def parse( self, abbreviation, biocyc, officialName, equation, subSystem="", proteinClass="", geneAssociation="" ):
reaction = Reaction()
reaction = self.parseEquation( equation )
#(left,right,direction,conversionType,compartment) = self.parseEquation( equation )
reaction = self.parseEquation(equation)
reaction.setId(abbreviation)
reaction.setName(officialName)
reaction.setEquation(equation)
geneAssociation = geneAssociation.strip()
if geneAssociation != "":
#print "GeneAssociation: %s" % geneAssociation
gpr = self.gp.parse( geneAssociation )
#print "GPR: %s" % gpr
else:
gpr = None
reaction.setGeneReference(gpr)
xref = {'biocyc': biocyc, }
#reaction.initialize( abbreviation, officialName, equation, left, right, direction, conversionType, gpr, proteinClass, subSystem, xref )
return reaction
def parseEquation( self, equation, name = ''):
result = Reaction()
result.setId(name)
result.setName(name)
( newEquation, compartment ) = self.parseEquationPrefix( equation )
( newEquation, conversionType ) = self.parseConversionType( newEquation )
( leftString, rightString, direction ) = self.parseDirection( newEquation )
left = self.parseParticipants( leftString, compartment )
right = self.parseParticipants( rightString, compartment )
result.addReactants(left)
result.addProducts(right)
result.setConversionType(conversionType)
result.direction = direction
return result
