def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
def performSampMoleComparison(adjlist, answer_smiles):
"""
Creates a sample molecule from the adjlist and returns if it is isomorphic to a molecule created from
the inputted smiles
"""
group = Group().fromAdjacencyList(adjlist)
result = group.makeSampleMolecule()
return (result.isIsomorphic(Molecule().fromSMILES(answer_smiles)))
########################################################################################################################
#tests adding implicit atoms
adjlist = """
1 *1 Cd u0
"""
answer_smiles = 'C=C'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2=naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a positively charged species
adjlist = """
1 *1 N5s u0
"""
answer_smiles = '[NH4+]'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test the creation of a negatively charged species
#commented out until new nitrogen atom types added in
# adjlist = """
# 1 *1 N2s u0
# """
# answer_smiles = '[NH2-]'
# self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
#test creation of charged species when some single bonds present
adjlist = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
answer_smiles = '[NH3+][CH2]'
self.assertTrue(performSampMoleComparison(adjlist, answer_smiles))
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
# result = self.group.makeSampleMolecule()
# print result.multiplicity
# self.assertTrue(result.isIsomorphic(Molecule().fromSMILES('OCC')))
#tests adding implicit atoms
adjlist1 = """
1 *1 Cd u0
"""
group1 = Group().fromAdjacencyList(adjlist1)
result1 = group1.makeSampleMolecule()
self.assertTrue(result1.isIsomorphic(Molecule().fromSMILES('C=C')))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2 = naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a charged species
adjlist3 = """
1 *1 N5s u0
"""
group3 = Group().fromAdjacencyList(adjlist3)
result3 = group3.makeSampleMolecule()
self.assertTrue(result3.isIsomorphic(Molecule().fromSMILES('[NH4+]')))
#test creation of charged species when some single bonds present
adjlist4 = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
group4 = Group().fromAdjacencyList(adjlist4)
result4 = group4.makeSampleMolecule()
self.assertTrue(
result4.isIsomorphic(Molecule().fromSMILES('[NH3+][CH2]')))
def testMakeSampleMolecule(self):
"""
Test the Group.makeSampleMolecule method
"""
# result = self.group.makeSampleMolecule()
# print result.multiplicity
# self.assertTrue(result.isIsomorphic(Molecule().fromSMILES('OCC')))
#tests adding implicit atoms
adjlist1 = """
1 *1 Cd u0
"""
group1 = Group().fromAdjacencyList(adjlist1)
result1 = group1.makeSampleMolecule()
self.assertTrue(result1.isIsomorphic(Molecule().fromSMILES('C=C')))
#test creating implicit benzene atoms
adjlist2 = """
1 *1 Cbf u0 {2,B}
2 Cbf u0 {1,B}
"""
group2 = Group().fromAdjacencyList(adjlist2)
result2 = group2.makeSampleMolecule()
naphthaleneMolecule = Molecule().fromSMILES('C1=CC=C2C=CC=CC2=C1')
resonanceList2=naphthaleneMolecule.generateResonanceIsomers()
self.assertTrue(any([result2.isIsomorphic(x) for x in resonanceList2]))
#test the creation of a charged species
adjlist3 = """
1 *1 N5s u0
"""
group3 = Group().fromAdjacencyList(adjlist3)
result3 = group3.makeSampleMolecule()
self.assertTrue(result3.isIsomorphic(Molecule().fromSMILES('[NH4+]')))
#test creation of charged species when some single bonds present
adjlist4 = """
1 *2 [N5s,N5d] u0 {2,S} {3,S}
2 *3 R!H u1 {1,S}
3 *4 H u0 {1,S}
"""
group4 = Group().fromAdjacencyList(adjlist4)
result4 = group4.makeSampleMolecule()
self.assertTrue(result4.isIsomorphic(Molecule().fromSMILES('[NH3+][CH2]')))
"""
Used to compare thermo data between high level calcs in a paper and those generated by group
additivity in RMG-Py
"""
from rmgpy.data.rmg import RMGDatabase
from rmgpy import settings
from rmgpy.molecule import Molecule
from rmgpy.species import Species
###################################
rmg_database = RMGDatabase()
rmg_database.load(settings['database.directory'],
kineticsFamilies='none',
reactionLibraries=[])
with open('/Users/belinda/Code/RMG-Py/SiH_rad_thermo_Katzer.txt',
'r') as thermo_data:
rad_species = thermo_data.read().split('\n\n')
for entry in rad_species:
label = entry.split('\n')[0]
adj_list = ""
for line in entry.split('\n')[1:]:
if 'u' in line: adj_list += line + '\n'
else: break
# print adj_list
H298 = entry.split('\n')[-1]
mol = Molecule().fromAdjacencyList(adj_list)
thermoData = rmg_database.thermo.getThermoDataFromGroups(
Species(molecule=mol.generateResonanceIsomers()))
print label + '\t' + H298 + '\t' + str(
thermoData.H298.value_si / 1000) + '\t' + thermoData.comment
