Merge pull request #566 from lilleswing/lazy-load-cr (782feb6d) · Commits · 钟慕尧 / deepchem

deepchem/dock/tests/test_binding_pocket.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ __copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import sys
		import mdtraj as md
		from deepchem.utils.dependencies import mdtraj as md
		import unittest
		import tempfile
		import os

+1 −1

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ __copyright__ = "Copyright 2016, Stanford University"
		__license__ = "LGPL v2.1+"

		import numpy as np
		import mdtraj
		from deepchem.utils.dependencies import mdtraj
		from deepchem.feat import Featurizer
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils import rdkit_util, pad_array

+1 −1

Original line number	Diff line number	Diff line
		@@ -10,7 +10,7 @@ __copyright__ = "Copyright 2017, Stanford University"
		__license__ = "MIT"

		import numpy as np
		import mdtraj as md
		from deepchem.utils.dependencies import mdtraj as md
		from deepchem.utils.save import log
		from deepchem.feat import Featurizer

+17 −8

Original line number	Diff line number	Diff line
		"""
		This file is for lazily importing optional dependencies
		"""
		import importlib


		def import_lazy(module_name):
		try:
		import xgboost as xgboost
		module = importlib.import_module(module_name)
		return module
		except:
		print("Warning: No XGBOOST installed on your system")
		print(
		"Attempting to run models with XGBOOST dependencies will throw runtime errors"
		)
		xgboost = None
		print("Warning: No %s installed on your system" % module_name)
		print("Attempting to run %s will throw runtime errors")
		return None


		xgboost = import_lazy("xgboost")
		pdbfixer = import_lazy("pdbfixer")
		simtk = import_lazy("simtk")
		mdtraj = import_lazy("mdtraj")

+5 −4

Original line number	Diff line number	Diff line
		@@ -4,11 +4,11 @@ import networkx as nx
		import numpy as np
		import os

		from pdbfixer import PDBFixer
		from deepchem.utils.dependencies import pdbfixer
		from deepchem.utils.dependencies import simtk
		from rdkit import Chem
		from rdkit.Chem import AllChem
		from rdkit.Chem import rdmolops
		from simtk.openmm.app import PDBFile

		try:
		from StringIO import StringIO
		@@ -50,11 +50,12 @@ def add_hydrogens_to_mol(mol):
		pdb_stringio = StringIO()
		pdb_stringio.write(pdbblock)
		pdb_stringio.seek(0)
		fixer = PDBFixer(pdbfile=pdb_stringio)
		fixer = pdbfixer.PDBFixer(pdbfile=pdb_stringio)
		fixer.addMissingHydrogens(7.4)

		hydrogenated_io = StringIO()
		PDBFile.writeFile(fixer.topology, fixer.positions, hydrogenated_io)
		simtk.openmm.app.PDBFile.writeFile(fixer.topology, fixer.positions,
		hydrogenated_io)
		hydrogenated_io.seek(0)
		return Chem.MolFromPDBBlock(
		hydrogenated_io.read(), sanitize=False, removeHs=False)