def setUpClass(cls):
cls.dv = DisVis()
cls.gdv = DisVis()
cls.gdv.queue = get_queue()
receptor = PDB.fromfile(join('data', 'O14250.pdb'))
ligand = PDB.fromfile(join('data', 'Q9UT97.pdb'))
restraints = parse_restraints(join('data', 'restraints.dat'), receptor,
ligand)
rselect, lselect = parse_interaction_selection(
join('data', 'selection.res'), receptor, ligand)
# Identity rotation and rotation around z-axis
rotations = np.asarray([[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
[[0, -1, 0], [1, 0, 0], [0, 0, 1]]],
dtype=np.float64)
cls.dv.receptor = receptor
cls.gdv.receptor = receptor
cls.dv.ligand = ligand
cls.gdv.ligand = ligand
cls.dv.distance_restraints = restraints
cls.gdv.distance_restraints = restraints
cls.dv.rotations = rotations
cls.gdv.rotations = rotations
cls.dv.occupancy_analysis = True
cls.gdv.occupancy_analysis = True
cls.dv.receptor_interaction_selection = rselect
cls.dv.ligand_interaction_selection = lselect
cls.gdv.receptor_interaction_selection = rselect
cls.gdv.ligand_interaction_selection = lselect
cls.dv._initialize()
cls.dv._cpu_init()
cls.gdv._initialize()
cls.gdv._gpu_init()
def setUp(self):
self.dv = DisVis()
self.receptor = PDB.fromfile('data/single-atom.pdb')
self.ligand = PDB.fromfile('data/single-atom.pdb')
class TestDisVis(TestCase):
def setUp(self):
self.dv = DisVis()
self.receptor = PDB.fromfile('data/single-atom.pdb')
self.ligand = PDB.fromfile('data/single-atom.pdb')
def test_minimal_volume_parameters(self):
coor1 = np.asarray([[1, 2, 3], [-2, -3, -4]], dtype=np.float64)
coor2 = np.asarray([[1, 0, 0], [-1, 0, 0]], dtype=np.float64)
offset = 0
voxelspacing = 1
shape, origin = self.dv._minimal_volume_parameters(
coor1, coor2, offset, voxelspacing)
offset = np.linalg.norm(coor2 - coor2.mean(axis=0), axis=1).max()
self.assertEqual(shape, [9, 8, 5])
self.assertTrue(np.allclose(origin, [-3.0, -4.0, -5.0]))
self.assertEqual(offset, 1.0)
def test_initialize(self):
dv = self.dv
# Test the Error raise when things are not set
with self.assertRaises(ValueError):
dv._initialize()
restraint = [self.receptor, self.ligand, 0, 1]
dv.receptor = self.receptor
dv.ligand = self.ligand
dv.add_distance_restraint(*restraint)
dv._initialize()
self.assertEqual(dv.interaction_restraints_cutoff, 1)
self.assertFalse(dv._interaction_analysis)
def test_cpu_init(self):
dv = self.dv
restraint = [self.receptor, self.ligand, 1, 4.5]
voxelspacing = 2
dv.receptor = self.receptor
dv.ligand = self.ligand
dv.add_distance_restraint(*restraint)
dv.voxelspacing = voxelspacing
dv._initialize()
dv._cpu_init()
self.assertEqual(dv._mindis[0], 0.5)
self.assertEqual(dv._maxdis[0], 2.25)
def test_rotate_lcore(self):
dv = self.dv
restraint = [self.receptor, self.ligand, 1, 4.5]
voxelspacing = 2
dv.receptor = self.receptor
dv.ligand = self.ligand
dv.add_distance_restraint(*restraint)
dv.voxelspacing = voxelspacing
dv._initialize()
dv._cpu_init()
rotmat = dv.rotations[0]
dv._rotate_lcore(rotmat)
# Identity rotation
self.assertTrue(np.allclose(dv._lcore, dv._rot_lcore))
def test_get_interaction_space(self):
dv = self.dv
restraint = [self.receptor, self.ligand, 1, 4.5]
dv.receptor = self.receptor
dv.ligand = self.ligand
dv.add_distance_restraint(*restraint)
dv.max_clash = 0.1
dv.min_interaction = 0.1
dv._initialize()
dv._cpu_init()
# Manually set rot_lcore for tests
dv._rot_lcore = np.zeros_like(dv._lcore)
dv._rot_lcore[0, 0, 0] = 1
dv._get_interaction_space()
self.assertTrue(np.allclose(dv._rsurf, dv._intervol))
self.assertTrue(np.allclose(dv._rcore, dv._clashvol))
self.assertTrue(np.allclose(dv._intervol, dv._interacting))
self.assertTrue(
np.allclose(dv._clashvol, np.logical_not(dv._not_clashing)))
self.assertTrue(
np.allclose(dv._interspace, dv._interacting - dv._clashvol))
def test_get_restraints_center(self):
dv = self.dv
# 90 degree rotation around Z-axis
rotmat = np.asarray([[0, -1, 0], [1, 0, 0], [0, 0, 1]],
dtype=np.float64)
restraint = [self.receptor, self.ligand, 0, 4.5]
# Set required attributes to test function
dv._lrestraints = np.asarray([[2, 0, 0]], dtype=np.float64)
dv._rot_lrestraints = np.zeros_like(dv._lrestraints)
dv._restraints_center = np.zeros_like(dv._lrestraints)
dv._rrestraints = np.asarray([[1, 0, 0]], dtype=np.float64)
dv._get_restraints_center(rotmat)
self.assertTrue(np.allclose(dv._rot_lrestraints, np.array([[0, 2,
0]])))
self.assertTrue(
np.allclose(dv._restraints_center, np.array([[1, -2, 0]])))
def test_get_restraint_space(self):
dv = self.dv
dv._restraints_center = np.array([[4, 3, 2]], dtype=np.float64)
dv._mindis = np.array([1], dtype=np.float64)
dv._maxdis = np.array([2], dtype=np.float64)
dv._restspace = np.empty((5, 7, 9), np.int32)
dv._get_restraint_space()
#print dv._restspace
def test_cpu_search(self):
dv = self.dv
restraint = [self.receptor, self.ligand, 1, 4.5]
voxelspacing = 2
dv.receptor = self.receptor
dv.ligand = self.ligand
dv.add_distance_restraint(*restraint)
dv.voxelspacing = voxelspacing
dv._initialize()
dv._cpu_init()
dv._cpu_search()
