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
|
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit test for Residues"""
import unittest
from Bio.SCOP.Residues import *
class ResiduesTests(unittest.TestCase):
res = (
("-", ()),
("A:", (("A", "", ""),)),
("1:", (("1", "", ""),)),
("1-100", (("", "1", "100"),)),
("B:1-101", (("B", "1", "101"),)),
("1:1a-100a", (("1", "1a", "100a"),)),
("a:-100a--1a", (("a", "-100a", "-1a"),)),
("-1-100", (("", "-1", "100"),)),
("-1-100", (("", "-1", "100"),)),
("A:12-19,A:23-25", (("A", "12", "19"), ("A", "23", "25"))),
("12-19,1:23-25", (("", "12", "19"), ("1", "23", "25"))),
("0-1,1:-1a-25a,T:", (("", "0", "1"), ("1", "-1a", "25a"), ("T", "", ""))),
)
def testParse(self):
for loc in self.res:
r = Residues(loc[0])
self.assertEqual(r.fragments, loc[1])
def testStr(self):
for loc in self.res:
r = Residues(loc[0])
self.assertEqual(str(r), loc[0])
def testAstralParse(self):
"""Test if we can parse residue subsets enclosed in brackets"""
for loc in self.res:
r = Residues("(" + loc[0] + ")")
self.assertEqual(r.fragments, loc[1])
def testPdbId(self):
pdbid = "1ddf"
for loc in self.res:
r = Residues("\t 1ddf \t" + loc[0] + "\t\n\n\n")
self.assertEqual(r.pdbid, pdbid)
self.assertEqual(str(r), pdbid + " " + loc[0])
r = Residues(pdbid + " " + loc[0])
self.assertEqual(r.pdbid, pdbid)
self.assertEqual(str(r), pdbid + " " + loc[0])
r = Residues("104l A:112-113")
self.assertEqual(r.pdbid, "104l")
self.assertEqual(r.fragments, (('A', '112', '113'),))
def testJustPdbId(self):
r = Residues("1sds")
self.assertEqual(r.pdbid, "1sds")
self.assertFalse(r.fragments)
def testParseError(self):
self.assertRaises(ValueError, Residues, "09324923423hh./;,.389")
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
