Partial python 3 fixes. (a8565122) · Commits · 钟慕尧 / deepchem

deepchem/featurizers/basic.py

+4 −2

Original line number	Diff line number	Diff line
		"""
		Basic molecular features.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Steven Kearnes"
		__copyright__ = "Copyright 2014, Stanford University"
		__license__ = "BSD 3-clause"
		__license__ = "LGPL v2.1+"

		from rdkit.Chem import Descriptors

		from deepchem.featurizers import Featurizer

deepchem/featurizers/coulomb_matrices.py

+4 −3

Original line number	Diff line number	Diff line
		@@ -3,15 +3,16 @@ Generate coulomb matrices for molecules.

		See Montavon et al., _New Journal of Physics_ __15__ (2013) 095003.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Steven Kearnes"
		__copyright__ = "Copyright 2014, Stanford University"
		__license__ = "BSD 3-clause"
		__license__ = "LGPL v2.1+"

		import numpy as np

		from rdkit import Chem

		from deepchem.featurizers import Featurizer
		from deepchem.utils import pad_array

deepchem/featurizers/fingerprints.py

+4 −2

Original line number	Diff line number	Diff line
		"""
		Topological fingerprints.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Steven Kearnes"
		__copyright__ = "Copyright 2014, Stanford University"
		__license__ = "BSD 3-clause"
		__license__ = "LGPL v2.1+"

		from rdkit import Chem
		from rdkit.Chem import rdMolDescriptors

		from deepchem.featurizers import Featurizer

deepchem/featurizers/nnscore.py

+3 −9

Original line number	Diff line number	Diff line
		"""
		The following code implements a featurizer based on NNScore 2.0.1

		## The following notice is copied from the original NNScore file.
		# NNScore 2.01 is released under the GNU General Public License (see
		# http://www.gnu.org/licenses/gpl.html).
		# If you have any questions, comments, or suggestions, please don't
		# hesitate to contact me, Jacob Durrant, at jdurrant [at] ucsd [dot]
		# edu. If you use NNScore 2.01 in your work, please cite [REFERENCE
		# HERE].
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import os
		import math
		import re
		@@ -368,7 +363,6 @@ def compute_hydrogen_bonds(ligand, receptor):
		< H_BOND_DIST):
		hydrogens.append(atom)

		#print "nearby hydrogens: " + str(hydrogens)
		# now we need to check the angles
		# TODO(rbharath): Rather than using this heuristic, it seems like
		# it might be better to just report the angle in the feature

deepchem/featurizers/nnscore_pdb.py

+5 −21

Original line number	Diff line number	Diff line
		"""
		Custom PDB class implementation.

		The code below contains heavily modified parts of Jacob Durrant's
		NNScore 2.0.1. The following notice is copied from the original NNScore
		file:
		# NNScore 2.01 is released under the GNU General Public License (see
		# http://www.gnu.org/licenses/gpl.html).
		# If you have any questions, comments, or suggestions, please don't
		# hesitate to contact me, Jacob Durrant, at jdurrant [at] ucsd [dot]
		# edu. If you use NNScore 2.01 in your work, please cite [REFERENCE
		# HERE].
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import ast
		import math
		import textwrap
		@@ -89,8 +82,8 @@ def print_warning(atom, residue, need):
		'active site, this warning may not affect the NNScore.')
		lines = textwrap.wrap(text, 80)
		for line in lines:
		print line
		print
		print(line)
		print()


		def bond_length(element1, element2):
		@@ -187,11 +180,6 @@ class MultiStructure(object):

		def _separate_into_models(self, lines, noisy):
		"""Separate lines into a list of models."""
		if noisy:
		print "len(lines)"
		print len(lines)
		for line in lines:
		print line
		models = []
		current = None
		for line in lines:
		@@ -203,9 +191,6 @@ class MultiStructure(object):
		current = None
		elif current is not None:
		current.append(line)
		if noisy:
		print "len(models)"
		print len(models)
		return models

		def load_from_files(self, pdb_filename, pdbqt_filename):
		@@ -1403,7 +1388,6 @@ class PDB(object):
		"""
		# first, we need to know what residues are available
		resids = []
		#print self.get_residues()
		for key in self.get_residues():
		_, resnum, chain = key.split("_")
		resids.append(resnum + "_" + chain)

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