Fixed bug for writer initialized by Chem.SDWriter(...).

[drivanov]

Without the writer.close() statement, the file written by writer will not be closed properly. As a result, in our test the end of the file /workspace/data/MoleculeGPT/raw/molecules.sdf is missing. This is what it looks like:

472184
     RDKit          2D

  1  0  0  0  0  0  0  0  0  0999 V2000
    2.0000    0.0000    0.0000 Os  0  0  0  0  0 15  0  0  0  0  0  0
M  CHG  1   1   4
M  END
>  <PUBCHEM_COMPOUND_CID>  (4303)
472184

>  <PUBCHEM_COMPOUND_CANONICALIZED>  (4303)
1

>  <PUBCHEM_CACTVS_COMPLEXITY>  (4303)
0

>  <PUBCHEM_CACTVS_HBOND_ACCEPTOR>  (4303)
0

>  <PUBCHEM_CACTVS_HBOND_DONOR>  (4303)
0

>  <PUBCHEM_CACTVS_ROTATABLE_BOND>  (4303)
0

>  <PUBCHEM_CACTVS_SUBSKEYS>  (4303)
AAADcQAAAAAAAAAAAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA==

>  <PUBCHEM_IUPAC_OPENEYE_NAME

Even the <PUBCHEM_IUPAC_OPENEYE_NAME tag does not end correctly with the > character, and the last molecule (#4303) is missing. As a result, we get a crash later when running the test:

Traceback (most recent call last):
  File "/workspace/examples/llm/molecule_gpt.py", line 187, in <module>
    train(
  File "/workspace/examples/llm/molecule_gpt.py", line 69, in train
    dataset = MoleculeGPTDataset(path)
              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/torch_geometric/datasets/molecule_gpt_dataset.py", line 217, in __init__
    super().__init__(root, transform, pre_transform, pre_filter,
  File "/usr/local/lib/python3.12/dist-packages/torch_geometric/data/in_memory_dataset.py", line 81, in __init__
    super().__init__(root, transform, pre_transform, pre_filter, log,
  File "/usr/local/lib/python3.12/dist-packages/torch_geometric/data/dataset.py", line 115, in __init__
    self._process()
  File "/usr/local/lib/python3.12/dist-packages/torch_geometric/data/dataset.py", line 262, in _process
    self.process()
  File "/usr/local/lib/python3.12/dist-packages/torch_geometric/datasets/molecule_gpt_dataset.py", line 436, in process
    CAN_SMILES = mol.GetProp("PUBCHEM_OPENEYE_CAN_SMILES")
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'PUBCHEM_OPENEYE_CAN_SMILES'

[puririshi98]

thanks for finding this fix