Merge branch 'a-r-j:master' into amorehead-pdbmanager-chain-interface…

…-filtering

CHANGELOG.md

@@ -22,6 +22,7 @@
 * Fixes initialisation of `Protein` objects. [#317](https://github.com/a-r-j/graphein/issues/317) [#318](https://github.com/a-r-j/graphein/pull/318)
 * Fixes incorrect `rad` and `embed` argument logic in `graphein.protein.tensor.angles.dihedrals/sidechain_torsion` [#321](https://github.com/a-r-j/graphein/pull/321)
 * Fixes incorrect start padding in pNeRF output [#321](https://github.com/a-r-j/graphein/pull/321)
+* Fixes setting ID for PyG data objects when loading from a path to a `.pdb` file [#332](https://github.com/a-r-j/graphein/pull/332)
 
 #### Other Changes
 * Adds transform composition to FoldComp Dataset [#312](https://github.com/a-r-j/graphein/pull/312)
@@ -35,6 +36,7 @@
 * Adds transform composition to FoldComp Dataset [#312](https://github.com/a-r-j/graphein/pull/312)
 * Improve FoldComp dataloading performance and include B factors (pLDDT) in output. [#313](https://github.com/a-r-j/graphein/pull/313) [#315](https://github.com/a-r-j/graphein/pull/315)
 * Add new helper functions to PDBManager [#322](https://github.com/a-r-j/graphein/pull/322) (@amorehead)
+* Add non-standard 'CYX' to `RESI_THREE_TO_1`.
 
 ### 1.7.0 - 10 /04/2023
 

graphein/protein/resi_atoms.py

@@ -652,6 +652,7 @@
     "CSX": "C",
     "CXM": "M",
     "CYS": "C",
+    "CYX": "C",
     "DAL": "A",
     "DAR": "R",
     "DCY": "C",

graphein/protein/tensor/io.py

@@ -166,9 +166,11 @@ def protein_to_pyg(
     # Get ID
     if path is not None:
         id = (
-            path.split("/")[-1] + "_" + "".join(chain_selection)
+            os.path.splitext(path)[0].split("/")[-1]
+            + "_"
+            + "".join(chain_selection)
             if chain_selection != "all"
-            else path
+            else os.path.splitext(path)[0].split("/")[-1]
         )
     elif pdb_code is not None:
         id = (