Sorry for my beginner question, but, I’d like to understand contents included in ConvMol object. I can’t understand relation of connection/bond among atoms of ConvMol object though I output the contents of the ConvMol object. I
(I was using pyg, and I understand edge_index, edge_features, which show the relation connection/bond among atoms)
I can see below using vars(obj), could you point which correspond to edge_index, edge_features? Thanks.
if 1:
obj = train_dataset.X[0]
# deepchem.feat.mol_graphs.ConvMol object
import sys, pprint
pprint.pprint(vars(obj))
-----
'canon_adj_list': [[9],
[10],
[10],
[8],
[8],
[10],
[9],
[8],
[9, 3, 4, 7],
[0, 6, 8, 10],
[9, 1, 2, 5]],
'deg_adj_lists': [array([], shape=(0, 0), dtype=int32),
array([[ 9],
[10],
[10],
[ 8],
[ 8],
[10],
[ 9],
[ 8]], dtype=int32),
array([], shape=(0, 2), dtype=int32),
array([], shape=(0, 3), dtype=int32),
array([[ 9, 3, 4, 7],
[ 0, 6, 8, 10],
[ 9, 1, 2, 5]], dtype=int32),
array([], shape=(0, 5), dtype=int32),
array([], shape=(0, 6), dtype=int32),
array([], shape=(0, 7), dtype=int32),
array([], shape=(0, 8), dtype=int32),
array([], shape=(0, 9), dtype=int32),
array([], shape=(0, 10), dtype=int32)],
'deg_block_indices': array([0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2], dtype=int32),
'deg_id_list': array([1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4], dtype=int32),
'deg_list': [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4],
'deg_slice': array([[0, 0],
[0, 8],
[0, 0],
[0, 0],
[8, 3],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0],
[0, 0]], dtype=int32),
'deg_start': array([ 0, 0, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11]),
'degree_list': [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4],
'max_deg': 10,
'min_deg': 0,