fixed single atom molecule issue

jtnn/chemutils.py

@@ -73,6 +73,9 @@ def get_clique_mol(mol, atoms):
 
 def tree_decomp(mol):
     n_atoms = mol.GetNumAtoms()
+    if n_atoms == 1:
+        return [[0]], []
+
     cliques = []
     for bond in mol.GetBonds():
         a1 = bond.GetBeginAtom().GetIdx()
@@ -330,6 +333,8 @@ def dfs_assemble(cur_mol, global_amap, fa_amap, cur_node, fa_node):
     lg.setLevel(rdkit.RDLogger.CRITICAL)
 
     smiles = ["O=C1[C@@H]2C=C[C@@H](C=CC2)C1(c1ccccc1)c1ccccc1","O=C([O-])CC[C@@]12CCCC[C@]1(O)OC(=O)CC2", "ON=C1C[C@H]2CC3(C[C@@H](C1)c1ccccc12)OCCO3", "C[C@H]1CC(=O)[C@H]2[C@@]3(O)C(=O)c4cccc(O)c4[C@@H]4O[C@@]43[C@@H](O)C[C@]2(O)C1", 'Cc1cc(NC(=O)CSc2nnc3c4ccccc4n(C)c3n2)ccc1Br', 'CC(C)(C)c1ccc(C(=O)N[C@H]2CCN3CCCc4cccc2c43)cc1', "O=c1c2ccc3c(=O)n(-c4nccs4)c(=O)c4ccc(c(=O)n1-c1nccs1)c2c34", "O=C(N1CCc2c(F)ccc(F)c2C1)C1(O)Cc2ccccc2C1"]
+    mol_tree = MolTree("C")
+    assert len(mol_tree.nodes) > 0
 
     def tree_test():
         for s in sys.stdin: