def __init__(self, halfBinding):
ParsedMzrToken.__init__(self, halfBinding)
self.is_bound = False
self.binding_token = 0
self.parse()
def __init__(self, complexTxt):
ParsedMzrToken.__init__(self, complexTxt)
self.parsed_mols_in_complex = []
self.parsed_bindings_in_complex = {}
self.parse()
def __init__(self, halfBinding):
ParsedMzrToken.__init__(self, halfBinding)
self.is_bound = False
self.binding_token = 0
self.parse()
def __init__(self, complexTxt):
ParsedMzrToken.__init__(self, complexTxt)
self.parsed_mols_in_complex = []
self.parsed_bindings_in_complex = {}
self.parse()
def __init__(self, bindingDefinition):
ParsedMzrToken.__init__(self, bindingDefinition)
self.binding_site_name = ""
self.has_specification = False
self.binding_site_specification = 0
self.parse()
def __init__(self, bindingDefinition ):
ParsedMzrToken.__init__(self, bindingDefinition)
self.binding_site_name = ""
self.has_specification = False
self.binding_site_specification = 0
self.parse()
def __init__(self, bindingShapeSpecification):
ParsedMzrToken.__init__(self, bindingShapeSpecification)
self.the_list = []
self.the_transformation = 0
self.is_transformation = False
self.is_shape_list = False
self.parse()
def __init__(self, bindingSiteSpec):
ParsedMzrToken.__init__(self, bindingSiteSpec)
self.has_half_binding = False
self.half_binding = 0
self.has_shape_specification = False
self.shape_specification = 0
self.parse()
def __init__(self, modSiteSpecToken):
ParsedMzrToken.__init__(self, modSiteSpecToken)
self.is_transformation = False
self.transformation_entry = ""
self.is_list = False
self.mod_value_list = []
self.parse()
def __init__(self, bindingSiteSpec):
ParsedMzrToken.__init__(self, bindingSiteSpec)
self.has_half_binding = False
self.half_binding = 0
self.has_shape_specification = False
self.shape_specification = 0
self.parse()
def __init__(self, bindingShapeSpecification):
ParsedMzrToken.__init__(self, bindingShapeSpecification)
self.the_list = []
self.the_transformation = 0
self.is_transformation = False
self.is_shape_list = False
self.parse()
def __init__(self, lineTxt):
ParsedMzrToken.__init__(self, lineTxt)
# A MzrRuleFileLine is a list of tokens (each of which can be a molDefinition,
#
self.tokens = []
# These are either ParsedReactions, ParsedComplexes, or (name = assignment) keys
self.parsed_content = []
self.__parse()
def __init__(self, lineTxt):
ParsedMzrToken.__init__(self, lineTxt)
# A MzrRuleFileLine is a list of tokens (each of which can be a molDefinition,
#
self.tokens = []
# These are either ParsedReactions, ParsedComplexes, or (name = assignment) keys
self.parsed_content = []
self.__parse()
def __init__(self, modificationSiteToken):
ParsedMzrToken.__init__(self, modificationSiteToken)
self.modification_site_name = ""
self.has_modification_site_spec = False
self.parsed_mod_site_specification = 0
self.parse()
return
def __init__(self, assignmentLine):
ParsedMzrToken.__init__(self, assignmentLine)
self.lhs = 0
self.has_value = False
self.has_expression = False
self.rhs_value = 0
self.rhs_expression = 0
self.parse()
def __init__(self, assignmentLine):
ParsedMzrToken.__init__(self, assignmentLine)
self.lhs = 0
self.has_value = False
self.has_expression = False
self.rhs_value = 0
self.rhs_expression = 0
self.parse()
def __init__(self, molDefinition ):
ParsedMzrToken.__init__(self, molDefinition )
# I want to be strict about forbidding bindings
# Parsing of complexes must factor them out first
self.is_small_mol = False
self.has_small_mol_binding = False
self.small_mol_binding = 0
self.mol_name = ""
self.the_parsed_bindings = []
self.the_parsed_modification_sites = []
self.parse()
def __init__(self, molDefinition):
ParsedMzrToken.__init__(self, molDefinition)
# I want to be strict about forbidding bindings
# Parsing of complexes must factor them out first
self.is_small_mol = False
self.has_small_mol_binding = False
self.small_mol_binding = 0
self.mol_name = ""
self.the_parsed_bindings = []
self.the_parsed_modification_sites = []
self.parse()
def ModSiteSpecificationPassesSanityCheck(ParsedMzrToken):
if ParsedMzrToken[0] == "{" and ParsedMzrToken[-1] == "}" and ParsedMzrToken.count("{") == 1 and ParsedMzrToken.count("}"):
return True
else:
return False