def test_guess_types(self):
out = guessers.guess_types(['MG2+', 'C12'])
assert isinstance(out, np.ndarray)
assert_equal(out, np.array(['MG', 'C'], dtype=object))
def test_guess_bonds_adk():
u = mda.Universe(datafiles.PSF, datafiles.DCD)
u.atoms.types = guessers.guess_types(u.atoms.names)
bonds = guessers.guess_bonds(u.atoms, u.atoms.positions)
assert_equal(np.sort(u.bonds.indices, axis=0), np.sort(bonds, axis=0))
def test_guess_bonds_peptide():
u = mda.Universe(datafiles.PSF_NAMD, datafiles.PDB_NAMD)
u.atoms.types = guessers.guess_types(u.atoms.names)
bonds = bond_sort(guessers.guess_bonds(u.atoms, u.atoms.positions))
assert_equal(np.sort(u.bonds.indices, axis=0), np.sort(bonds, axis=0))
def test_guess_types(self):
out = guessers.guess_types(['MG2+', 'C12'])
assert isinstance(out, np.ndarray)
assert_equal(out, np.array(['MG', 'C'], dtype=object))