Minor fixes (#310)

* add .ent support

* add entry for construction from dataframe

* add missing stage arg

* improve obsolete mapping retrieving to include entries with no replacement

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update changelog

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -4,7 +4,13 @@
 * Chain selections are now specified with either `"all"` or a list of strings (e.g. `["A", "B"]`) rather than a single selection string (e.g. `"AB"`). This is a necessary chain due to MMTF support which can have multicharacter chain identifiers. [#307](https://github.com/a-r-j/graphein/pull/307)
 
 
+#### Bugfixes
+* Adds missing `stage` parameter to `graphein.ml.datasets.foldcomp_data.FoldCompDataModule.setup()`. [#310](https://github.com/a-r-j/graphein/pull/310)
+
 #### Other Changes
+* Adds entry point for biopandas dataframes in `graphein.protein.tensor.io.protein_to_pyg`. [#310](https://github.com/a-r-j/graphein/pull/310)
+* Adds support for `.ent` files to `graphein.protein.graphs.read_pdb_to_dataframe`. [#310](https://github.com/a-r-j/graphein/pull/310)
+* Obsolete residues with no replacement are now returned by `graphein.protein.utils.get_obsolete_mapping`. [#310](https://github.com/a-r-j/graphein/pull/310)
 * Adds the ability to store a dictionary of HETATM positions in `Data`/`Protein` objects created in the `graphein.protein.tensor` module. [#307](https://github.com/a-r-j/graphein/pull/307)
 * Improved handling of non-standard residues in the `graphein.protein.tensor` module. [#307](https://github.com/a-r-j/graphein/pull/307)
 * Insertions retained by default in the `graphein.protein.tensor` module. I.e. `insertions=True` is now the default behaviour.[#307](https://github.com/a-r-j/graphein/pull/307)

graphein/ml/datasets/foldcomp_dataset.py

@@ -311,7 +311,7 @@ def __init__(
         self.num_workers = num_workers
         self.pin_memory = pin_memory
 
-    def setup(self, stage: str):
+    def setup(self, stage: Optional[str] = None):
         self.train_dataset()
         self.val_dataset()
         self.test_dataset()

graphein/protein/graphs.py

@@ -98,12 +98,18 @@ def read_pdb_to_dataframe(
     if path is not None:
         if isinstance(path, Path):
             path = os.fsdecode(path)
-        if path.endswith(".pdb") or path.endswith(".pdb.gz"):
+        if (
+            path.endswith(".pdb")
+            or path.endswith(".pdb.gz")
+            or path.endswith(".ent")
+        ):
             atomic_df = PandasPdb().read_pdb(path)
         elif path.endswith(".mmtf") or path.endswith(".mmtf.gz"):
             atomic_df = PandasMmtf().read_mmtf(path)
         else:
-            raise ValueError(f"File {path} must be either .pdb or .mmtf not")
+            raise ValueError(
+                f"File {path} must be either .pdb(.gz), .mmtf(.gz) or .ent, not {path.split('.')[-1]}"
+            )
     elif uniprot_id is not None:
         atomic_df = PandasPdb().fetch_pdb(
             uniprot_id=uniprot_id, source="alphafold2-v3"

graphein/protein/tensor/io.py

@@ -98,6 +98,7 @@ def protein_to_pyg(
     path: Optional[Union[str, os.PathLike]] = None,
     pdb_code: Optional[str] = None,
     uniprot_id: Optional[str] = None,
+    df: Optional[pd.DataFrame] = None,
     chain_selection: Union[str, List[str]] = "all",
     deprotonate: bool = True,
     keep_insertions: bool = True,
@@ -182,14 +183,15 @@ def protein_to_pyg(
             else uniprot_id
         )
     else:
-        raise ValueError("Must provide either a path, PDB code or uniprot ID.")
-
-    df = read_pdb_to_dataframe(
-        path=path,
-        pdb_code=pdb_code,
-        uniprot_id=uniprot_id,
-        model_index=model_index,
-    )
+        id = None
+
+    if df is None:
+        df = read_pdb_to_dataframe(
+            path=path,
+            pdb_code=pdb_code,
+            uniprot_id=uniprot_id,
+            model_index=model_index,
+        )
     if chain_selection != "all":
         if isinstance(chain_selection, str):
             chain_selection = [chain_selection]

graphein/protein/utils.py

@@ -54,6 +54,8 @@ def get_obsolete_mapping() -> Dict[str, str]:
             obs_dict[entry[2].lower().decode("utf-8")] = (
                 entry[3].lower().decode("utf-8")
             )
+        elif len(entry) == 3:
+            obs_dict[entry[2].lower().decode("utf-8")] = ""
     return obs_dict