exposed fill_value to protein_to_pyg function (#385)

* exposed fill_value to protein_to_pyg function

* added to CHANGELOG

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CHANGELOG.md

@@ -6,7 +6,8 @@
 * Fix bug where the `deprotonate` argument is not wired up to `graphein.protein.graphs.construct_graphs`. [#375](https://github.com/a-r-j/graphein/pull/375)
 
 #### Misc
-* Updated Foldcomp datasets with improved setup function and updated database choices such as ESMAtlas [#382](https://github.com/a-r-j/graphein/pull/382)
+* exposed `fill_value` option to `protein_to_pyg` function. [#385](https://github.com/a-r-j/graphein/pull/385)
+* Updated Foldcomp datasets with improved setup function and updated database choices such as ESMAtlas. [#382](https://github.com/a-r-j/graphein/pull/382)
 * Resolve issue with notebook version and `pluggy` in Dockerfile. [#372](https://github.com/a-r-j/graphein/pull/372)
 * Remove `typing_extension` as dependency since we now primarily support Python >=3.8 and `Literal` is included in `typing` there.
 

graphein/protein/tensor/io.py

@@ -108,6 +108,7 @@ def protein_to_pyg(
     atom_types: List[str] = PROTEIN_ATOMS,
     remove_nonstandard: bool = True,
     store_het: bool = False,
+    fill_value_coords: float = 1e-5,
 ) -> Data:
     """
     Parses a protein (from either: a PDB code, PDB file or a UniProt ID
@@ -237,7 +238,9 @@ def protein_to_pyg(
         df["residue_id"] = df.residue_id + ":" + df.insertion
 
     out = Data(
-        coords=protein_df_to_tensor(df, atoms_to_keep=atom_types),
+        coords=protein_df_to_tensor(
+            df, atoms_to_keep=atom_types, fill_value=fill_value_coords
+        ),
         residues=get_sequence(
             df,
             chains=chain_selection,