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Further network query functions #110

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Merged
merged 6 commits into from
Mar 13, 2019
Merged

Further network query functions #110

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c36a1fc
finish reaction_network accessors and start documenting
isaacsas Mar 12, 2019
fff7644
more comments
isaacsas Mar 12, 2019
2fcce0c
finishing comments
isaacsas Mar 12, 2019
57d5286
fix comment
isaacsas Mar 13, 2019
59bde8c
typo
isaacsas Mar 13, 2019
733d4db
commas...
isaacsas Mar 13, 2019
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5 changes: 3 additions & 2 deletions src/DiffEqBiological.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,9 @@ export @reaction_network, @reaction_func, @min_reaction_network

# functions to query network properties
export speciesmap, paramsmap, numspecies, numreactions, numparams
export odeexprs, jacobianexprs, noiseexprs, jumpexprs
export get_substrate_stoich, get_net_stoich
export oderhsfun, jacfun, paramjacfun, odefun, noisefun, sdefun, jumps, regularjumps
export odeexprs, jacobianexprs, noiseexprs, jumpexprs, rateexpr, oderatelawexpr, ssaratelawexpr
export substratestoich, productstoich, netstoich, ismassaction, dependants, dependents, substrates, products
export rxtospecies_depgraph, speciestorx_depgraph, rxtorx_depgraph

# functions to add mathematical equations to the network
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8 changes: 4 additions & 4 deletions src/massaction_jump_utils.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@

# given a ReactionStruct and a species map construct a MassActionJump
function make_majump(rs, specmap, ratemap, params, param_context)
reactant_stoich = get_substrate_stoich(rs, specmap)
net_stoich = get_net_stoich(rs, specmap)
reactant_stoich = substratestoich(rs, specmap)
net_stoich = netstoich(rs, specmap)
if isempty(net_stoich)
error("Empty net stoichiometry vectors for mass action reactions are not allowed.")
end
Expand Down Expand Up @@ -92,7 +92,7 @@ function jump_to_dep_specs_map(rn, rxidxs_jidxs)
jtos_vec = Vector{Vector{valtype(specmap)}}(undef, numrxs)
for rx in 1:numrxs
jidx = rxidxs_jidxs[rx]
jtos_vec[jidx] = sort!( [ns.first for ns in get_net_stoich(rn.reactions[rx], specmap)] )
jtos_vec[jidx] = sort!( [ns.first for ns in netstoich(rn.reactions[rx], specmap)] )
end

jtos_vec
Expand Down Expand Up @@ -125,7 +125,7 @@ function depgraph_from_network(rn, jset, rxidxs_to_jidxs, spec_to_dep_jumps)
jidx = rxidxs_to_jidxs[rx]

# get the net reaction stoichiometry
net_stoich = get_net_stoich(rn.reactions[rx], speciesmap(rn))
net_stoich = netstoich(rn.reactions[rx], speciesmap(rn))

# rx changes spec, hence rxs depending on spec depend on rx
for (spec,stoch) in net_stoich
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