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# 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
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