Merge pull request #582 from lilleswing/test-docs

  def test_carbon_nitrogen(self):

    """Test on carbon nitrogen molecule"""

    # Note there is a central carbon of degree 4, with 3 carbons and

    # one nitrogen of degree 1 (connected only to central carbon).

    # Note there is a central nitrogen of degree 4, with 4 carbons

    # of degree 1 (connected only to central nitrogen).

    raw_smiles = ['C[N+](C)(C)C']

    mols = [rdkit.Chem.MolFromSmiles(s) for s in raw_smiles]

    featurizer = ConvMolFeaturizer()

    # Get the adjacency lists grouped by degree

    deg_adj_lists = mol.get_deg_adjacency_lists()

    assert np.array_equal(deg_adj_lists[0], np.zeros([0, 0], dtype=np.int32))

    # The 4 outer atoms connected to central carbon

    # The 4 outer atoms connected to central nitrogen

    assert np.array_equal(deg_adj_lists[1],

                          np.array([[4], [4], [4], [4]], dtype=np.int32))

    assert np.array_equal(deg_adj_lists[2], np.zeros([0, 2], dtype=np.int32))

    assert np.array_equal(deg_adj_lists[3], np.zeros([0, 3], dtype=np.int32))

    # Central carbon connected to everything else.

    # Central nitrogen connected to everything else.

    assert np.array_equal(deg_adj_lists[4],

                          np.array([[0, 1, 2, 3]], dtype=np.int32))

    assert np.array_equal(deg_adj_lists[5], np.zeros([0, 5], dtype=np.int32))