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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.restraint
import ihm.geometry
class Tests(unittest.TestCase):
def test_restraint(self):
"""Test Restraint base class"""
r = ihm.restraint.Restraint() # does nothing
_ = r._get_report()
def test_em3d_restraint_fit(self):
"""Test EM3DRestraintFit class"""
f = ihm.restraint.EM3DRestraintFit(0.4)
self.assertAlmostEqual(f.cross_correlation_coefficient, 0.4, delta=0.1)
def test_em3d_restraint(self):
"""Test EM3DRestraint class"""
f = ihm.restraint.EM3DRestraint(dataset='foo', assembly='bar')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.assembly, 'bar')
self.assertEqual(f.fits, {})
self.assertEqual(f._get_report(),
"Fit to 3D electron microscopy density map")
f = ihm.restraint.EM3DRestraint(
dataset='foo', assembly='bar',
fitting_method="Gaussian mixture models")
self.assertEqual(f._get_report(),
"Fit to 3D electron microscopy density map "
"using Gaussian mixture models")
def test_sas_restraint_fit(self):
"""Test SASRestraintFit class"""
f = ihm.restraint.SASRestraintFit(0.4)
self.assertAlmostEqual(f.chi_value, 0.4, delta=0.1)
def test_sas_restraint(self):
"""Test SASRestraint class"""
f = ihm.restraint.SASRestraint(dataset='foo', assembly='bar')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.assembly, 'bar')
self.assertEqual(f.fits, {})
self.assertEqual(f._get_report(), "SAS restraint")
f = ihm.restraint.SASRestraint(dataset='foo', assembly='bar',
multi_state=False)
self.assertEqual(f._get_report(), "Single-state SAS restraint")
f = ihm.restraint.SASRestraint(dataset='foo', assembly='bar',
multi_state=True,
fitting_atom_type='residues')
self.assertEqual(f._get_report(),
"Multi-state SAS restraint on residues")
def test_em2d_restraint_fit(self):
"""Test EM2DRestraintFit class"""
f = ihm.restraint.EM2DRestraintFit(0.4)
self.assertAlmostEqual(f.cross_correlation_coefficient, 0.4, delta=0.1)
self.assertIsNone(f.rot_matrix)
self.assertIsNone(f.tr_vector)
def test_em2d_restraint(self):
"""Test EM2DRestraint class"""
f = ihm.restraint.EM2DRestraint(dataset='foo', assembly='bar')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.assembly, 'bar')
self.assertEqual(f.fits, {})
self.assertEqual(f._get_report(),
"Fit to 2D electron microscopy class average")
def test_distance_restraint(self):
"""Test DistanceRestraint class"""
_ = ihm.restraint.DistanceRestraint() # does nothing
def test_harmonic_distance_restraint(self):
"""Test HarmonicDistanceRestraint class"""
r = ihm.restraint.HarmonicDistanceRestraint(42.0)
self.assertAlmostEqual(r.distance, 42.0, delta=0.1)
self.assertAlmostEqual(r.distance_lower_limit, 42.0, delta=0.1)
self.assertAlmostEqual(r.distance_upper_limit, 42.0, delta=0.1)
self.assertEqual(r.restraint_type, "harmonic")
def test_upper_bound_distance_restraint(self):
"""Test UpperBoundDistanceRestraint class"""
r = ihm.restraint.UpperBoundDistanceRestraint(42.0)
self.assertAlmostEqual(r.distance, 42.0, delta=0.1)
self.assertIsNone(r.distance_lower_limit)
self.assertAlmostEqual(r.distance_upper_limit, 42.0, delta=0.1)
self.assertEqual(r.restraint_type, "upper bound")
def test_lower_bound_distance_restraint(self):
"""Test LowerBoundDistanceRestraint class"""
r = ihm.restraint.LowerBoundDistanceRestraint(42.0)
self.assertAlmostEqual(r.distance, 42.0, delta=0.1)
self.assertAlmostEqual(r.distance_lower_limit, 42.0, delta=0.1)
self.assertIsNone(r.distance_upper_limit)
self.assertEqual(r.restraint_type, "lower bound")
def test_lower_upper_bound_distance_restraint(self):
"""Test LowerUpperBoundDistanceRestraint class"""
r = ihm.restraint.LowerUpperBoundDistanceRestraint(20.0, 30.0)
self.assertAlmostEqual(r.distance_lower_limit, 20.0, delta=0.1)
self.assertAlmostEqual(r.distance_upper_limit, 30.0, delta=0.1)
self.assertEqual(r.restraint_type, "lower and upper bound")
def test_cross_link_restraint(self):
"""Test CrossLinkRestraint class"""
dss = ihm.ChemDescriptor('DSS')
f = ihm.restraint.CrossLinkRestraint(dataset='foo', linker=dss)
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.linker, dss)
self.assertEqual(f.experimental_cross_links, [])
self.assertEqual(
f._get_report(),
"0 DSS cross-links from 0 experimental identifications")
def test_experimental_cross_link(self):
"""Test ExperimentalCrossLink class"""
f = ihm.restraint.ExperimentalCrossLink('res1', 'res2')
self.assertEqual(f.residue1, 'res1')
self.assertEqual(f.residue2, 'res2')
def test_cross_link(self):
"""Test CrossLink class"""
_ = ihm.restraint.CrossLink() # does nothing
def test_residue_cross_link(self):
"""Test ResidueCrossLink class"""
e = ihm.Entity('AHCDAH')
asym1 = ihm.AsymUnit(e)
asym2 = ihm.AsymUnit(e)
ex_xl = ihm.restraint.ExperimentalCrossLink(e.residue(1), e.residue(2))
f = ihm.restraint.ResidueCrossLink(
experimental_cross_link=ex_xl, asym1=asym1, asym2=asym2,
distance='dist')
self.assertEqual(f.granularity, 'by-residue')
self.assertIsNone(f.atom1)
self.assertIsNone(f.atom2)
self.assertEqual(f.asym1, asym1)
self.assertEqual(f.asym2, asym2)
self.assertEqual(f.residue1.seq_id, 1)
self.assertEqual(f.residue1.asym, asym1)
self.assertEqual(f.residue2.seq_id, 2)
self.assertEqual(f.residue2.asym, asym2)
def test_feature_cross_link(self):
"""Test FeatureCrossLink class"""
f = ihm.restraint.FeatureCrossLink(
experimental_cross_link='ex', asym1='asym1', asym2='asym2',
distance='dist')
self.assertEqual(f.granularity, 'by-feature')
self.assertIsNone(f.atom1)
self.assertIsNone(f.atom2)
self.assertEqual(f.asym1, 'asym1')
self.assertEqual(f.asym2, 'asym2')
def test_atom_cross_link(self):
"""Test AtomCrossLink class"""
f = ihm.restraint.AtomCrossLink(
experimental_cross_link='ex', asym1='asym1', asym2='asym2',
atom1='C', atom2='N', distance='dist')
self.assertEqual(f.granularity, 'by-atom')
self.assertEqual(f.atom1, 'C')
self.assertEqual(f.atom2, 'N')
self.assertEqual(f.asym1, 'asym1')
self.assertEqual(f.asym2, 'asym2')
def test_feature(self):
"""Test Feature base class"""
f = ihm.restraint.Feature() # does nothing
self.assertEqual(f._all_entities_or_asyms(), [])
self.assertIs(f.type, ihm.unknown)
self.assertIs(f._get_entity_type(), ihm.unknown)
def test_residue_feature(self):
"""Test ResidueFeature class"""
e = ihm.Entity('AHCDAH')
a = ihm.AsymUnit(e)
f = ihm.restraint.ResidueFeature(ranges=[])
self.assertIsNone(f._get_entity_type())
# No ranges - type is 'residue'
f = ihm.restraint.ResidueFeature(ranges=[])
self.assertEqual(f.type, 'residue')
# All ranges are individual residues
f = ihm.restraint.ResidueFeature(ranges=[a(1, 1), a(2, 2)])
self.assertEqual(f.type, 'residue')
# Should work with actual Residue objects too
f = ihm.restraint.ResidueFeature(ranges=[a.residue(3)])
self.assertEqual(f.type, 'residue')
# At least one range is a true range
f = ihm.restraint.ResidueFeature(ranges=[a(3, 4)])
self.assertEqual(f.type, 'residue range')
def test_geometric_restraint(self):
"""Test GeometricRestraint class"""
dist = ihm.restraint.UpperBoundDistanceRestraint(42.0)
geom = ihm.geometry.XAxis(name='foo', description='bar')
f = ihm.restraint.GeometricRestraint(
dataset='foo', geometric_object=geom, feature='feat',
distance=dist)
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.object_characteristic, 'other')
self.assertIsNone(f.assembly)
self.assertEqual(f._get_report(), "Distance (upper bound) to axis")
def test_center_geometric_restraint(self):
"""Test CenterGeometricRestraint class"""
f = ihm.restraint.CenterGeometricRestraint(
dataset='foo', geometric_object='geom', feature='feat',
distance='dist')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.object_characteristic, 'center')
self.assertIsNone(f.assembly)
def test_inner_surface_geometric_restraint(self):
"""Test InnerSurfaceGeometricRestraint class"""
f = ihm.restraint.InnerSurfaceGeometricRestraint(
dataset='foo', geometric_object='geom', feature='feat',
distance='dist')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.object_characteristic, 'inner surface')
self.assertIsNone(f.assembly)
def test_outer_surface_geometric_restraint(self):
"""Test OuterSurfaceGeometricRestraint class"""
f = ihm.restraint.OuterSurfaceGeometricRestraint(
dataset='foo', geometric_object='geom', feature='feat',
distance='dist')
self.assertEqual(f.dataset, 'foo')
self.assertEqual(f.object_characteristic, 'outer surface')
self.assertIsNone(f.assembly)
self.assertEqual(f.feature, 'feat')
self.assertEqual(f._all_features, ('feat',))
def test_derived_distance_restraint(self):
"""Test DerivedDistanceRestraint class"""
f = ihm.restraint.DerivedDistanceRestraint(
dataset='foo', feature1='feat1', feature2='feat2', distance='dist')
self.assertEqual(f.dataset, 'foo')
self.assertIsNone(f.assembly)
self.assertEqual(f.feature1, 'feat1')
self.assertEqual(f.feature2, 'feat2')
self.assertEqual(f._all_features, ('feat1', 'feat2'))
def test_pseudo_site_signature(self):
"""Test signature of PseudoSite"""
p = ihm.restraint.PseudoSite(1.0, 2.0, 3.0)
self.assertEqual(p._signature(), ('1.000', '2.000', '3.000', None))
if __name__ == '__main__':
unittest.main()
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