def test_asa_calculator1(self):
myatoms = ATOMS[:12]
myatoms.extend( ATOMS[13:] )
mycoords = myatoms.extract_xyz()
myradii = RADII[:12] + RADII[13:]
calc = asa.calculator(
coordinate_adaptor = asa.coordinate_adaptor( array = mycoords ),
radius_adaptor = asa.radius_adaptor( array = myradii ),
probe = PROBE,
)
myvalues = self.ACCESSIBLES[:12] + self.ACCESSIBLES[13:]
for ( index, count, radius ) in zip( range( len( myatoms ) ), myvalues, myradii ):
self.assertEqual( calc.accessible_surface_points( index = index ), count )
self.assertAlmostEqual(
calc.accessible_surface_area( index = index ),
SAMPLING_POINTS.unit_area * count * ( radius + PROBE ) ** 2,
7,
)
self.assertTrue(
calc.is_overlapping_sphere( centre = mycoords[0], radius = myradii[0] )
)
self.assertFalse(
calc.is_overlapping_sphere( centre = ( 0, 0, 0 ), radius = 10 )
)
self.assertTrue(
calc.is_overlapping_sphere( centre = ( 0, 0, 0 ), radius = 15 )
)
def test_asa_calculator2(self):
myatoms = ATOMS[:12]
myatoms.extend(ATOMS[13:])
myradii = RADII[:12] + RADII[13:]
calc = asa.calculator(
coordinate_adaptor=asa.coordinate_adaptor(
array=myatoms,
transformation=lambda a: a.xyz,
),
radius_adaptor=asa.radius_adaptor(array=myradii),
probe=PROBE,
)
myvalues = self.ACCESSIBLES[:12] + self.ACCESSIBLES[13:]
for (index, count, radius) in zip(range(len(myatoms)), myvalues,
myradii):
self.assertEqual(calc.accessible_surface_points(index=index),
count)
self.assertAlmostEqual(
calc.accessible_surface_area(index=index),
SAMPLING_POINTS.unit_area * count * (radius + PROBE)**2,
7,
)
def test_asa_calculator1(self):
myatoms = ATOMS[:12]
myatoms.extend(ATOMS[13:])
mycoords = myatoms.extract_xyz()
myradii = RADII[:12] + RADII[13:]
calc = asa.calculator(
coordinate_adaptor=asa.coordinate_adaptor(array=mycoords),
radius_adaptor=asa.radius_adaptor(array=myradii),
probe=PROBE,
)
myvalues = self.ACCESSIBLES[:12] + self.ACCESSIBLES[13:]
for (index, count, radius) in zip(range(len(myatoms)), myvalues,
myradii):
self.assertEqual(calc.accessible_surface_points(index=index),
count)
self.assertAlmostEqual(
calc.accessible_surface_area(index=index),
SAMPLING_POINTS.unit_area * count * (radius + PROBE)**2,
7,
)
self.assertTrue(
calc.is_overlapping_sphere(centre=mycoords[0], radius=myradii[0]))
self.assertFalse(
calc.is_overlapping_sphere(centre=(0, 0, 0), radius=10))
self.assertTrue(calc.is_overlapping_sphere(centre=(0, 0, 0),
radius=15))
def test_asa_calculator0(self):
myatoms = ATOMS[:2]
myradii = ( 2, -2 )
calc = asa.calculator(
coordinate_adaptor = asa.coordinate_adaptor( array = myatoms.extract_xyz() ),
radius_adaptor = asa.radius_adaptor( array = myradii ),
probe = PROBE,
)
self.assertEqual( calc.accessible_surface_points( index = 0 ), 960 )
self.assertRaises( RuntimeError, calc.accessible_surface_points, index = 1 )
def test_asa_calculator0(self):
myatoms = ATOMS[:2]
myradii = (2, -2)
calc = asa.calculator(
coordinate_adaptor=asa.coordinate_adaptor(
array=myatoms.extract_xyz()),
radius_adaptor=asa.radius_adaptor(array=myradii),
probe=PROBE,
)
self.assertEqual(calc.accessible_surface_points(index=0), 960)
self.assertRaises(RuntimeError,
calc.accessible_surface_points,
index=1)
def test_is_overlapping_sphere(self):
mycoord = ATOMS.extract_xyz()[0]
myradius = 2
calc = asa.calculator(
coordinate_adaptor = asa.coordinate_adaptor( array = [ mycoord ] ),
radius_adaptor = asa.radius_adaptor( array = [ myradius ] ),
probe = PROBE,
)
self.assertTrue(
calc.is_overlapping_sphere( centre = mycoord, radius = myradius )
)
(x, y, z ) = mycoord
diff = 1.9 * myradius
self.assertTrue(
calc.is_overlapping_sphere( centre = ( x + diff, y, z ), radius = myradius )
)
self.assertTrue(
calc.is_overlapping_sphere( centre = ( x, y + diff, z ), radius = myradius )
)
self.assertTrue(
calc.is_overlapping_sphere( centre = ( x, y, z + diff ), radius = myradius )
)
diff = 2.1 * myradius
self.assertFalse(
calc.is_overlapping_sphere( centre = ( x + diff, y, z ), radius = myradius )
)
self.assertFalse(
calc.is_overlapping_sphere( centre = ( x, y + diff, z ), radius = myradius )
)
self.assertFalse(
calc.is_overlapping_sphere( centre = ( x, y, z + diff ), radius = myradius )
)
import math
diff = 1.9 * myradius / math.sqrt( 3 )
self.assertTrue(
calc.is_overlapping_sphere( centre = ( x + diff, y + diff, z + diff ), radius = myradius )
)
diff = 2.1 * myradius / math.sqrt( 3 )
self.assertFalse(
calc.is_overlapping_sphere( centre = ( x + diff, y + diff, z + diff ), radius = myradius )
)
def test_is_overlapping_sphere(self):
mycoord = ATOMS.extract_xyz()[0]
myradius = 2
calc = asa.calculator(
coordinate_adaptor=asa.coordinate_adaptor(array=[mycoord]),
radius_adaptor=asa.radius_adaptor(array=[myradius]),
probe=PROBE,
)
self.assertTrue(
calc.is_overlapping_sphere(centre=mycoord, radius=myradius))
(x, y, z) = mycoord
diff = 1.9 * myradius
self.assertTrue(
calc.is_overlapping_sphere(centre=(x + diff, y, z),
radius=myradius))
self.assertTrue(
calc.is_overlapping_sphere(centre=(x, y + diff, z),
radius=myradius))
self.assertTrue(
calc.is_overlapping_sphere(centre=(x, y, z + diff),
radius=myradius))
diff = 2.1 * myradius
self.assertFalse(
calc.is_overlapping_sphere(centre=(x + diff, y, z),
radius=myradius))
self.assertFalse(
calc.is_overlapping_sphere(centre=(x, y + diff, z),
radius=myradius))
self.assertFalse(
calc.is_overlapping_sphere(centre=(x, y, z + diff),
radius=myradius))
import math
diff = 1.9 * myradius / math.sqrt(3)
self.assertTrue(
calc.is_overlapping_sphere(centre=(x + diff, y + diff, z + diff),
radius=myradius))
diff = 2.1 * myradius / math.sqrt(3)
self.assertFalse(
calc.is_overlapping_sphere(centre=(x + diff, y + diff, z + diff),
radius=myradius))
def test_asa_calculator2(self):
myatoms = ATOMS[:12]
myatoms.extend( ATOMS[13:] )
myradii = RADII[:12] + RADII[13:]
calc = asa.calculator(
coordinate_adaptor = asa.coordinate_adaptor(
array = myatoms,
transformation = lambda a: a.xyz,
),
radius_adaptor = asa.radius_adaptor( array = myradii ),
probe = PROBE,
)
myvalues = self.ACCESSIBLES[:12] + self.ACCESSIBLES[13:]
for ( index, count, radius ) in zip( range( len( myatoms ) ), myvalues, myradii ):
self.assertEqual( calc.accessible_surface_points( index = index ), count )
self.assertAlmostEqual(
calc.accessible_surface_area( index = index ),
SAMPLING_POINTS.unit_area * count * ( radius + PROBE ) ** 2,
7,
)