printMath.py

Prints the rule, reaction, and event formulas in a given SBML document.

#!/usr/bin/env python
## 
## @file    printMath.py
## @brief   Prints Rule, Reaction, and Event formulas in a given SBML Document
## @author  Ben Bornstein
## @author  Sarah Keating
## 
## 
## <!--------------------------------------------------------------------------
## 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
from libsbml import *

def printFunctionDefinition(n, fd):
    if fd.isSetMath():
        print("FunctionDefinition " + str(n) + ", " + fd.getId())

        math = fd.getMath()

        # Print function arguments.
        if math.getNumChildren() > 1:
            print("(" + (math.getLeftChild()).getName())

            for n in range (1, math.getNumChildren()):
                print(", " + (math.getChild(n)).getName())

        print(") := ")

        # Print function body.
        if math.getNumChildren() == 0:
            print("(no body defined)")
        else:
            math = math.getChild(math.getNumChildren() - 1)
            formula = formulaToString(math)
            print(formula + "\n")


def printRuleMath(n, r):
    if r.isSetMath():
        formula = formulaToString(r.getMath())

        if len(r.getVariable()) > 0:
            print("Rule " + str(n) + ", formula: "
                             + r.getVariable() + " = " + formula + "\n")
        else:
            print("Rule " + str(n) + ", formula: "
                             + formula + " = 0" + "\n")


def printReactionMath(n, r):
    if r.isSetKineticLaw():
        kl = r.getKineticLaw()
        if kl.isSetMath():
            formula = formulaToString(kl.getMath())
            print("Reaction " + str(n) + ", formula: " + formula + "\n")


def printEventAssignmentMath(n, ea):
    if ea.isSetMath():
        variable = ea.getVariable()
        formula = formulaToString(ea.getMath())
        print("  EventAssignment " + str(n)
                              + ", trigger: " + variable + " = " + formula + "\n")


def printEventMath(n, e):
    if e.isSetDelay():
        formula = formulaToString(e.getDelay().getMath())
        print("Event " + str(n) + " delay: " + formula + "\n")

    if e.isSetTrigger():
        formula = formulaToString(e.getTrigger().getMath())
        print("Event " + str(n) + " trigger: " + formula + "\n")

    for i in range(0,e.getNumEventAssignments()):
        printEventAssignmentMath(i + 1, e.getEventAssignment(i))

    print()


def printMath(m):
    for n in range(0,m.getNumFunctionDefinitions()):
        printFunctionDefinition(n + 1, m.getFunctionDefinition(n))

    for n in range(0,m.getNumRules()):
        printRuleMath(n + 1, m.getRule(n))

    print()
    for n in range(0, m.getNumReactions()):
        printReactionMath(n + 1, m.getReaction(n))

    print()
    for n in range(0,m.getNumEvents()):
        printEventMath(n + 1, m.getEvent(n))


def main (args):
  """Usage: printMath filename
  """
  if len(args) != 2:
      print("\n" + "Usage: printMath filename" + "\n" + "\n")
      return 1

  filename = args[1]
  document = readSBML(filename)

  if document.getNumErrors() > 0:
      print("Encountered the following SBML errors:" + "\n")
      document.printErrors()
      return 1

  model = document.getModel()

  if model is None:
      print("No model present." + "\n")
      return 1

  printMath(model)
  print()
  return 0


if __name__ == '__main__':
  main(sys.argv)