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import utils
import os
import unittest
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import ihm.model
class Tests(unittest.TestCase):
def test_sphere(self):
"""Test Sphere class"""
s = ihm.model.Sphere(asym_unit='foo', seq_id_range=(1, 5), x=1.0,
y=2.0, z=3.0, radius=4.0)
self.assertEqual(s.asym_unit, 'foo')
self.assertEqual(s.seq_id_range, (1, 5))
def test_atom(self):
"""Test Atom class"""
s = ihm.model.Atom(asym_unit='foo', seq_id=1, atom_id='N',
type_symbol='N', x=1.0, y=2.0, z=3.0)
self.assertEqual(s.asym_unit, 'foo')
self.assertEqual(s.seq_id, 1)
def test_model(self):
"""Test Model class"""
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
self.assertIsNone(m.name)
self.assertEqual(m.protocol, 'bar')
def test_model_get_spheres(self):
"""Test Model.get_spheres()"""
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
spheres = ['sphere1', 'sphere2']
m._spheres = spheres[:]
new_spheres = [s for s in m.get_spheres()]
self.assertEqual(new_spheres, spheres)
def test_model_add_sphere(self):
"""Test Model.add_sphere()"""
spheres = ['sphere1', 'sphere2']
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
m.add_sphere(spheres[0])
m.add_sphere(spheres[1])
self.assertEqual(m._spheres, spheres)
def test_model_get_atoms(self):
"""Test Model.get_atoms()"""
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
atoms = ['atom1', 'atom2']
m._atoms = atoms[:]
new_atoms = [a for a in m.get_atoms()]
self.assertEqual(new_atoms, atoms)
def test_model_add_atom(self):
"""Test Model.add_atom()"""
atoms = ['atom1', 'atom2']
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
m.add_atom(atoms[0])
m.add_atom(atoms[1])
self.assertEqual(m._atoms, atoms)
def test_model_group(self):
"""Test ModelGroup class"""
m = ihm.model.Model(assembly='foo', protocol='bar',
representation='baz')
g = ihm.model.ModelGroup([m], name='foo', details='d')
self.assertEqual(g.name, 'foo')
self.assertEqual(g.details, 'd')
self.assertEqual(g[0].protocol, 'bar')
def test_ensemble(self):
"""Test Ensemble class"""
e = ihm.model.Ensemble(model_group=['m1', 'm2', 'm3'],
num_models=10, name='bar')
self.assertEqual(e.name, 'bar')
self.assertIsNone(e.precision)
self.assertEqual(e.num_models, 10)
self.assertEqual(e.num_models_deposited, 3)
self.assertEqual(e.densities, [])
def test_ensemble_invalid(self):
"""Test Ensemble class with invalid feaure/method"""
self.assertRaises(ValueError, ihm.model.Ensemble,
model_group=['m1', 'm2', 'm3'],
num_models=10, name='bar',
clustering_method="invalid")
self.assertRaises(ValueError, ihm.model.Ensemble,
model_group=['m1', 'm2', 'm3'],
num_models=10, name='bar',
clustering_feature="invalid")
def test_density(self):
"""Test LocalizationDensity class"""
e = ihm.model.LocalizationDensity(file='foo', asym_unit='bar')
self.assertEqual(e.file, 'foo')
self.assertEqual(e.asym_unit, 'bar')
def test_subsample(self):
"""Test Subsample classes"""
s = ihm.model.Subsample("foo", num_models=42)
self.assertEqual(s.name, 'foo')
self.assertEqual(s.sub_sampling_type, 'other')
self.assertEqual(s.num_models, 42)
self.assertIsNone(s.model_group)
self.assertIsNone(s.file)
self.assertEqual(s.num_models_deposited, 0)
mg = ihm.model.ModelGroup(['model1'], name='foo')
s = ihm.model.RandomSubsample("foo", num_models=4, model_group=mg)
self.assertEqual(s.name, 'foo')
self.assertEqual(s.sub_sampling_type, 'random')
self.assertEqual(s.num_models, 4)
self.assertIs(s.model_group, mg)
self.assertIsNone(s.file)
self.assertEqual(s.num_models_deposited, 1)
f = 'foo'
s = ihm.model.IndependentSubsample("foo", num_models=4, file=f)
self.assertEqual(s.sub_sampling_type, 'independent')
self.assertIs(s.file, f)
def test_state(self):
"""Test State class"""
s = ihm.model.State(name='foo')
self.assertEqual(s.name, 'foo')
self.assertEqual(s, [])
def test_state_group(self):
"""Test StateGroup class"""
s = ihm.model.StateGroup()
self.assertEqual(s, [])
def test_ordered_process(self):
"""Test OrderedProcess class"""
p = ihm.model.OrderedProcess("time steps", "test process")
self.assertEqual(p.ordered_by, "time steps")
self.assertEqual(p.description, "test process")
self.assertEqual(p.steps, [])
s = ihm.model.ProcessStep(description="foo")
self.assertEqual(s.description, "foo")
p.steps.append(s)
e = ihm.model.ProcessEdge('from', 'to')
s.append(e)
self.assertEqual(p.steps[0][0].group_begin, 'from')
self.assertEqual(p.steps[0][0].group_end, 'to')
self.assertIsNone(p.steps[0][0].description)
def test_dcd_writer(self):
"""Test DCDWriter class"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1, y=2, z=3),
ihm.model.Atom(None, None, None, None, x=4, y=5, z=6)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
d.add_model(m1)
with open(dcd, 'rb') as fh:
contents = fh.read()
self.assertEqual(len(contents), 452)
def test_dcd_writer_framesize_mismatch(self):
"""Test DCDWriter class with framesize mismatch"""
m1 = ihm.model.Model(None, None, None)
m1._atoms = [ihm.model.Atom(None, None, None, None, x=1, y=2, z=3),
ihm.model.Atom(None, None, None, None, x=4, y=5, z=6)]
m2 = ihm.model.Model(None, None, None)
m2._atoms = [ihm.model.Atom(None, None, None, None, x=1, y=2, z=3)]
with utils.temporary_directory() as tmpdir:
dcd = os.path.join(tmpdir, 'out.dcd')
with open(dcd, 'wb') as fh:
d = ihm.model.DCDWriter(fh)
d.add_model(m1)
self.assertRaises(ValueError, d.add_model, m2)
def test_not_modeled_residue_range(self):
"""Test construction of NotModeledResidueRange"""
e = ihm.Entity('ACGT')
asym = ihm.AsymUnit(e, 'foo')
rr = ihm.model.NotModeledResidueRange(asym, 1, 2)
self.assertEqual(rr.seq_id_begin, 1)
self.assertEqual(rr.seq_id_end, 2)
# Cannot create reversed range
self.assertRaises(ValueError, ihm.model.NotModeledResidueRange,
asym, 3, 1)
# Cannot create out-of-range range
self.assertRaises(IndexError, ihm.model.NotModeledResidueRange,
asym, -3, 1)
self.assertRaises(IndexError, ihm.model.NotModeledResidueRange,
asym, 1, 10)
if __name__ == '__main__':
unittest.main()
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