def test_mol2_parse():
name = "mol2"
target = [
"#Comment\n",
"@<TRIPOS>MOLECULE\n",
"MOL\n",
" 3 2 1 0 0\n",
"SMALL\n",
"resp\n",
"\n",
"\n",
"@<TRIPOS>ATOM\n",
" 1 O1 0.0000 0.0000 0.0000 o 1 MOL -0.830000\n",
" 2 H1 0.9572 0.0000 0.0000 h 1 MOL 0.415000\n",
" 3 H2 -0.2400 0.9266 0.0000 h 1 MOL 0.415000\n",
"@<TRIPOS>BOND\n",
" 1 1 2 1\n",
" 2 1 3 1\n",
"@<TRIPOS>SUBSTRUCTURE\n",
" 1 MOL 1 TEMP 0 **** **** 0 ROOT",
]
Mol, _ = mol2.parser(name, target)
print(Mol.getAtom(2, fmt="bohr"))
assert Mol.name == name
assert Mol.nat == 3
assert Mol.ntyp == 2
assert Mol.getTypes() == ["H", "O"]
assert Mol.getFmt() == "angstrom"
assert atom_equal(
Mol.getAtom(0, charge=True, fix=True, hidden=True), ["O", (0, 0, 0), -0.83, [False, False, False], False]
)
assert atom_equal(Mol.getAtom(2, charge=True, fmt="bohr"), ["H", (-0.4535, 1.7510, 0), 0.415])
assert len(Mol.getBonds(1.1)[0]) == 2
def test_turbomole_parse():
name = 'turbomole'
target = ["$coord\n",
" 0.0000 0.0000 0.0000 o\n",
" 1.8089 0.0000 0.0000 h\n",
"-0.4535 1.7511 0.0000 h\n",
"$end"]
Mol, _ = turbomole.parser(name, target)
assert Mol.name == name
assert Mol.nat == 3
assert Mol.ntyp == 2
assert Mol.getTypes() == ['H', 'O']
assert Mol.getFmt() == 'bohr'
assert atom_equal(Mol.getAtom(0, charge=True, fix=True, hidden=True),
['O', (0, 0, 0), 0.,
[False, False, False], False])
assert atom_equal(Mol.getAtom(2, fmt='bohr'),
['H', (-0.4535, 1.7511, 0)])
assert atom_equal(Mol.getAtom(1, fmt='angstrom'),
['H', (0.9572, 0, 0)])
assert len(Mol.getBonds(1.1)[0]) == 2