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from ase import Atoms
from ase.build import molecule
from ase.build.connected import connected_atoms, split_bond, separate
from ase.data.s22 import data
def test_split_biphenyl():
mol = molecule('biphenyl')
mol1, mol2 = split_bond(mol, 0, 14)
assert len(mol) == len(mol1) + len(mol2)
mol2s, mol1s = split_bond(mol, 14, 0)
assert mol1s == mol1
assert mol2s == mol2
# we cannot split within the ring
mol1, mol2 = split_bond(mol, 0, 1)
assert len(mol) < len(mol1) + len(mol2)
def test_connected_atoms():
CO = molecule('CO')
R = CO.get_distance(0, 1)
assert len(connected_atoms(CO, 0, 1.1 * R)) == 2
assert len(connected_atoms(CO, 0, 0.9 * R)) == 1
H2O = molecule('H2O')
assert len(connected_atoms(H2O, 0)) == 3
assert len(connected_atoms(H2O, 0, scale=0.9)) == 1
dimerdata = data['2-pyridoxine_2-aminopyridine_complex']
dimer = Atoms(dimerdata['symbols'], dimerdata['positions'])
atoms1 = connected_atoms(dimer, 0)
atoms2 = connected_atoms(dimer, -1)
assert len(dimer) == len(atoms1) + len(atoms2)
def test_separate_dimer():
dimerdata = data['Methanol-formaldehyde_complex']
dimer = Atoms(dimerdata['symbols'], dimerdata['positions'])
atoms_list = separate(dimer)
assert len(atoms_list) == 2
assert len(atoms_list[0]) + len(atoms_list[1]) == len(dimer)
# split into atoms
atoms_list = separate(dimer, scale=1e-5)
assert len(atoms_list) == len(dimer)
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