:,in) I(:,out)*-1];

The S-matrix is expanded with inverted versions of reversible reactions (the reducedModel.rev~=0 part), to consider that reactions can have a negative flux. But for the above case (backwards-only & irreversible), these reactions are not included. Arguably, it is not interesting anyway what the value of the rev field is, what is important is whether the reaction can carry a negative flux.

This should therefore be changed to:

revS=[reducedModel.S,reducedModel.S(:,reducedModel.lb<0)*-1 I(:,in) I(:,out)*-1];

I hereby confirm that I have:

• Checked that a similar issue does not already exist or is already discussed.