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wengong-jin / icml18-jtnn

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
MIT License
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Small molecule error #16

Closed bslakman closed 6 years ago

bslakman commented 6 years ago

Hi there,

When I have a molecule in training with a single character SMILES (such as "C" for methane), the encoder is failing with IndexError: list index out of range on the following:

def encode(self, mol_batch):
        set_batch_nodeID(mol_batch, self.vocab)
        root_batch = [mol_tree.nodes[0] for mol_tree in mol_batch]

because mol_tree.nodes is empty. From my understanding, I thought methane should be a single node graph. "C" is present in my vocabulary, and this also happens for other single character SMILES.

I removed these molecules from my training since they aren't helpful for my purposes anyway, but wasn't sure if this was a bug.

wengong-jin commented 6 years ago

I agree. It is some sort of bug. I will look into it.

wengong-jin commented 6 years ago

Hi, forgot to say I fixed it.