Feature request for Representing reactions with focus on intermediate complexes

[yewalenikhil65]

I think it would be nice to introduce another representation of chemical reactions in Catalyst which represents network with a focus on intermediate complexes.. Such way is very useful in modelling reduced order methods.

This shall enable in calculating certain incidence matrices of reaction graph, Laplacian matrices etc..This also helps in writing ODESystem in another alternate form that involves these matrices

On similar lines, it would be nice to visualize network with Graph(rn) representing intermediate complexes as nodes (naturally stoichometry is also taken care in the nodes) and edges as reaction arrows. It could be less messy for bigger reaction networks to visualize that way.

[isaacsas]

If you want to add new graph visualization options and/or a new system type with all the conversions it needs and such go ahead! PRs are welcome. I’d like to get a system type in, perhaps StoichMatSystem, that is the representation we’ve previously discussed, but right now I don’t have time to work on it. In ~ a month classes should end, and I can circle back to this if no one else has picked it up.

[yewalenikhil65]

If you want to add new graph visualization options and/or a new system type with all the conversions it needs and such go ahead! PRs are welcome. I’d like to get a system type in, perhaps StoichMatSystem, that is the representation we’ve previously discussed, but right now I don’t have time to work on it. In ~ a month classes should end, and I can circle back to this if no one else has picked it up.

I will like to try on following basis when i begin.. noting here for future purpose
"A network dynamics approach to chemical reaction networks" https://arxiv.org/pdf/1502.02247.pdf

[yewalenikhil65]

@isaacsas , I would like to know your thoughts on yewalenikhil65#2 whenever you are free.. Its based on what i said in #318 (comment)

i have written it in a form of example/demo, but not sure if it should suite networkapi.jl . Hopefully my writing in that explanation is understandable

[yewalenikhil65]

clsoed with #373