deepmodeling / deepmodeling/Uni-Mol
[BUG] Wrong calculation on feat["pair_type"] in Uni-Mol2
- Dominant language
- Python
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Description
### Describe the bug
The calculation of feat["pair_type"] in Uni-Mol2 at line 64 `unimol2/unimol2/data/unimol2_dataset.py` should calculate the atom-atom pair. Instead, it calculates the bond-bond pair. Is this the expected behavior?
```python
#unimol2/unimol2/data/unimol2_dataset.py
def get_graph_features(...):
atom_feat = convert_to_single_emb(x[:, 1:], atom_feat_sizes)
# The atom number has been removed in the above step
...
feat = {}
feat["atom_feat"] = torch.from_numpy(atom_feat).long()
...
atoms = feat["atom_feat"][..., 0]
# As a result, the above code does not retrieve the atom number.
pair_type = torch.cat(
[
atoms.view(-1, 1, 1).expand(-1, N, -1),
atoms.view(1, -1, 1).expand(N, -1, -1),
],
dim=-1,
)
```
### Uni-Mol Version
Uni-Mol2
### Expected behavior
`atoms` should get directly from `x[:, 0]` instead of `atom_feat`.
### To Reproduce
_No response_
### Environment
_No response_
### Additional Context
_No response_
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