1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
|
#!/usr/bin/python3
#
# @file groups_example1.py
# @brief SBML Groups example
# @author Akiya Jouraku
# @author Frank Bergmann (python port)
#
# $Id: example1.py 11938 2010-09-20 02:04:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/branches/libsbml-5/examples/groups/example1.py $
#
# This file is part of libSBML. Please visit http:# sbml.org for more
# information about SBML, and the latest version of libSBML.
#
from libsbml import *
#
# Creates an SBMLNamespaces object with the given SBML level, version
# package name, package version.
#
# (NOTE) By default, the name of package (i.e. "groups") will be used
# if the argument for the prefix is missing or empty. Thus the argument
# for the prefix can be added as follows:
#
# SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
#
sbmlns = SBMLNamespaces(3,1,"groups",1)
#
# (NOTES) The above code creating an SBMLNamespaces object can be replaced
# with one of the following other styles.
#
# (1) Creates an SBMLNamespace object with a SBML core namespace and then
# adds a groups package namespace to the object.
#
# SBMLNamespaces sbmlns(3,1);
# sbmlns.addPkgNamespace("groups",1);
#
# OR
#
# SBMLNamespaces sbmlns(3,1);
# sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
#
# (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
# groups package. The class is basically used for creating an SBase derived
# objects defined in the groups package) with the given SBML level, version,
# and package version
#
# GroupsPkgNamespaces sbmlns(3,1,1);
#
# create the document
document = SBMLDocument(sbmlns)
document.setPkgRequired('groups', False)
# create the Model
model= document.createModel()
# create the Compartment
compartment = model.createCompartment()
compartment.setId("cytosol")
compartment.setConstant(True)
compartment=model.createCompartment()
compartment.setId("mitochon")
compartment.setConstant(True)
# create the Species
species = model.createSpecies()
species.setId("ATPc")
species.setCompartment("cytosol")
species.setInitialConcentration(1)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
species = model.createSpecies()
species.setId("ATPm")
species.setCompartment("mitochon")
species.setInitialConcentration(2)
species.setHasOnlySubstanceUnits(False)
species.setBoundaryCondition(False)
species.setConstant(False)
# create the Groups
#
# Get a GroupsModelPlugin 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.
#
mplugin = model.getPlugin("groups")
#
# Creates a Group object via GroupsModelPlugin object.
#
group = mplugin.createGroup()
group.setId("ATP")
group.setKind("classification")
group.setSBOTerm("SBO:0000252")
member = group.createMember()
member.setIdRef("ATPc")
member = group.createMember()
member.setIdRef("ATPm")
writeSBML(document,"groups_example1-python.xml")
|
