def __init__(self, halfBinding):
        ParsedMzrToken.__init__(self, halfBinding)
        
        self.is_bound = False
        self.binding_token = 0

        self.parse()
Beispiel #2
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    def __init__(self, complexTxt):
        ParsedMzrToken.__init__(self, complexTxt)

        self.parsed_mols_in_complex = [] 
        self.parsed_bindings_in_complex = {}

        self.parse()
Beispiel #3
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    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()
Beispiel #5
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    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()
Beispiel #10
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    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()
Beispiel #11
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    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()
Beispiel #12
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    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()
Beispiel #13
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    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
Beispiel #15
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    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()
Beispiel #17
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    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()
Beispiel #18
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    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