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#
# @file printMulti.cs
# @brief multi print example
# @author Frank Bergmann
#
# <!--------------------------------------------------------------------------
# This file is part of libSBML. Please visit http://sbml.org for more
# information about SBML, and the latest version of libSBML.
#
# Copyright (C) 2009-2013 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
#
# Copyright (C) 2006-2008 by the California Institute of Technology,
# Pasadena, CA, USA
#
# Copyright (C) 2002-2005 jointly by the following organizations:
# 1. California Institute of Technology, Pasadena, CA, USA
# 2. Japan Science and Technology Agency, Japan
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation. A copy of the license agreement is provided
# in the file named "LICENSE.txt" included with this software distribution
# and also available online as http://sbml.org/software/libsbml/license.html
# ------------------------------------------------------------------------ -->
#
import sys
from libsbml import *
def printCompartmentInfo(compartment):
plugin = compartment.getPlugin("multi")
name = compartment.getName() if compartment.isSetName()else compartment.getId()
print("Compartment {0}: isType = {1}".format(name, plugin.getIsType()))
for i in range(plugin.getNumCompartmentReferences()):
current = plugin.getCompartmentReference(i)
print(" compartmentReference: {0}".format(current.getCompartment()))
print('')
def printSpeciesInfo(species):
plugin = species.getPlugin("multi")
name = species.getName() if species.isSetName() else species.getId()
print("Species {0}: speciesType = {1}".format(name, plugin.getSpeciesType()))
for i in range(plugin.getNumOutwardBindingSites()):
current = plugin.getOutwardBindingSite(i)
print(" outwardBindingSite bindingStatus={0} component={1}".format(
BindingStatus_toString(current.getBindingStatus()), current.getComponent()))
for i in range(plugin.getNumSpeciesFeatures()):
current = plugin.getSpeciesFeature(i)
print(" speciesFeature speciesFeatureType={0} occur={1}".format(current.getSpeciesFeatureType(), current.getOccur()))
for j in range(current.getNumSpeciesFeatureValues()):
element = current.getSpeciesFeatureValue(j)
print(" speciesFeatureValue value={0}".format(element.getValue()))
print('')
def printMultiMathReferences(node):
if node is None:
return
for i in range(node.getNumChildren()):
current = node.getChild(i)
printMultiMathReferences(current)
plugin = node.getPlugin("multi")
if plugin is None:
return
if plugin.isSetRepresentationType():
print(" math representationType={0}".format(plugin.getRepresentationType()))
if plugin.isSetSpeciesReference():
print(" math speciesReference={0}".format(plugin.getSpeciesReference()))
def printReactionInfo(reaction):
name = reaction.getName() if reaction.isSetName() else reaction.getId()
isIntraSpeciesReaction = isinstance(reaction, IntraSpeciesReaction)
print("Reaction {0}: isIntraSpeciesReaction={1}".format(name, isIntraSpeciesReaction))
for i in range(reaction.getNumReactants()):
current = reaction.getReactant(i)
plugin = current.getPlugin("multi")
if plugin is None:
continue
print(" reactant {0}: compartmentReference={1}".format(current.getSpecies(), plugin.getCompartmentReference()))
for j in range(plugin.getNumSpeciesTypeComponentMapInProducts()):
element = plugin.getSpeciesTypeComponentMapInProduct(j)
print(" speciesTypeComponentMapInProduct: reactant={0} reactantComponent={1} productComponent={2}".format(
element.getReactant(), element.getReactantComponent(), element.getProductComponent()))
print('')
for i in range(reaction.getNumProducts()):
current = reaction.getProduct(i)
plugin = current.getPlugin("multi")
if plugin is None:
continue
print(" product {0}: compartmentReference={1}".format(current.getSpecies(), plugin.getCompartmentReference()))
for j in range(plugin.getNumSpeciesTypeComponentMapInProducts()):
element = plugin.getSpeciesTypeComponentMapInProduct(j)
print(" speciesTypeComponentMapInProduct: reactant={0} reactantComponent={1} productComponent={2}".format(
element.getReactant(), element.getReactantComponent(), element.getProductComponent()))
print('')
if not reaction.isSetKineticLaw() or not reaction.getKineticLaw().isSetMath():
print('')
return
printMultiMathReferences(reaction.getKineticLaw().getMath())
print('')
def printModelInfo(model):
plugin = model.getPlugin("multi")
for i in range (plugin.getNumMultiSpeciesTypes()):
current = plugin.getMultiSpeciesType(i)
isBindingSiteSpeciesType = isinstance(current, BindingSiteSpeciesType)
print("speciesType id={0} name={1} compartment={2} isBindingSiteSpeciesType={3}".format(current.getId(), current.getName(), current.getCompartment(), isBindingSiteSpeciesType))
for j in range(current.getNumSpeciesTypeInstances()):
element = current.getSpeciesTypeInstance(j)
print(" speciesTypeInstance id={0} name={1} speciesType={2}".format(element.getId(), element.getName(), element.getSpeciesType()))
for j in range(current.getNumSpeciesTypeComponentIndexes()):
element = current.getSpeciesTypeComponentIndex(j)
print(" speciesTypeComponentIndex id={0} component={1}".format(element.getId(), element.getComponent()))
for j in range(current.getNumInSpeciesTypeBonds()):
element = current.getInSpeciesTypeBond(j)
print(" inSpeciesTypeBond bindingSite1={0} bindingSite2={1}".format(element.getBindingSite1(), element.getBindingSite2()))
print('')
print('')
def printMulti(fileName):
document = readSBMLFromFile(fileName)
if document.getNumErrors(LIBSBML_SEV_ERROR) > 0:
document.printErrors()
return
model = document.getModel()
# print multi model information
printModelInfo(model)
# print multi compartment information
for i in range(model.getNumCompartments()):
printCompartmentInfo(model.getCompartment(i))
# print multi species information
for i in range(model.getNumSpecies()):
printSpeciesInfo(model.getSpecies(i))
# print multi reaction information
for i in range(model.getNumReactions()):
printReactionInfo(model.getReaction(i))
if __name__ == "__main__":
if len(sys.argv) < 2:
print("usage: printMulti sbml-file")
else:
printMulti(sys.argv[1])
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