def test_origin_shape_6():
maker = GridMaker(cell=1.0,
box_origin=[-10, -10, -10],
box_shape=[20, 20, 20])
ag = prody.parsePDB(TEST_DATA / '1atom.pdb')
origin, shape = maker._get_origin_and_shape(ag)
assert np.array_equal(shape, np.array([20, 20, 20]))
assert np.array_equal(origin, np.array([-10, -10, -10]))
def test_grid_1atom_shape_3():
maker = GridMaker(cell=0.5,
atom_radius=2.0,
padding=3.0,
config='Elements')
g = maker.make_grids(prody.parsePDB(TEST_DATA / '1atom.pdb'))
assert np.all(np.array(g.grid.shape == np.array([4, 13, 13, 13])))
assert np.all(g.origin == np.array([-3] * 3))
def test_grid_1atom_values_point_out_of_bounds():
maker = GridMaker(cell=1.0,
box_origin=[-10, -10, -10],
box_shape=[3, 3, 3],
config='Elements',
mode='point')
g = maker.make_grids(prody.parsePDB(TEST_DATA / '1atom.pdb'))
assert np.all(g.grid < 0.00001)
def test_grid_1atom_values():
maker = GridMaker(cell=1.0,
atom_radius=2.0,
padding=3.0,
config='Elements')
g = maker.make_grids(prody.parsePDB(TEST_DATA / '1atom.pdb'))
assert np.all(g.grid[0] == 0)
assert np.all(g.grid[2] == 0)
assert np.all(g.grid[3] == 0)
assert g.grid[1][3, 3, 3] == pytest.approx(0.398, 0.01)
assert g.grid[1][3, 3, 2] == pytest.approx(0.241, 0.01)
assert np.all(g.grid[1].T - g.grid[1] < 0.001)
def test_grid_2atom_shape_2():
maker = GridMaker(cell=1.0,
atom_radius=2.0,
padding=3.0,
config='Elements')
g = maker.make_grids(prody.parsePDB(TEST_DATA / '2atom.pdb'))
assert np.all(g.grid.shape == np.array([4, 9, 9, 9]))
assert np.all(g.origin == np.array([-3] * 3))
assert np.all(g.grid[2] == 0)
assert np.all(g.grid[3] == 0)
assert g.grid[1][3, 3, 3] == pytest.approx(0.398, 0.01)
assert g.grid[1][3, 3, 2] == pytest.approx(0.241, 0.01)
assert g.grid[0][5, 5, 5] == pytest.approx(0.398, 0.01)
assert g.grid[0][5, 5, 4] == pytest.approx(0.241, 0.01)
assert np.all(g.grid[0][3:8, 3:8, 3:8] - g.grid[1][1:6, 1:6, 1:6] < 0.001)
def test_grid_1atom_values_point():
maker = GridMaker(cell=1.0, padding=3.0, config='Elements', mode='point')
g = maker.make_grids(prody.parsePDB(TEST_DATA / '1atom.pdb'))
assert g.grid[1, 3, 3, 3] == pytest.approx(1.0, 0.001)
g.grid[1, 3, 3, 3] = 0
assert np.all(g.grid < 0.00001)
def test_weights():
maker = GridMaker(cell=1.0, atom_radius=2.0, config=lambda x: [x])
g = maker.make_grids(prody.parsePDB(TEST_DATA / '1atom.pdb'),
weights=[2.0])
print(g.grid)
def test_create():
GridMaker()
def test_create_4():
with pytest.raises(RuntimeError):
GridMaker(cell=2.0, atom_radius=1.0)
def test_create_3():
GridMaker(config=lambda x: x.select('all'))
def test_create_2():
with pytest.raises(RuntimeError):
GridMaker(config='WrongConfigName')
def test_origin_shape_5():
maker = GridMaker(cell=1.0, box_center=[1, 1, 1])
ag = prody.parsePDB(TEST_DATA / '1atom.pdb')
origin, shape = maker._get_origin_and_shape(ag)
assert np.array_equal(shape, np.array([8, 8, 8]))
assert np.array_equal(origin, np.array([-3, -3, -3]))
def test_origin_shape_4():
maker = GridMaker(cell=1.25, box_shape=[8, 8, 8])
ag = prody.parsePDB(TEST_DATA / '1atom.pdb')
origin, shape = maker._get_origin_and_shape(ag)
assert np.array_equal(shape, np.array([8, 8, 8]))
assert np.array_equal(origin, np.array([-5, -5, -5]))
def test_create_1():
GridMaker(config='FuncGroups')