How to use the molgrid.ElementIndexTyper function in molgrid

def test_coordset_from_mol():
    m = pybel.readstring('smi','c1ccccc1CO')
    m.addh()
    m.make3D()
    
    c = molgrid.CoordinateSet(m,molgrid.ElementIndexTyper())
    oldcoord = c.coords.tonumpy()
    #simple translate
    t = molgrid.Transform(molgrid.Quaternion(), (0,0,0), (1,1,1))
    t.forward(c,c)
    newcoord = c.coords.tonumpy()
    assert np.sum(newcoord-oldcoord) == approx(48)

def test_example_merge():
    m = pybel.readstring('smi','c1ccccc1CO')
    m.addh()
    m.make3D()
    
    c = molgrid.CoordinateSet(m,molgrid.ElementIndexTyper())
    c2 = molgrid.CoordinateSet(m)

    c2.make_vector_types() #this should not screw up index types
    
    ex = molgrid.Example()
    ex.coord_sets.append(c)
    ex.coord_sets.append(c2)
    assert ex.num_types() == (c.max_type + c2.max_type)
    assert ex.num_coordinates() == (c.coords.dimension(0)+c2.type_index.size())
    
    c3 = ex.merge_coordinates()
    assert c3.coords.tonumpy().shape == (24,3)
    
    t = np.concatenate([c.type_index.tonumpy(),c2.type_index.tonumpy()+c.max_type])
    assert np.array_equal(t, c3.type_index.tonumpy())

def test_coordset_merge():
    m = pybel.readstring('smi','c1ccccc1CO')
    m.addh()
    m.make3D()
    
    c = molgrid.CoordinateSet(m,molgrid.ElementIndexTyper())
    c2 = molgrid.CoordinateSet(m)

    c3 = molgrid.CoordinateSet(c,c2)
    c4 = molgrid.CoordinateSet(c,c2,False)

    assert c3.max_type == (c.max_type + c2.max_type)
    assert c3.coords.dimension(0) == (c.coords.dimension(0)+c2.type_index.size())

    assert c4.max_type == max(c.max_type,c2.max_type)
    assert c4.coords.dimension(0) == (c.coords.dimension(0)+c2.type_index.size())
    
    t = np.concatenate([c.type_index.tonumpy(),c2.type_index.tonumpy()+c.max_type])
    assert np.array_equal(t, c3.type_index.tonumpy())
    
    #test merging without unique types, which makes no sense
    assert c4.coords.tonumpy().shape == (24,3)

def test_custom_typer_example_provider():
    fname = datadir+"/small.types"
    t = molgrid.ElementIndexTyper(80)
    e = molgrid.ExampleProvider(t,data_root=datadir+"/structs")
    e.populate(fname)
    batch = e.next_batch(10)
    c = batch[0].coord_sets[0]
    assert c.max_type == 80

def test_elementtyping():
    m = pybel.readstring('smi','c1ccccc1CO')
    m.addh()
    t = molgrid.ElementIndexTyper(17)
    assert t.num_types() == 17
    names = list(t.get_type_names())
    assert names[2] == 'Helium'
    typs = [t.get_atom_type_index(a.OBAtom) for a in m.atoms]
    assert len(typs) == 16
    ccnt = 0
    ocnt = 0
    hcnt = 0
    for t,r in typs:
        if names[t] == 'Carbon':
            ccnt += 1
            assert r == approx(.76)
        if names[t] == 'Oxygen':
            ocnt += 1
            assert r == approx(.66)
        if names[t] == 'Hydrogen':

def test_examplevec():
    m = pybel.readstring('smi','c1ccccc1CO')
    m.addh()
    m.make3D()
    
    c = molgrid.CoordinateSet(m,molgrid.ElementIndexTyper())
    c2 = molgrid.CoordinateSet(m)

    c2.make_vector_types() #this should not screw up index types
    
    ex = molgrid.Example()
    ex.coord_sets.append(c)
    ex.labels.append(0)
    
    ex2 = molgrid.Example()
    ex2.coord_sets.append(c2)
    ex2.labels.append(1)
    
    evec = molgrid.ExampleVec([ex,ex2])