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, 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, 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