data/features.py

# 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],
    'posible_explicit_valence': [1, 2, 3, 4, 5, 6, 7, 'misc'],
    'posible_implicit_valence': [1, 2, 3, 4, 5, 6, 7, 'misc']
}

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

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

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

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

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