Push to master for pre-release v0.6.0 - #64
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This is a list of reactions identified by the "constrainVariableMassReactions" script (and manually verified) that should be constrained in the model due to their introduction of mass imbalances into the model. This list is called by the second part of the constrainVariableMassRxns script to implement these constraints.
Previous version contained invisible line-break and other characters which were causing the associated function to not recognize some of the reaction IDs. This has now been corrected.
After further investigation, it was determined that the reactions which this script sought to "correct" still remained imbalanced for oxygen, causing other problems in the model. Therefore, this script will likely be deleted entirely.
Script will now make use of the "docRxnChanges" function, so a .txt report will be generated to document all the changes the script makes to each reaction.
After determining that these "ARTFR..." rxns could not be re-balanced by simply adjusting the soichiometric coefficient of the CoA metabolite, they have been added to this script so they will be constrained until they can be properly re-balanced or removed from the model.
Since the reactions involving degradation of two of the fatty acid pools were constrained, this resulted in an inability of the model to consume these pools. Therefore, reactions allowing export of each of the fatty acid pools will be added, and these are stored in a txt file for easier tracking/implementation.
Script is in a working state - should not be used by others at this point.
The beginning part of the script, which functioned to identify the mass variable reactions, was removed and reformulated as a separate function, "identifyMassVariableRxns". Also, comments were modified/expanded to improve descriptions.
Note: this function originated from a previous version of the "constrainVariableMassReactions.m" script. This function searches a model for sets of reactions that involve the same set of metabolites except for one, which indicates that one or more of the reactions in the set is mass-imbalanced. The metabolites that differ among the reactions in a set will be compared in their metFormulas; if they are different, the set will be classified as "mass variable reactions", otherwise the set will be classified as "mass consistent reactions".
Two of the rxn IDs were mistakenly duplicated. This has now been corrected.
Tune `repairModelLeaks` branch with master
Tune with master
Updated code with new versions of documentation (docRxnChanges) and writing (writeRxnChanges) functions
These reactions were originally planned to be constrained, but since they do not appear to violate any mass constraints, they will be left as is for the time being.
The original purpose of this script was to try and re-balance some of the R-group reactions involving CoA. It was later determined that, although carbon could be balanced by updating stoich coeffs, the oxygen remained unbalanced. Therefore, these changes will not be incorporated into the model.
- change the filename from `constrainVariableMassReactions.m` to `constrainReactions.m`
- Organize inactivated reactions and output into a unified log file `inactivationRxns.tsv`, instead of modifying the model.
- feat: move the Reaction inactivation section from repairModelLeaks.m to this script.
- A section with both reaction inactivation and stoich coeffs adjustment was located. Now this section is fixed by placing in both constrainReactions.m and repairModelLeaks.m with respective changes.
feat: repair model leaks
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