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Fix Kekulize error #30

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Fix Kekulize error #30

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e97faf1
Update chemutils.py
ConnorBarnhill Nov 26, 2021
2fa8d75
Merge pull request #1 from ConnorBarnhill/cpb/fix_kekulize
ConnorBarnhill Nov 26, 2021
9f51699
Update hgnn.py
ConnorBarnhill Nov 29, 2021
109960a
Merge pull request #2 from ConnorBarnhill/ConnorBarnhill-patch-1
ConnorBarnhill Nov 29, 2021
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2 changes: 1 addition & 1 deletion hgraph/chemutils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ def set_atommap(mol, num=0):

def get_mol(smiles):
mol = Chem.MolFromSmiles(smiles)
if mol is not None: Chem.Kekulize(mol)
if mol is not None: Chem.Kekulize(mol, clearAromaticFlags=True)
return mol

def get_smiles(mol):
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7 changes: 7 additions & 0 deletions hgraph/hgnn.py
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Expand Up @@ -48,6 +48,13 @@ def reconstruct(self, batch):

root_vecs, root_kl = self.rsample(root_vecs, self.R_mean, self.R_var, perturb=False)
return self.decoder.decode((root_vecs, root_vecs, root_vecs), greedy=True, max_decode_step=150)

def embed(self, batch):
graphs, tensors, _ = batch
tree_tensors, graph_tensors = tensors = make_cuda(tensors)
root_vecs, tree_vecs, _, graph_vecs = self.encoder(tree_tensors, graph_tensors)

return root_vecs

def forward(self, graphs, tensors, orders, beta, perturb_z=True):
tree_tensors, graph_tensors = tensors = make_cuda(tensors)
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