DGL molecule encoding

DGL-LifeSci
#1

Hi DGL Community :smile:

I have recently started exploring this wonderful library and the DGL extension, DGLLife.
As I am trying to familiarize myself, it seems I am running into an error that I cannot figure out.

When trying to create a graph with both node and edge features for Tox21

SMILESToBigraph(add_self_loop=True,node_featurizer=CanonicalAtomFeaturizer(),edge_featurizer=CanonicalBondFeaturizer())

I get the folowing error

4455 nfeats = F.shape(val)[0]
4456 if nfeats != num_edges:
→ 4457 raise DGLError(
4458 “Expect number of features to match number of edges.”
4459 " Got %d and %d instead." % (nfeats, num_edges)
DGLError: Expect number of features to match number of edges. Got 34 and 50 instead.

Maybe someone can help? :grinning:

#2

SMILESToBigraph(add_self_loop=True,node_featurizer=CanonicalAtomFeaturizer(),edge_featurizer=CanonicalBondFeaturizer(self_loop=True))

#3

as the error message indicates, you need to confirm the number of features and edges. please check if your raw data is correctly composed.