def test_add_from_range_2(self):
self.assertTrue(self.checker(point=(1, 1, 1)))
s = asa.sphere(centre=(1, 1, 1), radius=0.1, index=0)
indexer = asa.indexing.linear_spheres()
indexer.add(object=s, position=s.centre)
neighbours = asa.accessibility.filter(
range=indexer.close_to(centre=s.centre),
predicate=asa.accessibility.overlap_equality_predicate(
object=asa.sphere(centre=(2, 2, 2), radius=0.1, index=1)),
)
self.assertEqual(len(neighbours), 0)
self.checker.add(neighbours=neighbours)
self.assertTrue(self.checker(point=(1, 1, 1)))
neighbours = asa.accessibility.filter(
range=indexer.close_to(centre=s.centre),
predicate=asa.accessibility.overlap_equality_predicate(
object=asa.sphere(centre=(2, 2, 2), radius=1.64, index=2)),
)
self.assertEqual(len(neighbours), 1)
self.checker.add(neighbours=neighbours)
self.assertFalse(self.checker(point=(1, 1, 1)))
def test_add_from_range_2(self):
self.assertTrue( self.checker( point = ( 1, 1, 1 ) ) )
s = asa.sphere( centre = ( 1, 1, 1 ), radius = 0.1, index = 0 )
indexer = asa.indexing.linear_spheres()
indexer.add( object = s, position = s.centre )
neighbours = asa.accessibility.filter(
range = indexer.close_to( centre = s.centre ),
predicate = asa.accessibility.overlap_equality_predicate(
object = asa.sphere( centre = ( 2, 2, 2 ), radius = 0.1, index = 1 )
),
)
self.assertEqual( len( neighbours ), 0 )
self.checker.add( neighbours = neighbours )
self.assertTrue( self.checker( point = ( 1, 1, 1 ) ) )
neighbours = asa.accessibility.filter(
range = indexer.close_to( centre = s.centre ),
predicate = asa.accessibility.overlap_equality_predicate(
object = asa.sphere( centre = ( 2, 2, 2 ), radius = 1.64, index = 2 )
),
)
self.assertEqual( len( neighbours ), 1 )
self.checker.add( neighbours = neighbours )
self.assertFalse( self.checker( point = ( 1, 1, 1 ) ) )
def setUp(self):
self.sphere = asa.sphere( centre = ( 1, 1, 1 ), radius = 2, index = 0 )
self.predicate = asa.accessibility.overlap_equality_predicate( object = self.sphere )
self.overlap1 = asa.sphere( centre = ( 1, 1, 1 ), radius = 0.1, index = 1 )
self.overlap2 = asa.sphere( centre = ( 2, 2, 2 ), radius = 0.1, index = 1 )
self.no_overlap = asa.sphere( centre = ( -1, -1, -1 ), radius = 0.1, index = 1 )
def setUp(self):
self.sphere = asa.sphere(centre=(1, 1, 1), radius=2, index=0)
self.predicate = asa.accessibility.overlap_equality_predicate(
object=self.sphere)
self.overlap1 = asa.sphere(centre=(1, 1, 1), radius=0.1, index=1)
self.overlap2 = asa.sphere(centre=(2, 2, 2), radius=0.1, index=1)
self.no_overlap = asa.sphere(centre=(-1, -1, -1), radius=0.1, index=1)
def test_high(self):
self.assertIterablesAlmostEqual(
asa.sphere( centre = ( 1, 2, 3 ), radius = 4, index = 0 ).high,
( 5, 6, 7 ),
7,
)
def test_low(self):
self.assertIterablesAlmostEqual(
asa.sphere( centre = ( 1, 2, 3 ), radius = 4, index = 0 ).low,
( -3, -2, -1 ),
7,
)
def test_add_from_list(self):
self.assertTrue( self.checker( point = ( 1, 1, 1 ) ) )
s = asa.sphere( centre = ( 1, 1, 1 ), radius = 0.1, index = 0 )
self.checker.add( neighbours = [ s ] )
self.assertFalse( self.checker( point = ( 1, 1, 1 ) ) )
self.assertTrue( self.checker( point = ( 1.2, 1, 1 ) ) )
def test_high(self):
self.assertIterablesAlmostEqual(
asa.sphere(centre=(1, 2, 3), radius=4, index=0).high,
(5, 6, 7),
7,
)
def test_low(self):
self.assertIterablesAlmostEqual(
asa.sphere(centre=(1, 2, 3), radius=4, index=0).low,
(-3, -2, -1),
7,
)
def test_add_from_list(self):
self.assertTrue(self.checker(point=(1, 1, 1)))
s = asa.sphere(centre=(1, 1, 1), radius=0.1, index=0)
self.checker.add(neighbours=[s])
self.assertFalse(self.checker(point=(1, 1, 1)))
self.assertTrue(self.checker(point=(1.2, 1, 1)))
def test_creation(self):
s1 = asa.sphere( centre = ( 0, 0, 0 ), radius = 3, index = 1 )
s2 = asa.sphere( centre = ( 0, 0, 0 ), radius = 3, index = 2 )
self.assertTrue( s1.index != s2.index )
ATOMS = ROOT.atoms()
from mmtbx.geometry import sphere_surface_sampling
SAMPLING_POINTS = sphere_surface_sampling.golden_spiral( count = 960 )
from cctbx.eltbx import van_der_waals_radii
TABLE = van_der_waals_radii.vdw.table
PROBE = 1.4
RADII = [
TABLE[ atom.determine_chemical_element_simple().strip().capitalize() ]
for atom in ATOMS
]
SPHERES = [
asa.sphere( centre = atom.xyz, radius = radius + PROBE, index = index )
for ( index, ( atom, radius ) ) in enumerate( zip( ATOMS, RADII ) )
]
DESCRIPTIONS = [
altloc.Description(
data = s,
coordinates = s.centre,
altid = altloc.altid_for( atom = atom ),
)
for ( s, atom ) in zip( SPHERES, ATOMS )
]
class TestSphere(unittest.TestCase):
def test_creation(self):
def test_creation(self):
s1 = asa.sphere(centre=(0, 0, 0), radius=3, index=1)
s2 = asa.sphere(centre=(0, 0, 0), radius=3, index=2)
self.assertTrue(s1.index != s2.index)
from mmtbx.geometry import sphere_surface_sampling
SAMPLING_POINTS = sphere_surface_sampling.golden_spiral(count=960)
from cctbx.eltbx import van_der_waals_radii
TABLE = van_der_waals_radii.vdw.table
PROBE = 1.4
RADII = [
TABLE[atom.determine_chemical_element_simple().strip().capitalize()]
for atom in ATOMS
]
SPHERES = [
asa.sphere(centre=atom.xyz, radius=radius + PROBE, index=index)
for (index, (atom, radius)) in enumerate(zip(ATOMS, RADII))
]
DESCRIPTIONS = [
altloc.Description(
data=s,
coordinates=s.centre,
altid=altloc.altid_for(atom=atom),
) for (s, atom) in zip(SPHERES, ATOMS)
]
class TestSphere(unittest.TestCase):
def test_creation(self):
