Default charge of reactions containing unknown structures

[samseaver]

Due to the simple fact that we can, in theory, remove competing R groups from an equation, and thereafter balance the mass of the equation, we do have the problem, such as with fatty-acyl-ACPs, that we are still left with a charge imbalance (particularly if protons are added/removed to balance the mass).

The problem is exacerbated simply because changing the charge of any one compound to fix a single reaction may result in an imbalance of charge in another reaction. David Fell had an analogy for this, of trying to flatten a carpet, but getting the same bump to appear in different places on the floor.

Following on from the recent decision to default to a charge of zero for compounds with an unknown structure, we could make a decision concerning the charge balance of reactions that use such compounds. What I propose quite simply is that for reactions with unknown structures, that may still be mass balanced, we ignore the charge balance.

As such, for any reaction with the status of 'CI', I can check that it has R groups on both side of the equation, and update the status to be "OK|RG|CI' where RG stands for R group (or some other preferred code).

[chian]

@samseaver As long as we properly mark things so we can identify them later, I think that's a fine solution. I'm not sure if the mark should be 'OK' or unknown. I would have thought unknown, but not sure how you are defining these.

We can probably start our own internal FAQs at this rate. Or Chia FAQs.

Sent from my iPhone

On Jul 17, 2015, at 1:28 PM, samseaver [email protected] wrote:

Due to the simple fact that we can, in theory, remove competing R groups from an equation, and thereafter balance the mass of the equation, we do have the problem, such as with fatty-acyl-ACPs, that we are still left with a charge imbalance (particularly if protons are added/removed to balance the mass).

The problem is exacerbated simply because changing the charge of any one compound to fix a single reaction may result in an imbalance of charge in another reaction. David Fell had an analogy for this, of trying to flatten a carpet, but getting the same bump to appear in different places on the floor.

Following on from the recent decision to default to a charge of zero for compounds with an unknown structure, we could make a decision concerning the charge balance of reactions that use such compounds. What I propose quite simply is that for reactions with unknown structures, that may still be mass balanced, we ignore the charge balance.

As such, for any reaction with the status of 'CI', I can check that it has R groups on both side of the equation, and update the status to be "OK|RG|CI' where RG stands for R group (or some other preferred code).

—
Reply to this email directly or view it on GitHub.

[samseaver]

It used to be that the status has to be "OK" in order for the reaction to be included by the MFAToolkit. I'm unsure if this is still the case, @cshenry? If not, then merely including the reaction in a ModelTemplate would mean that it's "OK" by default.

[mmundy42]

Just a point of clarification for me, does the reaction status need to be only "OK" to be included by the MFAToolkit? Or would a reaction with "OK|RG|CI" also be included because there is an OK in the status string.

And we can document the status values and their meanings in https://github.com/ModelSEED/ModelSEEDDatabase/blob/master/Biochemistry/README.md

[samseaver]

The code uses the compare() function so it doesn't even have to be at the beginning of the status though that has been my preference:

https://github.com/ModelSEED/MFAToolkit/blob/master/src/MFAProblem.cpp#L6679