Merge branch 'protein_prediction' of https://github.com/ChEB-AI/pytho…

…n-chebai into protein_prediction
ChEB-AI · Feb 10, 2025 · e3659cb · e3659cb
2 parents e0bbb0e + a52d8de
commit e3659cb
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Showing 12 changed files with 2 additions and 2 deletions.
diff --git a/chebai/preprocessing/reader.py b/chebai/preprocessing/reader.py
@@ -509,7 +509,7 @@ class ESM2EmbeddingReader(DataReader):
 
     def __init__(
         self,
-        save_model_dir: str,
+        save_model_dir: str = os.path.join("data", "esm2_reader"),
         model_name: str = "esm2_t36_3B_UR50D",
         device: Optional[torch.device] = None,
         truncation_length: int = 1022,
@@ -617,7 +617,7 @@ def load_hub_workaround(self, url) -> torch.Tensor:
         return data
 
     @staticmethod
-    def name() -> None:
+    def name() -> str:
         """
         Returns the name of the data reader. This method identifies the specific type of data reader.
 

diff --git a/configs/data/chebi100.yml → configs/data/chebi/chebi100.yml b/configs/data/chebi100.yml → configs/data/chebi/chebi100.yml
diff --git a/configs/data/chebi100_SELFIES.yml → configs/data/chebi/chebi100_SELFIES.yml b/configs/data/chebi100_SELFIES.yml → configs/data/chebi/chebi100_SELFIES.yml
diff --git a/configs/data/chebi100_deepSMILES.yml → configs/data/chebi/chebi100_deepSMILES.yml b/configs/data/chebi100_deepSMILES.yml → configs/data/chebi/chebi100_deepSMILES.yml
diff --git a/configs/data/chebi100_mixed.yml → configs/data/chebi/chebi100_mixed.yml b/configs/data/chebi100_mixed.yml → configs/data/chebi/chebi100_mixed.yml
diff --git a/configs/data/chebi50.yml → configs/data/chebi/chebi50.yml b/configs/data/chebi50.yml → configs/data/chebi/chebi50.yml
diff --git a/configs/data/chebi50_mixed.yml → configs/data/chebi/chebi50_mixed.yml b/configs/data/chebi50_mixed.yml → configs/data/chebi/chebi50_mixed.yml
diff --git a/configs/data/chebi50_partial.yml → configs/data/chebi/chebi50_partial.yml b/configs/data/chebi50_partial.yml → configs/data/chebi/chebi50_partial.yml
diff --git a/configs/data/pubchem_SELFIES.yml → configs/data/pubchem/pubchem_SELFIES.yml b/configs/data/pubchem_SELFIES.yml → configs/data/pubchem/pubchem_SELFIES.yml
diff --git a/configs/data/pubchem_deepSMILES.yml → configs/data/pubchem/pubchem_deepSMILES.yml b/configs/data/pubchem_deepSMILES.yml → configs/data/pubchem/pubchem_deepSMILES.yml
diff --git a/configs/data/pubchem_dissimilar.yml → configs/data/pubchem/pubchem_dissimilar.yml b/configs/data/pubchem_dissimilar.yml → configs/data/pubchem/pubchem_dissimilar.yml
diff --git a/configs/data/tox21_moleculenet.yml → configs/data/tox21/tox21_moleculenet.yml b/configs/data/tox21_moleculenet.yml → configs/data/tox21/tox21_moleculenet.yml