1#!/usr/bin/env python
2##
3## @file    printMath.py
4## @brief   Prints Rule, Reaction, and Event formulas in a given SBML Document
5## @author  Ben Bornstein
6## @author  Sarah Keating
7##
8##
9## <!--------------------------------------------------------------------------
10## This sample program is distributed under a different license than the rest
11## of libSBML.  This program uses the open-source MIT license, as follows:
12##
13## Copyright (c) 2013-2018 by the California Institute of Technology
14## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
15## and the University of Heidelberg (Germany), with support from the National
16## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
17##
18## Permission is hereby granted, free of charge, to any person obtaining a
19## copy of this software and associated documentation files (the "Software"),
20## to deal in the Software without restriction, including without limitation
21## the rights to use, copy, modify, merge, publish, distribute, sublicense,
22## and/or sell copies of the Software, and to permit persons to whom the
23## Software is furnished to do so, subject to the following conditions:
24##
25## The above copyright notice and this permission notice shall be included in
26## all copies or substantial portions of the Software.
27##
28## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
29## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
30## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
31## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
32## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
33## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
34## DEALINGS IN THE SOFTWARE.
35##
36## Neither the name of the California Institute of Technology (Caltech), nor
37## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
38## of Heidelberg, nor the names of any contributors, may be used to endorse
39## or promote products derived from this software without specific prior
40## written permission.
41## ------------------------------------------------------------------------ -->
42##
43
44
45import sys
46import os.path
47from libsbml import *
48
49def printFunctionDefinition(n, fd):
50    if fd.isSetMath():
51        print("FunctionDefinition " + str(n) + ", " + fd.getId())
52
53        math = fd.getMath()
54
55        # Print function arguments.
56        if math.getNumChildren() > 1:
57            print("(" + (math.getLeftChild()).getName())
58
59            for n in range (1, math.getNumChildren()):
60                print(", " + (math.getChild(n)).getName())
61
62        print(") := ")
63
64        # Print function body.
65        if math.getNumChildren() == 0:
66            print("(no body defined)")
67        else:
68            math = math.getChild(math.getNumChildren() - 1)
69            formula = formulaToString(math)
70            print(formula + "\n")
71
72
73def printRuleMath(n, r):
74    if r.isSetMath():
75        formula = formulaToString(r.getMath())
76
77        if len(r.getVariable()) > 0:
78            print("Rule " + str(n) + ", formula: "
79                             + r.getVariable() + " = " + formula + "\n")
80        else:
81            print("Rule " + str(n) + ", formula: "
82                             + formula + " = 0" + "\n")
83
84
85def printReactionMath(n, r):
86    if r.isSetKineticLaw():
87        kl = r.getKineticLaw()
88        if kl.isSetMath():
89            formula = formulaToString(kl.getMath())
90            print("Reaction " + str(n) + ", formula: " + formula + "\n")
91
92
93def printEventAssignmentMath(n, ea):
94    if ea.isSetMath():
95        variable = ea.getVariable()
96        formula = formulaToString(ea.getMath())
97        print("  EventAssignment " + str(n)
98                              + ", trigger: " + variable + " = " + formula + "\n")
99
100
101def printEventMath(n, e):
102    if e.isSetDelay():
103        formula = formulaToString(e.getDelay().getMath())
104        print("Event " + str(n) + " delay: " + formula + "\n")
105
106    if e.isSetTrigger():
107        formula = formulaToString(e.getTrigger().getMath())
108        print("Event " + str(n) + " trigger: " + formula + "\n")
109
110    for i in range(0,e.getNumEventAssignments()):
111        printEventAssignmentMath(i + 1, e.getEventAssignment(i))
112
113    print()
114
115
116def printMath(m):
117    for n in range(0,m.getNumFunctionDefinitions()):
118        printFunctionDefinition(n + 1, m.getFunctionDefinition(n))
119
120    for n in range(0,m.getNumRules()):
121        printRuleMath(n + 1, m.getRule(n))
122
123    print()
124    for n in range(0, m.getNumReactions()):
125        printReactionMath(n + 1, m.getReaction(n))
126
127    print()
128    for n in range(0,m.getNumEvents()):
129        printEventMath(n + 1, m.getEvent(n))
130
131
132def main (args):
133  """Usage: printMath filename
134  """
135  if len(args) != 2:
136      print("\n" + "Usage: printMath filename" + "\n" + "\n")
137      return 1
138
139  filename = args[1]
140  document = readSBML(filename)
141
142  if document.getNumErrors() > 0:
143      print("Encountered the following SBML errors:" + "\n")
144      document.printErrors()
145      return 1
146
147  model = document.getModel()
148
149  if model is None:
150      print("No model present." + "\n")
151      return 1
152
153  printMath(model)
154  print()
155  return 0
156
157
158if __name__ == '__main__':
159  main(sys.argv)
160