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msneddon / nfsim

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

Multiple bonds per component #8

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
BNGL allows components to have multiple bonds. For example, a three-member ring 
can be constructed as A(a!0!1).A(a!1!2).A(a!2!0). NFsim does not currently 
allow this. It's unclear to me whether NFsim should be modified, whether 
multiple bonds should be deprecated from BNGL, or whether writeXML() can, or 
should, be modified to recast a model like this into a form that NFsim can 
handle. However, something should be done at some point to eliminate this 
incongruity between NFsim and BNGL.

Original issue reported on code.google.com by lh64@cornell.edu on 5 Jun 2013 at 12:03

GoogleCodeExporter commented 9 years ago 
This would require major code refactoring. Although multiple bodns per 
component is unofficially supported in BioNetGen, it is not officially 
recognized in the BNGL format. Therefore, this issue will not be fixed, except 
perhaps as part of a major rewrite in the future.

Original comment by justinshogg on 14 Aug 2013 at 2:50