def test_del(self):
"""
Test ParameterList __del__ overloading.
"""
p1 = ParameterType(smirks='[*:1]')
p2 = ParameterType(smirks='[#1:1]')
p3 = ParameterType(smirks='[#7:1]')
parameters = ParameterList([p1, p2, p3])
with pytest.raises(IndexError,
match='list assignment index out of range'):
del parameters[4]
with pytest.raises(
IndexError,
match=r'SMIRKS \[#6:1\] not found in ParameterList'):
del parameters['[#6:1]']
# Test that original list deletion behavior is preserved.
del parameters[2]
assert len(parameters) == 2
assert p1 in parameters
assert p2 in parameters
assert p3 not in parameters
# Test that we can delete elements by their smirks.
del parameters['[#1:1]']
assert len(parameters) == 1
assert p1 in parameters
assert p2 not in parameters
def test_base_parametertype_to_dict(self):
"""
Test ParameterType to_dict.
"""
p1 = ParameterType(smirks='[*:1]')
param_dict = p1.to_dict()
assert param_dict['smirks'] == '[*:1]'
assert len(param_dict.keys()) == 1
def test_insert(self):
"""
Test ParameterList.insert, ensuring that the new parameter was added to the proper spot in
the list and that it is propertly recorded as the most recently added.
"""
p1 = ParameterType(smirks='[*:1]-[*:2]')
p2 = ParameterType(smirks='[*:1]=[*:2]')
p3 = ParameterType(smirks='[*:1]#[*:2]')
param_list = ParameterList([p1, p2])
param_list.insert(1, p3)
assert param_list[1] == p3
def test_contains(self):
"""Test ParameterList __contains__ overloading.
"""
p1 = ParameterType(smirks='[*:1]')
p2 = ParameterType(smirks='[#1:1]')
p3 = ParameterType(smirks='[#7:1]')
parameters = ParameterList([p1, p2])
assert p1 in parameters
assert p2 in parameters
assert p3 not in parameters
assert p1.smirks in parameters
assert p2.smirks in parameters
assert p3.smirks not in parameters
def test_extend(self):
"""
Test ParameterList.extend, ensuring that the new parameter was added to the proper spot in
the list and that it is propertly recorded as the most recently added.
"""
p1 = ParameterType(smirks='[*:1]-[*:2]')
p2 = ParameterType(smirks='[*:1]=[*:2]')
param_list1 = ParameterList()
param_list2 = ParameterList([p1, p2])
param_list1.extend(param_list2)
assert len(param_list1) == 2
assert '[*:1]-[*:2]' in param_list1
assert '[*:1]=[*:2]' in param_list1
assert param_list1[-1] == p2
def test_append(self):
"""
Test ParameterList.append, ensuring that the new parameter was added to the bottom of the list
and that it is properly recorded as the most recently-added.
"""
p1 = ParameterType(smirks='[*:1]-[*:2]')
p2 = ParameterType(smirks='[*:1]=[*:2]')
param_list = ParameterList()
param_list.append(p1)
assert len(param_list) == 1
assert '[*:1]-[*:2]' in param_list
param_list.append(p2)
assert len(param_list) == 2
assert '[*:1]=[*:2]' in param_list
assert param_list[-1] == p2
def test_getitem(self):
"""Test ParameterList __getitem__ overloading.
"""
p1 = ParameterType(smirks='[*:1]')
p2 = ParameterType(smirks='[#1:1]')
parameters = ParameterList([p1, p2])
assert parameters[0] == p1
assert parameters[1] == p2
assert parameters[p1.smirks] == p1
assert parameters[p2.smirks] == p2
# Note that this call access __getitem__, not __setitem__.
parameters['[*:1]'].smirks = '[*X4:1]'
assert parameters[0].smirks == '[*X4:1]'
assert p1.smirks == '[*X4:1]'
def test_index(self):
"""
Tests the ParameterList.index() function by attempting lookups by SMIRKS and by ParameterType equivalence.
"""
p1 = ParameterType(smirks='[*:1]')
p2 = ParameterType(smirks='[#1:1]')
p3 = ParameterType(smirks='[#7:1]')
parameters = ParameterList([p1, p2, p3])
assert parameters.index(p1) == 0
assert parameters.index(p2) == 1
assert parameters.index(p3) == 2
assert parameters.index('[*:1]') == 0
assert parameters.index('[#1:1]') == 1
assert parameters.index('[#7:1]') == 2
with pytest.raises(IndexError, match=r'SMIRKS \[#2:1\] not found in ParameterList') as excinfo:
parameters.index('[#2:1]')
p4 = ParameterType(smirks='[#2:1]')
with pytest.raises(ValueError, match='is not in list') as excinfo:
parameters.index(p4)
def test_create(self):
"""Test creation of a parameter list.
"""
p1 = ParameterType(smirks='[*:1]')
p2 = ParameterType(smirks='[#1:1]')
parameters = ParameterList([p1, p2])