def testCarbeneIdentifiers(self):
"""
Test that singlet carbene molecules, bearing an electron pair rather than unpaired electrons
are correctly converted into rdkit molecules and identifiers.
"""
ch2_t = '''
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
'''
mol = Molecule().fromAdjacencyList(ch2_t)
self.assertEqual( mol.toAugmentedInChI(), 'InChI=1S/CH2/h1H2/mult3')
self.assertEqual( mol.toSMILES(), '[CH2]')
ch2_s = '''
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
'''
mol = Molecule().fromAdjacencyList(ch2_s)
self.assertEqual( mol.toAugmentedInChI(), 'InChI=1S/CH2/h1H2/mult1')
self.assertEqual( mol.toSMILES(), '[CH2]')
def testCarbeneIdentifiers(self):
"""
Test that singlet carbene molecules, bearing an electron pair rather than unpaired electrons
are correctly converted into rdkit molecules and identifiers.
"""
ch2_t = '''
multiplicity 3
1 C u2 p0 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
'''
mol = Molecule().fromAdjacencyList(ch2_t)
self.assertEqual(mol.toAugmentedInChI(), 'InChI=1S/CH2/h1H2/mult3')
self.assertEqual(mol.toSMILES(), '[CH2]')
ch2_s = '''
multiplicity 1
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
'''
mol = Molecule().fromAdjacencyList(ch2_s)
self.assertEqual(mol.toAugmentedInChI(), 'InChI=1S/CH2/h1H2/mult1')
self.assertEqual(mol.toSMILES(), '[CH2]')
def testHelium(self):
"""
adjlist: Test that the adjlist reading and writing works with Helium.
"""
smiles = '[He]'
inchi = 'InChI=1S/He'
adjlist = '1 He u0 p1 c0'
adjlist_old = '1 He 0'
adjlist_intermediate = '1 He 0 1'
mol_smiles = Molecule().fromSMILES(smiles)
mol_inchi = Molecule().fromInChI(inchi)
mol = Molecule().fromAdjacencyList(adjlist)
mol_old = Molecule().fromAdjacencyList(adjlist_old)
mol_intermediate = Molecule().fromAdjacencyList(adjlist_intermediate)
# Isomorphic check
self.assertTrue(mol_smiles.isIsomorphic(mol))
self.assertTrue(mol_smiles.isIsomorphic(mol_inchi))
self.assertTrue(mol_smiles.isIsomorphic(mol_old))
self.assertTrue(mol_smiles.isIsomorphic(mol_intermediate))
# Adjlist check
self.assertEqual(mol_smiles.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_inchi.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_old.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_intermediate.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toSMILES(), smiles)
self.assertEqual(mol.toInChI(), 'InChI=1S/He')
def testHelium(self):
"""
adjlist: Test that the adjlist reading and writing works with Helium.
"""
smiles = '[He]'
inchi = 'InChI=1S/He'
adjlist = '1 He u0 p1 c0'
adjlist_old = '1 He 0'
adjlist_intermediate = '1 He 0 1'
mol_smiles = Molecule().fromSMILES(smiles)
mol_inchi = Molecule().fromInChI(inchi)
mol = Molecule().fromAdjacencyList(adjlist)
mol_old = Molecule().fromAdjacencyList(adjlist_old)
mol_intermediate = Molecule().fromAdjacencyList(adjlist_intermediate)
# Isomorphic check
self.assertTrue(mol_smiles.isIsomorphic(mol))
self.assertTrue(mol_smiles.isIsomorphic(mol_inchi))
self.assertTrue(mol_smiles.isIsomorphic(mol_old))
self.assertTrue(mol_smiles.isIsomorphic(mol_intermediate))
# Adjlist check
self.assertEqual(mol_smiles.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_inchi.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_old.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol_intermediate.toAdjacencyList().strip(), adjlist)
self.assertEqual(mol.toSMILES(),smiles)
self.assertEqual(mol.toInChI(),'InChI=1S/He')
def toSMILES(self):
cutting_label_list = []
for vertex in self.vertices:
if isinstance(vertex, CuttingLabel):
cutting_label_list.append(vertex.symbol)
SMILES_before = self.copy(deep=True)
final_vertices = []
for ind, atom in enumerate(SMILES_before.atoms):
element_symbol = atom.symbol
if isinstance(atom, CuttingLabel):
substi_name = 'Si'
substi = Atom(element=substi_name)
substi.label = element_symbol
for bondedAtom, bond in atom.edges.iteritems():
new_bond = Bond(bondedAtom, substi, order=bond.order)
bondedAtom.edges[substi] = new_bond
del bondedAtom.edges[atom]
substi.edges[bondedAtom] = new_bond
substi.radicalElectrons = 3
final_vertices.append(substi)
else:
final_vertices.append(atom)
SMILES_before.vertices = final_vertices
mol_repr = Molecule()
mol_repr.atoms = SMILES_before.vertices
SMILES_after = mol_repr.toSMILES()
import re
smiles = re.sub('\[Si\]', '', SMILES_after)
return smiles
def test_restart(self):
"""
Test restarting ARC through the ARC class in main.py via the input_dict argument of the API
Rather than through ARC.py. Check that all files are in place and tst file content.
"""
restart_path = os.path.join(arc_path, 'arc', 'testing', 'restart(H,H2O2,N2H3,CH3CO2).yml')
project = 'arc_project_for_testing_delete_after_usage2'
project_directory = os.path.join(arc_path, 'Projects', project)
arc1 = ARC(project=project, ess_settings=dict(),
input_dict=restart_path, project_directory=project_directory)
arc1.execute()
with open(os.path.join(project_directory, 'output', 'thermo.info'), 'r') as f:
thermo_sft_ccsdtf12_bac = False
for line in f.readlines():
if 'thermo_DFT_CCSDTF12_BAC' in line:
thermo_sft_ccsdtf12_bac = True
break
self.assertTrue(thermo_sft_ccsdtf12_bac)
with open(os.path.join(project_directory, 'arc_project_for_testing_delete_after_usage2.info'), 'r') as f:
sts, n2h3, oet, lot, ap = False, False, False, False, False
for line in f.readlines():
if 'Considered the following species and TSs:' in line:
sts = True
elif 'Species N2H3' in line:
n2h3 = True
elif 'Overall time since project initiation:' in line:
oet = True
elif 'Levels of theory used:' in line:
lot = True
elif 'ARC project arc_project_for_testing_delete_after_usage2' in line:
ap = True
self.assertTrue(sts)
self.assertTrue(n2h3)
self.assertTrue(oet)
self.assertTrue(lot)
self.assertTrue(ap)
with open(os.path.join(project_directory, 'arc.log'), 'r') as f:
aei, ver, git, spc, rtm, ldb, therm, src, ter = False, False, False, False, False, False, False, False, False
for line in f.readlines():
if 'ARC execution initiated on' in line:
aei = True
elif '# Version:' in line:
ver = True
elif 'The current git HEAD for ARC is:' in line:
git = True
elif 'Considering species: CH3CO2_rad' in line:
spc = True
elif 'All jobs for species N2H3 successfully converged. Run time: 1:16:03' in line:
rtm = True
elif 'Loading the RMG database...' in line:
ldb = True
elif 'Thermodynamics for H2O2:' in line:
therm = True
elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line:
src = True
elif 'ARC execution terminated on' in line:
ter = True
self.assertTrue(aei)
self.assertTrue(ver)
self.assertTrue(git)
self.assertTrue(spc)
self.assertTrue(rtm)
self.assertTrue(ldb)
self.assertTrue(therm)
self.assertTrue(src)
self.assertTrue(ter)
self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'thermo_parity_plots.pdf')))
with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'species_dictionary.txt'), 'r') as f:
lines = f.readlines()
adj_list = str(''.join([line for line in lines if (line and 'H2O2' not in line)]))
mol1 = Molecule().fromAdjacencyList(adj_list)
self.assertEqual(mol1.toSMILES(), str('OO'))
thermo_library_path = os.path.join(project_directory, 'output', 'RMG libraries', 'thermo',
'arc_project_for_testing_delete_after_usage2.py')
new_thermo_library_path = os.path.join(settings['database.directory'], 'thermo', 'libraries',
'arc_project_for_testing_delete_after_usage2.py')
# copy the generated library to RMG-database
shutil.copyfile(thermo_library_path, new_thermo_library_path)
db = RMGDatabase()
db.load(
path=settings['database.directory'],
thermoLibraries=[str('arc_project_for_testing_delete_after_usage2')],
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
kineticsFamilies='none',
kineticsDepositories=[],
statmechLibraries=None,
depository=False,
solvation=False,
testing=True,
)
spc2 = Species().fromSMILES(str('CC([O])=O'))
spc2.generate_resonance_structures()
spc2.thermo = db.thermo.getThermoData(spc2)
self.assertAlmostEqual(spc2.getEnthalpy(298), -178003.44650359568, 1)
self.assertAlmostEqual(spc2.getEntropy(298), 283.5983103176096, 1)
self.assertAlmostEqual(spc2.getHeatCapacity(1000), 118.99753808225603, 1)
self.assertTrue('arc_project_for_testing_delete_after_usage2' in spc2.thermo.comment)
# delete the generated library from RMG-database
os.remove(new_thermo_library_path)
def test_aromatics(self):
"""Test that different aromatics representations returns different SMILES."""
mol1 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,D} {5,S} {11,S}
3 C u0 p0 c0 {2,D} {4,S} {12,S}
4 C u0 p0 c0 {3,S} {6,D} {13,S}
5 C u0 p0 c0 {2,S} {7,D} {10,S}
6 C u0 p0 c0 {1,S} {4,D} {7,S}
7 C u0 p0 c0 {5,D} {6,S} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol2 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,S} {5,D} {11,S}
3 C u0 p0 c0 {2,S} {4,D} {12,S}
4 C u0 p0 c0 {3,D} {6,S} {13,S}
5 C u0 p0 c0 {2,D} {7,S} {10,S}
6 C u0 p0 c0 {1,S} {4,S} {7,D}
7 C u0 p0 c0 {5,S} {6,D} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol3 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,B} {5,B} {11,S}
3 C u0 p0 c0 {2,B} {4,B} {12,S}
4 C u0 p0 c0 {3,B} {6,B} {13,S}
5 C u0 p0 c0 {2,B} {7,B} {10,S}
6 C u0 p0 c0 {1,S} {4,B} {7,B}
7 C u0 p0 c0 {5,B} {6,B} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
smiles1 = mol1.toSMILES()
smiles2 = mol2.toSMILES()
smiles3 = mol3.toSMILES()
self.assertNotEqual(smiles1, smiles2)
self.assertNotEqual(smiles2, smiles3)
self.assertNotEqual(smiles1, smiles3)
def test_empty_molecule(self):
"""Test that we can safely return a blank identifier for an empty molecule."""
mol = Molecule()
self.assertEqual(mol.toSMILES(), '')
self.assertEqual(mol.toInChI(), '')
def compare(self, adjlist, smiles):
mol = Molecule().fromAdjacencyList(adjlist)
self.assertEquals(smiles, mol.toSMILES())
def test_aromatics(self):
"""Test that different aromatics representations returns different SMILES."""
mol1 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,D} {5,S} {11,S}
3 C u0 p0 c0 {2,D} {4,S} {12,S}
4 C u0 p0 c0 {3,S} {6,D} {13,S}
5 C u0 p0 c0 {2,S} {7,D} {10,S}
6 C u0 p0 c0 {1,S} {4,D} {7,S}
7 C u0 p0 c0 {5,D} {6,S} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol2 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,S} {5,D} {11,S}
3 C u0 p0 c0 {2,S} {4,D} {12,S}
4 C u0 p0 c0 {3,D} {6,S} {13,S}
5 C u0 p0 c0 {2,D} {7,S} {10,S}
6 C u0 p0 c0 {1,S} {4,S} {7,D}
7 C u0 p0 c0 {5,S} {6,D} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
mol3 = Molecule().fromAdjacencyList("""
1 O u0 p2 c0 {6,S} {9,S}
2 C u0 p0 c0 {3,B} {5,B} {11,S}
3 C u0 p0 c0 {2,B} {4,B} {12,S}
4 C u0 p0 c0 {3,B} {6,B} {13,S}
5 C u0 p0 c0 {2,B} {7,B} {10,S}
6 C u0 p0 c0 {1,S} {4,B} {7,B}
7 C u0 p0 c0 {5,B} {6,B} {8,S}
8 C u0 p0 c0 {7,S} {14,S} {15,S} {16,S}
9 H u0 p0 c0 {1,S}
10 H u0 p0 c0 {5,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {4,S}
14 H u0 p0 c0 {8,S}
15 H u0 p0 c0 {8,S}
16 H u0 p0 c0 {8,S}
""")
smiles1 = mol1.toSMILES()
smiles2 = mol2.toSMILES()
smiles3 = mol3.toSMILES()
self.assertNotEqual(smiles1, smiles2)
self.assertNotEqual(smiles2, smiles3)
self.assertNotEqual(smiles1, smiles3)
def test_empty_molecule(self):
"""Test that we can safely return a blank identifier for an empty molecule."""
mol = Molecule()
self.assertEqual(mol.toSMILES(), '')
self.assertEqual(mol.toInChI(), '')
def compare(self, adjlist, smiles):
mol = Molecule().fromAdjacencyList(adjlist)
self.assertEquals(smiles, mol.toSMILES())