def test_heavy_constraint(self):
"""
Test that we can constrain the max number of heavy atoms.
"""
mol1 = Molecule(smiles='CCO')
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule(smiles='CCN=O')
self.assertTrue(fails_species_constraints(mol2))
def test_radical_constraint(self):
"""
Test that we can constrain the max number of radical electrons.
"""
mol1 = Molecule(smiles='[CH2][CH2]')
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule(smiles='[CH2][CH][CH2]')
self.assertTrue(fails_species_constraints(mol2))
def test_sulfur_constraint(self):
"""
Test that we can constrain the max number of sulfur atoms.
"""
mol1 = Molecule(smiles='CS')
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule(smiles='SCS')
self.assertTrue(fails_species_constraints(mol2))
def test_silicon_constraint(self):
"""
Test that we can constrain the max number of silicon atoms.
"""
mol1 = Molecule(smiles='[SiH4]')
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule(smiles='[SiH3][SiH3]')
self.assertTrue(fails_species_constraints(mol2))
def test_nitrogen_constraint(self):
"""
Test that we can constrain the max number of nitrogen atoms.
"""
mol1 = Molecule(smiles='CN')
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule(smiles='NCN')
self.assertTrue(fails_species_constraints(mol2))
def test_explicitly_allowed_molecules(self):
"""
Test that we can explicitly allow molecules in species constraints.
"""
mol = Molecule(smiles='CCCC')
self.assertTrue(fails_species_constraints(mol))
self.rmg.species_constraints['explicitlyAllowedMolecules'] = [Molecule(smiles='CCCC')]
self.assertFalse(fails_species_constraints(mol))
def test_surface_site_constraint(self):
"""
Test that we can constrain the max number of surface sites.
"""
mol_1site = Molecule().from_adjacency_list("""
1 O u0 p2 c0 {2,D}
2 C u0 p0 c0 {1,D} {3,D}
3 X u0 p0 c0 {2,D}
""")
mol_2site = Molecule().from_adjacency_list("""
1 C u0 p0 c0 {2,D} {3,D}
2 C u0 p0 c0 {1,D} {4,D}
3 X u0 p0 c0 {1,D}
4 X u0 p0 c0 {2,D}
""")
mol_3site_vdW = Molecule().from_adjacency_list("""
1 C u0 p0 c0 {2,D} {3,D}
2 C u0 p0 c0 {1,D} {4,D}
3 X u0 p0 c0 {1,D}
4 X u0 p0 c0 {2,D}
6 X u0 p0 c0
""")
mol_3site = Molecule().from_adjacency_list("""
1 C u0 p0 c0 {4,S} {2,D} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {5,S} {6,S} {9,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {3,S}
6 H u0 p0 c0 {3,S}
7 X u0 p0 c0 {1,S}
8 X u0 p0 c0 {2,S}
9 X u0 p0 c0 {3,S}
""")
max_carbon = self.rmg.species_constraints['maximumCarbonAtoms']
max_heavy_atoms = self.rmg.species_constraints['maximumHeavyAtoms']
self.rmg.species_constraints['maximumCarbonAtoms'] = 3
self.rmg.species_constraints['maximumHeavyAtoms'] = 6
self.assertFalse(fails_species_constraints(mol_1site))
self.assertFalse(fails_species_constraints(mol_2site))
self.assertTrue(fails_species_constraints(mol_3site_vdW))
self.assertTrue(fails_species_constraints(mol_3site))
self.rmg.species_constraints['maximumCarbonAtoms'] = max_carbon
self.rmg.species_constraints['maximumHeavyAtoms'] = max_heavy_atoms
def test_species_input(self):
"""
Test that fails_species_constraints can handle a Species object.
"""
spc = Species().from_smiles('C')
self.assertFalse(fails_species_constraints(spc))
def test_carbene_constraint(self):
"""
Test that we can constrain the max number of singlet carbenes.
"""
mol1 = Molecule().from_adjacency_list("""
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule().from_adjacency_list("""
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 C u0 p1 c0 {1,S} {4,S}
4 H u0 p0 c0 {3,S}
""")
self.assertTrue(fails_species_constraints(mol2))
def test_carbene_radical_constraint(self):
"""
Test that we can constrain the max number of radical electrons with a carbene.
"""
mol1 = Molecule().from_adjacency_list("""
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
""")
self.assertFalse(fails_species_constraints(mol1))
mol2 = Molecule().from_adjacency_list("""
1 C u0 p1 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 C u1 p0 c0 {1,S} {4,S} {5,S}
4 H u0 p0 c0 {3,S}
5 H u0 p0 c0 {3,S}
""")
self.assertTrue(fails_species_constraints(mol2))
def test_constraints_not_loaded(self, mock_logging):
"""
Test what happens when constraints are not loaded.
"""
# Reset module level rmg variable in rmgpy.rmg.input
rmgpy.rmg.input.rmg = None
mol = Molecule(smiles='C')
self.assertFalse(fails_species_constraints(mol))
mock_logging.debug.assert_called_with('Species constraints could not be found.')
# Restore module level rmg variable in rmgpy.rmg.input
rmgpy.rmg.input.rmg = self.rmg