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/tests/test_shape.py
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| a | b/tests/test_shape.py | ||
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| 1 | import os |
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| 2 | import numpy as np |
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| 3 | from numpy.testing import assert_array_almost_equal, assert_almost_equal |
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| 4 | import oddt |
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| 5 | from oddt.shape import usr, usr_cat, electroshape, usr_similarity |
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| 6 | |||
| 7 | test_data_dir = os.path.dirname(os.path.abspath(__file__)) |
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| 8 | benzene_sdf = """ |
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| 9 | RDKit 3D |
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| 10 | |||
| 11 | 6 6 0 0 0 0 0 0 0 0999 V2000 |
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| 12 | -1.0971 0.8220 0.2458 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 13 | 0.1708 1.3788 0.0966 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 14 | 1.2678 0.5568 -0.1492 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 15 | 1.0971 -0.8220 -0.2458 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 16 | -0.1708 -1.3788 -0.0966 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 17 | -1.2678 -0.5568 0.1491 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 18 | 1 2 2 0 |
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| 19 | 2 3 1 0 |
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| 20 | 3 4 2 0 |
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| 21 | 4 5 1 0 |
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| 22 | 5 6 2 0 |
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| 23 | 6 1 1 0 |
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| 24 | M END |
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| 25 | |||
| 26 | """ |
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| 27 | methylo_sdf = """ |
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| 28 | RDKit 3D |
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| 29 | |||
| 30 | 7 7 0 0 0 0 0 0 0 0999 V2000 |
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| 31 | 0.2879 -1.1465 0.0728 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 32 | -1.0997 -1.1111 0.1887 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 33 | -1.7974 0.0457 -0.1502 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 34 | -1.1081 1.1672 -0.6050 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 35 | 0.2795 1.1321 -0.7210 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 36 | 0.9778 -0.0249 -0.3821 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 37 | 2.4600 -0.0625 -0.5059 C 0 0 0 0 0 0 0 0 0 0 0 0 |
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| 38 | 1 2 2 0 |
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| 39 | 2 3 1 0 |
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| 40 | 3 4 2 0 |
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| 41 | 4 5 1 0 |
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| 42 | 5 6 2 0 |
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| 43 | 6 7 1 0 |
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| 44 | 6 1 1 0 |
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| 45 | M END |
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| 46 | |||
| 47 | """ |
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| 48 | benzene = oddt.toolkit.readstring('sdf', benzene_sdf) |
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| 49 | benzene.calccharges() |
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| 50 | methylo = oddt.toolkit.readstring('sdf', methylo_sdf) |
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| 51 | methylo.calccharges() |
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| 52 | |||
| 53 | |||
| 54 | def test_usr(): |
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| 55 | """USR test""" |
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| 56 | benzene_usr = np.array((1.392709, 0., 0., |
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| 57 | 1.732536, 0.877535, -0.580651, |
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| 58 | 1.732576, 0.877555, -0.580693, |
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| 59 | 1.732573, 0.877552, -0.580686)) |
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| 60 | methylo_usr = np.array((1.57291, 0.20536, 0.064638, |
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| 61 | 1.697949, 0.759765, -0.420457, |
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| 62 | 2.614764, 1.94016, -1.660038, |
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| 63 | 2.095664, 1.54289, 0.117823)) |
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| 64 | |||
| 65 | assert_array_almost_equal(usr(benzene), benzene_usr) |
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| 66 | assert_array_almost_equal(usr(methylo), methylo_usr) |
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| 67 | |||
| 68 | |||
| 69 | def test_usr_cat(): |
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| 70 | """USRCAT test""" |
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| 71 | benzene_usrcat = np.array((1.392709, 0., 0., |
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| 72 | 1.732536, 0.877535, -0.580651, |
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| 73 | 1.732576, 0.877555, -0.580693, |
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| 74 | 1.732573, 0.877552, -0.580686, |
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| 75 | 1.392709, 0., 0., |
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| 76 | 1.732536, 0.877535, -0.580651, |
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| 77 | 1.732576, 0.877555, -0.580693, |
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| 78 | 1.732573, 0.877552, -0.580686, |
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| 79 | 1.392709, 0., 0., |
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| 80 | 1.732536, 0.877535, -0.580651, |
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| 81 | 1.732576, 0.877555, -0.580693, |
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| 82 | 1.732573, 0.877552, -0.580686, |
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| 83 | 0., 0., 0., |
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| 84 | 0., 0., 0., |
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| 85 | 0., 0., 0., |
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| 86 | 0., 0., 0., |
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| 87 | 0., 0., 0., |
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| 88 | 0., 0., 0., |
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| 89 | 0., 0., 0., |
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| 90 | 0., 0., 0.)) |
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| 91 | methylo_usrcat = np.array((1.57291, 0.20536, 0.064638, |
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| 92 | 1.697949, 0.759765, -0.420457, |
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| 93 | 2.614764, 1.94016, -1.660038, |
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| 94 | 2.095664, 1.54289, 0.117823, |
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| 95 | 1.57291, 0.20536, 0.064638, |
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| 96 | 1.697949, 0.759765, -0.420457, |
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| 97 | 2.614764, 1.94016, -1.660038, |
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| 98 | 2.095664, 1.54289, 0.117823, |
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| 99 | 1.423502, 0.083326, -0.003973, |
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| 100 | 1.732968, 0.877809, -0.58125, |
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| 101 | 3.050558, 0.934105, -0.26119, |
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| 102 | 1.732674, 0.877707, -0.58073, |
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| 103 | 0., 0., 0., |
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| 104 | 0., 0., 0., |
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| 105 | 0., 0., 0., |
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| 106 | 0., 0., 0., |
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| 107 | 0., 0., 0., |
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| 108 | 0., 0., 0., |
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| 109 | 0., 0., 0., |
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| 110 | 0., 0., 0.)) |
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| 111 | |||
| 112 | assert_array_almost_equal(usr_cat(benzene), benzene_usrcat) |
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| 113 | assert_array_almost_equal(usr_cat(methylo), methylo_usrcat) |
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| 114 | |||
| 115 | |||
| 116 | def test_electroshape(): |
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| 117 | """Electroshape test""" |
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| 118 | if oddt.toolkit.backend == 'rdk': |
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| 119 | benzene_usr = np.array((1.392709, 0.000024, 0.000021, |
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| 120 | 1.732576, 0.936779, -0.834287, |
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| 121 | 1.732573, 0.936777, -0.834284, |
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| 122 | 1.482042, 0.477624, -0.293458, |
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| 123 | 1.482042, 0.477624, -0.293458)) |
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| 124 | methylo_usr = np.array((1.58227, 0.461717, 0.417984, |
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| 125 | 2.649053, 1.404615, -1.20629, |
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| 126 | 2.103215, 1.252546, 0.544395, |
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| 127 | 2.009275, 0.651085, -0.488366, |
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| 128 | 1.955503, 0.693917, -0.521708)) |
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| 129 | else: |
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| 130 | benzene_usr = np.array((1.39270878, 0.000023678, 0.0000208289, |
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| 131 | 1.73257649, 0.936778843, -0.834286869, |
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| 132 | 1.73257256, 0.936777234, -0.834283948, |
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| 133 | 1.48204167, 0.477623908, -0.293458485, |
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| 134 | 1.48204167, 0.477623908, -0.293458485)) |
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| 135 | methylo_usr = np.array((1.61146379, 0.46305567, 0.46938854, |
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| 136 | 2.76274943, 1.37034833, -1.2889241, |
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| 137 | 2.11388564, 1.2641263, 0.57394201, |
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| 138 | 2.18083588, 0.57593416, -0.48947371, |
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| 139 | 2.06548012, 0.71989938, -0.44118673)) |
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| 140 | |||
| 141 | assert_array_almost_equal(electroshape(benzene), benzene_usr) |
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| 142 | assert_array_almost_equal(electroshape(methylo), methylo_usr) |
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| 143 | |||
| 144 | |||
| 145 | def test_usr_similarity(): |
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| 146 | """Similarity function for USR test""" |
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| 147 | similarity_usr = 0.68517293875665453 |
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| 148 | assert_almost_equal(usr_similarity(usr(benzene), usr(methylo)), similarity_usr) |
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| 149 | |||
| 150 | |||
| 151 | def test_usrcat_similarity(): |
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| 152 | """Similarity function for USRCAT test""" |
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| 153 | similarity_usrcat = 0.82370755989115707 |
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| 154 | assert_almost_equal(usr_similarity(usr_cat(benzene), usr_cat(methylo)), |
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| 155 | similarity_usrcat) |
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| 156 | |||
| 157 | |||
| 158 | def test_elecroshape_similarity(): |
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| 159 | """Similarity function for Electroshape test""" |
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| 160 | if oddt.toolkit.backend == 'rdk': |
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| 161 | similarity_electroshape = 0.69110953340712389 |
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| 162 | else: |
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| 163 | similarity_electroshape = 0.67710967360721197 |
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| 164 | |||
| 165 | assert_almost_equal(usr_similarity(electroshape(benzene), electroshape(methylo)), |
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| 166 | similarity_electroshape) |