Integerating few utils (4ee456d3) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/mol_graph_conv_featurizer.py

+16 −27

Original line number	Diff line number	Diff line
		@@ -18,6 +18,10 @@ 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
		from deepchem.utils.molecule_feature_utils import get_bond_stereo_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.rdkit_utils import compute_all_pairs_shortest_path
		from deepchem.utils.rdkit_utils import compute_pairwise_ring_info


		def _construct_atom_feature(
		@@ -219,27 +223,10 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
		edge_features=bond_features)


		from deepchem.feat import MolecularFeaturizer
		import numpy as np
		from deepchem.feat.graph_data import GraphData


		class PAGTNFeaturizer(MolecularFeaturizer):

		def __init__(self, max_length=5):

		try:
		from rdkit import Chem
		from dgllife.utils import ConcatFeaturizer
		from dgllife.utils import atom_formal_charge_one_hot, atom_type_one_hot, atom_degree_one_hot
		from dgllife.utils import atom_explicit_valence_one_hot, atom_implicit_valence_one_hot
		from dgllife.utils import atom_is_aromatic
		from functools import partial
		from dgllife.utils import one_hot_encoding
		from dgllife.utils import bond_type_one_hot, ConcatFeaturizer, bond_is_conjugated, bond_is_in_ring
		except:
		raise ImportError(
		"This class requires Rdkit & DGLLifeSci to be installed.")
		self.SYMBOLS = [
		'C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na', 'Ca', 'Fe',
		'As', 'Al', 'I', 'B', 'V', 'K', 'Tl', 'Yb', 'Sb', 'Sn', 'Ag', 'Pd',
		@@ -251,15 +238,13 @@ class PAGTNFeaturizer(MolecularFeaturizer):

		self.RING_TYPES = [(5, False), (5, True), (6, False), (6, True)]
		self.ordered_pair = lambda a, b: (a, b) if a < b else (b, a)
		self.bond_featurizer = ConcatFeaturizer(
		[bond_type_one_hot, bond_is_conjugated, bond_is_in_ring])
		self.max_length = 5

		def PAGTNAtomFeaturizer(atom):
		def PAGTNAtomFeaturizer(self, atom):
		atom_type = get_atom_type_one_hot(atom, self.SYMBOLS, False)
		formal_charge = get_atom_formal_charge(atom)
		degree = get_atom_total_degree_one_hot(atom, 10, False)
		exp_valence = atom_explicit_valence_one_hot(atom, list(range(7)), 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([
		@@ -291,7 +276,10 @@ class PAGTNFeaturizer(MolecularFeaturizer):

		for path_idx in range(self.max_length):
		if path_idx < len(path_bonds):
		features.append(self.bond_featurizer(path_bonds[path_idx]))
		bond_type = get_bond_type_one_hot(path_bonds[path_idx])
		conjugacy = get_bond_is_conjugated_one_hot(path_bonds[path_idx])
		ring_attach = get_bond_is_in_same_ring_one_hot(path_bonds[path_idx])
		features.append(np.concatenate([bond_type, conjugacy, ring_attach]))
		else:
		features.append([0, 0, 0, 0, 0, 0])

		@@ -302,14 +290,15 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		features.append(position_feature)
		if ring_info:
		rfeat = [
		one_hot_encoding(r, allowable_set=self.RING_TYPES) for r in ring_info
		get_atom_type_one_hot(r, allowable_set=self.RING_TYPES)
		for r in ring_info
		]
		rfeat = [True] + np.any(rfeat, axis=0).tolist()
		features.append(rfeat)
		else:
		# This will return a boolean vector with all entries False
		features.append(
		[False] + one_hot_encoding(ring_info, allowable_set=self.RING_TYPES))
		features.append([False] + get_atom_type_one_hot(
		ring_info, allowable_set=self.RING_TYPES))
		return np.concatenate(features, axis=0)

		def PAGTNBondFeaturizer(self, mol):
		@@ -327,9 +316,9 @@ class PAGTNFeaturizer(MolecularFeaturizer):

		n_atoms = mol.GetNumAtoms()
		# To get the shortest paths between two nodes.
		paths_dict = utils.compute_all_pairs_shortest_path(mol)
		paths_dict = compute_all_pairs_shortest_path(mol)
		# To get info if two nodes belong to the same ring.
		rings_dict = utils.compute_pairwise_ring_info(mol)
		rings_dict = compute_pairwise_ring_info(mol)
		# Featurizer
		feats = []
		src = []

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