search

msneddon / nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks
MIT License
17 stars 18 forks source link

Molecularity is not enforced on the product side of reaction rules #2

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Write a BNGL model with a dissociation rule that applies to rings and 
chains, e.g. molecule types: A(x,y); seed species A(x!0,y!1).A(x!1,y!0) rules: 
A(x!0).A(y!0) -> A(x) + A(y).
2. Simulate the model in NFsim (with or without complex bookkeeping)

What is the expected output? What do you see instead?

The rule should not apply to the seed species since breaking one bond will not 
result in two distinct complexes. However, NFsim does not check for the 
violation of molecularity and the reaction proceeds. This behavior is not in 
conformity with BNGL.

This is a low priority issue since there are work-arounds for most models that 
require product-side molecularity checks.

Please use labels and text to provide additional information.

Original issue reported on code.google.com by justinshogg on 27 Mar 2013 at 11:10