Project: s41467-025-62235-6 | Function: get_atom_value (python)

system: You are an expert Python programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow Python best practices and maintain consistent code style.
Return **only** the complete Python function code.

user: Complete this Python function:

**DESCRIPTION:** Implements comprehensive molecular atom feature extraction for drug representation learning. This function extracts multiple atomic properties including electronic configuration, chemical bonding characteristics, ring topology, and stereochemistry to create rich molecular representations essential for drug-target interaction prediction.

**KEY TERMS:** {
  "atomic_num": "atomic number for element identification",
  "degree": "number of bonded neighbors",
  "formal_charge": "formal charge on atom",
  "hybridization": "orbital hybridization state",
  "is_aromatic": "aromaticity flag",
  "valence_out_shell": "outer shell electron count",
  "chiral_tag": "stereochemical configuration",
  "total_numHs": "total hydrogen count"
}

**CONTEXT CODE:** 
class CompoundKit(object):
    """
    CompoundKit
    """
    atom_vocab_dict = {
        "atomic_num": list(range(1, 200)) + ['misc'],
        "chiral_tag": rdchem_enum_to_list(rdchem.ChiralType.values),
        "degree": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 'misc'],
        "explicit_valence": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 'misc'],
        "formal_charge": [-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 'misc'],
        "hybridization": rdchem_enum_to_list(rdchem.HybridizationType.values),
        "implicit_valence": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 'misc'],
        "is_aromatic": [0, 1],
        "total_numHs": [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'num_radical_e': [0, 1, 2, 3, 4, 'misc'],
        'atom_is_in_ring': [0, 1],
        'valence_out_shell': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size3': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size4': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size5': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size6': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size7': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
        'in_num_ring_with_size8': [0, 1, 2, 3, 4, 5, 6, 7, 8, 'misc'],
    }
    bond_vocab_dict = {
        "bond_dir": rdchem_enum_to_list(rdchem.BondDir.values),
        "bond_type": rdchem_enum_to_list(rdchem.BondType.values),
        "is_in_ring": [0, 1],

        'bond_stereo': rdchem_enum_to_list(rdchem.BondStereo.values),
        'is_conjugated': [0, 1],
    }
    # float features
    atom_float_names = ["van_der_waals_radis", "partial_charge", 'mass']
    # bond_float_feats= ["bond_length", "bond_angle"]     # optional

    ### functional groups
    # day_light_fg_smarts_list = DAY_LIGHT_FG_SMARTS_LIST
    # day_light_fg_mo_list = [Chem.MolFromSmarts(smarts) for smarts in day_light_fg_smarts_list]

    morgan_fp_N = 200
    morgan2048_fp_N = 2048
    maccs_fp_N = 167

    period_table = Chem.GetPeriodicTable()

    ### atom

    @staticmethod
    def get_atom_value(atom, name):
        raise NotImplementedError("get_atom_value function has been masked for testing purposes")
        """get atom values"""
        if name == 'atomic_num':
            return atom.GetAtomicNum()
        elif name == 'chiral_tag':
            return atom.GetChiralTag()
        elif name == 'degree':
            return atom.GetDegree()
        elif name == 'explicit_valence':
            return atom.GetExplicitValence()
        elif name == 'formal_charge':
            return atom.GetFormalCharge()
        elif name == 'hybridization':
            return atom.GetHybridization()
        elif name == 'implicit_valence':
            return atom.GetImplicitValence()
        elif name == 'is_aromatic':
            return int(atom.GetIsAromatic())
        elif name == 'mass':
            return int(atom.GetMass())
        elif name == 'total_numHs':
            return atom.GetTotalNumHs()
        elif name == 'num_radical_e':
            return atom.GetNumRadicalElectrons()
        elif name == 'atom_is_in_ring':
            return int(atom.IsInRing())
        elif name == 'valence_out_shell':
            return CompoundKit.period_table.GetNOuterElecs(atom.GetAtomicNum())
        else:
            raise ValueError(name)

    @staticmethod
    def get_atom_feature_id(atom, name):
        """get atom features id"""
        assert name in CompoundKit.atom_vocab_dict, "%s not found in atom_vocab_dict" % name
        return safe_index(CompoundKit.atom_vocab_dict[name], CompoundKit.get_atom_value(atom, name))

    @staticmethod
    def get_atom_feature_size(name):
        """get atom features size"""
        assert name in CompoundKit.atom_vocab_dict, "%s not found in atom_vocab_dict" % name
        return len(CompoundKit.atom_vocab_dict[name])

    ### bond

    @staticmethod
    def get_bond_value(bond, name):
        """get bond values"""
        if name == 'bond_dir':
            return bond.GetBondDir()
        elif name == 'bond_type':
            return bond.GetBondType()
        elif name == 'is_in_ring':
            return int(bond.IsInRing())
        elif name == 'is_conjugated':
            return int(bond.GetIsConjugated())
        elif name == 'bond_stereo':
            return bond.GetStereo()
        else:
            raise ValueError(name)

    @staticmethod
    def get_bond_feature_id(bond, name):
        """get bond features id"""
        assert name in CompoundKit.bond_vocab_dict, "%s not found in bond_vocab_dict" % name
        return safe_index(CompoundKit.bond_vocab_dict[name], CompoundKit.get_bond_value(bond, name))

    @staticmethod
    def get_bond_feature_size(name):
        """get bond features size"""
        assert name in CompoundKit.bond_vocab_dict, "%s not found in bond_vocab_dict" % name
        return len(CompoundKit.bond_vocab_dict[name])

    ### fingerprint

    @staticmethod
    def get_morgan_fingerprint(mol, radius=2):
        """get morgan fingerprint"""
        nBits = CompoundKit.morgan_fp_N
        mfp = AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=nBits)
        return [int(b) for b in mfp.ToBitString()]

    @staticmethod
    def get_morgan2048_fingerprint(mol, radius=2):
        """get morgan2048 fingerprint"""
        nBits = CompoundKit.morgan2048_fp_N
        mfp = AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=nBits)
        return [int(b) for b in mfp.ToBitString()]

    @staticmethod
    def get_maccs_fingerprint(mol):
        """get maccs fingerprint"""
        fp = AllChem.GetMACCSKeysFingerprint(mol)
        return [int(b) for b in fp.ToBitString()]

    ### functional groups

    @staticmethod
    def get_daylight_functional_group_counts(mol):


Complete the function implementation replacing "raise NotImplementedError".