def get_input_features(self, mol):
type_check_num_atoms(mol, self.max_atoms)
atoms = self.create_atoms(mol)
i_jbond_dict = self.create_ijbonddict(mol)
subgraph_array = self.extract_subgraph(atoms, i_jbond_dict,
self.radius)
adj_array = construct_discrete_edge_matrix(mol)
return subgraph_array, adj_array
def get_input_features(self, mol):
"""get input features
Args:
mol (Mol):
Returns:
"""
type_check_num_atoms(mol, self.max_atoms)
atom_array = construct_atomic_number_array(mol, out_size=self.out_size)
adj_array = construct_discrete_edge_matrix(mol, out_size=self.out_size)
return atom_array, adj_array
def get_input_features(self, mol):
"""get input features
Args:
mol (Mol): Molecule input
Returns:
"""
type_check_num_atoms(mol, self.max_atoms)
atom_array = construct_atomic_number_array(mol, out_size=self.out_size)
adj_array = construct_discrete_edge_matrix(mol, out_size=self.out_size)
return atom_array, adj_array
def get_input_features(self, mol):
"""get input features
Args:
mol (Mol): Molecule input
Returns:
"""
type_check_num_atoms(mol, self.max_atoms)
atom_array = construct_atomic_number_array(mol, out_size=self.out_size)
adj_array = construct_discrete_edge_matrix(mol, out_size=self.out_size)
super_node_x = construct_supernode_feature(
mol, atom_array, adj_array, out_size=self.out_size_super)
return atom_array, adj_array, super_node_x
def test_construct_super_node_feature_adj_ndim3(sample_molecule):
adj = common.construct_discrete_edge_matrix(sample_molecule)
atom_array = common.construct_atomic_number_array(sample_molecule)
s = common.construct_supernode_feature(sample_molecule, atom_array, adj)
assert s.shape == (MAX_ATOMIC_NUM * 2 + 10, )
assert s[0] == len(atom_array)
assert s[1] == adj.sum()
assert s[2] == 1
assert s[3] == 1
assert s[4] == 0
assert s[5] == 0
assert pytest.approx(s[6], 1 * 2 / adj.sum()) # symmetric
assert pytest.approx(s[7], 2 * 2 / adj.sum()) # symmetric
assert s[8] == 0
assert s[9] == 0
assert s[9 + 6] == 1 # C
assert s[9 + 6] == 1 # N
assert s[9 + 7] == 1 # O
assert s[9 + MAX_ATOMIC_NUM] == 0 # other
assert s[9 + MAX_ATOMIC_NUM + 6] == 2 / len(atom_array)
assert s[9 + MAX_ATOMIC_NUM + 7] == 1 / len(atom_array)
assert s[9 + MAX_ATOMIC_NUM + 8] == 1 / len(atom_array)
assert s[9 + MAX_ATOMIC_NUM * 2] == 0
def get_input_features(self, mol):
"""get input features
Args:
mol (Mol):
Returns: (atom, feature_dim)
"""
# type_check_num_atoms(mol, self.max_atoms)
# atom_array = construct_atomic_number_array(mol, out_size=self.out_size)
# adj_array = construct_adj_matrix(mol, out_size=self.out_size)
# return atom_array, adj_array
graph = MolGraph()
atoms_by_rd_idx = {}
for atom in mol.GetAtoms():
new_atom_node = graph.new_node('atom',
features=atom_features(atom),
rdkit_ix=atom.GetIdx())
atoms_by_rd_idx[atom.GetIdx()] = new_atom_node
for bond in mol.GetBonds():
atom1_node = atoms_by_rd_idx[bond.GetBeginAtom().GetIdx()]
atom2_node = atoms_by_rd_idx[bond.GetEndAtom().GetIdx()]
new_bond_node = graph.new_node('bond',
features=bond_features(bond))
new_bond_node.add_neighbors((atom1_node, atom2_node))
atom1_node.add_neighbors((atom2_node, ))
mol_node = graph.new_node('molecule')
mol_node.add_neighbors(graph.nodes['atom'])
atom_array = graph.feature_array('atom')
atom_array = atom_array.astype(dtype=np.float32)
adj_array = construct_discrete_edge_matrix(mol, out_size=self.out_size)
return atom_array, adj_array
def test_truncated(self, sample_molecule_2):
with pytest.raises(ValueError):
adj = common.construct_discrete_edge_matrix(sample_molecule_2,
6) # NOQA
def test_padding(self, sample_molecule_2):
adj = common.construct_discrete_edge_matrix(sample_molecule_2, 8)
assert adj.shape == (4, 8, 8)
expect = extend_adj(self.expect_adj, out_size=8, axis=[-1, -2])
numpy.testing.assert_equal(adj, expect)
def test_add_self_connection_channel(self, sample_molecule_2):
adj = common.construct_discrete_edge_matrix(
sample_molecule_2, add_self_connection_channel=True)
assert adj.shape == (5, 7, 7)
numpy.testing.assert_equal(adj[:4], self.expect_adj)
numpy.testing.assert_equal(adj[4], numpy.eye(7, 7))
def test_default(self, sample_molecule_2):
adj = common.construct_discrete_edge_matrix(sample_molecule_2)
assert adj.shape == (4, 7, 7)
numpy.testing.assert_equal(adj, self.expect_adj)
def test_truncated(self, sample_molecule_2):
with pytest.raises(ValueError):
adj = common.construct_discrete_edge_matrix(sample_molecule_2, 6) # NOQA
def test_padding(self, sample_molecule_2):
adj = common.construct_discrete_edge_matrix(sample_molecule_2, 8)
assert adj.shape == (4, 8, 8)
expect = extend_adj(self.expect_adj, out_size=8, axis=[-1, -2])
numpy.testing.assert_equal(adj, expect)
def test_default(self, sample_molecule_2):
adj = common.construct_discrete_edge_matrix(sample_molecule_2)
assert adj.shape == (4, 7, 7)
numpy.testing.assert_equal(adj, self.expect_adj)
