Пример #1
0
    def testGetRingGroupsFromComments(self):
        """
        Test that getRingGroupsFromComments method works for fused polycyclics.
        """
        # set-up RMG object
        rmg = RMG()

        # load kinetic database and forbidden structures
        rmg.database = RMGDatabase()
        path = os.path.join(settings['database.directory'])

        # forbidden structure loading
        rmg.database.loadThermo(os.path.join(path, 'thermo'))

        smi = 'C12C(C3CCC2C3)C4CCC1C4'#two norbornane rings fused together
        spc = Species().fromSMILES(smi)

        spc.generateThermoData(rmg.database)

        thermodb = rmg.database.thermo
        thermodb.getRingGroupsFromComments(spc.thermo)

        import rmgpy.data.rmg
        rmgpy.data.rmg.database = None
Пример #2
0
    def testGetRingGroupsFromComments(self):
        """
        Test that getRingGroupsFromComments method works for fused polycyclics.
        """
        # set-up RMG object
        rmg = RMG()

        # load kinetic database and forbidden structures
        rmg.database = RMGDatabase()
        path = os.path.join(settings['database.directory'])

        # forbidden structure loading
        rmg.database.loadThermo(os.path.join(path, 'thermo'))

        smi = 'C12C(C3CCC2C3)C4CCC1C4'  #two norbornane rings fused together
        spc = Species().fromSMILES(smi)

        spc.generateThermoData(rmg.database)

        thermodb = rmg.database.thermo
        thermodb.getRingGroupsFromComments(spc.thermo)

        import rmgpy.data.rmg
        rmgpy.data.rmg.database = None
    print 'Loading {0} library'.format(libraryName)
    kineticLibrary = database.kinetics.libraries[libraryName]
    
    reactionList = []    
    for index, entry in kineticLibrary.entries.iteritems():
        reaction = entry.item
        reaction.kinetics = entry.data
        reactionList.append(reaction)

    speciesList = []
    index = 0
    for spec in kineticLibrary.getSpecies().values():
        index = index + 1
        species = Species(molecule = spec.molecule)
        species.generateThermoData(database)
        species.index = index
        speciesList.append(species)

    for reaction in reactionList:
        for reactant in reaction.reactants:
            for spec in speciesList:
                if reactant.isIsomorphic(spec):
                    reactant.index = spec.index
                    spec.label = reactant.label
        for product in reaction.products:
            for spec in speciesList:
                if product.isIsomorphic(spec):
                    product.index = spec.index
                    spec.label = product.label
            
Пример #4
0
    reactionList = []
    for index, entry in kineticLibrary.entries.iteritems():
        reaction = entry.item
        reaction.kinetics = entry.data
        reactionList.append(reaction)

    speciesList = []
    index = 0
    speciesDict = kineticLibrary.getSpecies(
        os.path.join(settings['database.directory'], 'kinetics', 'libraries',
                     libraryName, 'dictionary.txt'))
    for spec in speciesDict.values():
        index = index + 1
        species = Species(molecule=spec.molecule)
        species.generateThermoData(database)
        species.index = index
        speciesList.append(species)

    for reaction in reactionList:
        for reactant in reaction.reactants:
            for spec in speciesList:
                if reactant.isIsomorphic(spec):
                    reactant.index = spec.index
                    spec.label = reactant.label
        for product in reaction.products:
            for spec in speciesList:
                if product.isIsomorphic(spec):
                    product.index = spec.index
                    spec.label = product.label