def test_ASTNode_replaceChild(self): node = libsbml.ASTNode() c1 = libsbml.ASTNode() c2 = libsbml.ASTNode() c3 = libsbml.ASTNode() newc = libsbml.ASTNode() i = 0 node.setType(libsbml.AST_LOGICAL_AND) c1.setName( "a") c2.setName( "b") c3.setName( "c") node.addChild(c1) node.addChild(c2) node.addChild(c3) self.assert_( node.getNumChildren() == 3 ) self.assert_(( "and(a, b, c)" == libsbml.formulaToString(node) )) newc.setName( "d") i = node.replaceChild(0,newc) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( node.getNumChildren() == 3 ) self.assert_(( "and(d, b, c)" == libsbml.formulaToString(node) )) i = node.replaceChild(3,newc) self.assert_( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE ) self.assert_( node.getNumChildren() == 3 ) self.assert_(( "and(d, b, c)" == libsbml.formulaToString(node) )) i = node.replaceChild(1,c1) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( node.getNumChildren() == 3 ) self.assert_(( "and(d, a, c)" == libsbml.formulaToString(node) )) _dummyList = [ node ]; _dummyList[:] = []; del _dummyList pass
def test_ASTNode_swapChildren(self): node = libsbml.ASTNode() c1 = libsbml.ASTNode() c2 = libsbml.ASTNode() node_1 = libsbml.ASTNode() c1_1 = libsbml.ASTNode() c2_1 = libsbml.ASTNode() i = 0 node.setType(libsbml.AST_LOGICAL_AND) c1.setName( "a") c2.setName( "b") node.addChild(c1) node.addChild(c2) self.assert_( node.getNumChildren() == 2 ) self.assert_(( "and(a, b)" == libsbml.formulaToString(node) )) node_1.setType(libsbml.AST_LOGICAL_AND) c1_1.setName( "d") c2_1.setName( "f") node_1.addChild(c1_1) node_1.addChild(c2_1) self.assert_( node_1.getNumChildren() == 2 ) self.assert_(( "and(d, f)" == libsbml.formulaToString(node_1) )) i = node.swapChildren(node_1) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( node.getNumChildren() == 2 ) self.assert_(( "and(d, f)" == libsbml.formulaToString(node) )) self.assert_( node_1.getNumChildren() == 2 ) self.assert_(( "and(a, b)" == libsbml.formulaToString(node_1) )) _dummyList = [ node_1 ]; _dummyList[:] = []; del _dummyList _dummyList = [ node ]; _dummyList[:] = []; del _dummyList pass
def test_read_l2v4_new(self):
reader = libsbml.SBMLReader()
filename = "../../sbml/test/test-data/"
filename += "l2v4-new.xml"
d = reader.readSBML(filename)
if (d == None):
pass
self.assert_( d.getLevel() == 2 )
self.assert_( d.getVersion() == 4 )
m = d.getModel()
self.assert_( m != None )
self.assert_( m.getId() == "l2v4_all" )
self.assert_( m.getNumCompartments() == 1 )
c = m.getCompartment(0)
self.assert_( c != None )
self.assert_( c.getId() == "a" )
self.assert_( c.getSize() == 1 )
self.assertEqual( False, c.getConstant() )
self.assert_( m.getNumEvents() == 1 )
e = m.getEvent(0)
self.assert_( e != None )
self.assertEqual( True, e.getUseValuesFromTriggerTime() )
self.assertEqual( True, e.isSetTrigger() )
trigger = e.getTrigger()
self.assert_( trigger != None )
ast = trigger.getMath()
self.assert_(( "lt(x, 3)" == libsbml.formulaToString(ast) ))
self.assert_( e.getNumEventAssignments() == 1 )
ea = e.getEventAssignment(0)
self.assert_( ea != None )
self.assert_( ea.getVariable() == "a" )
ast = ea.getMath()
self.assert_(( "x * p3" == libsbml.formulaToString(ast) ))
d = None
def stoichToString(species, stoich):
if stoich is None:
stoich = str(species.getStoichiometry())
elif hasattr(stoich, 'getMath'): # libsbml > 3.0
stoich = libsbml.formulaToString(stoich.getMath())
else: # libsbml 2.3.4
stoich = libsbml.formulaToString(stoich)
return stoich
def __getRawAssignmentRules(self,arule):
variable = arule.getVariable()
rate = libsbml.formulaToString(arule.getMath())
#try to separate into positive and negative sections
if arule.getMath().getCharacter() == '-' and arule.getMath().getNumChildren() > 1 and not arule.isAssignment():
rateL = libsbml.formulaToString(arule.getMath().getLeftChild())
if(arule.getMath().getRightChild().getCharacter()) == '*':
if libsbml.formulaToString(arule.getMath().getRightChild().getLeftChild()) == variable:
rateR = libsbml.formulaToString(arule.getMath().getRightChild().getRightChild())
elif libsbml.formulaToString(arule.getMath().getRightChild().getRightChild()) == variable:
rateR = libsbml.formulaToString(arule.getMath().getRightChild().getLeftChild())
else:
rateR = 'if({0} >0,{1}/{0} ,0)'.format(variable,libsbml.formulaToString(arule.getMath().getRightChild()))
else:
rateR = 'if({0} >0,{1}/{0} ,0)'.format(variable,libsbml.formulaToString((arule.getMath().getRightChild())))
else:
rateL = libsbml.formulaToString(arule.getMath())
rateR = '0'
if not self.useID:
rateL = self.convertToName(rateL)
rateR = self.convertToName(rateR)
variable = self.convertToName(variable).strip()
#print arule.isAssignment(),arule.isRate()
return variable,[rateL,rateR],arule.isAssignment(),arule.isRate()
def create_value_dictionary(model):
values = dict()
# parse all the initial assignments
for assignment in model.getListOfInitialAssignments():
sid = assignment.getId()
math = ' = {}'.format(libsbml.formulaToString(assignment.getMath()))
values[sid] = math
# rules
for rule in model.getListOfRules():
sid = rule.getVariable()
math = ' = {}'.format(libsbml.formulaToString(rule.getMath()))
values[sid] = math
return values
def test_read_MathML_1(self):
reader = libsbml.SBMLReader()
filename = "../../sbml/math/test/test-data/"
filename += "mathML_1-invalid.xml"
d = reader.readSBML(filename)
if (d == None):
pass
m = d.getModel()
self.assert_( m != None )
self.assert_( m.getNumFunctionDefinitions() == 2 )
self.assert_( m.getNumInitialAssignments() == 1 )
self.assert_( m.getNumRules() == 2 )
self.assert_( m.getNumReactions() == 1 )
fd = m.getFunctionDefinition(0)
fd_math = fd.getMath()
self.assert_( fd_math.getType() == libsbml.AST_LAMBDA )
self.assert_( fd_math.getNumChildren() == 2 )
self.assert_(( "lambda(x, )" == libsbml.formulaToString(fd_math) ))
self.assert_( fd_math.getParentSBMLObject() == fd )
child = fd_math.getRightChild()
self.assert_( child.getType() == libsbml.AST_UNKNOWN )
self.assert_( child.getNumChildren() == 0 )
self.assert_(( "" == libsbml.formulaToString(child) ))
fd = m.getFunctionDefinition(1)
fd1_math = fd.getMath()
self.assert_( fd1_math.getType() == libsbml.AST_LAMBDA )
self.assert_( fd1_math.getNumChildren() == 2 )
self.assert_(( "lambda(x, true)" == libsbml.formulaToString(fd1_math) ))
self.assert_( fd1_math.getParentSBMLObject() == fd )
child1 = fd1_math.getRightChild()
self.assert_( child1.getType() == libsbml.AST_CONSTANT_TRUE )
self.assert_( child1.getNumChildren() == 0 )
self.assert_(( "true" == libsbml.formulaToString(child1) ))
ia = m.getInitialAssignment(0)
ia_math = ia.getMath()
self.assert_( ia_math.getType() == libsbml.AST_UNKNOWN )
self.assert_( ia_math.getNumChildren() == 0 )
self.assert_(( "" == libsbml.formulaToString(ia_math) ))
self.assert_( ia_math.getParentSBMLObject() == ia )
r = m.getRule(0)
r_math = r.getMath()
self.assert_( r_math.getType() == libsbml.AST_CONSTANT_TRUE )
self.assert_( r_math.getNumChildren() == 0 )
self.assert_(( "true" == libsbml.formulaToString(r_math) ))
self.assert_( r_math.getParentSBMLObject() == r )
r = m.getRule(1)
r1_math = r.getMath()
self.assert_( r1_math.getType() == libsbml.AST_REAL )
self.assert_( r1_math.getNumChildren() == 0 )
self.assert_(( "INF" == libsbml.formulaToString(r1_math) ))
self.assert_( r1_math.getParentSBMLObject() == r )
kl = m.getReaction(0).getKineticLaw()
kl_math = kl.getMath()
self.assert_( kl_math.getType() == libsbml.AST_REAL )
self.assert_( kl_math.getNumChildren() == 0 )
self.assert_(( "4.5" == libsbml.formulaToString(kl_math) ))
self.assert_( kl_math.getParentSBMLObject() == kl )
d = None
pass
def getPrunnedTree(math,remainderPatterns):
while math.getCharacter() == '*' and len(remainderPatterns) > 0:
if libsbml.formulaToString(math.getLeftChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getLeftChild()))
math = math.getRightChild()
elif libsbml.formulaToString(math.getRightChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getRightChild()))
math = math.getLeftChild()
else:
if(math.getLeftChild().getCharacter()) == '*':
math.replaceChild(0,getPrunnedTree(math.getLeftChild(),remainderPatterns))
if(math.getRightChild().getCharacter()) == '*':
math.replaceChild(math.getNumChildren() - 1,getPrunnedTree(math.getRightChild(),remainderPatterns))
break
return math
def convert_SBML_Formula_to_ecell_Expression( self, formula, aModel, aLocalParameterList = [], aDenominator = 1.0 ):
'''## =================================================
formula: string or libsbml.ASTNode
'''## =================================================
if isinstance( formula, str ):
if aDenominator != 1.0:
formula = '( 1.0 / %s ) * ( %s )' % ( aDenominator, formula )
preprocessedFormula = formula.replace( '<t>', self.Model.TimeSymbol )
aASTRootNode = libsbml.parseFormula( preprocessedFormula )
elif isinstance( formula, libsbml.ASTNode ):
if aDenominator != 1.0:
aASTRootNode = libsbml.parseFormula( '( 1.0 / %s ) * ( x )' % aDenominator )
aASTRootNode.removeChild( 1 )
aASTRootNode.addChild( formula.deepCopy() )
else:
aASTRootNode = formula
else:
raise Exception,"DEBUG : Formula must be str or libsbml.ASTNode instance."
## dump_tree_construction_of_AST_node( aASTRootNode )
aASTRootNode = preprocess_math_tree( aASTRootNode, aModel.TimeSymbol )
convertedAST = self._convert_SBML_variable_to_ecell_Expression( aASTRootNode, aLocalParameterList )
return postprocess_math_string( libsbml.formulaToString( convertedAST ), aModel.TimeSymbol )
def test_element_not(self):
s = wrapMathML("<apply> <not/> <ci> TooShabby </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "not(TooShabby)" == self.F ))
pass
def test_element_function_call_1(self):
s = wrapMathML("<apply> <ci> foo </ci> <ci> x </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "foo(x)" == self.F ))
pass
def removeFactorFromMath(self, math, reactants, products):
ifStack = Counter()
remainderPatterns = []
highStoichoiMetryFactor = 1
for x in reactants:
highStoichoiMetryFactor *= factorial(x[1])
y = [i[1] for i in products if i[0] == x[0]]
y = y[0] if len(y) > 0 else 0
#TODO: check if this actually keeps the correct dynamics
# this is basically there to address the case where theres more products
#than reactants (synthesis)
if x[1] > y:
highStoichoiMetryFactor /= comb(int(x[1]), int(y), exact=True)
for counter in range(0, int(x[1])):
remainderPatterns.append(x[0])
#for x in products:
# highStoichoiMetryFactor /= math.factorial(x[1])
#remainderPatterns = [x[0] for x in reactants]
math = self.getPrunnedTree(math,remainderPatterns)
rateR = libsbml.formulaToString(math)
for element in remainderPatterns:
ifStack.update([element])
for element in ifStack:
if ifStack[element] > 1:
rateR = 'if({0}>0,{1}/({0}^{2}),0)'.format(element,rateR,ifStack[element])
else:
rateR = 'if({0}>0,{1}/{0},0)'.format(element,rateR)
if highStoichoiMetryFactor != 1:
rateR = '{0}*{1}'.format(rateR, int(highStoichoiMetryFactor))
return rateR,math.getNumChildren()
def test_element_root_2(self):
s = wrapMathML("<apply> <root/> <ci> a </ci> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "sqrt(a)" == self.F ))
pass
def initializeVariableReferenceList(self):
self.theVariableReferenceList = []
formulaString = self.theSBase.getFormula()
anASTNode = libsbml.parseFormula(formulaString)
self.__convertFormulaToExpression(anASTNode)
self.theExpression = libsbml.formulaToString(anASTNode)
# SBML_ASSIGNMENT_RULE or SBML_RATE_RULE
## if self.theSBase.getType() == 1 \
## or self.theSBase.getType() == 2:
if type(self.theSBase) == libsbml.AssignmentRulePtr or type(self.theSBase) == libsbml.RateRulePtr:
variable = self.theSBase.getVariable()
(fullIDString, sbaseType) = self.rootobj.theSBMLIdManager.searchFullIDFromId(variable)
if sbaseType == libsbml.SBML_SPECIES or sbaseType == libsbml.SBML_PARAMETER:
pass
elif sbaseType == libsbml.SBML_COMPARTMENT:
fullID = ecell.ecssupport.createFullID(fullIDString)
systemPath = ecell.ecssupport.createSystemPathFromFullID(fullID)
fullIDString = "Variable:%s:SIZE" % (systemPath)
else:
raise SBMLConvertError, "SBase [%s] is not found" % (variable)
self.__addVariableReference(fullIDString, 1)
def test_element_power(self):
s = wrapMathML("<apply><power/> <ci>x</ci> <cn>3</cn> </apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "pow(x, 3)" == self.F ))
pass
def test_element_ceiling(self):
s = wrapMathML("<apply><ceiling/><cn> 1.6 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "ceil(1.6)" == self.F ))
pass
def test_element_factorial(self):
s = wrapMathML("<apply><factorial/><cn> 5 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "factorial(5)" == self.F ))
pass
def test_element_tanh(self):
s = wrapMathML("<apply><tanh/><ci> x </ci></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "tanh(x)" == self.F ))
pass
def test_element_floor(self):
s = wrapMathML("<apply><floor/><cn> 1.2 </cn></apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "floor(1.2)" == self.F ))
pass
def removeFactorFromMath(self,math,reactants):
'''
walks through a series of * nodes and removes the remainder reactant factors
'''
def getPrunnedTree(math,remainderPatterns):
while math.getCharacter() == '*' and len(remainderPatterns) > 0:
if libsbml.formulaToString(math.getLeftChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getLeftChild()))
math = math.getRightChild()
elif libsbml.formulaToString(math.getRightChild()) in remainderPatterns:
remainderPatterns.remove(libsbml.formulaToString(math.getRightChild()))
math = math.getLeftChild()
else:
if(math.getLeftChild().getCharacter()) == '*':
math.replaceChild(0,getPrunnedTree(math.getLeftChild(),remainderPatterns))
if(math.getRightChild().getCharacter()) == '*':
math.replaceChild(math.getNumChildren() - 1,getPrunnedTree(math.getRightChild(),remainderPatterns))
break
return math
remainderPatterns = [x[0] for x in reactants]
math = getPrunnedTree(math,remainderPatterns)
rateR = libsbml.formulaToString(math)
for element in remainderPatterns:
rateR = 'if({0} >0,{1}/{0} ,0)'.format(element,rateR)
return rateR
def function_definitions(self, evalfunc=None, kwargs={}):
for func in self.model.function_definitions:
args = [func.getArgument(i).getName() for i in range(func.getNumArguments())]
formula = libsbml.formulaToString(func.getBody())
if evalfunc is None:
yield (func.id, (args, formula))
else:
yield (func.id, LambdaFunction(args, formula, evalfunc))
def test_element_operator_times(self):
s = wrapMathML("<apply> <times/> <ci> x </ci> <ci> y </ci> <ci> z </ci> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "x * y * z" == self.F ))
pass
def test_element_leq(self):
s = wrapMathML("<apply> <leq/> <cn>0</cn> <ci>x</ci> <cn>1</cn> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "leq(0, x, 1)" == self.F ))
pass
def test_element_neq(self):
s = wrapMathML("<apply> <neq/> <notanumber/> <notanumber/> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "neq(NaN, NaN)" == self.F ))
pass
def convertRuleFormula( self, aFormula ):
aASTRootNode = libsbml.parseFormula( aFormula )
convertedAST = self.__convertVariableName( aASTRootNode )
convertedFormula = libsbml.formulaToString( convertedAST )
return convertedFormula
def getReactionMath(self, reaction):
try:
kineticLaw = reaction.getKineticLaw()
mathNode = kineticLaw.getMath()
mathString = libsbml.formulaToString(mathNode)
return mathString
except: # most often happens when creating a new reaction that does not have a kinetic law
return
def test_element_operator_plus(self):
s = wrapMathML("<apply> <plus/> <cn> 1 </cn> <cn> 2 </cn> <cn> 3 </cn> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "1 + 2 + 3" == self.F ))
pass
def test_element_xor(self):
s = wrapMathML("<apply> <xor/> <ci>a</ci> <ci>b</ci> <ci>b</ci> <ci>a</ci> </apply>"
)
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "xor(a, b, b, a)" == self.F ))
pass
def test_element_root_1(self):
s = wrapMathML("<apply> <root/> <degree> <cn type='integer'> 3 </cn> </degree>" +
" <ci> a </ci>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "root(3, a)" == self.F ))
pass
def test_element_lt(self):
s = wrapMathML("<apply> <lt/> <apply> <minus/> <infinity/> <infinity/> </apply>" +
" <cn>1</cn>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_( self.N != None )
self.F = libsbml.formulaToString(self.N)
self.assert_(( "lt(INF - INF, 1)" == self.F ))
pass
def test_element_lambda(self):
s = wrapMathML(
"<lambda>" + " <bvar> <ci>x</ci> </bvar>" + " <apply> <sin/>" +
" <apply> <plus/> <ci>x</ci> <cn>1</cn> </apply>" +
" </apply>" + "</lambda>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("lambda(x, sin(x + 1))" == self.F))
pass
def test_element_piecewise_otherwise(self):
s = wrapMathML("<piecewise>" + " <piece>" + " <cn>0</cn>" +
" <apply> <lt/> <ci>x</ci> <cn>0</cn> </apply>" +
" </piece>" + " <otherwise>" + " <ci>x</ci>" +
" </otherwise>" + "</piecewise>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("piecewise(0, lt(x, 0), x)" == self.F))
pass
def test_element_function_call_2(self):
s = wrapMathML(
"<apply> <plus/> <cn> 1 </cn>" +
" <apply> <ci> f </ci> <ci> x </ci> </apply>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("1 + f(x)" == self.F))
pass
def test_element_gt(self):
s = wrapMathML(
"<apply> <gt/> <infinity/>" +
" <apply> <minus/> <infinity/> <cn>1</cn> </apply>" +
"</apply>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("gt(INF, INF - 1)" == self.F))
pass
def test_element_csymbol_delay_2(self):
s = wrapMathML(
"<apply>" +
" <csymbol encoding='text' definitionURL='http://www.sbml.org/sbml/"
+ "symbols/delay'> my_delay </csymbol>" + " <ci> x </ci>" +
" <cn> 0.1 </cn>" + "</apply>\n")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("my_delay(x, 0.1)" == self.F))
pass
def test_ValidASTNode_infix_nary_times0(self):
n = libsbml.readMathMLFromString(
"<math xmlns='http://www.w3.org/1998/Math/MathML'>" + " <apply>" +
" <times/>" + " </apply>" + "</math>")
self.assert_(n != None)
formula = libsbml.formulaToString(n)
node = libsbml.parseFormula(formula)
self.assert_(node != None)
n = None
node = None
pass
def test_element_bug_math_xmlns(self):
s = wrapXML(
"<foo:math xmlns:foo='http://www.w3.org/1998/Math/MathML'>" +
" <foo:apply>" +
" <foo:plus/> <foo:cn>1</foo:cn> <foo:cn>2</foo:cn>" +
" </foo:apply>" + "</foo:math>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("1 + 2" == self.F))
pass
def test_read_MathML_1(self):
reader = libsbml.SBMLReader()
filename = "../../sbml/math/test/test-data/"
filename += "mathML_1-invalid.xml"
d = reader.readSBML(filename)
if (d == None):
pass
m = d.getModel()
self.assert_(m != None)
self.assert_(m.getNumFunctionDefinitions() == 2)
self.assert_(m.getNumInitialAssignments() == 1)
self.assert_(m.getNumRules() == 2)
self.assert_(m.getNumReactions() == 1)
fd = m.getFunctionDefinition(0)
fd_math = fd.getMath()
self.assert_(fd_math.getType() == libsbml.AST_LAMBDA)
self.assert_(fd_math.getNumChildren() == 2)
self.assert_(("lambda(x, )" == libsbml.formulaToString(fd_math)))
self.assert_(fd_math.getParentSBMLObject() == fd)
child = fd_math.getRightChild()
self.assert_(child.getType() == libsbml.AST_UNKNOWN)
self.assert_(child.getNumChildren() == 0)
self.assert_(("" == libsbml.formulaToString(child)))
fd = m.getFunctionDefinition(1)
fd1_math = fd.getMath()
self.assert_(fd1_math.getType() == libsbml.AST_LAMBDA)
self.assert_(fd1_math.getNumChildren() == 2)
self.assert_(("lambda(x, true)" == libsbml.formulaToString(fd1_math)))
self.assert_(fd1_math.getParentSBMLObject() == fd)
child1 = fd1_math.getRightChild()
self.assert_(child1.getType() == libsbml.AST_CONSTANT_TRUE)
self.assert_(child1.getNumChildren() == 0)
self.assert_(("true" == libsbml.formulaToString(child1)))
ia = m.getInitialAssignment(0)
ia_math = ia.getMath()
self.assert_(ia_math.getType() == libsbml.AST_UNKNOWN)
self.assert_(ia_math.getNumChildren() == 0)
self.assert_(("" == libsbml.formulaToString(ia_math)))
self.assert_(ia_math.getParentSBMLObject() == ia)
r = m.getRule(0)
r_math = r.getMath()
self.assert_(r_math.getType() == libsbml.AST_CONSTANT_TRUE)
self.assert_(r_math.getNumChildren() == 0)
self.assert_(("true" == libsbml.formulaToString(r_math)))
self.assert_(r_math.getParentSBMLObject() == r)
r = m.getRule(1)
r1_math = r.getMath()
self.assert_(r1_math.getType() == libsbml.AST_REAL)
self.assert_(r1_math.getNumChildren() == 0)
self.assert_(("INF" == libsbml.formulaToString(r1_math)))
self.assert_(r1_math.getParentSBMLObject() == r)
# kl = m.getReaction(0).getKineticLaw()
# kl_math = kl.getMath()
# self.assert_( kl_math == None )
d = None
pass
def function_definitions(self, evalfunc=None, kwargs=None):
kwargs = kwargs or {}
for func in self.model.function_definitions:
args = [
func.getArgument(i).getName()
for i in range(func.getNumArguments())
]
formula = libsbml.formulaToString(func.getBody())
if evalfunc is None:
yield (func.id, (args, formula))
else:
yield (func.id, LambdaFunction(args, formula, evalfunc))
def test_element_csymbol_delay_3(self):
s = wrapMathML(
"<apply>" + " <power/>" + " <apply>" +
" <csymbol encoding='text' definitionURL='http://www.sbml.org/sbml/"
+ "symbols/delay'> delay </csymbol>" + " <ci> P </ci>" +
" <ci> delta_t </ci>" + " </apply>\n" + " <ci> q </ci>" +
"</apply>\n")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(("pow(delay(P, delta_t), q)" == self.F))
pass
def test_Delay_setMath(self):
math = libsbml.parseFormula("lambda(x, x^3)")
self.D.setMath(math)
math1 = self.D.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("lambda(x, x^3)" == formula))
self.assert_(self.D.getMath() != math)
self.assertEqual(True, self.D.isSetMath())
self.D.setMath(self.D.getMath())
math1 = self.D.getMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1)
self.assert_(formula != None)
self.assert_(("lambda(x, x^3)" == formula))
self.D.setMath(None)
self.assertEqual(False, self.D.isSetMath())
if (self.D.getMath() != None):
pass
pass
def initial_assignments(self, evalfunc=None, kwargs=None):
evalfunc = evalfunc or None
kwargs = kwargs.copy() if kwargs else {}
for assignment in self.model.initial_assignments:
formula = libsbml.formulaToString(assignment.math)
if evalfunc is None:
yield (assignment.id, formula)
else:
val = evalfunc(formula, kwargs)
kwargs[assignment.id] = val
yield (assignment.id, val)
def test_SpeciesReference_setStoichiometryMath(self):
math = libsbml.parseFormula("k3 / k2")
stoich = libsbml.StoichiometryMath(2, 4)
stoich.setMath(math)
self.SR.setStoichiometryMath(stoich)
math1 = self.SR.getStoichiometryMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1.getMath())
self.assert_(formula != None)
self.assert_(("k3 / k2" == formula))
self.assertEqual(True, self.SR.isSetStoichiometryMath())
pass
def __get_rules(sbml_model, gillespy_model, errors):
for i in range(sbml_model.getNumRules()):
rule = sbml_model.getRule(i)
rule_name = rule.getId()
rule_variable = rule.getVariable()
rule_string = __get_math(rule.getMath())
if rule_variable in gillespy_model.listOfParameters:
# Treat Non-Constant Parameters as Species
value = gillespy_model.listOfParameters[rule_variable].expression
species = gillespy2.Species(name=rule_variable,
initial_value=value,
allow_negative_populations=True,
mode='continuous')
gillespy_model.delete_parameter(rule_variable)
gillespy_model.add_species([species])
t = []
if rule.isAssignment():
assign_value = eval(rule_string, {**eval_globals, **init_state})
postponed_evals[rule_variable] = rule_string
gillespy_rule = gillespy2.AssignmentRule(name=rule_name,
variable=rule_variable,
formula=rule_string)
gillespy_model.add_assignment_rule(gillespy_rule)
init_state[gillespy_rule.variable] = eval(gillespy_rule.formula, {
**init_state,
**eval_globals
})
if rule.isRate():
gillespy_rule = gillespy2.RateRule(name=rule_name,
variable=rule_variable,
formula=rule_string)
gillespy_model.add_rate_rule(gillespy_rule)
if rule.isAlgebraic():
t.append('algebraic')
if len(t) > 0:
t[0] = t[0].capitalize()
msg = ", ".join(t)
msg += " rule"
else:
msg = "Rule"
errors.append([
"{0} '{1}' found on line '{2}' with equation '{3}'. gillespy does not support SBML Algebraic Rules"
.format(msg, rule.getId(), rule.getLine(),
libsbml.formulaToString(rule.getMath())), -5
])
def generate_functions(self, model):
# global parameters
for f in model.getListOfFunctionDefinitions():
ast = f.getMath()
idx = ast.getNumChildren() - 1
ast_func = ast.getChild(idx) # most right child is the function
self.functions[f.getId()] = formulaToString(ast_func)
arglist = []
for i in range(ast.getNumChildren() - 1):
child = ast.getChild(i)
arglist.append(child.getName())
self.funcargs[f.getId()] = arglist
def parse_mathML_to_annonymous(mathML):
mathML = ET.tostring(mathML).decode().replace('ns0:', '')
ast = libsbml.readMathMLFromString(mathML)
result = libsbml.formulaToString(ast)
parsed_equation = lambda x: eval(result, {
"x": x,
"exp": math.exp,
"lt": lt,
"gt": gt
})
return parsed_equation, result
def test_EventAssignment_setMath(self):
math = libsbml.parseFormula("2 * k")
self.EA.setMath(math)
math1 = self.EA.getMath()
self.assert_( math1 != None )
formula = libsbml.formulaToString(math1)
self.assert_( formula != None )
self.assert_(( "2 * k" == formula ))
self.assert_( self.EA.getMath() != math )
self.assertEqual( True, self.EA.isSetMath() )
self.EA.setMath(self.EA.getMath())
math1 = self.EA.getMath()
self.assert_( math1 != None )
formula = libsbml.formulaToString(math1)
self.assert_( formula != None )
self.assert_(( "2 * k" == formula ))
self.assert_( self.EA.getMath() != math )
self.EA.setMath(None)
self.assertEqual( False, self.EA.isSetMath() )
if (self.EA.getMath() != None):
pass
_dummyList = [ math ]; _dummyList[:] = []; del _dummyList
pass
def generate_varspecs(self, model):
# Generate Rate equation for all variable Species (ex. dx/dt = v1 - v2 + v3).
for s in model.getListOfSpecies():
#if s.isSetBoundaryCondition() or s.isSetConstant:
# continue
root = None
for r in model.getListOfReactions():
if self.is_species_reactant_of(s, r):
root = self.add_ast_as_reactant(root, r)
if self.is_species_product_of(s, r):
root = self.add_ast_as_product(root, r)
if root is not None:
self.varspecs[s.getId()] = formulaToString(root)
def test_element_piecewise(self):
s = wrapMathML("<piecewise>" + " <piece>" +
" <apply> <minus/> <ci>x</ci> </apply>" +
" <apply> <lt/> <ci>x</ci> <cn>0</cn> </apply>" +
" </piece>" + " <piece>" + " <cn>0</cn>" +
" <apply> <eq/> <ci>x</ci> <cn>0</cn> </apply>" +
" </piece>" + " <piece>" + " <ci>x</ci>" +
" <apply> <gt/> <ci>x</ci> <cn>0</cn> </apply>" +
" </piece>" + "</piecewise>")
self.N = libsbml.readMathMLFromString(s)
self.assert_(self.N != None)
self.F = libsbml.formulaToString(self.N)
self.assert_(
("piecewise(-x, lt(x, 0), 0, eq(x, 0), x, gt(x, 0))" == self.F))
pass
def test_AlgebraicRule_createWithFormula(self):
ar = libsbml.AlgebraicRule(2, 4)
ar.setFormula("1 + 1")
self.assert_(ar.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE)
self.assert_(ar.getMetaId() == "")
math = ar.getMath()
self.assert_(math != None)
formula = libsbml.formulaToString(math)
self.assert_(formula != None)
self.assert_(("1 + 1" == formula))
self.assert_((formula == ar.getFormula()))
_dummyList = [ar]
_dummyList[:] = []
del _dummyList
pass
def test_AssignmentRule_createWithFormula(self):
ar = libsbml.AssignmentRule(2, 4)
ar.setVariable("s")
ar.setFormula("1 + 1")
self.assert_(ar.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE)
self.assert_(ar.getMetaId() == "")
self.assert_(("s" == ar.getVariable()))
math = ar.getMath()
self.assert_(math != None)
formula = libsbml.formulaToString(math)
self.assert_(formula != None)
self.assert_(("1 + 1" == formula))
self.assert_((formula == ar.getFormula()))
_dummyList = [ar]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_setMath1(self): math = libsbml.ASTNode(libsbml.AST_TIMES) a = libsbml.ASTNode() b = libsbml.ASTNode() a.setName( "a") b.setName( "b") math.addChild(a) math.addChild(b) i = self.kl.setMath(math) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, self.kl.isSetMath() ) math1 = self.kl.getMath() self.assert_( math1 != None ) formula = libsbml.formulaToString(math1) self.assert_( formula != None ) self.assert_(( "a * b" == formula )) _dummyList = [ math ]; _dummyList[:] = []; del _dummyList pass
def test_ASTNode_freeName(self):
node = libsbml.ASTNode()
i = 0
i = node.setName("a")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(("a" == libsbml.formulaToString(node)))
self.assert_(("a" == node.getName()))
i = node.freeName()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getName() == None)
i = node.freeName()
self.assert_(i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE)
self.assert_(node.getName() == None)
node.setType(libsbml.AST_UNKNOWN)
i = node.freeName()
self.assert_(i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE)
self.assert_(node.getName() == None)
_dummyList = [node]
_dummyList[:] = []
del _dummyList
pass
def test_FunctionDefinition_createWith(self):
math = libsbml.parseFormula("lambda(x, x^3)")
fd = libsbml.FunctionDefinition(2,4)
fd.setId( "pow3")
fd.setMath(math)
self.assert_( fd.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION )
self.assert_( fd.getMetaId() == "" )
self.assert_( fd.getNotes() == None )
self.assert_( fd.getAnnotation() == None )
self.assert_( fd.getName() == "" )
math1 = fd.getMath()
self.assert_( math1 != None )
formula = libsbml.formulaToString(math1)
self.assert_( formula != None )
self.assert_(( "lambda(x, x^3)" == formula ))
self.assert_( fd.getMath() != math )
self.assertEqual( True, fd.isSetMath() )
self.assert_(( "pow3" == fd.getId() ))
self.assertEqual( True, fd.isSetId() )
_dummyList = [ math ]; _dummyList[:] = []; del _dummyList
_dummyList = [ fd ]; _dummyList[:] = []; del _dummyList
pass
def ParseFunction(functionIndex, function):
newFunction = sbmltoodepy.dataclasses.FunctionData()
# outputFile.write("Function; " + str(functionIndex + 1) + "\n")
if function.isSetName():
newFunction.name = function.getName()
else:
newFunction.name = ''
# outputFile.write(function.getId() + ";" + functionName + "\n")
newFunction.Id = function.getId()
newFunction.mathString = libsbml.formulaToL3String(function.getMath())
numArguments = function.getNumArguments()
funcStringIter = re.finditer(",", newFunction.mathString)
newFunction.arguments = []
for i in range(numArguments):
match = next(funcStringIter)
newFunction.arguments.append(
libsbml.formulaToString(function.getArgument(i)))
newFunction.mathString = newFunction.mathString[match.end() + 1:-1]
# functionMath = formulaToL3String(function.getMath())
# numArguments = function.getNumArguments()
# funcStringIter = re.finditer(",", functionMath)
# argumentString = ""
# for i in range(numArguments):
# match = next(funcStringIter)
# argumentString += formulaToString(function.getArgument(i))
# if i != numArguments-1:
# argumentString += ";"
# argumentString += "\n"
# functionMath = functionMath[match.end()+1:-1]
# outputFile.write(argumentString)
# outputFile.write(functionMath + "\n")
return newFunction
def analyseModelStructure(self):
Parser.analyseModelStructure(self)
for i in range(0, len(self.listOfReactions)):
for n in range(0, self.numLocalParameters[i]):
self.parameterId.append(
self.listOfReactions[i].getKineticLaw().getParameter(
n).getId())
if ((len(self.writer.parsedModel.parameterId) - self.comp) <
10):
self.writer.parsedModel.parameterId.append(
"parameter0" + repr(len(self.parameterId) - self.comp))
else:
self.writer.parsedModel.parameterId.append(
"parameter" + repr(len(self.parameterId) - self.comp))
name = self.listOfReactions[i].getKineticLaw().getParameter(
n).getId()
new_name = 'parameter' + repr(
len(self.parameterId) - self.comp)
node = self.sbmlModel.getReaction(i).getKineticLaw().getMath()
new_node = self.rename(node, name, new_name)
self.writer.parsedModel.kineticLaw[i] = formulaToString(
new_node)
def initializeVariableReferenceList(self):
self.theVariableReferenceList = []
formulaString = self.theSBase.getFormula()
anASTNode = libsbml.parseFormula(formulaString)
self.__convertFormulaToExpression(anASTNode)
self.theExpression = libsbml.formulaToString(anASTNode)
# SBML_ASSIGNMENT_RULE or SBML_RATE_RULE
## if self.theSBase.getType() == 1 \
## or self.theSBase.getType() == 2:
if type( self.theSBase ) == libsbml.AssignmentRulePtr \
or type( self.theSBase ) == libsbml.RateRulePtr:
variable = self.theSBase.getVariable()
( fullIDString, sbaseType ) \
= self.rootobj.theSBMLIdManager.searchFullIDFromId( variable )
if sbaseType == libsbml.SBML_SPECIES \
or sbaseType == libsbml.SBML_PARAMETER:
pass
elif sbaseType == libsbml.SBML_COMPARTMENT:
fullID = ecell.ecssupport.createFullID(fullIDString)
systemPath = ecell.ecssupport.createSystemPathFromFullID(
fullID)
fullIDString = 'Variable:%s:SIZE' % (systemPath)
else:
raise SBMLConvertError, \
'SBase [%s] is not found' % ( variable )
self.__addVariableReference(fullIDString, 1)
def _get_sbml_ini_dict(sbml_model):
return {
ini.getId(): libsbml.formulaToString(ini.getMath())
for ini in sbml_model.getListOfInitialAssignments()
}
def __init__(self, rule: libsbml.AssignmentRule):
super().__init__(rule)
self.variable = rule.getVariable() # target variable
self.formula_string = libsbml.formulaToString(rule.math)
self.formula = compile(self.formula_string, "<string>", "eval")
def _get_sbml_allrules_dict(sbml_model):
return {
rule.getId(): libsbml.formulaToString(rule.getMath())
for rule in sbml_model.getListOfRules()
}
