def tmp_population():
bb1, bb2, bb3, bb4, c1, c2, c3, c4 = _population_members()
return stk.Population(
c3, stk.BuildingBlock('NCCCN'), bb1,
stk.BuildingBlock('NCCCN', ['amine']), c1,
stk.BuildingBlock('O=CCC=O'), c1,
stk.BuildingBlock('O=CCC=O', ['aldehyde']),
stk.Population(c1, stk.BuildingBlock('[Br]CC[Br]'), bb1, bb2, bb1), c2,
stk.Population(bb1, stk.BuildingBlock('CCCC'),
stk.Population(bb3, stk.BuildingBlock('NNNN'), c4)))
def progress():
pop = stk.Population()
for i in range(15):
subpop = stk.Population(*(stk.BuildingBlock('C') for j in range(5)))
pop.subpopulations.append(subpop)
for i, mol in enumerate(pop):
mol.fitness = i
return pop
def test_init(amine2, aldehyde2, amine3):
"""
Tests the __init__ method of the stk.Population class.
"""
pop = stk.Population(
NewMol(), amine2, NewMol(),
stk.Population(NewMol(), NewMol(), aldehyde2), stk.Population(),
stk.Population(amine3, stk.Population(NewMol(), NewMol())), NewMol())
assert len(pop) == 10
assert len(pop.direct_members) == 4
assert len(pop.subpopulations) == 3
def test_init():
"""
Tests the __init__ method of the stk.Population class.
"""
def NewMol():
return stk.MacroMolecule.__new__(stk.MacroMolecule)
pop = stk.Population(NewMol(), NewMol(),
stk.Population(NewMol(), NewMol()), stk.Population(),
stk.Population(stk.Population(NewMol(), NewMol())),
NewMol())
assert len(pop) == 7
assert len(pop.members) == 3
assert len(pop.populations) == 3
def test_remove_duplicates_not_across_subpopulations():
x = stk.BuildingBlock('C')
y = stk.BuildingBlock('N')
subpop = stk.Population(x, x, y, stk.Population(y, y))
pop = subpop.clone() + subpop.clone()
counts = Counter(pop)
assert counts[x] == 4
assert counts[y] == 6
subpop_counts = Counter(pop.subpopulations[0].direct_members)
assert subpop_counts[x] == 2
assert subpop_counts[y] == 1
pop.remove_duplicates(across_subpopulations=False)
counts = Counter(pop)
assert counts[x] == 2
assert counts[y] == 4
subpop_counts = Counter(pop.subpopulations[0].direct_members)
assert subpop_counts[x] == 1
assert subpop_counts[y] == 1
def parallel_pop_update(collection, population_files):
update_fn = globals()['update']
with mp.Pool() as pool:
p = stk.Population()
for pop_file in population_files:
p.add_members(stk.Population.load(pop_file,
stk.Molecule.from_dict))
updates = pool.map(update_fn, p)
for mol, update in updates:
key = (macromol_key
if isinstance(mol, stk.MacroMolecule) else struct_unit_key)
collection.update_one(key(mol), **update)
def generation():
pop = stk.Population(*(stk.BuildingBlock('C') for i in range(10)))
for i, mol in enumerate(pop):
mol.fitness = i
return pop