def test_get_atom_is_in_aromatic_one_hot(self):
atoms = self.mol.GetAtoms()
assert atoms[0].GetSymbol() == "C"
one_hot = get_atom_is_in_aromatic_one_hot(atoms[0])
assert one_hot == [0.0]
atoms = self.mol_benzene.GetAtoms()
assert atoms[0].GetSymbol() == "C"
one_hot = get_atom_is_in_aromatic_one_hot(atoms[0])
assert one_hot == [1.0]
def _pagtn_atom_featurizer(self, atom: RDKitAtom) -> np.ndarray:
"""Calculate Atom features from RDKit atom object.
Parameters
----------
mol: rdkit.Chem.rdchem.Mol
RDKit mol object.
Returns
-------
atom_feat: np.ndarray
numpy vector of atom features.
"""
atom_type = get_atom_type_one_hot(atom, self.SYMBOLS, False)
formal_charge = get_atom_formal_charge_one_hot(
atom, include_unknown_set=False)
degree = get_atom_total_degree_one_hot(atom, list(range(11)), False)
exp_valence = get_atom_explicit_valence_one_hot(
atom, list(range(7)), False)
imp_valence = get_atom_implicit_valence_one_hot(
atom, list(range(6)), False)
armoticity = get_atom_is_in_aromatic_one_hot(atom)
atom_feat = np.concatenate([
atom_type, formal_charge, degree, exp_valence, imp_valence,
armoticity
])
return atom_feat
def _construct_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int,
str]],
sssr: List[Sequence]) -> List[float]:
"""Construct an atom feature from a RDKit atom object.
Parameters
----------
atom: rdkit.Chem.rdchem.Atom
RDKit atom object
h_bond_infos: List[Tuple[int, str]]
A list of tuple `(atom_index, hydrogen_bonding_type)`.
Basically, it is expected that this value is the return value of
`construct_hydrogen_bonding_info`. The `hydrogen_bonding_type`
value is "Acceptor" or "Donor".
sssr: List[Sequence]
The return value of `Chem.GetSymmSSSR(mol)`.
The value is a sequence of rings.
Returns
-------
List[float]
A one-hot vector of the atom feature.
"""
atom_type = get_atom_type_one_hot(atom)
chirality = get_atom_chirality_one_hot(atom)
formal_charge = get_atom_formal_charge(atom)
partial_charge = get_atom_partial_charge(atom)
ring_size = get_atom_ring_size_one_hot(atom, sssr)
hybridization = get_atom_hybridization_one_hot(atom)
acceptor_donor = get_atom_hydrogen_bonding_one_hot(atom, h_bond_infos)
aromatic = get_atom_is_in_aromatic_one_hot(atom)
degree = get_atom_total_degree_one_hot(atom)
total_num = get_atom_total_num_Hs_one_hot(atom)
return atom_type + chirality + formal_charge + partial_charge + \
ring_size + hybridization + acceptor_donor + aromatic + degree + total_num
def _construct_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int,
str]],
use_chirality: bool,
use_partial_charge: bool) -> np.ndarray:
"""Construct an atom feature from a RDKit atom object.
Parameters
----------
atom: rdkit.Chem.rdchem.Atom
RDKit atom object
h_bond_infos: List[Tuple[int, str]]
A list of tuple `(atom_index, hydrogen_bonding_type)`.
Basically, it is expected that this value is the return value of
`construct_hydrogen_bonding_info`. The `hydrogen_bonding_type`
value is "Acceptor" or "Donor".
use_chirality: bool
Whether to use chirality information or not.
use_partial_charge: bool
Whether to use partial charge data or not.
Returns
-------
np.ndarray
A one-hot vector of the atom feature.
"""
atom_type = get_atom_type_one_hot(atom)
formal_charge = get_atom_formal_charge(atom)
hybridization = get_atom_hybridization_one_hot(atom)
acceptor_donor = get_atom_hydrogen_bonding_one_hot(atom, h_bond_infos)
aromatic = get_atom_is_in_aromatic_one_hot(atom)
degree = get_atom_total_degree_one_hot(atom)
total_num_Hs = get_atom_total_num_Hs_one_hot(atom)
atom_feat = np.concatenate([
atom_type, formal_charge, hybridization, acceptor_donor, aromatic,
degree, total_num_Hs
])
if use_chirality:
chirality = get_atom_chirality_one_hot(atom)
atom_feat = np.concatenate([atom_feat, chirality])
if use_partial_charge:
partial_charge = get_atom_partial_charge(atom)
atom_feat = np.concatenate([atom_feat, partial_charge])
return atom_feat
def _construct_atom_feature(atom: RDKitAtom, h_bond_infos: List[Tuple[int,
str]],
use_chirality: bool,
use_partial_charge: bool) -> np.ndarray:
"""Construct an atom feature from a RDKit atom object.
Parameters
----------
atom: rdkit.Chem.rdchem.Atom
RDKit atom object
h_bond_infos: List[Tuple[int, str]]
A list of tuple `(atom_index, hydrogen_bonding_type)`.
Basically, it is expected that this value is the return value of
`construct_hydrogen_bonding_info`. The `hydrogen_bonding_type`
value is "Acceptor" or "Donor".
use_chirality: bool
Whether to use chirality information or not.
use_partial_charge: bool
Whether to use partial charge data or not.
Returns
-------
np.ndarray
A one-hot vector of the atom feature.
44+1+5+2+1+12+6+8+7+1+1+2+1 = 91 features
"""
atom_type = get_atom_type_one_hot(atom,
USER_ATOM_TYPE_SET,
include_unknown_set=True)
formal_charge = get_atom_formal_charge(atom)
hybridization = get_atom_hybridization_one_hot(atom,
USER_HYBRIDIZATION_SET,
include_unknown_set=False)
acceptor_donor = get_atom_hydrogen_bonding_one_hot(atom, h_bond_infos)
aromatic = get_atom_is_in_aromatic_one_hot(atom)
degree = get_atom_total_degree_one_hot(atom,
USER_TOTAL_DEGREE_SET,
include_unknown_set=True)
total_num_Hs = get_atom_total_num_Hs_one_hot(atom,
DEFAULT_TOTAL_NUM_Hs_SET,
include_unknown_set=True)
atom_feat = np.concatenate([
atom_type, formal_charge, hybridization, acceptor_donor, aromatic,
degree, total_num_Hs
])
### user additional features ####
if True:
imp_valence = get_atom_implicit_valence_one_hot(
atom, DEFAULT_ATOM_IMPLICIT_VALENCE_SET, include_unknown_set=True)
exp_valence = get_atom_explicit_valence_one_hot(
atom, DEFAULT_ATOM_EXPLICIT_VALENCE_SET, include_unknown_set=True)
atom_feat = np.concatenate([
atom_feat,
imp_valence,
exp_valence,
[
atom.HasProp('_ChiralityPossible'),
atom.GetNumRadicalElectrons()
],
])
########### END ############
if use_chirality:
# chirality = get_atom_chirality_one_hot(atom)
chirality = get_atom_chirality_one_hot(atom)
atom_feat = np.concatenate([atom_feat, np.array(chirality)])
if use_partial_charge:
partial_charge = get_atom_partial_charge(atom)
atom_feat = np.concatenate([atom_feat, np.array(partial_charge)])
return atom_feat
