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LCSB-BioCore
SBML.jl
Commits
b101210c
Commit
b101210c
authored
Jul 13, 2021
by
Miroslav Kratochvil
🚴
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document the previous
parent
67f64299
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src/utils.jl
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b101210c
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...
@@ -103,12 +103,25 @@ initial_concentrations(m::SBML.Model; convert_amounts = false) = (
"""
extensive_kinetic_math(m::SBML.Model, formula::SBML.Math)
function extensive_kinetic_math(
m::SBML.Model,
formula::SBML.Math;
handle_empty_compartment_size = (id::String) -> throw(
DomainError(
"
Non
-
substance
-
only
-
unit
reference
to
species
`\$id' in an unsized compartment `
\$
(
m
.
species
[
id
]
.
compartment
)
'
",
),
),
)
Convert a SBML math `formula` to "
extensive
" kinetic laws, where the references
to species that are marked as not having only substance units are converted
from amounts to concentrations.
If the data is missing, you can supply a function that adds them. A common way
to handle errors is to assume that unsized compartments have volume 1.0 (of
whatever units), you can specify that behavior by supplying
`handle_empty_compartment_size = _ -> 1.0`.
Handling of units in the conversion process is ignored in this version.
"""
function
extensive_kinetic_math
(
...
...
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