def _parse_rules(self, model, comp, node):
"""
Parses the rules (equations) in this model
"""
parent = node
formulas = {}
# Create variables with assignment rules (all except derivatives)
node = dom_child(parent, 'assignmentRule')
while node:
var = self._convert_name(str(node.getAttribute('variable')).strip())
if var in comp:
self.log('Parsing assignment rule for <' + str(var) + '>.')
var = comp[var]
var.set_rhs(parse_mathml_rhs(
dom_child(node, 'math'), comp, self))
else:
raise SBMLError('Assignment found for unknown parameter: "'
+ var + '".')
node = dom_next(node, 'assignmentRule')
# Create variables with rate rules (states)
node = dom_child(parent, 'rateRule')
while node:
var = self._convert_name(str(node.getAttribute('variable')).strip())
if var in comp:
self.log('Parsing rate rule for <' + var + '>.')
var = comp[var]
ini = var.rhs()
ini = ini.eval() if ini else 0
var.promote(ini)
var.set_rhs(parse_mathml_rhs(
dom_child(node, 'math'), comp, self))
else:
raise SBMLError('Derivative found for unknown parameter: <'
+ var + '>.')
node = dom_next(node, 'rateRule')
def _parse_initial_assignments(self, model, comp, refs, node):
"""
Parses any initial values specified outside of the rules section.
"""
node = dom_child(node, 'initialAssignment')
while node:
var = str(node.getAttribute('symbol')).strip()
var = self._convert_name(var)
if var in comp:
self.logger().log('Parsing initial assignment for "' + var +
'".')
var = comp[var]
expr = parse_mathml_rhs(dom_child(node, 'math'), refs,
self.logger())
if var.is_state():
# Initial value
var.set_state_value(expr)
else:
# Change of value
var.set_rhs(expr)
else: # pragma: no cover
raise SBMLError( # pragma: no cover
'Initial assignment found for unknown parameter <' + var +
'>.')
node = dom_next(node, 'initialAssignment')
def mathml(node, rfs):
return parse_mathml_rhs(node,
var_table=rfs,
logger=self,
number_post_processor=npp,
derivative_post_processor=dpp)