Removing old-style prints and making build only on py 2.7 (d9739cdf) · Commits · 钟慕尧 / deepchem

.travis.yml

+1 −8

Original line number	Diff line number	Diff line
		language: python
		python:
		# We don't actually use the Travis Python, but this keeps it organized.
		- "2.6"
		- "2.7"
		install:
		- sudo apt-get update
		# We do this conditionally because it saves us some downloading if the
		# version is the same.
		- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
		wget http://repo.continuum.io/archive/Anaconda2-2.4.1-Linux-x86_64.sh -O anaconda.sh;
		else
		wget http://repo.continuum.io/archive/Anaconda3-2.4.1-Linux-x86_64.sh -O anaconda.sh;
		fi
		- wget http://repo.continuum.io/archive/Anaconda2-2.4.1-Linux-x86_64.sh -O anaconda.sh;
		- bash anaconda.sh -b -p $HOME/anaconda
		- export PATH="$HOME/anaconda/bin:$PATH"
		- hash -r

deepchem/featurizers/tests/test_binana.py

+18 −36

Original line number	Diff line number	Diff line
		@@ -6,6 +6,9 @@ salt-bridge interactions. There might be a bug in the pi-T interaction
		finger, and the H-bonds are known to miss some potential bonds with an
		overly-conservative bond-angle cutoff.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals
		import os
		import unittest
		from deepchem.featurizers.nnscore import Binana
		@@ -135,7 +138,7 @@ class TestBinana(unittest.TestCase):
		hbonds_dict[name] = compute_hydrogen_bonds(
		ligand, protein)
		for name, hbonds in hbonds_dict.iteritems():
		print "Processing hydrogen bonds for %s" % name
		print("Processing hydrogen bonds for %s" % name)
		assert len(hbonds) == 12
		assert "HDONOR-LIGAND_BACKBONE_ALPHA" in hbonds
		assert "HDONOR-LIGAND_BACKBONE_BETA" in hbonds
		@@ -159,13 +162,7 @@ class TestBinana(unittest.TestCase):
		counts_dict[name] = compute_ligand_atom_counts(
		ligand)
		for name, counts in counts_dict.iteritems():
		print "Processing ligand atom counts for %s" % name
		# TODO(rbharath): This code is useful for debugging. Remove once
		# codebase is stable enough.
		#for key in Binana.atom_types:
		# if key in counts:
		# del counts[key]
		#print "Residual counts:"
		print("Processing ligand atom counts for %s" % name)
		#print counts
		assert len(counts) == len(Binana.atom_types)

		@@ -179,33 +176,18 @@ class TestBinana(unittest.TestCase):
		ligand, protein)
		num_atoms = len(Binana.atom_types)
		for name, (close_contacts, contacts) in contacts_dict.iteritems():
		print "Processing contacts for %s" % name
		print "close_contacts"
		print("Processing contacts for %s" % name)
		print("close_contacts")
		for key, val in close_contacts.iteritems():
		if val != 0:
		print (key, val)
		print "len(close_contacts): " + str(len(close_contacts))
		print "contacts"
		print("len(close_contacts): " + str(len(close_contacts)))
		print("contacts")
		for key, val in contacts.iteritems():
		if val != 0:
		print (key, val)
		print "len(contacts): " + str(len(contacts))
		print "Desired Number: " + str(num_atoms*(num_atoms+1)/2)
		# TODO(rbharath): The following code has proved very useful for
		# debugging. Remove once the code is stable enough that it's not
		# required.
		#if name == '1pi5':
		# for first, second in itertools.product(Binana.atom_types,
		# Binana.atom_types):
		# key = "_".join(sorted([first, second]))
		# if key in close_contacts:
		# del close_contacts[key]
		# if key in contacts:
		# del contacts[key]
		# print "Residuals close_contacts:"
		# print close_contacts
		# print "Residuals contacts:"
		# print contacts
		print("len(contacts): " + str(len(contacts)))
		print("Desired Number: " + str(num_atoms*(num_atoms+1)/2))
		assert len(close_contacts) == num_atoms*(num_atoms+1)/2
		assert len(contacts) == num_atoms*(num_atoms+1)/2

		@@ -219,9 +201,9 @@ class TestBinana(unittest.TestCase):
		pi_stacking_dict[name] = compute_pi_pi_stacking(
		ligand, protein)
		for name, pi_stacking in pi_stacking_dict.iteritems():
		print "Processing pi-stacking for %s" % name
		print("Processing pi-stacking for %s" % name)
		assert len(pi_stacking) == 3
		print pi_stacking
		print(pi_stacking)
		assert "STACKING_ALPHA" in pi_stacking
		assert "STACKING_BETA" in pi_stacking
		assert "STACKING_OTHER" in pi_stacking
		@@ -240,7 +222,7 @@ class TestBinana(unittest.TestCase):
		pi_t_dict[name] = compute_pi_t(
		ligand, protein)
		for name, pi_t in pi_t_dict.iteritems():
		print "Processing pi-T for %s" % name
		print("Processing pi-T for %s" % name)
		assert len(pi_t) == 3
		assert "T-SHAPED_ALPHA" in pi_t
		assert "T-SHAPED_BETA" in pi_t
		@@ -255,7 +237,7 @@ class TestBinana(unittest.TestCase):
		pi_cation_dict[name] = compute_pi_cation(
		ligand, protein)
		for name, pi_cation in pi_cation_dict.iteritems():
		print "Processing pi-cation for %s" % name
		print("Processing pi-cation for %s" % name)
		assert len(pi_cation) == 6
		assert 'PI-CATION_LIGAND-CHARGED_ALPHA' in pi_cation
		assert 'PI-CATION_LIGAND-CHARGED_BETA' in pi_cation
		@@ -276,9 +258,9 @@ class TestBinana(unittest.TestCase):
		salt_bridges_dict[name] = compute_salt_bridges(
		ligand, protein)
		for name, salt_bridges in salt_bridges_dict.iteritems():
		print "Processing salt-bridges for %s" % name
		print("Processing salt-bridges for %s" % name)
		assert len(salt_bridges) == 3
		print salt_bridges
		print(salt_bridges)
		assert 'SALT-BRIDGE_ALPHA' in salt_bridges
		assert 'SALT-BRIDGE_BETA' in salt_bridges
		assert 'SALT-BRIDGE_OTHER' in salt_bridges
		@@ -308,5 +290,5 @@ class TestBinana(unittest.TestCase):
		total_len = (3num_atoms(num_atoms+1)/2 + num_atoms
		+ 12 + 6 + 3 + 6 + 3 + 6 + 3 + 1)
		for name, input_vector in features_dict.iteritems():
		print "Processing input-vector for %s" % name
		print("Processing input-vector for %s" % name)
		assert len(input_vector) == total_len

deepchem/utils/init.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,6 @@ __author__ = "Steven Kearnes"
		__copyright__ = "Copyright 2014, Stanford University"
		__license__ = "BSD 3-clause"

		import cPickle
		import gzip
		import numpy as np
		import os

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