Merge pull request #2484 from VIGNESHinZONE/util (f8ded19b) · Commits · 钟慕尧 / deepchem

deepchem/utils/molecule_feature_utils.py

+56 −0

Original line number	Diff line number	Diff line
		@@ -35,6 +35,8 @@ DEFAULT_RING_SIZE_SET = [3, 4, 5, 6, 7, 8]
		DEFAULT_BOND_TYPE_SET = ["SINGLE", "DOUBLE", "TRIPLE", "AROMATIC"]
		DEFAULT_BOND_STEREO_SET = ["STEREONONE", "STEREOANY", "STEREOZ", "STEREOE"]
		DEFAULT_GRAPH_DISTANCE_SET = [1, 2, 3, 4, 5, 6, 7]
		DEFAULT_ATOM_IMPLICIT_VALENCE_SET = [0, 1, 2, 3, 4, 5, 6]
		DEFAULT_ATOM_EXPLICIT_VALENCE_SET = [1, 2, 3, 4, 5, 6]


		class _ChemicalFeaturesFactory:
		@@ -356,6 +358,60 @@ def get_atom_total_degree_one_hot(
		include_unknown_set)


		def get_atom_implicit_valence_one_hot(
		atom: RDKitAtom,
		allowable_set: List[int] = DEFAULT_ATOM_IMPLICIT_VALENCE_SET,
		include_unknown_set: bool = True) -> List[float]:
		"""Get an one-hot feature of implicit valence of an atom.

		Parameters
		---------
		atom: rdkit.Chem.rdchem.Atom
		RDKit atom object
		allowable_set: List[int]
		Atom implicit valence to consider. The default set is `[0, 1, ..., 6]`
		include_unknown_set: bool, default True
		If true, the index of all types not in `allowable_set` is `len(allowable_set)`.

		Returns
		-------
		List[float]
		A one-hot vector of implicit valence an atom has.
		If `include_unknown_set` is False, the length is `len(allowable_set)`.
		If `include_unknown_set` is True, the length is `len(allowable_set) + 1`.

		"""
		return one_hot_encode(atom.GetImplicitValence(), allowable_set,
		include_unknown_set)


		def get_atom_explicit_valence_one_hot(
		atom: RDKitAtom,
		allowable_set: List[int] = DEFAULT_ATOM_EXPLICIT_VALENCE_SET,
		include_unknown_set: bool = True) -> List[float]:
		"""Get an one-hot feature of explicit valence of an atom.

		Parameters
		---------
		atom: rdkit.Chem.rdchem.Atom
		RDKit atom object
		allowable_set: List[int]
		Atom explicit valence to consider. The default set is `[1, ..., 6]`
		include_unknown_set: bool, default True
		If true, the index of all types not in `allowable_set` is `len(allowable_set)`.

		Returns
		-------
		List[float]
		A one-hot vector of explicit valence an atom has.
		If `include_unknown_set` is False, the length is `len(allowable_set)`.
		If `include_unknown_set` is True, the length is `len(allowable_set) + 1`.

		"""
		return one_hot_encode(atom.GetExplicitValence(), allowable_set,
		include_unknown_set)


		#################################################################
		# bond (edge) featurization
		#################################################################

deepchem/utils/rdkit_utils.py

+68 −0

Original line number	Diff line number	Diff line
		@@ -626,3 +626,71 @@ def compute_ring_normal(mol, ring_indices):
		v2 = points[2] - points[0]
		normal = np.cross(v1, v2)
		return normal


		def compute_all_pairs_shortest_path(
		mol) -> Dict[Tuple[int, int], Tuple[int, int]]:
		"""Computes the All pair shortest between every pair of nodes
		in terms of Rdkit Atom indexes.

		Parameters:
		-----------
		mol: rdkit.rdchem.Mol
		Molecule containing a ring

		Returns:
		--------
		paths_dict: Dict representing every atom-atom pair as key in Rdkit index
		and value as the shortest path between each atom pair in terms of Atom index.
		"""
		try:
		from rdkit import Chem
		except:
		raise ImportError("This class requires RDkit installed")
		n_atoms = mol.GetNumAtoms()
		paths_dict = {(i, j): Chem.rdmolops.GetShortestPath(mol, i, j)
		for i in range(n_atoms) for j in range(n_atoms) if i < j}
		return paths_dict


		def compute_pairwise_ring_info(mol):
		""" Computes all atom-atom pair belong to same ring with
		its ring size and its aromaticity.

		Parameters:
		-----------
		mol: rdkit.rdchem.Mol
		Molecule containing a ring

		Returns:
		--------
		rings_dict: Key consisting of all node-node pair sharing the same ring
		and value as a tuple of size of ring and its aromaticity.
		"""
		try:
		from rdkit import Chem
		except:
		raise ImportError("This class requires RDkit installed")
		rings_dict = {}

		def ordered_pair(a, b):
		return (a, b) if a < b else (b, a)

		ssr = [list(x) for x in Chem.GetSymmSSSR(mol)]
		for ring in ssr:
		ring_sz = len(ring)
		is_aromatic = True
		for atom_idx in ring:
		if not mol.GetAtoms()[atom_idx].GetIsAromatic():
		is_aromatic = False
		break
		for ring_idx, atom_idx in enumerate(ring):
		for other_idx in ring[ring_idx:]:
		atom_pair = ordered_pair(atom_idx, other_idx)
		if atom_pair not in rings_dict:
		rings_dict[atom_pair] = [(ring_sz, is_aromatic)]
		else:
		if (ring_sz, is_aromatic) not in rings_dict[atom_pair]:
		rings_dict[atom_pair].append((ring_sz, is_aromatic))

		return rings_dict

deepchem/utils/test/test_molecule_feature_utils.py

+22 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,8 @@ from deepchem.utils.molecule_feature_utils import get_atom_chirality_one_hot
		from deepchem.utils.molecule_feature_utils import get_atom_formal_charge
		from deepchem.utils.molecule_feature_utils import get_atom_partial_charge
		from deepchem.utils.molecule_feature_utils import get_atom_total_degree_one_hot
		from deepchem.utils.molecule_feature_utils import get_atom_implicit_valence_one_hot
		from deepchem.utils.molecule_feature_utils import get_atom_explicit_valence_one_hot
		from deepchem.utils.molecule_feature_utils import get_bond_type_one_hot
		from deepchem.utils.molecule_feature_utils import get_bond_is_in_same_ring_one_hot
		from deepchem.utils.molecule_feature_utils import get_bond_is_conjugated_one_hot
		@@ -140,6 +142,26 @@ class TestGraphConvUtils(unittest.TestCase):
		one_hot = get_atom_total_degree_one_hot(atoms[3])
		assert one_hot == [0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0]

		def test_get_atom_implicit_valence_one_hot(self):
		atoms = self.mol.GetAtoms()
		assert atoms[0].GetSymbol() == "C"
		one_hot = get_atom_implicit_valence_one_hot(atoms[0])
		assert one_hot == [0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0]

		assert atoms[3].GetSymbol() == "O"
		one_hot = get_atom_implicit_valence_one_hot(atoms[3])
		assert one_hot == [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]

		def test_get_atom_explicit_valence_one_hot(self):
		atoms = self.mol.GetAtoms()
		assert atoms[0].GetSymbol() == "C"
		one_hot = get_atom_explicit_valence_one_hot(atoms[0])
		assert one_hot == [1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]

		assert atoms[3].GetSymbol() == "O"
		one_hot = get_atom_explicit_valence_one_hot(atoms[3])
		assert one_hot == [0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0]

		def test_get_bond_type_one_hot(self):
		bonds = self.mol.GetBonds()
		one_hot = get_bond_type_one_hot(bonds[0])

deepchem/utils/test/test_rdkit_utils.py

+25 −0

Original line number	Diff line number	Diff line
		@@ -162,3 +162,28 @@ class TestRdkitUtil(unittest.TestCase):

		def test_strip_hydrogens(self):
		pass

		def test_all_shortest_pairs(self):
		from rdkit import Chem
		mol = Chem.MolFromSmiles("CN=C=O")
		valid_dict = {
		(0, 1): (0, 1),
		(0, 2): (0, 1, 2),
		(0, 3): (0, 1, 2, 3),
		(1, 2): (1, 2),
		(1, 3): (1, 2, 3),
		(2, 3): (2, 3)
		}
		assert rdkit_utils.compute_all_pairs_shortest_path(mol) == valid_dict

		def test_pairwise_ring_info(self):
		from rdkit import Chem
		mol = Chem.MolFromSmiles("c1ccccc1")
		predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
		assert all(pair == [(6, True)] for pair in predict_dict.values())
		mol = Chem.MolFromSmiles("c1c2ccccc2ccc1")
		predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
		assert all(pair == [(6, True)] for pair in predict_dict.values())
		mol = Chem.MolFromSmiles("CN=C=O")
		predict_dict = rdkit_utils.compute_pairwise_ring_info(mol)
		assert not predict_dict

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