def add_dependency_edges(g: Dict[str, Set], variable: str,
astnode: libsbml.ASTNode) -> None:
"""Add the dependency edges to the graph."""
# variable --depends_on--> v2
for k in range(astnode.getNumChildren()):
child: libsbml.ASTNode = astnode.getChild(k)
if child.getType() == libsbml.AST_NAME:
# add to dependency graph if id is not a defined parameter or state variable
sid = child.getName()
if sid not in filtered_ids:
g[variable].add(sid)
# recursive adding of children
add_dependency_edges(g, variable, child)
def _remove_lambda2(astnode: libsbml.ASTNode) -> libsbml.ASTNode:
"""Replace lambda function with function expression.
Removes the lambda and argument parts from lambda expressions;
lambda(x, y, x+y) -> x+y
:param formula: SBML formula string
:return: formula string
"""
if astnode.isLambda():
num_children = astnode.getNumChildren()
# get function with arguments
f = astnode.getChild(num_children - 1) # type: libsbml.ASTNode
return f.deepCopy()
return astnode
def _get_variables(astnode: libsbml.ASTNode, variables: Set[str] = None) -> Set[str]:
"""Get variables from ASTNode."""
if variables is None:
variables: Set[str] = set() # type: ignore
num_children = astnode.getNumChildren()
if num_children == 0:
if astnode.isName():
name = astnode.getName()
variables.add(name) # type: ignore
else:
for k in range(num_children):
child: libsbml.ASTNode = astnode.getChild(k)
_get_variables(child, variables=variables)
return variables # type: ignore
def evaluableMathML(astnode: libsbml.ASTNode, variables: Optional[Dict] = None) -> str:
"""Create evaluable python formula string from ASTNode."""
if variables is None:
variables = {}
# replace variables with provided values
for key, value in variables.items():
astnode.replaceArgument(key, libsbml.parseFormula(str(value)))
# parse formula
settings = libsbml.L3ParserSettings() # type: libsbml.L3ParserSettings
settings.setParseUnits(False)
settings.setParseCollapseMinus(True)
formula: str = libsbml.formulaToL3StringWithSettings(astnode, settings)
# <replacements>
formula = formula.replace("&&", "and")
formula = formula.replace("||", "or")
formula = formula.replace("^", "**")
return formula
def find_names_in_ast(ast: libsbml.ASTNode,
names: Optional[List[str]] = None) -> List[str]:
"""Find all names in given astnode.
Names are the variables in the formula.
:param ast:
:param names:
:return:
"""
if names is None:
names = []
# name for this node
if ast.getType() == libsbml.AST_NAME:
names.append(ast.getName())
for k in range(ast.getNumChildren()):
ast_child = ast.getChild(k)
find_names_in_ast(ast_child, names)
return names
def add_ast_as_product(self, ast, r):
if ast is None: # if there is no parent, return v1.
root = r.getKineticLaw().getMath().deepCopy()
else:
root = ASTNode(AST_PLUS)
root.addChild(ast)
root.addChild(r.getKineticLaw().getMath().deepCopy())
return root
def ast_info(ast: libsbml.ASTNode) -> None:
"""Print ASTNode information."""
print(ast)
print(ast.getType(), ast.getName())
def add_ast_as_reactant(self, ast, r):
if ast is None: # if there is no parent, return -1 * v1.
root = ASTNode(AST_TIMES)
l = ASTNode()
l.setValue(-1.0)
root.addChild(l)
root.addChild(r.getKineticLaw().getMath().deepCopy())
else:
root = ASTNode(AST_MINUS)
root.addChild(ast)
root.addChild(r.getKineticLaw().getMath().deepCopy())
return root