import os
import numpy as np
from numpy.testing import assert_array_almost_equal, assert_almost_equal
import oddt
from oddt.shape import usr, usr_cat, electroshape, usr_similarity
test_data_dir = os.path.dirname(os.path.abspath(__file__))
benzene_sdf = """
RDKit 3D
6 6 0 0 0 0 0 0 0 0999 V2000
-1.0971 0.8220 0.2458 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1708 1.3788 0.0966 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2678 0.5568 -0.1492 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0971 -0.8220 -0.2458 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1708 -1.3788 -0.0966 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2678 -0.5568 0.1491 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END
"""
methylo_sdf = """
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
0.2879 -1.1465 0.0728 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0997 -1.1111 0.1887 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7974 0.0457 -0.1502 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1081 1.1672 -0.6050 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2795 1.1321 -0.7210 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9778 -0.0249 -0.3821 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4600 -0.0625 -0.5059 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
6 1 1 0
M END
"""
benzene = oddt.toolkit.readstring('sdf', benzene_sdf)
benzene.calccharges()
methylo = oddt.toolkit.readstring('sdf', methylo_sdf)
methylo.calccharges()
def test_usr():
"""USR test"""
benzene_usr = np.array((1.392709, 0., 0.,
1.732536, 0.877535, -0.580651,
1.732576, 0.877555, -0.580693,
1.732573, 0.877552, -0.580686))
methylo_usr = np.array((1.57291, 0.20536, 0.064638,
1.697949, 0.759765, -0.420457,
2.614764, 1.94016, -1.660038,
2.095664, 1.54289, 0.117823))
assert_array_almost_equal(usr(benzene), benzene_usr)
assert_array_almost_equal(usr(methylo), methylo_usr)
def test_usr_cat():
"""USRCAT test"""
benzene_usrcat = np.array((1.392709, 0., 0.,
1.732536, 0.877535, -0.580651,
1.732576, 0.877555, -0.580693,
1.732573, 0.877552, -0.580686,
1.392709, 0., 0.,
1.732536, 0.877535, -0.580651,
1.732576, 0.877555, -0.580693,
1.732573, 0.877552, -0.580686,
1.392709, 0., 0.,
1.732536, 0.877535, -0.580651,
1.732576, 0.877555, -0.580693,
1.732573, 0.877552, -0.580686,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.))
methylo_usrcat = np.array((1.57291, 0.20536, 0.064638,
1.697949, 0.759765, -0.420457,
2.614764, 1.94016, -1.660038,
2.095664, 1.54289, 0.117823,
1.57291, 0.20536, 0.064638,
1.697949, 0.759765, -0.420457,
2.614764, 1.94016, -1.660038,
2.095664, 1.54289, 0.117823,
1.423502, 0.083326, -0.003973,
1.732968, 0.877809, -0.58125,
3.050558, 0.934105, -0.26119,
1.732674, 0.877707, -0.58073,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.,
0., 0., 0.))
assert_array_almost_equal(usr_cat(benzene), benzene_usrcat)
assert_array_almost_equal(usr_cat(methylo), methylo_usrcat)
def test_electroshape():
"""Electroshape test"""
if oddt.toolkit.backend == 'rdk':
benzene_usr = np.array((1.392709, 0.000024, 0.000021,
1.732576, 0.936779, -0.834287,
1.732573, 0.936777, -0.834284,
1.482042, 0.477624, -0.293458,
1.482042, 0.477624, -0.293458))
methylo_usr = np.array((1.58227, 0.461717, 0.417984,
2.649053, 1.404615, -1.20629,
2.103215, 1.252546, 0.544395,
2.009275, 0.651085, -0.488366,
1.955503, 0.693917, -0.521708))
else:
benzene_usr = np.array((1.39270878, 0.000023678, 0.0000208289,
1.73257649, 0.936778843, -0.834286869,
1.73257256, 0.936777234, -0.834283948,
1.48204167, 0.477623908, -0.293458485,
1.48204167, 0.477623908, -0.293458485))
methylo_usr = np.array((1.61146379, 0.46305567, 0.46938854,
2.76274943, 1.37034833, -1.2889241,
2.11388564, 1.2641263, 0.57394201,
2.18083588, 0.57593416, -0.48947371,
2.06548012, 0.71989938, -0.44118673))
assert_array_almost_equal(electroshape(benzene), benzene_usr)
assert_array_almost_equal(electroshape(methylo), methylo_usr)
def test_usr_similarity():
"""Similarity function for USR test"""
similarity_usr = 0.68517293875665453
assert_almost_equal(usr_similarity(usr(benzene), usr(methylo)), similarity_usr)
def test_usrcat_similarity():
"""Similarity function for USRCAT test"""
similarity_usrcat = 0.82370755989115707
assert_almost_equal(usr_similarity(usr_cat(benzene), usr_cat(methylo)),
similarity_usrcat)
def test_elecroshape_similarity():
"""Similarity function for Electroshape test"""
if oddt.toolkit.backend == 'rdk':
similarity_electroshape = 0.69110953340712389
else:
similarity_electroshape = 0.67710967360721197
assert_almost_equal(usr_similarity(electroshape(benzene), electroshape(methylo)),
similarity_electroshape)
Datasets
Models
