Partial cleanup (9ce499f2) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+6 −3

Original line number	Diff line number	Diff line
		@@ -10,9 +10,6 @@ import numpy as np
		import csv
		import numbers
		import tempfile
		from rdkit.Chem import rdmolfiles
		from rdkit.Chem import rdmolops
		from rdkit import Chem
		import time
		import sys
		from deepchem.utils.save import log
		@@ -66,6 +63,9 @@ def featurize_smiles_df(df, featurizer, field, log_every_N=1000, verbose=True):
		sample_elems = df[field].tolist()

		features = []
		from rdkit import Chem
		from rdkit.Chem import rdmolfiles
		from rdkit.Chem import rdmolops
		for ind, elem in enumerate(sample_elems):
		mol = Chem.MolFromSmiles(elem)
		# TODO (ytz) this is a bandage solution to reorder the atoms so
		@@ -91,6 +91,9 @@ def featurize_smiles_np(arr, featurizer, log_every_N=1000, verbose=True):
		features array
		"""
		features = []
		from rdkit import Chem
		from rdkit.Chem import rdmolfiles
		from rdkit.Chem import rdmolops
		for ind, elem in enumerate(arr.tolist()):
		mol = Chem.MolFromSmiles(elem)
		if mol:

+1 −2

Original line number	Diff line number	Diff line
		from collections import deque

		from rdkit import Chem

		import sys
		import tensorflow as tf
		import pickle
		@@ -160,6 +158,7 @@ class AdjacencyFingerprint(Featurizer):
		def featurize(self, rdkit_mols):
		featurized_mols = np.empty((len(rdkit_mols)), dtype=object)

		from rdkit import Chem
		for idx, mol in enumerate(rdkit_mols):
		if self.add_hydrogens:
		mol = Chem.AddHs(mol)

+0 −2

Original line number	Diff line number	Diff line
		@@ -4,8 +4,6 @@ Feature calculations.
		import logging
		import types
		import numpy as np
		from rdkit import Chem
		from rdkit.Chem import rdGeometry, rdMolTransforms
		import multiprocessing

		__author__ = "Steven Kearnes"

+2 −1

Original line number	Diff line number	Diff line
		@@ -8,7 +8,6 @@ __author__ = "Steven Kearnes"
		__copyright__ = "Copyright 2014, Stanford University"
		__license__ = "MIT"

		from rdkit.Chem import Descriptors
		from deepchem.feat import Featurizer


		@@ -27,6 +26,7 @@ class MolecularWeight(Featurizer):
		mol : RDKit Mol
		Molecule.
		"""
		from rdkit.Chem import Descriptors
		wt = Descriptors.ExactMolWt(mol)
		wt = [wt]
		return wt
		@@ -74,6 +74,7 @@ class RDKitDescriptors(Featurizer):
		def __init__(self):
		self.descriptors = []
		self.descList = []
		from rdkit.Chem import Descriptors
		for descriptor, function in Descriptors.descList:
		if descriptor in self.allowedDescriptors:
		self.descriptors.append(descriptor)

+1 −1

Original line number	Diff line number	Diff line
		@@ -12,7 +12,6 @@ __license__ = "MIT"

		import numpy as np
		import deepchem as dc
		from rdkit import Chem
		from deepchem.feat import Featurizer
		from deepchem.utils import pad_array
		from deepchem.feat.atomic_coordinates import AtomicCoordinates
		@@ -118,6 +117,7 @@ class CoulombMatrix(Featurizer):
		mol : RDKit Mol
		Molecule.
		"""
		from rdkit import Chem
		if self.remove_hydrogens:
		mol = Chem.RemoveHs(mol)
		n_atoms = mol.GetNumAtoms()