libSBML C++ API
libSBML 5.18.0 C++ API
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Simple example of writing a model that uses the SBML Level 3 Groups package and also the SBML Level 3 Layout package.
int main(int argc,char** argv){
sbmlns.addPkgNamespace("layout",1);
sbmlns.addPkgNamespace("groups",1);
model->
setId(
"TestModel");
compartment->
setId(
"Compartment_1");
species1->
setId(
"Species_1");
species2->
setId(
"Species_2");
reaction1->
setId(
"Reaction_1");
reference1->
setId(
"SpeciesReference_1");
reference2->
setId(
"SpeciesReference_2");
reaction2->
setId(
"Reaction_2");
reference3->
setId(
"SpeciesReference_3");
reference4->
setId(
"SpeciesReference_4");
layout->
setId(
"Layout_1");
compartmentGlyph->
setId(
"CompartmentGlyph_1");
speciesGlyph1->
setId(
"SpeciesGlyph_1");
textGlyph1->
setId(
"TextGlyph_01");
speciesGlyph2->
setId(
"SpeciesGlyph_2");
textGlyph2->
setId(
"TextGlyph_02");
reactionGlyph1->
setId(
"ReactionGlyph_1");
Point p(&layoutns,165,105);
p=
Point(&layoutns,165,115);
reactionGlyph2->
setId(
"ReactionGlyph_1");
p=
Point(&layoutns,235,105);
p=
Point(&layoutns,235,115);
speciesReferenceGlyph1->
setId(
"SpeciesReferenceGlyph_1");
Curve* speciesReferenceCurve1=speciesReferenceGlyph1->
getCurve();
p=
Point(&layoutns,165,105);
p=
Point(&layoutns,165,90);
p=
Point(&layoutns,165,90);
p=
Point(&layoutns,195,60);
speciesReferenceGlyph2->
setId(
"SpeciesReferenceGlyph_2");
Curve* speciesReferenceCurve2=speciesReferenceGlyph2->
getCurve();
p=
Point(&layoutns,165,115);
p=
Point(&layoutns,165,130);
p=
Point(&layoutns,165,130);
p=
Point(&layoutns,195,160);
speciesReferenceGlyph3->
setId(
"SpeciesReferenceGlyph_3");
Curve* speciesReferenceCurve3=speciesReferenceGlyph3->
getCurve();
p=
Point(&layoutns,235,115);
p=
Point(&layoutns,235,130);
p=
Point(&layoutns,235,130);
p=
Point(&layoutns,205,160);
speciesReferenceGlyph4->
setId(
"SpeciesReferenceGlyph_4");
Curve* speciesReferenceCurve4=speciesReferenceGlyph4->
getCurve();
p=
Point(&layoutns,235,105);
p=
Point(&layoutns,235,90);
p=
Point(&layoutns,235,90);
p=
Point(&layoutns,205,60);
group->
setId(
"role_substrate");
member->
setIdRef(
"SpeciesReferenceGlyph_1");
member->
setIdRef(
"SpeciesReferenceGlyph_3");
group->
setId(
"role_product");
member->
setIdRef(
"SpeciesReferenceGlyph_2");
member->
setIdRef(
"SpeciesReferenceGlyph_4");
delete document;
}
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:275
@ GROUP_KIND_CLASSIFICATION
Definition: GroupsExtension.h:400
int setModel(const Model *m)
Sets the Model for this SBMLDocument to a copy of the given Model.
Definition: SBMLDocument.cpp:599
int setConstant(bool value)
Sets the value of the "constant" attribute of this Compartment object.
Definition: Compartment.cpp:681
void setRole(const std::string &role)
Sets the role based on a string.
Definition: SpeciesReferenceGlyph.cpp:338
Spatial dimensions of a 2D or 3D shape.
Definition: Dimensions.h:65
An SBML reaction between species in an SBML model.
Definition: Reaction.h:218
void setBasePoint1(const Point *p)
Initializes first base point with a copy of the given point.
Definition: CubicBezier.cpp:403
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:385
A Cubic Bézier smooth curve.
Definition: CubicBezier.h:65
Representation of a point.
Definition: Point.h:59
A curve connecting elements in a diagram.
Definition: Curve.h:211
Member * createMember()
Creates a new Member object, adds it to this Group object and returns the Member object created.
Definition: Group.cpp:443
virtual const std::string & getId() const
Returns the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:128
int setKind(const GroupKind_t kind)
Sets the value of the "kind" attribute of this Group.
Definition: Group.cpp:229
CompartmentGlyph * createCompartmentGlyph()
Creates a CompartmentGlyph object, adds it to the end of the compartment glyph objects list and retur...
Definition: Layout.cpp:1380
SpeciesReferenceGlyph * createSpeciesReferenceGlyph()
Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objec...
Definition: ReactionGlyph.cpp:496
LineSegment * createLineSegment()
Creates a new LineSegment and adds it to the end of the list.
Definition: Curve.cpp:359
Include all SBML types in a single header file.
Reaction * createReaction()
Creates a new Reaction inside this Model and returns it.
Definition: Model.cpp:1779
Extension of Model.
Definition: LayoutModelPlugin.h:62
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:375
int setReversible(bool value)
Sets the value of the "reversible" attribute of this Reaction.
Definition: Reaction.cpp:607
A glyph for an SBML reaction.
Definition: ReactionGlyph.h:249
@ SPECIES_ROLE_SUBSTRATE
Definition: SpeciesReferenceRole.h:56
Extension of Model.
Definition: GroupsModelPlugin.h:60
void setSpeciesId(const std::string &id)
Sets the id of the associated species object.
Definition: SpeciesGlyph.cpp:201
The Member class defines what objects are parts of a Group.
Definition: Member.h:79
Model * createModel(const std::string sid="")
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Definition: SBMLDocument.cpp:643
Layout * createLayout()
Creates a new layout object and adds it to the list of layout objects and returns it.
Definition: LayoutModelPlugin.cpp:475
void setEnd(const Point *end)
Initializes the end point with a copy of the given Point object.
Definition: LineSegment.cpp:369
Curve * getCurve()
Returns the curve object for the species reference glyph.
Definition: SpeciesReferenceGlyph.cpp:365
int setFast(bool value)
Sets the value of the "fast" attribute of this Reaction.
Definition: Reaction.cpp:620
Species * createSpecies()
Creates a new Species inside this Model and returns it.
Definition: Model.cpp:1590
void setSpeciesGlyphId(const std::string &speciesGlyphId)
Sets the id of the associated species glyph.
Definition: SpeciesReferenceGlyph.cpp:284
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:210
Representation of a group of SBML components.
Definition: Group.h:171
Definition of GroupsExtensionTypes.
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Compartment object.
Definition: Compartment.cpp:474
TextGlyph * createTextGlyph()
Creates a TextGlyph object, adds it to the end of the text glyph objects list and returns a pointer t...
Definition: Layout.cpp:1443
SpeciesReference * createReactant()
Creates a new SpeciesReference, adds it to this Reaction's list of reactants, and returns it.
Definition: Reaction.cpp:955
void setSpeciesReferenceId(const std::string &id)
Sets the id of the associated species reference.
Definition: SpeciesReferenceGlyph.cpp:304
int setConstant(bool value)
Sets the "constant" attribute of this Species object.
Definition: Species.cpp:824
void setBasePoint2(const Point *p)
Initializes second base point with a copy of the given point.
Definition: CubicBezier.cpp:452
An SBML compartment, where species are located.
Definition: Compartment.h:484
A glyph for an SBML species.
Definition: SpeciesGlyph.h:59
ReactionGlyph * createReactionGlyph()
Creates a ReactionGlyph object, adds it to the end of the reaction glyph objects list and returns a p...
Definition: Layout.cpp:1412
virtual int setId(const std::string &id)
Sets the value of the "id" attribute of this Group.
Definition: Group.cpp:208
int setSpecies(const std::string &sid)
Sets the "species" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:192
The layout of a diagram of an SBML model.
Definition: Layout.h:783
An SBML model.
Definition: Model.h:479
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Species.
Definition: Species.cpp:586
SBMLNamespaces extension for the package.
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Layout.
Definition: Layout.cpp:449
int setGraphicalObjectId(const std::string &id)
Sets the id of the associated graphical object.
Definition: TextGlyph.cpp:241
Group * createGroup()
Creates a new Group object, adds it to this GroupsModelPlugin object and returns the Group object cre...
Definition: GroupsModelPlugin.cpp:227
virtual const std::string & getId() const
Returns the value of the "id" attribute of this GraphicalObject.
Definition: GraphicalObject.cpp:367
Include all SBML types of layout extension in a single header file.
A glyph for an SBML compartment.
Definition: CompartmentGlyph.h:54
A bounding box for an item in a diagram.
Definition: BoundingBox.h:58
Representation of a line.
Definition: LineSegment.h:63
SpeciesReference * createProduct()
Creates a new SpeciesReference, adds it to this Reaction's list of products, and returns it.
Definition: Reaction.cpp:983
int setReactionId(const std::string &id)
Sets the id of the associated reaction.
Definition: ReactionGlyph.cpp:319
void setStart(const Point *start)
Initializes the start point with a copy of the given Point object.
Definition: LineSegment.cpp:322
int setPackageRequired(const std::string &package, bool flag)
Sets the required attribute value of the given package extension.
Definition: SBMLDocument.cpp:1439
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:516
int setOriginOfTextId(const std::string &orig)
Sets the id of the origin of text.
Definition: TextGlyph.cpp:261
void setDimensions(const Dimensions *dimensions)
Sets the dimensions of the layout.
Definition: Layout.cpp:515
const Curve * getCurve() const
Returns the curve object for the reaction glyph.
Definition: ReactionGlyph.cpp:447
int setConstant(bool flag)
Sets the "constant" attribute of this SpeciesReference to the given boolean flag.
Definition: SpeciesReference.cpp:395
Set of SBML Level + Version + namespace triples.
Definition: SBMLNamespaces.h:139
CubicBezier * createCubicBezier()
Creates a new CubicBezier and adds it to the end of the list.
Definition: Curve.cpp:374
int setCompartmentId(const std::string &id)
Sets the id of the associated compartment.
Definition: CompartmentGlyph.cpp:218
SpeciesGlyph * createSpeciesGlyph()
Creates a SpeciesGlyph object, adds it to the end of the species glyph objects list and returns a poi...
Definition: Layout.cpp:1396
int setCompartment(const std::string &sid)
Sets the "compartment" attribute of this Species object.
Definition: Species.cpp:665
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Compartment.
Definition: Compartment.cpp:238
A glyph for a text label.
Definition: TextGlyph.h:59
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Model.
Definition: Model.cpp:717
Compartment * createCompartment()
Creates a new Compartment inside this Model and returns it.
Definition: Model.cpp:1563
A glyph for an SBML species reference.
Definition: SpeciesReferenceGlyph.h:65
int setIdRef(const std::string &idRef)
Sets the value of the "idRef" attribute of this Member.
Definition: Member.cpp:234
void setBoundingBox(const BoundingBox *bb)
Sets the boundingbox for the GraphicalObject.
Definition: GraphicalObject.cpp:470
@ SPECIES_ROLE_PRODUCT
Definition: SpeciesReferenceRole.h:57
An SBML species – a pool of entities.
Definition: Species.h:423
virtual const std::string & getId() const
Returns the value of the "id" attribute of this Species.
Definition: Species.cpp:273
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
Overall SBML container object.
Definition: SBMLDocument.h:342
SBasePlugin * getPlugin(const std::string &package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given p...
Definition: SBase.cpp:3460
int setBoundaryCondition(bool value)
Sets the "boundaryCondition" attribute of this Species object.
Definition: Species.cpp:791
int setHasOnlySubstanceUnits(bool value)
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
Definition: Species.cpp:771
int writeSBML(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file named by filename.