def test_spectrophore_run_1(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="all",
stereo="none",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-1.1031914, -1.0750767, -1.3654453, -0.42381215, 0.59894806,
0.5699494, -0.55262715, -0.57715636, 0.4276119, 1.0509295,
2.2181115, 0.23175779, -1.6306345, -1.4963043, -0.92958903,
-0.32305473, 0.4869356, 0.55584854, -0.5126002, -0.16577469,
0.8719677, 1.4856232, 1.5202019, 0.13738069, -1.5233064,
-1.2432761, -0.27087742, -0.07694667, 0.31983256, 0.36887285,
-0.885755, -0.791568, 0.14561523, 1.1058402, 2.1657825, 0.6857875,
-1.6640162, -1.4057074, -0.42076126, -0.08906693, 0.00726358,
0.6733182, -0.780978, -0.28257385, 0.0892069, 1.3344021, 1.9459364,
0.59297746
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_6(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="all",
stereo="unique",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-2.0392199, -1.0451725, -0.28498945, -1.2991787, -0.47926974,
-1.2253278, -0.8954297, 0.1003789, 1.0659237, 0.19154277,
0.02370401, 0.499685, 1.3921181, 1.2063197, 0.0598392, 0.52852434,
0.42327705, 1.777275, -1.9831187, -0.93960583, -1.0471339,
-0.58259386, -0.6017486, -1.3884957, -0.664746, 0.03728981,
1.0724077, 0.20224081, -0.45646247, 0.00250024, 1.5450943,
0.95032066, 0.47626516, 0.68226475, 1.3573786, 1.3381474,
-1.8927505, -0.37909365, -0.8576261, -0.3310822, -0.54383785,
-1.4202882, -1.1178166, 0.52769566, 1.6502874, 0.45543864,
-0.9291761, 0.2235955, 1.9028864, 0.20087405, 0.10442823,
0.65212655, 0.64576787, 1.1085755, -2.140659, -0.16367035,
-1.1340805, -0.1692811, -0.6985873, -1.1200222, -1.2796654,
0.14967908, 0.9537448, 0.92984784, -0.7686497, 0.01253645,
1.7815126, 0.22271025, 0.5704576, 0.9154165, 0.8240188, 1.1146964
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_7(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="all",
stereo="mirror",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-1.9092162, -0.9825288, -0.90366286, -0.9143438, -0.7486751,
-0.8012937, -0.9516235, 0.28901854, 1.3555537, 0.6454737,
-0.549702, -0.2771643, 1.6498784, 0.88433164, 0.14506489,
0.8713128, 0.7724476, 1.4251299, -2.2960248, -0.8243914,
-0.8502815, -0.52425385, -0.4224533, -1.4565605, -0.6545931,
0.23557016, 1.1703192, 0.11799809, -0.36495772, 0.27398908,
1.6857136, 0.3137505, 0.48427516, 0.76461554, 0.89003146,
1.4572529, -2.2340105, -0.7796255, -0.73147553, -0.17699519,
-0.45110518, -1.2328252, -0.95921105, 0.31719577, 1.718044,
0.29338098, -0.65229195, 0.41400814, 1.7445465, 0.28271115,
0.37067434, 0.65412444, 0.09685306, 1.3260028, -2.5056496,
-0.70145863, -0.9819242, -0.22952928, -0.69301647, -1.0164218,
-0.7544724, 0.30910036, 1.0584307, 0.16536063, -0.36628118,
0.8994829, 1.7892605, 0.434241, 0.19778353, 0.55352926, 0.41452837,
1.4270407
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_9(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="all",
stereo="none",
resolution=5.0)
spec = calculator.calculate(mol)
refe = np.array([
-1.1769704, -1.1675407, -1.3753582, -0.3884973, 0.62028074,
0.50084645, -0.46682152, -0.477354, 0.44754717, 1.0362803,
2.187679, 0.25990626, -1.7077427, -1.6246742, -0.87070256,
-0.20418099, 0.6459274, 0.47249973, -0.5150156, -0.12306376,
0.88154876, 1.3598802, 1.424343, 0.2611806, -1.6462182, -1.4651036,
-0.1785752, 0.06534798, 0.33775648, 0.34625006, -0.85368073,
-0.64889866, 0.2699157, 1.000516, 2.0210416, 0.75164795,
-1.7681832, -1.5752606, -0.35909587, 0.07542755, 0.0941598,
0.56239283, -0.7233517, -0.16622925, 0.11416941, 1.2129686,
1.8534594, 0.6795451
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_4(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="mean",
stereo="none",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-3.1576002e+00, -3.0771291e+00, -3.9082341e+00, -1.2130527e+00,
1.7143340e+00, 1.6313329e+00, -1.5817523e+00, -1.6519608e+00,
1.2239285e+00, 3.0080142e+00, 6.3487706e+00, 6.6334677e-01,
-7.3344212e+00, -6.7302179e+00, -4.1811929e+00, -1.4530659e+00,
2.1901846e+00, 2.5001478e+00, -2.3056211e+00, -7.4563694e-01,
3.9220181e+00, 6.6821756e+00, 6.8377066e+00, 6.1792374e-01,
-1.2800018e+01, -1.0446983e+01, -2.2761250e+00, -6.4656639e-01,
2.6874847e+00, 3.0995598e+00, -7.4428101e+00, -6.6513767e+00,
1.2235737e+00, 9.2921391e+00, 1.8198606e+01, 5.7625256e+00,
-2.0945449e+00, -1.7694041e+00, -5.2962422e-01, -1.1211109e-01,
9.1428757e-03, 8.4752488e-01, -9.8303938e-01, -3.5568380e-01,
1.1228728e-01, 1.6796501e+00, 2.4494059e+00, 7.4639773e-01
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_8(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="all",
stereo="all",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-1.8868657, -1.0286354, -0.37231636, -1.2479366, -0.54005206,
-1.1841761, -0.89935195, -0.03960101, 0.7940211, 0.03910712,
-0.10579979, 0.3051478, 1.0756475, 0.91523474, -0.07460175,
0.33004677, 0.23917948, 1.4081802, -1.9848713, -0.9601767,
-0.8729698, -0.88478035, -0.7015905, -0.759774, -0.9260028,
0.44585046, 1.6251832, 0.8400046, -0.48157376, -0.18021232,
1.9506359, 1.1041243, 0.28667217, 1.0897286, 0.9804073, 1.7021178,
-2.0215762, -0.92931026, -1.041862, -0.55561876, -0.5756684,
-1.3991723, -0.641609, 0.09322588, 1.1767044, 0.2658834,
-0.4235945, 0.05681095, 1.6714748, 1.0489135, 0.5527102,
0.76833403, 1.4749892, 1.4548595, -2.2305825, -0.83562994,
-0.86017096, -0.5511313, -0.45463514, -1.4348592, -0.67467904,
0.16910143, 1.0551445, 0.05765557, -0.4001354, 0.20551851,
1.543684, 0.24320813, 0.40484744, 0.6705804, 0.78946143, 1.3271272,
-1.9042444, -0.3714665, -0.85604393, -0.3228485, -0.5382918,
-1.425814, -1.1195213, 0.54677784, 1.6835508, 0.47360805,
-0.92849785, 0.23883615, 1.9393407, 0.21582766, 0.1181635,
0.67278063, 0.6663416, 1.1349957, -2.217496, -0.7819456,
-0.7344192, -0.18711956, -0.45767972, -1.2292762, -0.9592055,
0.30067146, 1.6833782, 0.27716509, -0.6562611, 0.3962301,
1.7095375, 0.26663342, 0.35345745, 0.6332368, 0.08318226,
1.2964141, -2.1362412, -0.10708191, -1.1031003, -0.11284073,
-0.6561148, -1.0886708, -1.2525269, 0.21453649, 1.0398207,
1.0152931, -0.72802603, 0.0737748, 1.8894325, 0.28949487,
0.64641887, 1.0004809, 0.90667135, 1.2050197, -2.48907,
-0.74067366, -1.0124658, -0.2833388, -0.7324926, -1.0458965,
-0.792048, 0.23863365, 0.9647909, 0.0993391, -0.4158616,
0.81075853, 1.6730196, 0.35990432, 0.13075931, 0.4755036,
0.3408013, 1.3220016
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_5(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="std",
stereo="none",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
0.87864834, 0.906763, 0.6163945, 1.5580276, 2.580788, 2.551789,
1.4292126, 1.4046834, 2.4094517, 3.0327692, 4.199951, 2.2135975,
0.7984234, 0.9327537, 1.4994689, 2.1060033, 2.9159937, 2.9849064,
1.9164578, 2.2632833, 3.3010256, 3.9146812, 3.9492598, 2.5664387,
1.6037147, 1.8837451, 2.8561437, 3.0500743, 3.4468536, 3.495894,
2.241266, 2.335453, 3.2726364, 4.2328615, 5.2928033, 3.8128085,
1.2476672, 1.5059761, 2.4909222, 2.8226166, 2.918947, 3.5850017,
2.1307054, 2.6291096, 3.0008903, 4.2460856, 4.85762, 3.5046608
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_3(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=20,
normalization="none",
stereo="none",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
2.5149038, 2.5953748, 1.76427, 4.459451, 7.386838, 7.303837,
4.0907516, 4.020543, 6.8964324, 8.680518, 12.021275, 6.3358507,
3.5912237, 4.195427, 6.744452, 9.472579, 13.115829, 13.425793,
8.620024, 10.180008, 14.847663, 17.60782, 17.763351, 11.543569,
13.475672, 15.828707, 23.999565, 25.629124, 28.963175, 29.37525,
18.83288, 19.624313, 27.499264, 35.56783, 44.474297, 32.038216,
1.5704744, 1.8956152, 3.135395, 3.5529082, 3.6741621, 4.512544,
2.68198, 3.3093355, 3.7773066, 5.3446693, 6.114425, 4.411417
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_run_2(self):
"""
Test the output data
"""
mol = Chem.MolFromSmiles("ClC(F)(Br)I")
AllChem.EmbedMolecule(mol, randomSeed=1)
calculator = spectrophore.SpectrophoreCalculator(accuracy=10,
normalization="all",
stereo="none",
resolution=3.0)
spec = calculator.calculate(mol)
refe = np.array([
-1.0970671, -1.0719464, -1.3717929, -0.44025284, 0.5940364,
0.57050735, -0.5535874, -0.5920576, 0.43895695, 1.0622, 2.2018838,
0.25912088, -1.6827124, -1.5546383, -0.8647143, -0.25011283,
0.4348574, 0.53342175, -0.57047194, -0.12031432, 0.847524,
1.4454637, 1.49618, 0.28551823, -1.5919987, -1.3039782,
-0.28732124, 0.12322673, 0.27585822, 0.23473941, -1.0049644,
-0.56039035, 0.15567124, 0.840308, 2.115431, 1.0034201, -1.7006627,
-1.4457755, -0.527023, 0.13723296, -0.06602039, 0.63088846,
-0.8454364, -0.15673935, 0.0565788, 1.3564981, 1.7587292, 0.8017287
],
dtype=np.float32)
np.testing.assert_allclose(spec, refe, rtol=TOLERANCE)
def test_spectrophore_creation_stereo_3(self):
"""
Test the stereo 'unique' setting
"""
calculator = spectrophore.SpectrophoreCalculator(stereo="unique")
self.assertEqual(calculator.stereo(), "unique")
def test_spectrophore_creation_stereo_1(self):
"""
Test the stereo default setting
"""
calculator = spectrophore.SpectrophoreCalculator()
self.assertEqual(calculator.stereo(), "none")
def test_spectrophore_creation_normalization_5(self):
"""
Test the normalization 'mean' setting
"""
calculator = spectrophore.SpectrophoreCalculator(normalization='mean')
self.assertEqual(calculator.normalization(), "mean")
def test_spectrophore_creation_normalization_3(self):
"""
Test the normalization 'none' setting
"""
calculator = spectrophore.SpectrophoreCalculator(normalization='none')
self.assertEqual(calculator.normalization(), "none")
def test_spectrophore_creation_accuracy_2(self):
"""
Test the accuracy setting
"""
calculator = spectrophore.SpectrophoreCalculator(accuracy=30)
self.assertEqual(calculator.accuracy(), 30)
def test_spectrophore_creation_resolution_1(self):
"""
Test the resolution default setting
"""
calculator = spectrophore.SpectrophoreCalculator()
self.assertEqual(calculator.resolution(), 3.0)
def test_spectrophore_creation_stereo_4(self):
"""
Test the stereo 'mirror' setting
"""
calculator = spectrophore.SpectrophoreCalculator(stereo="mirror")
self.assertEqual(calculator.stereo(), "mirror")
def test_spectrophore_creation_normalization_1(self):
"""
Test the normalization default setting
"""
calculator = spectrophore.SpectrophoreCalculator()
self.assertEqual(calculator.normalization(), "all")
def test_spectrophore_creation_default(self):
"""
Test that a spectrophore calculator can be created
"""
calculator = spectrophore.SpectrophoreCalculator()
self.assertIsInstance(calculator, spectrophore.SpectrophoreCalculator)
def test_spectrophore_creation_stereo_5(self):
"""
Test the stereo 'all' setting
"""
calculator = spectrophore.SpectrophoreCalculator(stereo="all")
self.assertEqual(calculator.stereo(), "all")
def test_spectrophore_creation_normalization_2(self):
"""
Test the normalization 'all' setting
"""
calculator = spectrophore.SpectrophoreCalculator(normalization='all')
self.assertEqual(calculator.normalization(), "all")
def test_spectrophore_creation_resolution_2(self):
"""
Test the resolution setting
"""
calculator = spectrophore.SpectrophoreCalculator(resolution=5.0)
self.assertEqual(calculator.resolution(), 5.0)
def test_spectrophore_creation_accuracy_1(self):
"""
Test the accuracy default setting
"""
calculator = spectrophore.SpectrophoreCalculator()
self.assertEqual(calculator.accuracy(), 20)