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
|
#!/usr/bin/python3
##
## @file replaceOneFD.py
## @brief replaces a given function definition in a specific part of the model
## @author Frank 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.
## ------------------------------------------------------------------------ -->
##
import sys
import os.path
import libsbml
def main (args):
"""Usage: replaceOneFD filename functionDefinitionId reactionId outfile
"""
if len(args) != 5:
print("Usage: replaceOneFD filename functionDefinitionId reactionId outfile")
return 1
filename = args[1]
outFile = args[4]
functionDefinitionId = args[2]
reactionId = args[3]
document = libsbml.readSBML(filename)
if document.getNumErrors(libsbml.LIBSBML_SEV_ERROR) > 0:
print("The models contains errors, please correct them before continuing.")
document.printErrors()
return 1
model = document.getModel()
functionDefinition = model.getFunctionDefinition(functionDefinitionId)
if functionDefinition is None:
print()
print("No functiondefinition with the given id can be found.")
return 1
reaction = model.getReaction(reactionId)
if reaction is None:
print()
print("No reaction with the given id can be found.")
return 1
if reaction.isSetKineticLaw() == False or reaction.getKineticLaw().isSetMath()== False:
print()
print("The reaction has no math set. ")
return 1
# Until here it was all setup, all we needed was an ASTNode, in which we wanted to
# replace calls to a function definition, with the function definitions content.
#
libsbml.SBMLTransforms.replaceFD(reaction.getKineticLaw().getMath(), functionDefinition)
# finally write to file
libsbml.writeSBML(document, outFile)
if __name__ == '__main__':
main(sys.argv)
|
