1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
import unittest
import os
import ost
from ost import io
from ost import seq
from ost.mol.alg import scoring_base
def _GetTestfilePath(filename):
"""Get the path to the test file given filename"""
return os.path.join('testfiles', filename)
class TestLigandScoringFancy(unittest.TestCase):
def test_MMCIFPrep(self):
poly_ent = scoring_base.MMCIFPrep(_GetTestfilePath("1r8q.cif.gz"))
self.assertEqual(poly_ent.GetChainCount(), 4)
cnames = [ch.name for ch in poly_ent.chains]
self.assertEqual(cnames, ["A", "B", "C", "D"])
# test enabling extract_nonpoly flag
poly_ent, non_poly_entities = scoring_base.MMCIFPrep(_GetTestfilePath("1r8q.cif.gz"),
extract_nonpoly=True)
self.assertEqual(poly_ent.GetChainCount(), 4)
cnames = [ch.name for ch in poly_ent.chains]
self.assertEqual(cnames, ["A", "B", "C", "D"])
self.assertEqual(len(non_poly_entities), 7)
nonpoly_names = [ent.residues[0].name for ent in non_poly_entities]
self.assertEqual(nonpoly_names, ["MG", "G3D", "AFB", "ZN", "MG", "G3D", "AFB"])
# test enabling extract_seqres_mapping flag
poly_ent, seqres, trg_seqres_mapping = scoring_base.MMCIFPrep(_GetTestfilePath("1r8q.cif.gz"),
extract_seqres_mapping=True)
self.assertEqual(poly_ent.GetChainCount(), 4)
cnames = [ch.name for ch in poly_ent.chains]
self.assertEqual(cnames, ["A", "B", "C", "D"])
self.assertEqual(len(seqres), 2)
seqres_1 = seq.CreateSequence("1", "MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTIL"
"YKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDV"
"GGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNE"
"AREELMRMLAEDELRDAVLLVFANKQDLPNAMNA"
"AEITDKLGLHSLRHRNWYIQATCATSGDGLYEGL"
"DWLSNQLRNQK")
seqres_2 = seq.CreateSequence("2", "LEANEGSKTLQRNRKMAMGRKKFNMDPKKGIQFL"
"VENELLQNTPEEIARFLYKGEGLNKTAIGDYLGE"
"REELNLAVLHAFVDLHEFTDLNLVQALRQFLWSF"
"RLPGEAQKIDRMMEAFAQRYCLCNPGVFQSTDTC"
"YVLSYSVIMLNTDLHNPNVRDKMGLERFVAMNRG"
"INEGGDLPEELLRNLYDSIRNEPFKIPEDDGND")
self.assertEqual(seqres[0].GetName(), seqres_1.GetName())
self.assertEqual(seqres[0].GetGaplessString(), seqres_1.GetGaplessString())
self.assertEqual(seqres[1].GetName(), seqres_2.GetName())
self.assertEqual(seqres[1].GetGaplessString(), seqres_2.GetGaplessString())
expected_trg_seqres_mapping = {"A": "1",
"B": "2",
"C": "1",
"D": "2"}
self.assertEqual(len(expected_trg_seqres_mapping), len(trg_seqres_mapping))
for k,v in trg_seqres_mapping.items():
self.assertEqual(expected_trg_seqres_mapping[k], v)
# specify biounit and enable EVERYTHING
poly_ent, non_poly_entities, seqres, trg_seqres_mapping =\
scoring_base.MMCIFPrep(_GetTestfilePath("1r8q.cif.gz"),
extract_nonpoly=True,
extract_seqres_mapping=True,
biounit="1")
self.assertEqual(poly_ent.GetChainCount(), 2)
cnames = [ch.name for ch in poly_ent.chains]
self.assertEqual(cnames, ["1.A", "1.B"])
self.assertEqual(len(non_poly_entities), 4)
nonpoly_names = [ent.residues[0].name for ent in non_poly_entities]
self.assertEqual(nonpoly_names, ["MG", "G3D", "AFB", "ZN"])
self.assertEqual(seqres[0].GetName(), seqres_1.GetName())
self.assertEqual(seqres[0].GetGaplessString(), seqres_1.GetGaplessString())
self.assertEqual(seqres[1].GetName(), seqres_2.GetName())
self.assertEqual(seqres[1].GetGaplessString(), seqres_2.GetGaplessString())
expected_trg_seqres_mapping = {"1.A": "1",
"1.B": "2"}
self.assertEqual(len(expected_trg_seqres_mapping), len(trg_seqres_mapping))
for k,v in trg_seqres_mapping.items():
self.assertEqual(expected_trg_seqres_mapping[k], v)
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound lib available. Ignoring test_scoring_base.py tests.')
|
