Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def test_make_vector_types_ex_provider(capsys):
fname = datadir+"/ligonly.types"
e = molgrid.ExampleProvider(molgrid.NullIndexTyper(),molgrid.defaultGninaLigandTyper, data_root=datadir+"/structs",make_vector_types=True)
e.populate(fname)
batch_size = 10
b = e.next_batch(batch_size)
gmaker = molgrid.GridMaker(dimension=23.5,radius_type_indexed=True)
shape = gmaker.grid_dimensions(molgrid.defaultGninaLigandTyper.num_types())
mgrid = molgrid.MGrid5f(batch_size,*shape)
c = b[0].merge_coordinates()
tv = c.type_vector.tonumpy()
assert tv.shape == (10,14)
assert tv[0].sum() == 1.0
assert tv[0][8] == 1.0
e2 = molgrid.ExampleProvider(data_root=datadir+"/structs",make_vector_types=True)
e = molgrid.ExampleProvider(data_root=datadir+"/structs",make_vector_types=True)
e.populate(fname)
batch_size = 10
b = e.next_batch(batch_size)
sum = molgrid.MGrid2f(batch_size, e.num_types())
b.sum_types(sum)
sum2 = np.zeros(sum.shape,np.float32)
b.sum_types(sum2)
sum3 = torch.empty(sum.shape,dtype=torch.float32,device='cuda')
b.sum_types(sum3)
np.testing.assert_allclose(sum.tonumpy(),sum3.detach().cpu().numpy(),atol=1e-5)
np.testing.assert_allclose(sum.tonumpy(),sum2,atol=1e-5)
np.testing.assert_allclose(sum[0].tonumpy(), [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 2., 3., 0.,
0., 0., 0., 0., 0., 2., 2., 1., 0., 0., 0.], atol=1e-5)
e = molgrid.ExampleProvider(molgrid.NullIndexTyper(), molgrid.defaultGninaLigandTyper, data_root=datadir+"/structs",make_vector_types=True)
e.populate(fname)
b = e.next_batch(batch_size)
sum = molgrid.MGrid2f(batch_size, e.num_types())
b.sum_types(sum)
np.testing.assert_allclose(sum[0].tonumpy(), [ 2., 3., 0.,
0., 0., 0., 0., 0., 2., 2., 1., 0., 0., 0.], atol=1e-5)
def test_nulltyping():
m = pybel.readstring('smi','c1ccccc1CO')
m.addh()
t = molgrid.NullIndexTyper()
typs = [t.get_atom_type_index(a.OBAtom) for a in m.atoms]
assert t.num_types() == 0
for t,r in typs:
assert t == -1
assert r == 0.0