def test_2(self):
dummy_prediction = """###
D U M M Y
100 8 5.382865
"""
with self.assertRaises(InvalidFormat):
output = ContactParser(dummy_prediction, 'BCLCONTACTS')
def test_5(self):
dummy_prediction = """112 X 145 X 0 0.99560225
38 X 49 X 0 0.99520814
24 X 56 X 0 0.995158
109 X 145 X 0 0.99344337
109 X 141 X 0 0.99096644
64 X 125 X 0 0.98981607
128 X 138 X 0 0.9892521
34 X 53 X 0 0.98918885
75 X 81 X 0 0.9883262
57 X 146 X 0 0.98828995"""
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [
0.99560225, 0.99520814, 0.995158, 0.99344337, 0.99096644,
0.98981607, 0.9892521, 0.98918885, 0.9883262, 0.98828995
]
output = ContactParser(dummy_prediction, 'EVFOLD')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_1(self):
dummy_prediction = """5 I 9 Q 0.000 0.286 0.185 0.836 0.875 0.749
5 I 10 R 0.000 0.000 0.105 0.875 0.482 0.634
5 I 11 I 0.000 0.178 0.066 0.730 0.876 0.727
5 I 21 I 0.030 0.021 0.233 0.645 0.733 0.557
5 I 58 G 0.000 0.054 0.010 0.642 0.799 0.535
6 T 62 V 0.000 0.000 0.027 0.485 0.428 0.585
6 T 63 S 0.000 0.004 0.051 0.547 0.387 0.529
6 T 78 L 0.000 0.000 0.039 0.624 0.384 0.581
6 T 79 T 0.000 0.000 0.036 0.657 0.415 0.679
6 T 80 I 0.000 0.076 0.003 0.513 0.386 0.578
6 T 94 Q 0.000 0.068 0.041 0.534 0.489 0.679
11 T 5 Q 0.000 0.178 0.066 0.730 0.876 0.727
"""
expected_res2 = [5, 6, 6, 5, 6, 6, 6, 5, 5, 6]
expected_res1 = [11, 79, 94, 10, 62, 78, 80, 21, 58, 63]
expected_score = [
0.727, 0.679, 0.679, 0.634, 0.585, 0.581, 0.578, 0.557, 0.535,
0.529
]
output = ContactParser(dummy_prediction, 'BCLCONTACTS')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_12(self):
dummy_prediction = """
i j i_id j_id r_sco s_sco prob
112 145 112_X 145_X 0.99560225 1.0 1.0
38 49 38_X 49_X 0.99520814 1.0 1.0
24 56 24_X 56_X 0.995158 1.0 1.0
109 145 109_X 145_X 0.99344337 1.0 1.0
109 141 109_X 141_X 0.99096644 1.0 1.0
64 125 64_X 125_X 0.98981607 1.0 1.0
128 138 128_X 138_X 0.9892521 1.0 1.0
34 53 34_X 53_X 0.98918885 1.0 1.0
75 81 75_X 81_X 0.9883262 1.0 1.0
57 146 57_X 146_X 0.98828995 1.0 1.0
"""
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [
0.99560225, 0.99520814, 0.995158, 0.99344337, 0.99096644,
0.98981607, 0.9892521, 0.98918885, 0.9883262, 0.98828995
]
output = ContactParser(dummy_prediction, 'GREMLIN')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_10(self):
dummy_prediction = """LEN 146
CON 112 145 0.995602
CON 38 49 0.995208
CON 24 56 0.995158
CON 109 145 0.993443
CON 109 141 0.990966
CON 64 125 0.989816
CON 128 138 0.989252
CON 34 53 0.989189
CON 75 81 0.988326
CON 57 146 0.988290
PRF 0 T X 0.0321 0.0078 0.0582 0.1021 0.0207 0.0384 0.038 0.0386 0.0697 0.0376 0.0586
PRF 1 M X 0.0228 0.0052 0.0103 0.0112 0.1236 0.0083 0.0106 0.1182 0.0104 0.3046 0.1922
PRF 2 K X 0.0322 0.0048 0.0563 0.128 0.0116 0.0481 0.0332 0.0319 0.1099 0.0366 0.0228
PRF 3 I X 0.0147 0.0062 0.0025 0.0034 0.2786 0.0058 0.0057 0.1876 0.0053 0.2779 0.0302
PRF 4 I X 0.0404 0.0057 0.1139 0.2398 0.0104 0.028 0.0275 0.0278 0.0491 0.0283 0.0051
"""
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [
0.995602, 0.995208, 0.995158, 0.993443, 0.990966, 0.989816,
0.989252, 0.989189, 0.988326, 0.98829
]
output = ContactParser(dummy_prediction, 'MAPALIGN')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_7(self):
dummy_prediction = """112 145 0.99560225
38 49 0.99520814
24 56 0.995158
109 145 0.99344337
109 141 0.99096644
64 125 0.98981607
128 138 0.9892521
34 53 0.98918885
75 81 0.9883262
57 146 0.98828995"""
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [
0.99560225, 0.99520814, 0.995158, 0.99344337, 0.99096644,
0.98981607, 0.9892521, 0.98918885, 0.9883262, 0.98828995
]
output = ContactParser(dummy_prediction, 'PCONS')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_3(self):
dummy_prediction = """#identifier diversity direction viterbiscore indexpred state res1 res2
1EAZ 0.65 Antiparallel 9.860725 1 first 29 24
1EAZ 0.65 Antiparallel 9.860725 1 internal 30 23
1EAZ 0.65 Antiparallel 9.860725 1 last 31 22
1EAZ 0.65 Parallel -6.855870 29 first 87 54
1EAZ 0.65 Parallel -6.855870 29 internal 88 55
1EAZ 0.65 Parallel -6.855870 29 last 89 56
1EAZ 0.65 Parallel -6.855870 29 last 56 89
"""
expected_res1 = [29, 30, 31, 87, 88, 89]
expected_res2 = [24, 23, 22, 54, 55, 56]
expected_score = [0, 0, 0, 0, 0, 0]
output = ContactParser(dummy_prediction, 'BBCONTACTS')
self.assertEqual(6, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_4(self):
dummy_prediction = """112 X 145 X Hx-Hx
38 X 49 X Hx-Hx
24 X 56 X Hx-Hx
109 X 145 X Hx-Hx
109 X 141 X Hx-Hx
64 X 125 X Hx-Hx
128 X 138 X Hx-Hx
34 X 53 X Hx-Hx
75 X 81 X Hx-Hx
57 X 146 X Hx-Hx
146 X 57 X Hx-Hx """
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
output = ContactParser(dummy_prediction, 'COMSAT')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])
def test_11(self):
dummy_prediction = """147
112 145
38 49
24 56
109 145
109 141
64 125
128 138
34 53
75 81
57 146
"""
expected_res2 = [112, 38, 24, 109, 109, 64, 128, 34, 75, 57]
expected_res1 = [145, 49, 56, 145, 141, 125, 138, 53, 81, 146]
expected_score = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
output = ContactParser(dummy_prediction, 'ALEIGEN')
self.assertEqual(10, len(output))
self.assertListEqual(expected_res1, [contact[0] for contact in output])
self.assertListEqual(expected_res2, [contact[1] for contact in output])
self.assertListEqual(expected_score,
[contact[2] for contact in output])