Unexpected behavior for reversible reaction

[formersbach]

Description:

Text2Model of reversible reaction with one reactant and one product fails.

Reproduce:

Text file containing:

A + C <--> B
A <--> B

Convert to model:

from biomass import Text2Model
model = Text2Model("test.txt")
model.convert(overwrite=True)

Raises:

DetectionError
Unregistered words in line2: A <--> B

[formersbach]

Hey @himoto could you take a look at this? Am I missing something or is this indeed a bug?

[formersbach]

The same behavior appears for uni-directional reactions such as:

A --> B

[himoto]

Hi @formersbach,
This is NotImplementedError rather than a bug.
Currently, the arrows, e.g., <--> and --> are used for determining reaction directionality and specifying the name of the product in a reaction, not for identifying reaction rules.
Therefore in your example above Text2Model cannot choose which reaction rule to assign.
The solution is to use @rxn prefix:

@rxn A --> B: kfi * u[A]

And I think it would be dangerous to use arrows for identifying reaction rules, which will destroy Text2Model.

[formersbach]

I see! But how can Text2Model identify the reaction rule for:

A + E <--> C + E

Is the plus symbol used to infer the reaction rule?

[himoto]

Yes, it is assigned for complex association and dissociation (see below).

biomass/biomass/construction/reaction_rules.py

Lines 214 to 219 in fc464df

	# Words to identify reaction rules
	rule_words: Dict[str, List[str]] = field(
	default_factory=lambda: dict(
	_bind_and_dissociate=[
	" +",
	],

Note that currently I do not allow to have the plus symbol in both left and right hand side of the arrow.
Therefore in your example above, if the reaction is unidirectional you can write:

@rxn A --> C: (rate depending on [E])

However, I found that the latest biomass does not raise any warning and errors.
This is a bug and I have fixed it in the kinetics branch. Can you please see it?

[formersbach]

Note that currently I do not allow to have the plus symbol in both left and right hand side of the arrow.

Correctly raises "Cannot put the plus symbol in both left and right hand side of arrow" error!

Currently, the arrows, e.g., <--> and --> are used for determining reaction directional and specifying the name of the product in a reaction, not for identifying reaction rules.

Wouldn't it make sense to use simple mass action kinetics by default? At least the other modelling programs I've used do it like that, so it was quite unexpected.
Would it be possible to implement mass action kinetics as the default when reaction rules are not infer-able?
E.g. if no words indicating a reaction are found try to assign reactants and products (if it fails raise error) and then construct mass action equation with them.

[himoto]

Would it be possible to implement mass action kinetics as the default when reaction rules are not infer-able?
E.g. if no words indicating a reaction are found try to assign reactants and products (if it fails raise error) and then construct mass action equation with them.

This sounds reasonable. To be able to describe simple state transition via arrows, I added state_transition rule in progress at PR #169. I confirmed that this worked fine with the EGFR signaling model:

EGF + EGFR <--> Ra | kf=0.003, kr=0.06 | EGFR=100
Ra + Ra <--> R2 | kf=0.01, kr=0.1
R2 <--> RP | kf=1, kr=0.01
RP is dephosphorylated --> R2 | V=450, K=50
RP + PLCg <--> RPL | kf=0.06, kr=0.2 | PLCg=105
RPL <--> RPLP | kf=1, kr=0.05
RPLP <--> RP + PLCgP | kf=0.3, kr=0.006
PLCgP is dephosphorylated --> PLCg | V=1, K=100
RP + Grb2 <--> RG | kf=0.003, kr=0.05 | Grb2=85
RG + SOS <--> RGS | kf=0.01, kr=0.06 | SOS=34
RGS <--> RP + GS | kf=0.03, kr=4.5e-3
GS <--> Grb2 + SOS | kf=1.5e-3, kr=1e-4
RP + Shc <--> RSh | kf=0.09, kr=0.6 | Shc=150
RSh <--> RShP | kf=6, kr=0.06
RShP <--> ShP + RP | kf=0.3, kr=9e-4
ShP is dephosphorylated --> Shc | V=1.7, K=340
RShP + Grb2 <--> RShG | kf=0.003, kr=0.1
RShG <--> RP + ShG | kf=0.3, kr=9e-4
RShG + SOS <--> RShGS | kf=0.01, kr=2.14e-2
RShGS <--> ShGS + RP | kf=0.12, kr=2.4e-4
ShP + Grb2 <--> ShG | kf=0.003, kr=0.1
ShG + SOS <--> ShGS | kf=0.03, kr=0.064
ShGS <--> ShP + GS | kf=0.1, kr=0.021
RShP + GS <--> RShGS | kf=0.009, kr=4.29e-2
PLCgP is translocated to cytoskeletal or membrane structures <--> PLCgP_I | kf=1, kr=0.03

[himoto]

I have fixed this issue in #169