def test_complicated_torsion():
"""
Test ChemicalEnvironment objects with complicated torsion
test methods that add atoms, remove atoms
add ORtypes and ANDtypes to existing atoms
This is the SMIRK for the final torsion
"[*:1] - [#6:2](=[#8,#7;H0]) - [#6:3](-[#7X3,#8X2;+0]-[#1])(-[#1]) - [*:4]"
"""
torsion_smirks = "[*:1]-[#6:2]-[#6:3]-[*:4]"
torsion = ChemicalEnvironment(torsion_smirks)
# save atoms (use selectAtom)
atom1 = torsion.selectAtom(1)
atom2 = torsion.selectAtom(2)
atom3 = torsion.selectAtom(3)
# Add atoms with names so I can try to remove them
atom2alpha = torsion.addAtom(atom2, [('=',[])], None, [('#8',[]),('#7',[])], ['H0'])
atom3alpha1 = torsion.addAtom(atom3)
atom3beta1 = torsion.addAtom(atom3alpha1, [('-',[])], None, [('#1',[])])
atom3alpha2 = torsion.addAtom(atom3, [('-',[])], None, [('#1',[])])
# Get bond for atom3 and alpha and add ANDtype
bond = torsion.getBond(atom3, atom3alpha1)
assert bond is not None
bond.addORtype('-', [])
# Add ORtypes and ANDtypes to atom3 alpha atom
atom3alpha1.addORtype('#7', ['X3'])
atom3alpha1.addORtype('#8', ['X2'])
atom3alpha1.addANDtype('+0')
# Call getAtoms and getBonds just to make sure they work
torsion.getAtoms()
torsion.getBonds()
# get smarts and smirks for the large torsion
smarts = torsion.asSMIRKS(smarts=True)
assert is_valid_smirks(smarts)
smirks = torsion.asSMIRKS()
assert is_valid_smirks(smirks)
# Try removing atoms
# if it was labeled:
removed = torsion.removeAtom(atom1)
assert not removed
removed = torsion.removeAtom(atom3alpha1)
assert not removed
removed = torsion.removeAtom(atom3beta1)
assert removed
def isValid(self, smirks=None):
"""
Returns if the environment is valid, that is if it
creates a parseable SMIRKS string.
"""
if smirks is None:
smirks = self._asSMIRKS()
from chemper.chemper_utils import is_valid_smirks
return is_valid_smirks(smirks)
def test_other_cluster_graph(graph1, graph2):
"""
Check graphs build successfully by looking at minimal examples
"""
# check that a duplicate of the graph is treated as identical
assert graph1 == graph2
# check that some of the extraction functions work as expected
bonds = graph1.get_bonds()
atom = graph1.get_atoms()[0]
neighbor = graph1.get_neighbors(atom)[0]
bond = graph1.get_connecting_bond(atom, neighbor)
assert bond is not None
# check graph makes a valid smirks
assert is_valid_smirks(graph1.as_smirks())
def test_smirks_validity(smirks, is_valid):
assert chemper_utils.is_valid_smirks(smirks) == is_valid