:construction: wip commit (9ba11701) · Commits · 钟慕尧 / deepchem

deepchem/splits/splitters.py

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		@@ -5,11 +5,8 @@ __author__ = "Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__license__ = "MIT"

		import tempfile
		import numpy as np
		from deepchem.utils import ScaffoldGenerator
		from deepchem.data import NumpyDataset
		from deepchem.utils.save import load_data
		from deepchem.splits import Splitter

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		@@ -189,34 +189,3 @@ def unzip_file(file, dest_dir=None, name=None):
		dest_dir = os.path.join(get_data_dir, name)
		with zipfile.ZipFile(file, "r") as zip_ref:
		zip_ref.extractall(dest_dir)


		class ScaffoldGenerator(object):
		"""
		Generate molecular scaffolds.

		Parameters
		----------
		include_chirality : : bool, optional (default False)
		Include chirality in scaffolds.
		"""

		def __init__(self, include_chirality=False):
		self.include_chirality = include_chirality

		def get_scaffold(self, mol):
		"""
		Get Murcko scaffolds for molecules.

		Murcko scaffolds are described in DOI: 10.1021/jm9602928.
		They are essentially that part of the molecule consisting of
		rings and the linker atoms between them.

		Parameters
		----------
		mols : array_like
		Molecules.
		"""
		from rdkit.Chem.Scaffolds import MurckoScaffold
		return MurckoScaffold.MurckoScaffoldSmiles(
		mol=mol, includeChirality=self.include_chirality)

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		@@ -67,9 +67,6 @@ File Handling
		Molecular Utilities
		-------------------

		.. autoclass:: deepchem.utils.ScaffoldGenerator
		:members:

		.. autoclass:: deepchem.utils.conformers.ConformerGenerator
		:members: