Fail to train synthon completion in retrosynthesis: Pre-condition Violation

[KiddoZhu]

Following the tutorial in the doc, I got error on this line.

synthon_solver = core.Engine(synthon_task, synthon_train, synthon_valid, synthon_test, synthon_optimizer , gpus=[0], batch_size=128)

The error message is

****
Pre-condition Violation
bgnIdx not connected to begin atom of bond
Violation occurred on line 292 in file /opt/conda/conda-bld/rdkit_1603173682698/work/Code/GraphMol/Bond.cpp
Failed Expression: getOwningMol().getBondBetweenAtoms(getBeginAtomIdx(), bgnIdx) != nullptr
****

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/zhuzhaoc/torchdrug/torchdrug/core/engine.py", line 143, in train
    loss, metric = model(batch)
  File "/home/zhuzhaoc/.local/envs/ogb/lib/python3.7/site-packages/torch/nn/modules/module.py", line 889, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/home/zhuzhaoc/torchdrug/torchdrug/tasks/retrosynthesis.py", line 596, in forward
    pred, target = self.predict_and_target(batch, all_loss, metric)
  File "/home/zhuzhaoc/torchdrug/torchdrug/tasks/retrosynthesis.py", line 993, in predict_and_target
    graph2, node_in_target2, node_out_target2, bond_target2, stop_target2 = self.all_stop(reactant, synthon)
  File "/home/zhuzhaoc/.local/envs/ogb/lib/python3.7/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
    return func(*args, **kwargs)
  File "/home/zhuzhaoc/torchdrug/torchdrug/tasks/retrosynthesis.py", line 586, in all_stop
    graph, feature_valid = self._update_molecule_feature(graph)
  File "/home/zhuzhaoc/torchdrug/torchdrug/tasks/retrosynthesis.py", line 385, in _update_molecule_feature
    mols = graphs.to_molecule(ignore_error=True)
  File "/home/zhuzhaoc/torchdrug/torchdrug/data/molecule.py", line 788, in to_molecule
    bond.SetStereoAtoms(*stereo_atoms[j])
RuntimeError: Pre-condition Violation
        bgnIdx not connected to begin atom of bond
        Violation occurred on line 292 in file Code/GraphMol/Bond.cpp
        Failed Expression: getOwningMol().getBondBetweenAtoms(getBeginAtomIdx(), bgnIdx) != nullptr
        RDKIT: 2020.09.1
        BOOST: 1_73

This is because some molecules in USPTO50k have stereo bonds.

[KiddoZhu]

Fixed in d4b7883