def test_same_molecule(self):
# Exact same
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom + 1,
altloc=self.altloc,
symop=self.symop,
)
)
)
# Symmetry equivalent
self.assertTrue(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom + 1,
altloc=self.altloc,
symop=self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=(0, 0, 3 * self.radius),
radius=self.radius,
molecule=self.molecule,
atom=self.atom + 1,
altloc=self.altloc,
symop=self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom + 1,
altloc=clash.altloc_strategy.alternate(identifier="B"),
symop=self.symop2,
)
)
)
def test_same_molecule(self):
# Exact same
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom + 1,
altloc = self.altloc,
symop = self.symop,
)
)
)
# Symmetry equivalent
self.assertTrue(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom + 1,
altloc = self.altloc,
symop = self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = ( 0, 0, 3 * self.radius ),
radius = self.radius,
molecule = self.molecule,
atom = self.atom + 1,
altloc = self.altloc,
symop = self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom + 1,
altloc = clash.altloc_strategy.alternate( identifier = "B" ),
symop = self.symop2,
)
)
)
def test_structure(self):
self.assertEqual( len( self.indexer ), 0 )
sphere = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.altloc,
symop = self.symop,
)
self.indexer.add( object = sphere, position = sphere.centre )
self.assertEqual( len( self.indexer ), 1 )
closeby = self.indexer.close_to( centre = sphere.centre )
self.assertEqual( len( closeby ), 1 )
spheres = list( closeby )
self.assertEqual( sphere.atom, spheres[0].atom )
self.assertEqual( sphere.molecule, spheres[0].molecule )
self.assertEqual( sphere.symop, spheres[0].symop )
closeby = self.indexer.close_to( centre = [ c + 3 for c in self.centre ] )
self.assertEqual( len( closeby ), 0 )
def test_structure(self):
self.assertEqual(len(self.indexer), 0)
sphere = clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc,
symop=self.symop,
)
self.indexer.add(object=sphere, position=sphere.centre)
self.assertEqual(len(self.indexer), 1)
closeby = self.indexer.close_to(centre=sphere.centre)
self.assertEqual(len(closeby), 1)
spheres = list(closeby)
self.assertEqual(sphere.atom, spheres[0].atom)
self.assertEqual(sphere.molecule, spheres[0].molecule)
self.assertEqual(sphere.symop, spheres[0].symop)
closeby = self.indexer.close_to(centre=[c + 3 for c in self.centre])
self.assertEqual(len(closeby), 0)
def test_same_atom(self):
# Exact same
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.altloc,
symop = self.symop,
)
)
)
# Symmetry equivalent
self.assertTrue(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.altloc,
symop = self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = ( 0, 0, 3 * self.radius ),
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.altloc,
symop = self.symop2,
)
)
)
def test_same_atom(self):
# Exact same
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc,
symop=self.symop,
)
)
)
# Symmetry equivalent
self.assertTrue(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc,
symop=self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=(0, 0, 3 * self.radius),
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc,
symop=self.symop2,
)
)
)
def test_altloc_a(self):
sphere = clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc_a,
symop=self.symop,
)
self.check_sphere(sphere=sphere)
self.check_altloc(sphere=sphere, interacting=[self.regular, self.altloc_a], noninteracting=[self.altloc_b])
def test_altloc_c(self):
sphere = clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=clash.altloc_strategy.alternate(identifier="C"),
symop=self.symop,
)
self.check_sphere(sphere=sphere)
self.check_altloc(sphere=sphere, interacting=[self.regular], noninteracting=[self.altloc_a, self.altloc_b])
def test_other_molecules(self):
self.assertTrue(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule + 1,
atom = self.atom,
altloc = self.altloc,
symop = self.symop,
)
)
)
self.assertTrue(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule + 1,
atom = self.atom,
altloc = self.altloc,
symop = self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule + 1,
atom = self.atom,
altloc = clash.altloc_strategy.alternate( identifier = "B" ),
symop = self.symop,
)
)
)
def test_other_molecules(self):
self.assertTrue(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule + 1,
atom=self.atom,
altloc=self.altloc,
symop=self.symop,
)
)
)
self.assertTrue(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule + 1,
atom=self.atom,
altloc=self.altloc,
symop=self.symop2,
)
)
)
self.assertFalse(
self.predicate(
other=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule + 1,
atom=self.atom,
altloc=clash.altloc_strategy.alternate(identifier="B"),
symop=self.symop,
)
)
)
def test_regular(self):
sphere = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.regular,
symop = self.symop,
)
self.check_sphere( sphere = sphere )
self.check_altloc(
sphere = sphere,
interacting = [ self.regular, self.altloc_a, self.altloc_b],
)
def test_altloc_c(self):
sphere = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = clash.altloc_strategy.alternate( identifier = "C" ),
symop = self.symop,
)
self.check_sphere( sphere = sphere )
self.check_altloc(
sphere = sphere,
interacting = [ self.regular ],
noninteracting = [ self.altloc_a, self.altloc_b ],
)
def setUp(self):
self.centre = ( 0, 0, 0 )
self.radius = 1.7
self.molecule = 0
self.atom = 0
self.symop = clash.sgtbx.rt_mx( ( 1, 0, 0, 0, 1, 0, 0, 0, 1 ), ( 0, 0, 0 ) )
self.symop2 = clash.sgtbx.rt_mx( ( 1, 0, 0, 0, 1, 0, 0, 0, 1 ), ( 0, 0, 1 ) )
self.altloc = clash.altloc_strategy.alternate( identifier = "A" )
self.predicate = clash.overlap_interaction_predicate(
object = clash.sphere(
centre = self.centre,
radius = self.radius,
molecule = self.molecule,
atom = self.atom,
altloc = self.altloc,
symop = self.symop,
),
tolerance = 0,
)
def setUp(self):
self.centre = (0, 0, 0)
self.radius = 1.7
self.molecule = 0
self.atom = 0
self.symop = clash.sgtbx.rt_mx((1, 0, 0, 0, 1, 0, 0, 0, 1), (0, 0, 0))
self.symop2 = clash.sgtbx.rt_mx((1, 0, 0, 0, 1, 0, 0, 0, 1), (0, 0, 1))
self.altloc = clash.altloc_strategy.alternate(identifier="A")
self.predicate = clash.overlap_interaction_predicate(
object=clash.sphere(
centre=self.centre,
radius=self.radius,
molecule=self.molecule,
atom=self.atom,
altloc=self.altloc,
symop=self.symop,
),
tolerance=0,
)