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LCSB-BioCore
SBML.jl
Commits
68a2fadd
Commit
68a2fadd
authored
Jun 25, 2021
by
Miroslav Kratochvil
🚴
Browse files
stylistic changes to docs of other helper functions
parent
bd5db6b5
Changes
1
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Inline
Side-by-side
src/utils.jl
View file @
68a2fadd
...
...
@@ -25,33 +25,29 @@ function getS(
end
"""
function
getLBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
getLBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
Extract a vector of lower bounds of reaction rates from the model. All bounds
are accompanied with the unit of the corresponding value (this behavior is
based on SBML specification).
"""
function
getLBs
(
m
::
SBML
.
Model
)
::
Vector
{
Tuple
{
Float64
,
String
}}
return
broadcast
(
x
->
x
.
lb
,
values
(
m
.
reactions
))
end
getLBs
(
m
::
SBML
.
Model
)
::
Vector
{
Tuple
{
Float64
,
String
}}
=
broadcast
(
x
->
x
.
lb
,
values
(
m
.
reactions
))
"""
function
getUBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
getUBs(m::SBML.Model)::Vector{Tuple{Float64,String}}
Likewise to `getLBs`, extract the upper bounds.
Likewise to
[
`getLBs`
](@ref)
, extract the upper bounds.
"""
function
getUBs
(
m
::
SBML
.
Model
)
::
Vector
{
Tuple
{
Float64
,
String
}}
return
broadcast
(
x
->
x
.
ub
,
values
(
m
.
reactions
))
end
getUBs
(
m
::
SBML
.
Model
)
::
Vector
{
Tuple
{
Float64
,
String
}}
=
broadcast
(
x
->
x
.
ub
,
values
(
m
.
reactions
))
"""
function
getOCs(m::SBML.Model)::Vector{Float64}
getOCs(m::SBML.Model)::Vector{Float64}
Extract the vector of objective coefficients of each reaction.
"""
function
getOCs
(
m
::
SBML
.
Model
)
::
Vector
{
Float64
}
return
broadcast
(
x
->
x
.
oc
,
values
(
m
.
reactions
))
end
getOCs
(
m
::
SBML
.
Model
)
::
Vector
{
Float64
}
=
broadcast
(
x
->
x
.
oc
,
values
(
m
.
reactions
))
"""
initial_amounts(m::SBML.Model; convert_concentrations = false)
...
...
@@ -73,7 +69,7 @@ Dict(initial_amounts(model, convert_concentrations = true))
Dict(k => v for (k,v) in initial_amounts(model) if !isnothing(v))
```
"""
const
initial_amounts
(
m
::
SBML
.
Model
;
convert_concentrations
=
false
)
=
(
initial_amounts
(
m
::
SBML
.
Model
;
convert_concentrations
=
false
)
=
(
k
=>
if
!
isnothing
(
s
.
initial_amount
)
s
.
initial_amount
[
1
]
elseif
convert_concentrations
&&
...
...
@@ -92,7 +88,7 @@ const initial_amounts(m::SBML.Model; convert_concentrations = false) = (
Return initial concentrations of the species in the model. Refer to work-alike
[`initial_amounts`](@ref) for details.
"""
const
initial_concentrations
(
m
::
SBML
.
Model
;
convert_amounts
=
false
)
=
(
initial_concentrations
(
m
::
SBML
.
Model
;
convert_amounts
=
false
)
=
(
k
=>
if
!
isnothing
(
s
.
initial_concentration
)
s
.
initial_concentration
[
1
]
elseif
convert_amounts
&&
...
...
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