def test_add_to_cache(tmp_amine2):
mmff = stk.MMFF(use_cache=True)
mmff_energy = stk.MMFFEnergy()
init_energy = mmff_energy.get_energy(tmp_amine2)
mmff.add_to_cache(tmp_amine2)
mmff.optimize(tmp_amine2)
assert mmff_energy.get_energy(tmp_amine2) == init_energy
mmff2 = stk.MMFF(use_cache=True)
mmff2.optimize(tmp_amine2)
assert mmff_energy.get_energy(tmp_amine2) != init_energy
def test_optimizer_sequence(tmp_polymer):
tmp_polymer.write(join(odir, 'optimize_sequence_before.mol'))
etkdg = stk.RDKitEmbedder(rdkit.ETKDG())
mmff = stk.MMFF()
sequence = stk.OptimizerSequence(etkdg, mmff)
sequence.optimize(tmp_polymer)
tmp_polymer.write(join(odir, 'optimize_sequence_after.mol'))
def test_mmff(tmp_polymer):
# If the optimization was successful the energy should be lowered.
energy_calculator = stk.MMFFEnergy()
init_energy = energy_calculator.get_energy(tmp_polymer)
tmp_polymer.write(join(odir, 'mmff_before.mol'))
mmff = stk.MMFF()
mmff.optimize(tmp_polymer)
tmp_polymer.write(join(odir, 'mmff_after.mol'))
assert energy_calculator.get_energy(tmp_polymer) < init_energy
def test_optimizer_sequence(tmp_polymer):
# If the optimization was successful the energy should be lowered.
energy_calculator = stk.MMFFEnergy()
init_energy = energy_calculator.get_energy(tmp_polymer)
tmp_polymer.write(join(odir, 'optimize_sequence_before.mol'))
etkdg = stk.ETKDG()
mmff = stk.MMFF()
sequence = stk.OptimizerSequence(etkdg, mmff)
sequence.optimize(tmp_polymer)
tmp_polymer.write(join(odir, 'optimize_sequence_after.mol'))
assert energy_calculator.get_energy(tmp_polymer) < init_energy
def test_cage_optimizer_sequence(tmp_opt_cc3, tmp_cc3):
energy_calculator = stk.MMFFEnergy()
init_opt_cc3 = energy_calculator.get_energy(tmp_opt_cc3)
init_cc3 = energy_calculator.get_energy(tmp_cc3)
mmff = stk.MMFF()
sequence = stk.CageOptimizerSequence(mmff)
sequence.optimize(tmp_opt_cc3)
sequence.optimize(tmp_cc3)
# opt_cc3 should have found all windows so energy should be lowered
# due to optimization.
assert energy_calculator.get_energy(tmp_opt_cc3) < init_opt_cc3
# cc3 should have not found all windows so energy should be the
# same as if no optimization happened.
assert energy_calculator.get_energy(tmp_cc3) == init_cc3
def test_raising_optimizer(tmp_polymer):
mmff = stk.MMFF()
always_raiser = stk.RaisingOptimizer(
optimizer=mmff,
fail_chance=1
)
with pytest.raises(stk.RaisingOptimizerError):
always_raiser.optimize(tmp_polymer)
never_raiser = stk.RaisingOptimizer(
optimizer=mmff,
fail_chance=0
)
tmp_polymer.write(join(odir, 'raising_optimizer_before.mol'))
energy_calculator = stk.MMFFEnergy()
energy_before = energy_calculator.get_energy(tmp_polymer)
never_raiser.optimize(tmp_polymer)
tmp_polymer.write(join(odir, 'raising_optimizer_after.mol'))
assert energy_before > energy_calculator.get_energy(tmp_polymer)
def test_cage_optimizer_sequence(tmp_cc3, tmp_cage):
mmff = stk.MMFF()
etkdg = stk.RDKitEmbedder(rdkit.ETKDG())
sequence = stk.CageOptimizerSequence(etkdg, mmff)
sequence.optimize(tmp_cage)
sequence.optimize(tmp_cc3)
def test_mmff(tmp_polymer):
tmp_polymer.write(join(odir, 'mmff_before.mol'))
mmff = stk.MMFF()
mmff.optimize(tmp_polymer)
tmp_polymer.write(join(odir, 'mmff_after.mol'))