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import os
import unittest
import utils
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import modelcif
import modelcif.protocol
import modelcif.descriptor
import modelcif.associated
import ihm
class Tests(unittest.TestCase):
def test_all_data(self):
"""Test _all_data() method"""
s = modelcif.System()
e1 = modelcif.Entity("D")
e2 = modelcif.Entity("M")
s.entities.extend((e1, e2))
e3 = modelcif.Entity("A")
s.data.extend((e1, e3))
s.data_groups.append('something not a group')
e4 = modelcif.Entity("M")
s.data_groups.append(modelcif.data.DataGroup([e1, e4]))
e5 = modelcif.Entity("M")
f = modelcif.associated.File(path='foo', details='bar', data=e5)
s.repositories.append(modelcif.associated.Repository('/', [f]))
d = s._all_data()
# List may contain duplicates
self.assertEqual(list(d), [e1, e3, e1, e2, e1, e4, e5])
def test_all_asym_units(self):
"""Test _all_asym_units() method"""
s = modelcif.System()
e1 = modelcif.Entity("DDDD")
e2 = modelcif.Entity("MMMM")
a1 = modelcif.AsymUnit(e1)
a2 = modelcif.AsymUnit(e2)
s.asym_units.append(a1)
asmb = modelcif.Assembly((a1, a2(1, 2)))
s.assemblies.append(asmb)
asyms = s._all_asym_units()
# List may contain duplicates and should be all AsymUnit,
# not AsymUnitRange
self.assertEqual(list(asyms), [a1, a1, a2])
def test_all_entities(self):
"""Test _all_entities() method"""
s = modelcif.System()
e1 = modelcif.Entity("DDDD")
e2 = modelcif.Entity("MMMM")
s.entities.append(e1)
a1 = modelcif.AsymUnit(e1)
s.asym_units.append(a1)
t2 = modelcif.Template(e2, asym_id='A', model_num=1,
transformation=None)
s.templates.append(t2)
es = s._all_entities()
# List may contain duplicates, but does not contain template entity e2
self.assertEqual(list(es), [e1, e1])
def test_all_data_groups(self):
"""Test _all_data_groups() method"""
s = modelcif.System()
e1 = modelcif.Entity("A")
s.data_groups.append(e1)
e2 = modelcif.Entity("C")
p = modelcif.protocol.Protocol()
p.steps.append(modelcif.protocol.ModelingStep(
input_data=e1, output_data=e2))
p.steps.append(modelcif.protocol.ModelingStep(
input_data=None, output_data=None))
s.protocols.append(p)
d = s._all_data_groups()
self.assertEqual(list(d), [e1, e1, e2])
def test_all_template_transformations(self):
"""Test _all_template_transformations() method"""
s = modelcif.System()
tr1 = 'tr1'
tr2 = 'tr2'
s.template_transformations.extend((tr1, tr2))
template = modelcif.Template('mockentity', asym_id="A", model_num=1,
name="test template",
transformation=tr1)
s.templates.append(template)
tt = s._all_template_transformations()
# List may contain duplicates
self.assertEqual(list(tt), [tr1, tr2, tr1])
def test_transformation(self):
"""Test Transformation class"""
_ = modelcif.Transformation([[1, 0, 0], [0, 1, 0], [0, 0, 1]],
[1, 2, 3])
def test_identity_transformation(self):
"""Test identity transformation"""
t = modelcif.Transformation.identity()
for i in range(3):
self.assertAlmostEqual(t.tr_vector[i], 0., delta=0.1)
for j in range(3):
self.assertAlmostEqual(t.rot_matrix[i][j],
1. if i == j else 0., delta=0.1)
# Should always get the same object
t2 = modelcif.Transformation.identity()
self.assertIs(t, t2)
def test_all_software_groups(self):
"""Test _all_software_groups() method"""
s = modelcif.System()
sg1 = 'sg1'
sg2 = 'sg2'
s.software_groups.extend((sg1, sg2))
p = modelcif.protocol.Protocol()
p.steps.append(modelcif.protocol.ModelingStep(
input_data=None, output_data=None, software=sg1))
s.protocols.append(p)
allsg = s._all_software_groups()
# List may contain duplicates
self.assertEqual(list(allsg), [sg1, sg2, sg1])
def test_all_ref_software(self):
"""Test _all_ref_software() method"""
s1 = modelcif.Software(
name='foo', version='1.0',
classification='1', description='2', location='3')
s2 = modelcif.Software(
name='foo', version='2.0',
classification='4', description='5', location='6')
p = modelcif.SoftwareParameter(name='foo', value='bar')
s2param = modelcif.SoftwareWithParameters(s2, [p])
s = modelcif.System()
s.software_groups.append(modelcif.SoftwareGroup((s1, s2param)))
s.software_groups.append(s1)
e1 = modelcif.Entity("DDDD")
t1 = modelcif.Template(e1, asym_id='A', model_num=1,
transformation=None)
s.templates.append(t1)
# Old-style ChemComp without descriptors
c1 = ihm.NonPolymerChemComp('C1', name='C1')
if hasattr(c1, 'descriptors'):
del c1.descriptors
# ChemComp with descriptor without software
c2 = ihm.NonPolymerChemComp('C2', name='C2')
c2.descriptors = [modelcif.descriptor.IUPACName('foo')]
# ChemComp with descriptor with software
c3 = ihm.NonPolymerChemComp('C3', name='C3')
s3 = modelcif.Software(
name='foo', version='2.0',
classification='4', description='5', location='6')
c3.descriptors = [modelcif.descriptor.IUPACName('foo', software=s3)]
e2 = modelcif.Entity([c1, c2, c3])
s.entities.append(e2)
alls = s._all_ref_software()
# List may contain duplicates
self.assertEqual(list(alls), [s1, s2, s1, s3])
def test_software_parameter(self):
"""Test SoftwareParameter class"""
p = modelcif.SoftwareParameter(name='foo', value=42)
self.assertEqual(p.name, 'foo')
self.assertEqual(p.value, 42)
self.assertIsNone(p.description)
_ = repr(p)
def test_software_with_parameters(self):
"""Test SoftwareWithParameters class"""
s = modelcif.Software(
name='foo', version='1.0',
classification='1', description='2', location='3')
p = modelcif.SoftwareParameter(name='foo', value=42)
swp = modelcif.SoftwareWithParameters(software=s, parameters=[p])
self.assertEqual(swp.software.name, 'foo')
self.assertEqual(swp.parameters, [p])
self.assertEqual(swp.name, 'foo')
self.assertEqual(swp.classification, '1')
self.assertEqual(swp.description, '2')
self.assertEqual(swp.location, '3')
self.assertEqual(swp.type, 'program')
self.assertEqual(swp.version, '1.0')
self.assertIsNone(swp.citation)
def test_template(self):
"""Test Template class"""
e1 = modelcif.Entity("DDDD")
t1 = modelcif.Template(e1, asym_id='A', model_num=1,
transformation=None)
self.assertEqual(t1.seq_id_range, (1, 4))
self.assertEqual(t1.template, t1)
def test_software_group_parameters(self):
"""Test old-style SoftwareGroup construction with parameters"""
s = modelcif.Software(
name='foo', version='1.0',
classification='1', description='2', location='3')
p = modelcif.SoftwareParameter(name='foo', value=42)
self.assertWarns(UserWarning,
modelcif.SoftwareGroup, [s], parameters=[p])
def test_feature(self):
"""Test Feature base class"""
f = modelcif.Feature()
self.assertIs(f._get_entity_type(), ihm.unknown)
if __name__ == '__main__':
unittest.main()
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