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

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GoogleCodeExporter opened this issue Mar 19, 2015 · 0 comments
Open

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

GoogleCodeExporter opened this issue Mar 19, 2015 · 0 comments
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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
msneddon pushed a commit that referenced this issue Sep 15, 2015
@jjtapia
Changing templateMolecule::compare to return a vector of mappingSets …
b6cb7fc 
…instead of returning different mapping sets with each iteration

Also chabnged compare return type to bool back from pair<bool,bool>. Finally, the updated conmpare method and related functionality
is now used in the basic reaction class. This issue should address most of the remaining problems found in issue #2.
rasi added a commit to rasilab/nfsim that referenced this issue Jan 1, 2019
@rasi
Search polymer neighborhood of all specified comps
60b304a 
For my polymer neighborhood search, I was previously looking at only the
molecule components that got changed by a transformation. This results
in searching of only polymer neighborhoods of the changed component, but
not other unchanged components which might nevertheless be constrained
by the reaction rule.
So I now look at all molecule components that are constrained as well.
This is done by looking at the template molecule corresponding to the
transformation reactant.

Alter search to only polymeric constrained comps and
Search neighborhood of only bonded polymeric comps

Trying to speed up the polymer search but not very useful

This is the commit message msneddon#2:

This is done to avoid slow searching of all specified components
of all molecules.
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