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
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
|
import unittest
from ost import geom, mol
class TestInvalidHandleOrView(unittest.TestCase):
""" Test some basic behavior of invalid (chain|residue|atom|bond)
(view|handle)s. in Python. This test checks the behavior
of valid and IsValid() as well as presence and behavior of hash_code
and GetHashCode() on relevant handles."""
def setUp(self):
""" Setup some test data."""
# Create an entity with 3 atoms and 1 bond.
self.entity = mol.CreateEntity()
ed = self.entity.EditXCS()
ch = ed.InsertChain("A")
res = ed.AppendResidue(ch, "ALA")
self.at0 = ed.InsertAtom(res, "A", geom.Vec3(0, 0, 0))
self.at1 = ed.InsertAtom(res, "B", geom.Vec3(1, 0, 0))
self.at2 = ed.InsertAtom(res, "C", geom.Vec3(2, 0, 0))
ed.Connect(self.at0, self.at1)
ed.UpdateICS()
self.entity_view = self.entity.Select("cname=A")
def assertValidHandleOrView(self, x):
"""Assertion for valid handles: valid and IsValid() are True,
hash_code and GetHashCode() work and return a positive integer.
This test also ensures the hash code is > 0. Although we make no
promise about the exact value of the hash, an earlier behavior was to
return a hash_code of 0 (null pointer) for some invalid handles. If you
get a hash code of 0, your installation of OpenStructure is most likely
buggy.
"""
self.assertTrue(x.valid)
self.assertTrue(x.IsValid())
self.assertIsInstance(x.GetHashCode(), int)
self.assertTrue(x.hash_code, int)
self.assertTrue(x.GetHashCode() > 0)
self.assertTrue(x.hash_code > 0)
def assertInvalidHandleOrView(self, x):
"""Assertion for invalid handles: valid and IsValid() are False,
hash_code and GetHashCode() raise an InvalidHandle error (which
is converted to an Exception in Python with a specific error
message).
"""
self.assertFalse(x.valid)
self.assertFalse(x.IsValid())
with self.assertRaises(Exception, msg="Can not access invalid handle or view"):
x.hash_code
with self.assertRaises(Exception, msg="Can not access invalid handle or view"):
x.GetHashCode()
def test_InvalidChainHandle(self):
""" Test behavior of chain handles"""
# Valid
ch = self.entity.FindChain("A")
self.assertValidHandleOrView(ch)
# Invalid
ch = self.entity.FindChain("X")
self.assertInvalidHandleOrView(ch)
def test_InvalidChainView(self):
""" Test behavior of chain views"""
# Valid
ch = self.entity_view.FindChain("A")
self.assertValidHandleOrView(ch)
# Invalid
ch = self.entity_view.FindChain("X")
self.assertInvalidHandleOrView(ch)
def test_InvalidResidueHandle(self):
""" Test behavior of residue handles"""
# Valid
res = self.entity.FindResidue("A", 1)
self.assertValidHandleOrView(res)
# Invalid
res = self.entity.FindResidue("X", 1)
self.assertInvalidHandleOrView(res)
def test_InvalidResidueView(self):
""" Test behavior of residue views"""
# Valid
res = self.entity_view.FindResidue("A", 1)
self.assertValidHandleOrView(res)
# Invalid
res = self.entity_view.FindResidue("X", 1)
self.assertInvalidHandleOrView(res)
def test_InvalidAtomHandle(self):
""" Test behavior of atom handles"""
# Valid
at = self.entity.FindAtom("A", 1, "A")
self.assertValidHandleOrView(at)
# Invalid
at = self.entity.FindAtom("X", 1, "A")
self.assertInvalidHandleOrView(at)
def test_InvalidAtomView(self):
""" Test behavior of atom views"""
# Valid
at = self.entity_view.FindAtom("A", 1, "A")
self.assertValidHandleOrView(at)
# Invalid
at = self.entity_view.FindAtom("X", 1, "A")
self.assertInvalidHandleOrView(at)
def test_InvalidBondHandle(self):
""" Test behavior of atom handles"""
# Valid
bond = self.at0.FindBondToAtom(self.at1)
self.assertValidHandleOrView(bond)
# Invalid
bond = self.at0.FindBondToAtom(self.at0)
self.assertInvalidHandleOrView(bond)
if __name__ == "__main__":
unittest.main()
|
