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
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
|
import unittest
import utils
import os
from io import StringIO
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm
import ihm.report
import ihm.reference
import ihm.location
import ihm.representation
import ihm.protocol
import ihm.analysis
import ihm.restraint
import ihm.geometry
import ihm.model
class Tests(unittest.TestCase):
def test_report(self):
"""Test System.report()"""
sio = StringIO()
s = ihm.System(title='test system')
s.report(sio)
def test_entities(self):
"""Test report_entities"""
sio = StringIO()
s = ihm.System(title='test system')
e = ihm.Entity("ACG")
a = ihm.AsymUnit(e, "my asym")
a.id = 'A'
s.asym_units.append(a)
s.entities.append(e)
r = ihm.report.Reporter(s, sio)
# Should warn about missing references
self.assertWarns(ihm.report.MissingDataWarning, r.report_entities)
uniprot = ihm.reference.UniProtSequence(
db_code='testcode', accession='testacc', sequence='CCCG')
e.references.append(uniprot)
r.report_entities()
def test_asyms(self):
"""Test report_asyms"""
sio = StringIO()
s = ihm.System(title='test system')
e = ihm.Entity("ACG")
s.entities.append(e)
a = ihm.AsymUnit(e, "my asym")
s.asym_units.append(a)
r = ihm.report.Reporter(s, sio)
r.report_asyms()
def test_representations(self):
"""Test report_representations"""
sio = StringIO()
s = ihm.System(title='test system')
e = ihm.Entity("ACGT")
s.entities.append(e)
a = ihm.AsymUnit(e, "my asym")
s.asym_units.append(a)
s1 = ihm.representation.ResidueSegment(
a(1, 2), starting_model=None,
rigid=False, primitive='sphere')
s2 = ihm.representation.FeatureSegment(
a(3, 4), starting_model=None,
rigid=True, primitive='other', count=3)
r1 = ihm.representation.Representation((s1, s2), name='foo')
s.orphan_representations.append(r1)
r = ihm.report.Reporter(s, sio)
# Test report of representation without ID
r.report_representations()
# Test report of representation with ID
r1._id = 42
r.report_representations()
def test_citations(self):
"""Test report_citations"""
sio = StringIO()
s = ihm.System(title='test system')
c = ihm.Citation(pmid="foo", title="bar", journal="j", volume=1,
page_range=(10, 20), year=2023,
authors=["foo", "bar"], doi="test")
s.citations.append(c)
r = ihm.report.Reporter(s, sio)
r.report_citations()
def test_software(self):
"""Test report_software"""
sio = StringIO()
s = ihm.System(title='test system')
soft = ihm.Software(name='foo', version='1.0',
classification='1', description='2', location='3')
s.software.append(soft)
r = ihm.report.Reporter(s, sio)
# Should warn about missing citation
self.assertWarns(ihm.report.MissingDataWarning, r.report_software)
c = ihm.Citation(pmid="foo", title="bar", journal="j", volume=1,
page_range=(10, 20), year=2023,
authors=["foo", "bar"], doi="test")
soft.citation = c
soft.version = None
r.report_software()
def test_databases(self):
"""Test report_databases"""
sio = StringIO()
s = ihm.System(title='test system')
s.locations.append(
ihm.location.BMRBLocation('27600', version='foo', details='bar'))
s.locations.append(
ihm.location.FileLocation(repo='mydoi', path='a'))
r = ihm.report.Reporter(s, sio)
r.report_databases()
def test_files(self):
"""Test report_files"""
sio = StringIO()
s = ihm.System(title='test system')
repo = ihm.location.Repository(doi='1.2.3.4')
s.locations.append(
ihm.location.BMRBLocation('27600', version='foo', details='bar'))
s.locations.append(
ihm.location.FileLocation(repo=repo, path='a'))
r = ihm.report.Reporter(s, sio)
r.report_files()
def test_files_local(self):
"""Test report_files with local files"""
sio = StringIO()
s = ihm.System(title='test system')
s.locations.append(
ihm.location.BMRBLocation('27600', version='foo', details='bar'))
s.locations.append(
ihm.location.FileLocation(repo=None, path='.'))
r = ihm.report.Reporter(s, sio)
# Should warn about local files
self.assertWarns(ihm.report.LocalFilesWarning, r.report_files)
def test_protocols(self):
"""Test report_protocols"""
sio = StringIO()
s = ihm.System(title='test system')
prot = ihm.protocol.Protocol(name='foo')
prot.steps.append(ihm.protocol.Step(
assembly='foo', dataset_group='bar',
method='baz', num_models_begin=0, num_models_end=42))
analysis = ihm.analysis.Analysis()
analysis.steps.append(ihm.analysis.ClusterStep(
feature='RMSD', num_models_begin=42, num_models_end=5))
prot.analyses.append(analysis)
s.orphan_protocols.append(prot)
r = ihm.report.Reporter(s, sio)
r.report_protocols()
def test_restraints(self):
"""Test report_restraints"""
sio = StringIO()
s = ihm.System(title='test system')
dist = ihm.restraint.UpperBoundDistanceRestraint(42.0)
geom = ihm.geometry.XAxis(name='foo', description='bar')
rsr = ihm.restraint.GeometricRestraint(
dataset='foo', geometric_object=geom, feature='feat',
distance=dist)
s.restraints.append(rsr)
r = ihm.report.Reporter(s, sio)
r.report_restraints()
def test_models(self):
"""Test report_models"""
sio = StringIO()
s = ihm.System(title='test system')
sg = ihm.model.StateGroup()
state = ihm.model.State(name='foo')
mg = ihm.model.ModelGroup(name='bar')
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
mg.append(m)
state.append(mg)
sg.append(state)
s.state_groups.append(sg)
r = ihm.report.Reporter(s, sio)
r.report_models()
def test_ensembles(self):
"""Test report_ensembles"""
sio = StringIO()
s = ihm.System(title='test system')
e = ihm.Entity("ACG")
a = ihm.AsymUnit(e, "my asym")
a.id = 'A'
s.asym_units.append(a)
s.entities.append(e)
e1 = ihm.model.Ensemble(model_group=None, num_models=10)
e2 = ihm.model.Ensemble(model_group=None, num_models=5, precision=1.0,
name='test ensemble')
mg = ihm.model.ModelGroup(name='bar')
e3 = ihm.model.Ensemble(model_group=mg, num_models=1, file='file')
e3.densities.append(ihm.model.LocalizationDensity(
file='foo', asym_unit=a(1, 2)))
s.ensembles.extend((e1, e2, e3))
r = ihm.report.Reporter(s, sio)
r.report_ensembles()
# Should warn about extra models but no external file
e4 = ihm.model.Ensemble(model_group=mg, num_models=1)
s.ensembles.append(e4)
self.assertWarns(ihm.report.MissingFileWarning, r.report_ensembles)
if __name__ == '__main__':
unittest.main()
|
