def testSulfurConstraint(self):
"""
Test that we can constrain the max number of sulfur atoms.
"""
mol1 = Molecule(SMILES='CS')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='SCS')
self.assertTrue(failsSpeciesConstraints(mol2))
def testCarbonConstraint(self):
"""
Test that we can constrain the max number of carbon atoms.
"""
mol1 = Molecule(SMILES='CC')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='CCC')
self.assertTrue(failsSpeciesConstraints(mol2))
def testCarbonConstraint(self):
"""
Test that we can constrain the max number of carbon atoms.
"""
mol1 = Molecule(SMILES='CC')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='CCC')
self.assertTrue(failsSpeciesConstraints(mol2))
def testSiliconConstraint(self):
"""
Test that we can constrain the max number of silicon atoms.
"""
mol1 = Molecule(SMILES='[SiH4]')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='[SiH3][SiH3]')
self.assertTrue(failsSpeciesConstraints(mol2))
def testRadicalConstraint(self):
"""
Test that we can constrain the max number of radical electrons.
"""
mol1 = Molecule(SMILES='[CH2][CH2]')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='[CH2][CH][CH2]')
self.assertTrue(failsSpeciesConstraints(mol2))
def testHeavyConstraint(self):
"""
Test that we can constrain the max number of heavy atoms.
"""
mol1 = Molecule(SMILES='CCO')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='CCN=O')
self.assertTrue(failsSpeciesConstraints(mol2))
def testHeavyConstraint(self):
"""
Test that we can constrain the max number of heavy atoms.
"""
mol1 = Molecule(SMILES='CCO')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='CCN=O')
self.assertTrue(failsSpeciesConstraints(mol2))
def testRadicalConstraint(self):
"""
Test that we can constrain the max number of radical electrons.
"""
mol1 = Molecule(SMILES='[CH2][CH2]')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='[CH2][CH][CH2]')
self.assertTrue(failsSpeciesConstraints(mol2))
def testSulfurConstraint(self):
"""
Test that we can constrain the max number of sulfur atoms.
"""
mol1 = Molecule(SMILES='CS')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='SCS')
self.assertTrue(failsSpeciesConstraints(mol2))
def testSiliconConstraint(self):
"""
Test that we can constrain the max number of silicon atoms.
"""
mol1 = Molecule(SMILES='[SiH4]')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='[SiH3][SiH3]')
self.assertTrue(failsSpeciesConstraints(mol2))
def testNitrogenConstraint(self):
"""
Test that we can constrain the max number of nitrogen atoms.
"""
mol1 = Molecule(SMILES='CN')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='NCN')
self.assertTrue(failsSpeciesConstraints(mol2))
def testNitrogenConstraint(self):
"""
Test that we can constrain the max number of nitrogen atoms.
"""
mol1 = Molecule(SMILES='CN')
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule(SMILES='NCN')
self.assertTrue(failsSpeciesConstraints(mol2))
def testExplicitlyAllowedMolecules(self):
"""
Test that we can explicitly allow molecules in species constraints.
"""
mol = Molecule(SMILES='CCCC')
self.assertTrue(failsSpeciesConstraints(mol))
self.rmg.speciesConstraints['explicitlyAllowedMolecules'] = [Molecule(SMILES='CCCC')]
self.assertFalse(failsSpeciesConstraints(mol))
def testExplicitlyAllowedMolecules(self):
"""
Test that we can explicitly allow molecules in species constraints.
"""
mol = Molecule(SMILES='CCCC')
self.assertTrue(failsSpeciesConstraints(mol))
self.rmg.speciesConstraints['explicitlyAllowedMolecules'] = [
Molecule(SMILES='CCCC')
]
self.assertFalse(failsSpeciesConstraints(mol))
def testSpeciesInput(self):
"""
Test that failsSpeciesConstraints can handle a Species object.
"""
spc = Species().fromSMILES('C')
self.assertFalse(failsSpeciesConstraints(spc))
def testSpeciesInput(self):
"""
Test that failsSpeciesConstraints can handle a Species object.
"""
spc = Species().fromSMILES('C')
self.assertFalse(failsSpeciesConstraints(spc))
def testCarbeneConstraint(self):
"""
Test that we can constrain the max number of singlet carbenes.
"""
mol1 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol2))
def testCarbeneConstraint(self):
"""
Test that we can constrain the max number of singlet carbenes.
"""
mol1 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol2))
def testCarbeneRadicalConstraint(self):
"""
Test that we can constrain the max number of radical electrons with a carbene.
"""
mol1 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol2))
def testCarbeneRadicalConstraint(self):
"""
Test that we can constrain the max number of radical electrons with a carbene.
"""
mol1 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
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(failsSpeciesConstraints(mol2))
def testIsotopeConstraint(self):
"""
Test that we can constrain the max number of isotopic atoms.
"""
mol1 = Molecule().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 D u0 p0 c0 {1,S}
3 D u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 D u0 p0 c0 {1,S}
3 D u0 p0 c0 {1,S}
4 D u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
self.assertTrue(failsSpeciesConstraints(mol2))
def testIsotopeConstraint(self):
"""
Test that we can constrain the max number of isotopic atoms.
"""
mol1 = Molecule().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 D u0 p0 c0 {1,S}
3 D u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
self.assertFalse(failsSpeciesConstraints(mol1))
mol2 = Molecule().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 D u0 p0 c0 {1,S}
3 D u0 p0 c0 {1,S}
4 D u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
""")
self.assertTrue(failsSpeciesConstraints(mol2))
def testConstraintsNotLoaded(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(failsSpeciesConstraints(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
def testConstraintsNotLoaded(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(failsSpeciesConstraints(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
