def test_boron_cof(diol2, boronic_acid4):
cof = stk.Periodic([diol2, boronic_acid4], stk.Square())
path = join(test_dir, 'boron.sdf')
cof.write(path)
island = cof.island([3, 3, 1])
rdkit.MolToMolFile(island, path.replace('.sdf', '_island.sdf'))
assert cof.bonds_made == 4
assert (cof.mol.GetNumAtoms() == diol2.mol.GetNumAtoms() * 2 +
boronic_acid4.mol.GetNumAtoms() * 1 - cof.bonds_made * 3)
assert (cof.mol.GetNumBonds() == diol2.mol.GetNumBonds() * 2 +
boronic_acid4.mol.GetNumBonds() * 1 - cof.bonds_made * 2)
assert cof.bb_counter[diol2] == 2
assert cof.bb_counter[boronic_acid4] == 1
assert cof.topology == stk.Square()
def test_kagome(amine2, aldehyde4):
cof = stk.Periodic([amine2, aldehyde4], stk.Kagome())
path = os.path.join(test_dir, 'kagome.sdf')
cof.write(path)
island = cof.island([3, 3, 1])
rdkit.MolToMolFile(island, path.replace('.sdf', '_island.sdf'))
assert cof.bonds_made == 9
assert (cof.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * 6 +
aldehyde4.mol.GetNumAtoms() * 3 - cof.bonds_made * 3)
assert (cof.mol.GetNumBonds() == amine2.mol.GetNumBonds() * 6 +
aldehyde4.mol.GetNumBonds() * 3 - cof.bonds_made * 2)
assert cof.bb_counter[amine2] == 6
assert cof.bb_counter[aldehyde4] == 3
assert cof.topology == stk.Kagome()
def test_hexagonal(amine2, aldehyde6):
cof = stk.Periodic([amine2, aldehyde6], stk.Hexagonal())
path = os.path.join(test_dir, 'hexagonal.sdf')
cof.write(path)
island = cof.island([3, 3, 1])
rdkit.MolToMolFile(island, path.replace('.sdf', '_island.sdf'))
assert cof.bonds_made == 17
assert (cof.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * 12 +
aldehyde6.mol.GetNumAtoms() * 4 - cof.bonds_made * 3)
assert (cof.mol.GetNumBonds() == amine2.mol.GetNumBonds() * 12 +
aldehyde6.mol.GetNumBonds() * 4 - cof.bonds_made * 2)
assert cof.bb_counter[amine2] == 12
assert cof.bb_counter[aldehyde6] == 4
assert cof.topology == stk.Hexagonal()
def test_honeycomb(amine2, aldehyde3):
cof = stk.Periodic([amine2, aldehyde3], stk.Honeycomb())
path = join(test_dir, 'honeycomb.sdf')
cof.write(path)
island = cof.island([3, 3, 1])
rdkit.MolToMolFile(island, path.replace('.sdf', '_island.sdf'))
assert cof.bonds_made == 4
assert (cof.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * 3 +
aldehyde3.mol.GetNumAtoms() * 2 - cof.bonds_made * 3)
assert (cof.mol.GetNumBonds() == amine2.mol.GetNumBonds() * 3 +
aldehyde3.mol.GetNumBonds() * 2 - cof.bonds_made * 2)
assert cof.bb_counter[amine2] == 3
assert cof.bb_counter[aldehyde3] == 2
assert cof.topology == stk.Honeycomb()
def test_nolinkerhoneycomb(amine3, aldehyde3):
cof = stk.Periodic([amine3, aldehyde3], stk.NoLinkerHoneycomb())
path = join(test_dir, 'nolinkerhoneycomb.sdf')
cof.write(path)
island = cof.island([3, 3, 1])
rdkit.MolToMolFile(island, path.replace('.sdf', '_island.sdf'))
assert cof.bonds_made == 1
assert (cof.mol.GetNumAtoms() == amine3.mol.GetNumAtoms() +
aldehyde3.mol.GetNumAtoms() - cof.bonds_made * 3)
assert (cof.mol.GetNumBonds() == amine3.mol.GetNumBonds() * 1 +
aldehyde3.mol.GetNumBonds() * 1 - cof.bonds_made * 2)
assert cof.bb_counter[amine3] == 1
assert cof.bb_counter[aldehyde3] == 1
assert cof.topology == stk.NoLinkerHoneycomb()
def test_aligning(amine2, aldehyde4_alt1):
for i in range(4):
top = stk.Kagome(multitopic_aligners=[i, 0, 0])
cof = stk.Periodic([amine2, aldehyde4_alt1], top)
cof.write(join(test_dir, f'aligning_{i}.sdf'))