def test_mol2graph_single_rings():
mol = me.get_mol(
'O=C(Cn1nc(C(=O)[O-])c2ccccc2c1=O)Nc1ccc2c(c1)C(=O)c1ccccc1C2=O')
result = mr.mol2graph_single(mol, include_rings=True)
assert 'ring_bond_idx' in result
assert 'ring_bond_order' in result
assert len(result['ring_bond_idx']) == 27 * 2
def test_combine_graphs_leaf_rings_singleton_sequence():
mol = me.get_mol(
'O=C(Cn1nc(C(=O)[O-])c2ccccc2c1=O)Nc1ccc2c(c1)C(=O)c1ccccc1C2=O')
result = mr.mol2graph_single(mol, include_leaves=True)
result = mr.combine_mol_graph([result])
assert 'leaf_ring' in result
assert 'leaf_atom' in result
assert np.all(result['leaf_ring_scope'] == np.array([[0, 2]]))
def test_combine_graphs_bond_rings():
mol = me.get_mol(
'O=C(Cn1nc(C(=O)[O-])c2ccccc2c1=O)Nc1ccc2c(c1)C(=O)c1ccccc1C2=O')
result = mr.mol2graph_single(mol, include_leaves=True, include_rings=True)
result = mr.combine_mol_graph([result])
assert 'ring_bond_idx' in result
assert 'ring_bond_order' in result
assert np.allclose(result['ring_scope'], np.array([[0, 27 * 2]]))
def test_combine_graphs(request):
data = get_data(request)
result = list(
mr.combine_mol_graph([
mr.mol2graph_single(me.get_mol(s)) for s in data['smiles']
]).values())
expected = data['graph_stereo']
def _compare_tensor(a, b):
return np.allclose(a, b[:a.shape[0], :])
assert _compare_tensor(result[0], expected[0])
def test_mol2graph_single(request):
data = get_data(request)
mol = me.get_mol(data['smiles'][0])
result = list(mr.mol2graph_single(mol).values())
expected = data['graph_nostereo']
def _compare_tensor(a, b):
return np.allclose(a, b[:a.shape[0], :])
assert _compare_tensor(result[0], expected[0])
assert _compare_tensor(result[1], expected[1][1:])
def test_mol2graph_single_rings_leaves():
mol = me.get_mol(
'O=C(Cn1nc(C(=O)[O-])c2ccccc2c1=O)Nc1ccc2c(c1)C(=O)c1ccccc1C2=O')
result = mr.mol2graph_single(mol, include_leaves=True)
assert 'leaf_ring' in result
assert 'leaf_atom' in result
assert result['leaf_atom'].tolist() == [0, 7, 8, 16, 25, 33]
assert result['leaf_ring'][0][0].tolist() == [0] * 6 + [1] * 6
assert result['leaf_ring'][0][1].tolist() == [9, 10, 11, 12, 13, 14
] + [26, 27, 28, 29, 30, 31]
assert result['leaf_ring'][1].tolist() == [pytest.approx(1 / np.sqrt(6))
] * 12
