# allowable multiple choice node and edge features
allowable_features = {
    "possible_atomic_num_list": list(range(1, 119)) + ["misc"],
    "possible_chirality_list": [
        "CHI_UNSPECIFIED",
        "CHI_TETRAHEDRAL_CW",
        "CHI_TETRAHEDRAL_CCW",
        "CHI_OTHER",
    ],
    "possible_degree_list": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, "misc"],
    "possible_formal_charge_list": [-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, "misc"],
    "possible_numH_list": [0, 1, 2, 3, 4, 5, 6, 7, 8, "misc"],
    "possible_number_radical_e_list": [0, 1, 2, 3, 4, "misc"],
    "possible_hybridization_list": ["SP", "SP2", "SP3", "SP3D", "SP3D2", "misc"],
    "possible_is_aromatic_list": [False, True],
    "possible_is_in_ring_list": [False, True],
    "possible_bond_type_list": ["SINGLE", "DOUBLE", "TRIPLE", "AROMATIC", "misc"],
    "possible_bond_stereo_list": [
        "STEREONONE",
        "STEREOZ",
        "STEREOE",
        "STEREOCIS",
        "STEREOTRANS",
        "STEREOANY",
    ],
    "possible_is_conjugated_list": [False, True],
}


def safe_index(l, e):
    """
    Return index of element e in list l. If e is not present, return the last index
    """
    try:
        return l.index(e)
    except:
        return len(l) - 1


# # miscellaneous case
# i = safe_index(allowable_features['possible_atomic_num_list'], 'asdf')
# assert allowable_features['possible_atomic_num_list'][i] == 'misc'
# # normal case
# i = safe_index(allowable_features['possible_atomic_num_list'], 2)
# assert allowable_features['possible_atomic_num_list'][i] == 2


def atom_to_feature_vector(atom):
    """
    Converts rdkit atom object to feature list of indices
    :param mol: rdkit atom object
    :return: list
    """
    atom_feature = [
        safe_index(allowable_features["possible_atomic_num_list"], atom.GetAtomicNum()),
        allowable_features["possible_chirality_list"].index(str(atom.GetChiralTag())),
        safe_index(allowable_features["possible_degree_list"], atom.GetTotalDegree()),
        safe_index(allowable_features["possible_formal_charge_list"], atom.GetFormalCharge()),
        safe_index(allowable_features["possible_numH_list"], atom.GetTotalNumHs()),
        safe_index(
            allowable_features["possible_number_radical_e_list"], atom.GetNumRadicalElectrons()
        ),
        safe_index(allowable_features["possible_hybridization_list"], str(atom.GetHybridization())),
        allowable_features["possible_is_aromatic_list"].index(atom.GetIsAromatic()),
        allowable_features["possible_is_in_ring_list"].index(atom.IsInRing()),
    ]
    return atom_feature


# from rdkit import Chem
# mol = Chem.MolFromSmiles('Cl[C@H](/C=C/C)Br')
# atom = mol.GetAtomWithIdx(1)  # chiral carbon
# atom_feature = atom_to_feature_vector(atom)
# assert atom_feature == [5, 2, 4, 5, 1, 0, 2, 0, 0]


def get_atom_feature_dims():
    return list(
        map(
            len,
            [
                allowable_features["possible_atomic_num_list"],
                allowable_features["possible_chirality_list"],
                allowable_features["possible_degree_list"],
                allowable_features["possible_formal_charge_list"],
                allowable_features["possible_numH_list"],
                allowable_features["possible_number_radical_e_list"],
                allowable_features["possible_hybridization_list"],
                allowable_features["possible_is_aromatic_list"],
                allowable_features["possible_is_in_ring_list"],
            ],
        )
    )


def bond_to_feature_vector(bond):
    """
    Converts rdkit bond object to feature list of indices
    :param mol: rdkit bond object
    :return: list
    """
    bond_feature = [
        safe_index(allowable_features["possible_bond_type_list"], str(bond.GetBondType())),
        allowable_features["possible_bond_stereo_list"].index(str(bond.GetStereo())),
        allowable_features["possible_is_conjugated_list"].index(bond.GetIsConjugated()),
    ]
    return bond_feature


# uses same molecule as atom_to_feature_vector test
# bond = mol.GetBondWithIdx(2)  # double bond with stereochem
# bond_feature = bond_to_feature_vector(bond)
# assert bond_feature == [1, 2, 0]


def get_bond_feature_dims():
    return list(
        map(
            len,
            [
                allowable_features["possible_bond_type_list"],
                allowable_features["possible_bond_stereo_list"],
                allowable_features["possible_is_conjugated_list"],
            ],
        )
    )


def atom_feature_vector_to_dict(atom_feature):
    [
        atomic_num_idx,
        chirality_idx,
        degree_idx,
        formal_charge_idx,
        num_h_idx,
        number_radical_e_idx,
        hybridization_idx,
        is_aromatic_idx,
        is_in_ring_idx,
    ] = atom_feature

    feature_dict = {
        "atomic_num": allowable_features["possible_atomic_num_list"][atomic_num_idx],
        "chirality": allowable_features["possible_chirality_list"][chirality_idx],
        "degree": allowable_features["possible_degree_list"][degree_idx],
        "formal_charge": allowable_features["possible_formal_charge_list"][formal_charge_idx],
        "num_h": allowable_features["possible_numH_list"][num_h_idx],
        "num_rad_e": allowable_features["possible_number_radical_e_list"][number_radical_e_idx],
        "hybridization": allowable_features["possible_hybridization_list"][hybridization_idx],
        "is_aromatic": allowable_features["possible_is_aromatic_list"][is_aromatic_idx],
        "is_in_ring": allowable_features["possible_is_in_ring_list"][is_in_ring_idx],
    }

    return feature_dict


# # uses same atom_feature as atom_to_feature_vector test
# atom_feature_dict = atom_feature_vector_to_dict(atom_feature)
# assert atom_feature_dict['atomic_num'] == 6
# assert atom_feature_dict['chirality'] == 'CHI_TETRAHEDRAL_CCW'
# assert atom_feature_dict['degree'] == 4
# assert atom_feature_dict['formal_charge'] == 0
# assert atom_feature_dict['num_h'] == 1
# assert atom_feature_dict['num_rad_e'] == 0
# assert atom_feature_dict['hybridization'] == 'SP3'
# assert atom_feature_dict['is_aromatic'] == False
# assert atom_feature_dict['is_in_ring'] == False


def bond_feature_vector_to_dict(bond_feature):
    [bond_type_idx, bond_stereo_idx, is_conjugated_idx] = bond_feature

    feature_dict = {
        "bond_type": allowable_features["possible_bond_type_list"][bond_type_idx],
        "bond_stereo": allowable_features["possible_bond_stereo_list"][bond_stereo_idx],
        "is_conjugated": allowable_features["possible_is_conjugated_list"][is_conjugated_idx],
    }

    return feature_dict


# # uses same bond as bond_to_feature_vector test
# bond_feature_dict = bond_feature_vector_to_dict(bond_feature)
# assert bond_feature_dict['bond_type'] == 'DOUBLE'
# assert bond_feature_dict['bond_stereo'] == 'STEREOE'
# assert bond_feature_dict['is_conjugated'] == False
