def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NEXT-STEP": # NOT USED FOR THE MOMENT...
self.next_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STEP-INTERACTIONS":
self.step_interactions_xref.append(current_child.attrs["rdf:resource"])
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CONTROLLER":
self.controller_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROLLED":
self.controlled_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROL-TYPE":
control_type = current_child.getValue()
if control_type == "ACTIVATION":
self.control_type = "activates"
elif control_type == "INHIBITION":
self.control_type = "inhibits"
elif control_type == "INHIBITION-ALLOSTERIC":
self.control_type = "allosteric_inhibition"
elif control_type == "INHIBITION-COMPETITIVE":
self.control_type = "competitive_inhibition"
elif control_type == "INHIBITION-IRREVERSIBLE":
self.control_type = "irreversible_inhibition"
elif control_type == "INHIBITION-NONCOMPETITIVE":
self.control_type = "non_competitive_inhibition"
elif control_type == "INHIBITION-OTHER":
self.control_type = "inhibits"
elif control_type == "INHIBITION-UNCOMPETITIVE":
self.control_type = "uncompetitive_inhibition"
elif control_type == "ACTIVATION-NONALLOSTERIC":
self.control_type = "nonallosteric_activation"
elif control_type == "ACTIVATION-ALLOSTERIC":
self.control_type = "allosteric_activation"
else:
raise ValueError("Control type %s not recognized" %
control_type)
BiopaxPhysicalInteraction.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CONTROLLER":
self.controller_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROLLED":
self.controlled_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:CONTROL-TYPE":
control_type = current_child.getValue()
if control_type == "ACTIVATION":
self.control_type = "activates"
elif control_type == "INHIBITION":
self.control_type = "inhibits"
elif control_type == "INHIBITION-ALLOSTERIC":
self.control_type = "allosteric_inhibition"
elif control_type == "INHIBITION-COMPETITIVE":
self.control_type = "competitive_inhibition"
elif control_type == "INHIBITION-IRREVERSIBLE":
self.control_type = "irreversible_inhibition"
elif control_type == "INHIBITION-NONCOMPETITIVE":
self.control_type = "non_competitive_inhibition"
elif control_type == "INHIBITION-OTHER":
self.control_type = "inhibits"
elif control_type == "INHIBITION-UNCOMPETITIVE":
self.control_type = "uncompetitive_inhibition"
elif control_type == "ACTIVATION-NONALLOSTERIC":
self.control_type = "nonallosteric_activation"
elif control_type == "ACTIVATION-ALLOSTERIC":
self.control_type = "allosteric_activation"
else:
raise ValueError("Control type %s not recognized" %control_type)
BiopaxPhysicalInteraction.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NEXT-STEP": # NOT USED FOR THE MOMENT...
self.next_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STEP-INTERACTIONS":
self.step_interactions_xref.append(current_child.attrs["rdf:resource"])
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:PATHWAY-COMPONENTS":
#print "Adding component ",current_child.attrs["rdf:resource"]
self.pathway_components.append(
current_child.attrs["rdf:resource"])
BiopaxEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:TAXON-XREF":
self.tax_ref = current_child.attrs["rdf:resource"]
else:
print current_child.name, " not recognized"
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:TAXON-XREF":
self.tax_ref = current_child.attrs["rdf:resource"]
else:
print current_child.name," not recognized"
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:LEFT":
self.left_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:RIGHT":
self.right_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:EC-NUMBER":
self.ec_number.append(current_child.getValue())
BiopaxEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COFACTOR":
self.cofactor = current_child.attrs["rdf:resource"]
# NOT IMPLEMENTED YET!!!
elif current_child.name == "bp:DIRECTION":
self.direction = current_child.getValue()
# NOT IMPLEMENTED YET!!!
BiopaxControl.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:LEFT":
self.left_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:RIGHT":
self.right_xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:EC-NUMBER":
self.ec_number.append(current_child.getValue())
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COFACTOR":
self.cofactor = current_child.attrs["rdf:resource"]
# NOT IMPLEMENTED YET!!!
elif current_child.name == "bp:DIRECTION":
self.direction = current_child.getValue()
# NOT IMPLEMENTED YET!!!
BiopaxControl.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CELLULAR-LOCATION":
self.cellular_location_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:PHYSICAL-ENTITY":
self.physical_entity_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STOICHIOMETRIC-COEFFICIENT":
self.stoichiometric_coefficient = current_child.getValue()
elif current_child.name == "bp:SEQUENCE-FEATURE-LIST":
# TO CHECK WHAT TO DO
pass
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:CELLULAR-LOCATION":
self.cellular_location_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:PHYSICAL-ENTITY":
self.physical_entity_xref = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:STOICHIOMETRIC-COEFFICIENT":
self.stoichiometric_coefficient = current_child.getValue()
elif current_child.name == "bp:SEQUENCE-FEATURE-LIST":
# TO CHECK WHAT TO DO
pass
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
"""
"""
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:ORGANISM":
self.organism = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:XREF":
self.xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:SYNONYMS":
self.synonyms.append(current_child.getValue())
elif current_child.name == "bp:SHORT_NAME":
self.short_name = current_child.getValue()
elif current_child.name == "bp:COMMENT":
self.comments.append(current_child.getValue())
def set_attributes(self, XMLNode):
"""
"""
for current_child in XMLNode.getChilds():
if current_child.name == "bp:NAME":
self.name = current_child.getValue()
elif current_child.name == "bp:ORGANISM":
self.organism = current_child.attrs["rdf:resource"]
elif current_child.name == "bp:XREF":
self.xrefs.append(current_child.attrs["rdf:resource"])
elif current_child.name == "bp:SYNONYMS":
self.synonyms.append(current_child.getValue())
elif current_child.name == "bp:SHORT_NAME":
self.short_name = current_child.getValue()
elif current_child.name == "bp:COMMENT":
self.comments.append(current_child.getValue())
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:TERM":
self.term = current_child.getValue()
elif current_child.name == "bp:XREF":
self.xref = current_child.attrs["rdf:resource"]
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:DB":
self.db = current_child.getValue()
elif current_child.name == "bp:ID":
self.id = current_child.getValue()
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COMPONENTS":
self.components.append(current_child.attrs["rdf:resource"])
BiopaxPhysicalEntity.set_attributes(self, XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:PATHWAY-COMPONENTS":
#print "Adding component ",current_child.attrs["rdf:resource"]
self.pathway_components.append(current_child.attrs["rdf:resource"])
BiopaxEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:COMPONENTS":
self.components.append( current_child.attrs["rdf:resource"] )
BiopaxPhysicalEntity.set_attributes(self,XMLNode)
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:DB":
self.db = current_child.getValue()
elif current_child.name == "bp:ID":
self.id = current_child.getValue()
def set_attributes(self, XMLNode):
for current_child in XMLNode.getChilds():
if current_child.name == "bp:TERM":
self.term = current_child.getValue()
elif current_child.name == "bp:XREF":
self.xref = current_child.attrs["rdf:resource"]
