def test_alignments(amine2, amine2_alt3, aldehyde3, aldehyde3_alt3):
# Regular cage topology.
bb_positions = {
amine2: [0, 1, 2, 3, 4],
amine2_alt3: [5],
aldehyde3: [0, 1, 2],
aldehyde3_alt3: [3]
}
bbs = [amine2, amine2_alt3, aldehyde3, aldehyde3_alt3]
for fg in range(3):
top = stk.FourPlusSix(bb_positions=bb_positions,
A_alignments=[0, 0, 0, fg],
B_alignments=[1, 1, 1, 1, 1, 1])
c = stk.Cage(bbs, top)
c.write(join(test_dir, f'4p6_valignment_{fg}.mol'))
top = stk.FourPlusSix(bb_positions=bb_positions,
A_alignments=[0, 0, 0, 0],
B_alignments=[1, 1, 1, 1, 1, -1])
c = stk.Cage(bbs, top)
c.write(join(test_dir, f'4p6_edge_alignment.mol'))
# No linker topology.
bbs = [aldehyde3, aldehyde3_alt3]
bb_positions = {aldehyde3: [1, 2, 3], aldehyde3_alt3: [0]}
for fg in range(3):
top = stk.TwoPlusTwo(bb_positions=bb_positions,
alignments=[fg, 0, 0, 0])
c = stk.Cage(bbs, top)
c.write(join(test_dir, f'2p2_valignment_{fg}.mol'))
def test_multiconformer(tmp_amine2, tmp_aldehyde3):
top = stk.FourPlusSix()
amine_fg_count = 2
amine_count = 6
aldehyde_count = 4
c = stk.Cage([tmp_amine2, tmp_aldehyde3],
stk.FourPlusSix(),
bb_conformers=[0, 0])
c.add_conformer([1, 0])
c.add_conformer([0, 1])
c.add_conformer([1, 1])
c.write(join(test_dir, 'FourPlusSix_conf1.mol'), 0)
c.write(join(test_dir, 'FourPlusSix_conf2.mol'), 1)
c.write(join(test_dir, 'FourPlusSix_conf3.mol'), 2)
c.write(join(test_dir, 'FourPlusSix_conf4.mol'), 3)
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == tmp_amine2.mol.GetNumAtoms() * amine_count +
tmp_aldehyde3.mol.GetNumAtoms() * aldehyde_count -
c.bonds_made * 3)
assert (c.mol.GetNumBonds() == tmp_amine2.mol.GetNumBonds() * amine_count +
tmp_aldehyde3.mol.GetNumBonds() * aldehyde_count -
c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[tmp_amine2] == amine_count
assert c.bb_counter[tmp_aldehyde3] == aldehyde_count
def test_multiFourPlusFour(aldehyde3, aldehyde3_alt1, aldehyde3_alt2):
top = stk.FourPlusFour(bb_positions={
aldehyde3: [0, 1],
aldehyde3_alt1: [2, 3, 4, 6, 7],
aldehyde3_alt2: [5]
})
bbs = [aldehyde3, aldehyde3_alt1, aldehyde3_alt2]
c = stk.Cage(bbs, top)
c.write(join(test_dir, 'multi_FourPlusFour.mol'))
assert c.bb_counter[aldehyde3] == 2
assert c.bb_counter[aldehyde3_alt1] == 5
assert c.bb_counter[aldehyde3_alt2] == 1
def test_cage_complex(amine2, amine2_alt1, aldehyde3, chained_c60):
c = stk.Cage(
[amine2, amine2_alt1, aldehyde3],
stk.FourPlusSix(bb_positions={
amine2: [5],
amine2_alt1: [0, 1, 2, 3, 4],
aldehyde3: [0, 1, 2, 3]
}))
n = 3
for i in range(n):
cage_complex = stk.CageComplex([c, chained_c60],
stk.CageWithGuest(
axis=[1, 0, 0],
angle=2 * np.pi * i / n,
displacement=[2 * i, 0, 0]))
cage_complex.write(join(test_dir, f'cage_with_guest_{i}.mol'))
def test_SixPlusEight(aldehyde3, amine4):
top = stk.SixPlusEight()
amine_fg_count = 4
amine_count = 6
aldehyde_count = 8
c = stk.Cage([aldehyde3, amine4], top)
c.write(join(test_dir, 'SixPlusEight.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine4.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine4.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine4] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_Dodecahedron(amine2, aldehyde3):
top = stk.Dodecahedron()
amine_fg_count = 2
amine_count = 30
aldehyde_count = 20
c = stk.Cage([amine2, aldehyde3], top)
c.write(join(test_dir, 'Dodecahedron.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine2.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine2] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_EightPlusTwelve(amine2, aldehyde3):
top = stk.EightPlusTwelve()
amine_fg_count = 2
amine_count = 12
aldehyde_count = 8
c = stk.Cage([amine2, aldehyde3], top)
c.write(join(test_dir, 'EightPlusTwelve.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine2.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine2] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_FourPlusSix2(amine2, aldehyde3):
top = stk.FourPlusSix2()
amine_fg_count = 2
amine_count = 6
aldehyde_count = 4
c = stk.Cage([amine2, aldehyde3], top)
c.write(join(test_dir, 'FourPlusSix2.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine2.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine2] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_FourPlusFour(amine3, aldehyde3):
top = stk.FourPlusFour(bb_positions={0: [4, 1, 6, 3], 1: [0, 5, 2, 7]})
amine_fg_count = 3
amine_count = 4
aldehyde_count = 4
c = stk.Cage([aldehyde3, amine3], top)
c.write(join(test_dir, 'FourPlusFour.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine3.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine3.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine3] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_TwoPlusTwo(amine3, aldehyde3):
top = stk.TwoPlusTwo(bb_positions={0: [0, 1], 1: [2, 3]})
amine_fg_count = 3
amine_count = 2
aldehyde_count = 2
c = stk.Cage([aldehyde3, amine3], top)
c.write(join(test_dir, 'TwoPlusTwo.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine3.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine3.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine3] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_OnePlusOne(amine3, aldehyde3):
top = stk.OnePlusOne(bb_positions={0: [0], 1: [1]})
amine_fg_count = 3
amine_count = 1
aldehyde_count = 1
c = stk.Cage([aldehyde3, amine3], top)
c.write(join(test_dir, 'OnePlusOne.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine3.mol.GetNumAtoms() * amine_count +
aldehyde3.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine3.mol.GetNumBonds() * amine_count +
aldehyde3.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine3] == amine_count
assert c.bb_counter[aldehyde3] == aldehyde_count
def test_TenPlusTwenty(aldehyde2, amine4):
top = stk.TenPlusTwenty()
amine_fg_count = 4
amine_count = 10
aldehyde_count = 20
c = stk.Cage([amine4, aldehyde2], top)
c.write(join(test_dir, 'TenPlusTwenty.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine4.mol.GetNumAtoms() * amine_count +
aldehyde2.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine4.mol.GetNumBonds() * amine_count +
aldehyde2.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine4] == amine_count
assert c.bb_counter[aldehyde2] == aldehyde_count
def test_FivePlusTen(aldehyde2, amine4):
top = stk.FivePlusTen()
amine_fg_count = 4
amine_count = 5
aldehyde_count = 10
c = stk.Cage([aldehyde2, amine4], top)
c.write(join(test_dir, 'FivePlusTen.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine4.mol.GetNumAtoms() * amine_count +
aldehyde2.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine4.mol.GetNumBonds() * amine_count +
aldehyde2.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine4] == amine_count
assert c.bb_counter[aldehyde2] == aldehyde_count
def test_ThreePlusSix(aldehyde2, amine4):
top = stk.ThreePlusSix()
amine_fg_count = 4
amine_count = 3
aldehyde_count = 6
c = stk.Cage([aldehyde2, amine4], top)
c.write(join(test_dir, 'ThreePlusSix.mol'))
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == amine4.mol.GetNumAtoms() * amine_count +
aldehyde2.mol.GetNumAtoms() * aldehyde_count - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine4.mol.GetNumBonds() * amine_count +
aldehyde2.mol.GetNumBonds() * aldehyde_count - c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[amine4] == amine_count
assert c.bb_counter[aldehyde2] == aldehyde_count
def test_multiFourPlusSix(amine2, amine2_alt1, amine2_alt2, aldehyde3,
aldehyde3_alt1, aldehyde3_alt2):
top = stk.FourPlusSix(bb_positions={
0: [0, 1],
1: [2, 3, 4],
2: [5],
3: [0],
4: [1, 2],
5: [3]
})
amine_fg_count = 2
bbs = [
amine2, amine2_alt1, amine2_alt2, aldehyde3, aldehyde3_alt1,
aldehyde3_alt2
]
c = stk.Cage(bbs, top)
c.write(join(test_dir, 'multi_FourPlusSix.mol'))
assert c.bonds_made == amine_fg_count * 6
assert c.topology == top
assert c.bb_counter[amine2] == 2
assert c.bb_counter[amine2_alt1] == 3
assert c.bb_counter[amine2_alt2] == 1
assert c.bb_counter[aldehyde3] == 1
assert c.bb_counter[aldehyde3_alt1] == 2
assert c.bb_counter[aldehyde3_alt2] == 1
assert (c.mol.GetNumAtoms() == amine2.mol.GetNumAtoms() * 2 +
amine2_alt1.mol.GetNumAtoms() * 3 +
amine2_alt2.mol.GetNumAtoms() * 1 +
aldehyde3.mol.GetNumAtoms() * 1 +
aldehyde3_alt1.mol.GetNumAtoms() * 2 +
aldehyde3_alt2.mol.GetNumAtoms() * 1 - c.bonds_made * 3)
assert (c.mol.GetNumBonds() == amine2.mol.GetNumBonds() * 2 +
amine2_alt1.mol.GetNumBonds() * 3 +
amine2_alt2.mol.GetNumBonds() * 1 +
aldehyde3.mol.GetNumBonds() * 1 +
aldehyde3_alt1.mol.GetNumBonds() * 2 +
aldehyde3_alt2.mol.GetNumBonds() * 1 - c.bonds_made * 2)
def test_multiconformer(tmp_amine2, tmp_aldehyde3):
top = stk.FourPlusSix()
amine_fg_count = 2
amine_count = 6
aldehyde_count = 4
# Add conformers.
tmp_amine2.mol.AddConformer(tmp_amine2.mol.GetConformer(), True)
tmp_aldehyde3.mol.AddConformer(tmp_aldehyde3.mol.GetConformer(), True)
# Give conformers distinct geometries.
tmp_amine2.set_position_from_matrix(
pos_mat=tmp_amine2.mol.GetConformer().GetPositions().T * 4,
conformer=1)
tmp_aldehyde3.set_position_from_matrix(
pos_mat=tmp_aldehyde3.mol.GetConformer().GetPositions().T * 4,
conformer=1)
c = stk.Cage([tmp_amine2, tmp_aldehyde3],
stk.FourPlusSix(),
bb_conformers=[0, 0])
c.add_conformer([1, 0])
c.add_conformer([0, 1])
c.add_conformer([1, 1])
c.write(join(test_dir, 'FourPlusSix_conf1.mol'), 0)
c.write(join(test_dir, 'FourPlusSix_conf2.mol'), 1)
c.write(join(test_dir, 'FourPlusSix_conf3.mol'), 2)
c.write(join(test_dir, 'FourPlusSix_conf4.mol'), 3)
assert c.bonds_made == amine_fg_count * amine_count
assert (c.mol.GetNumAtoms() == tmp_amine2.mol.GetNumAtoms() * amine_count +
tmp_aldehyde3.mol.GetNumAtoms() * aldehyde_count -
c.bonds_made * 3)
assert (c.mol.GetNumBonds() == tmp_amine2.mol.GetNumBonds() * amine_count +
tmp_aldehyde3.mol.GetNumBonds() * aldehyde_count -
c.bonds_made * 2)
assert c.topology == top
assert c.bb_counter[tmp_amine2] == amine_count
assert c.bb_counter[tmp_aldehyde3] == aldehyde_count
def tmp_cage(amine2, aldehyde3):
return stk.Cage([amine2, aldehyde3], stk.FourPlusSix(), 'tmp_cage')
