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5.18.0
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Examples
fbc_example1.cpp
Simple example of writing a model that uses the SBML Level 3 Flux Balance Constraints package.
/**
* @file example1.cpp
* @brief SBML FBC example
* @author Frank T. Bergmann
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2018 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
#include <
sbml/SBMLTypes.h
>
#include <
sbml/packages/fbc/common/FbcExtensionTypes.h
>
LIBSBML_CPP_NAMESPACE_USE
int
main(
int
argc,
char
** argv)
{
SBMLNamespaces
sbmlns(3,1,
"fbc"
,1);
// create the document
SBMLDocument
*document =
new
SBMLDocument
(&sbmlns);
document->
setPackageRequired
(
"fbc"
,
false
);
// create the Model
Model
* model=document->
createModel
();
// create the Compartment
Compartment
* compartment = model->
createCompartment
();
compartment->
setId
(
"compartment"
);
compartment->
setConstant
(
true
);
compartment->
setSize
(1);
// create the Species
Species
* species = model->
createSpecies
();
species->
setId
(
"Node1"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node2"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node3"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node4"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node5"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node6"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node7"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node8"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
false
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node0"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
true
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
species = model->
createSpecies
();
species->
setId
(
"Node9"
);
species->
setCompartment
(
"compartment"
);
species->
setBoundaryCondition
(
true
);
species->
setConstant
(
false
);
species->
setHasOnlySubstanceUnits
(
false
);
Reaction
* reaction = model->
createReaction
();
reaction->
setId
(
"J0"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
SpeciesReference
* reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node0"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
SpeciesReference
* product = reaction->
createProduct
();
product->
setSpecies
(
"Node1"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J1"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node1"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node2"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J2"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node2"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node3"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J3"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node1"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node4"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J4"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node4"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node3"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J5"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node3"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node5"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J6"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node5"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node6"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J7"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node6"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node7"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J8"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node5"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node8"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J9"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node8"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node7"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
reaction = model->
createReaction
();
reaction->
setId
(
"J10"
);
reaction->
setReversible
(
false
);
reaction->
setFast
(
false
);
reactant = reaction->
createReactant
();
reactant->
setSpecies
(
"Node7"
);
reactant->
setStoichiometry
(1);
reactant->
setConstant
(
true
);
product = reaction->
createProduct
();
product->
setSpecies
(
"Node9"
);
product->
setStoichiometry
(1);
product->
setConstant
(
true
);
//
// Get a FbcModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is
// SBasePlugin*, and thus the value needs to be casted for the
// corresponding derived class.
//
FbcModelPlugin
* mplugin
=
static_cast<
FbcModelPlugin
*
>
(model->
getPlugin
(
"fbc"
));
FluxBound
* bound= mplugin->
createFluxBound
();
bound->
setId
(
"bound1"
);
bound->
setReaction
(
"J0"
);
bound->
setOperation
(
"equal"
);
bound->
setValue
(10);
Objective
* objective = mplugin->
createObjective
();
objective->
setId
(
"obj1"
);
objective->
setType
(
"maximize"
);
// mark obj1 as active objective
mplugin->
setActiveObjectiveId
(
"obj1"
);
FluxObjective
* fluxObjective = objective->
createFluxObjective
();
fluxObjective->
setReaction
(
"J8"
);
fluxObjective->
setCoefficient
(1);
writeSBML
(document,
"fbc_example1.xml"
);
delete
document;
}
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