def test_vector_sum_types():
fname = datadir + "/ligonly.types"
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_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)
e2.populate(fname)
b2 = e2.next_batch(batch_size)
c2 = b2[0].merge_coordinates(unique_index_types=True)
tv2 = c2.type_vector.tonumpy()
assert tv2.shape == (10, 28)
gmaker.forward(b, mgrid)
assert b[0].coord_sets[0].has_vector_types()
assert b[0].coord_sets[1].has_vector_types()
assert b[0].num_types() == 14
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
