def test_init_one_residue(self, molecule_top_bmim: MoleculeTop,
residue_bmim: Residue):
"""
Tests Molecule initialization with only one residue and some basic
attributes and methods.
"""
# Wrong residue
new_residue = Residue(residue_bmim[:-1])
with pytest.raises(IOError):
molec = Molecule(molecule_top_bmim, [new_residue])
molec = Molecule(molecule_top_bmim, [residue_bmim])
assert len(molec) == len(molecule_top_bmim)
assert len(molec) == len(residue_bmim)
assert len(molec) == 25
assert str(molec) == 'Molecule of BMIM.'
for atom, atom_top, atom_gro in zip(molec, molecule_top_bmim,
residue_bmim):
atom_compare = Atom(atom_top, atom_gro)
assert atom == atom_compare
for atom, atom_comp in zip(molec, molec.atoms):
assert atom == atom_comp
assert molec[-1] == atom_compare
assert atom_compare != molec[0]
assert molec.index(atom_compare) == 24
with pytest.raises(ValueError):
_ = molec.index(34) # type: ignore
assert molec._each_atom_resid == [0] * len(molec)
assert molec == molec
assert molec is molec
copy_mol = molec.copy()
assert copy_mol == molec
assert copy_mol is not molec
assert len(molec.residues) == 1
assert molec.residues[0] == residue_bmim
assert molec.residues[0] is not residue_bmim
assert molec.molecule_top is molecule_top_bmim
with pytest.raises(NotImplementedError):
_ = molec + 1 # type: ignore
with pytest.raises(NotImplementedError):
_ = 1 + molec # type: ignore
for key in dir(molec.molecule_top):
assert key in dir(molec)
def test_copy(self, molecule_bmim: Molecule):
"""
Test the copy method of Molecule class.
"""
copy_mol = molecule_bmim.copy()
assert copy_mol == molecule_bmim
assert copy_mol.resnames == molecule_bmim.resnames
assert copy_mol.molecule_top == molecule_bmim.molecule_top
assert copy_mol.molecule_top is molecule_bmim.molecule_top
assert copy_mol.residues == molecule_bmim.residues
assert copy_mol.residues is not molecule_bmim.residues
# Tricky change in the resname of the topology
copy_mol.molecule_top.resnames = ['Test']
assert molecule_bmim.molecule_top.resnames == ['Test']
def test_init_multi_residue(self, molecule_top_protein: MoleculeTop,
residue_protein: List[Residue]):
"""
Tests Molecule initialization with multiple residues and some basic
attributes and methods.
"""
molec = Molecule(molecule_top_protein, residue_protein)
assert len(molec) == len(molecule_top_protein)
assert len(molec) == sum(len(res) for res in residue_protein)
assert len(molec) == 34
index = 0
for res in residue_protein:
for atom_gro in res:
atom_compare = Atom(molecule_top_protein[index], atom_gro)
assert molec[index] == atom_compare
index += 1
for atom, atom_comp in zip(molec, molec.atoms):
assert atom == atom_comp
assert molec[-1] == atom_compare
assert molec.index(atom_compare) == 33
assert molec._each_atom_resid == [0, 0, 0, 1, 1, 1, 2, 2, 3,
3, 3, 4, 4, 4, 5, 5, 6, 6, 7, 7, 7,
8, 8, 8, 9, 9, 10, 10, 10, 11, 11,
11, 12, 12]
assert molec != 0
assert molec == molec
assert molec is molec
assert molec.copy() == molec
assert molec.copy() is not molec
assert len(molec.residues) == 13
for res1, res2 in zip(molec.residues, residue_protein):
assert res1 == res2
assert res1 is not res2
assert molec.molecule_top is molecule_top_protein