changes (659631da) · Commits · 钟慕尧 / deepchem

deepchem/feat/graph_features.py

+2 −0

Original line number	Diff line number	Diff line
		@@ -116,6 +116,7 @@ def atom_features(atom,
		if bool_id_feat:
		return np.array([atom_to_id(atom)])
		else:
		from rdkit import Chem
		results = one_of_k_encoding_unk(
		atom.GetSymbol(),
		[
		@@ -189,6 +190,7 @@ def atom_features(atom,


		def bond_features(bond, use_chirality=False):
		from rdkit import Chem
		bt = bond.GetBondType()
		bond_feats = [
		bt == Chem.rdchem.BondType.SINGLE, bt == Chem.rdchem.BondType.DOUBLE,

+1 −1

Original line number	Diff line number	Diff line
		@@ -3,7 +3,6 @@
		from __future__ import division
		from __future__ import unicode_literals

		from rdkit import Chem
		from deepchem.feat import Featurizer


		@@ -13,6 +12,7 @@ class RawFeaturizer(Featurizer):
		self.smiles = smiles

		def _featurize(self, mol):
		from rdkit import Chem
		if self.smiles:
		return Chem.MolToSmiles(mol)
		else:

+4 −2

Original line number	Diff line number	Diff line
		@@ -14,8 +14,6 @@ import tempfile
		import hashlib
		import multiprocessing
		from collections import Counter
		from rdkit import Chem
		from rdkit.Chem import AllChem
		from deepchem.utils.rdkit_util import load_molecule
		from deepchem.utils.rdkit_util import MoleculeLoadException

		@@ -194,6 +192,7 @@ def compute_all_ecfp(mol, indices=None, degree=2):
		"""

		ecfp_dict = {}
		from rdkit import Chem
		for i in range(mol.GetNumAtoms()):
		if indices is not None and i not in indices:
		continue
		@@ -224,6 +223,7 @@ def compute_ecfp_features(mol, ecfp_degree=2, ecfp_power=11):
		that ECFP fragment is found in the molecule and array at index j has a 0
		if ECFP fragment not in molecule.
		"""
		from rdkit.Chem import AllChem
		bv = AllChem.GetMorganFingerprintAsBitVect(
		mol, ecfp_degree, nBits=2**ecfp_power)
		return np.array(bv)
		@@ -511,6 +511,7 @@ def compute_pi_stack(protein,

		protein_aromatic_rings = []
		ligand_aromatic_rings = []
		from rdkit import Chem
		for mol, ring_list in ((protein, protein_aromatic_rings),
		(ligand, ligand_aromatic_rings)):
		aromatic_atoms = {atom.GetIdx() for atom in mol.GetAromaticAtoms()}
		@@ -630,6 +631,7 @@ def compute_cation_pi(mol1, mol2, charge_tolerance=0.01, **kwargs):
		conformer = mol2.GetConformer()

		aromatic_atoms = set(atom.GetIdx() for atom in mol1.GetAromaticAtoms())
		from rdkit import Chem
		rings = [list(r) for r in Chem.GetSymmSSSR(mol1)]

		for ring in rings:

+3 −3

Original line number	Diff line number	Diff line
		from unittest import TestCase

		from nose.tools import assert_equals
		from rdkit import Chem

		import deepchem as dc
		from nose.tools import assert_equals


		class TestOneHotFeaturizer(TestCase):
		"""Tests for the one-hot featurizer."""

		def test_featurize(self):
		from rdkit import Chem
		smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]
		mols = [Chem.MolFromSmiles(smile) for smile in smiles]
		featurizer = dc.feat.one_hot.OneHotFeaturizer(dc.feat.one_hot.zinc_charset)

+1 −1

Original line number	Diff line number	Diff line
		@@ -5,7 +5,6 @@ import os
		import logging
		import numpy as np
		import unittest
		from rdkit import Chem
		from deepchem.utils import conformers
		from deepchem.feat.atomic_coordinates import get_coords
		from deepchem.feat.atomic_coordinates import AtomicCoordinates
		@@ -26,6 +25,7 @@ class TestAtomicCoordinates(unittest.TestCase):
		Set up tests.
		"""
		smiles = 'CC(=O)OC1=CC=CC=C1C(=O)O'
		from rdkit import Chem
		mol = Chem.MolFromSmiles(smiles)
		engine = conformers.ConformerGenerator(max_conformers=1)
		self.mol = engine.generate_conformers(mol)