Fixes padding in pNerF computations (#320)

* add PSW to nonstandard residues

* improve insertion and non-standard residue handling

* refactor chain selection

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* remove unused verbosity arg

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* fix chain selection in tests

* fix chain selection in tutorial notebook

* fix notebook chain selection

* fix chain selection typehint

* Update changelog

* Add NLW to non-standard residues

* add .ent support

* add entry for construction from dataframe

* add missing stage arg

* improve obsolete mapping retrieving to include entries with no replacement

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* update changelog

* add transforms to foldcomp datasets

* fix jaxtyping syntax

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* Update changelog

* fix double application of transforms

* improve foldcomp data loading performance

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* remove unused imports

* linting

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* Update changelog

* add B factors to FC parsing output

* bugfix to alpha & kappa angle embedding

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* update changelog

* handle selenocysteine in sidechain torsion angle computation

* fix protein data object initialisation #317

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* restore eq dunder

* update changelog

* add x to foldcomp examples for correct batching

* fix pnerf padding

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---------

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

graphein/protein/tensor/pnerf.py

@@ -277,13 +277,14 @@ def extend(prev_three_coords, point, multi_m):
         )
         coords_trans = torch.cat([coords_pretrans[i], transformed_coords], 0)
 
-    # coords = F.pad(
-    #    coords_trans[: total_num_angles - 1], (0, 0, 0, 0, 1, 0)
-    # )  # original
+    coords = F.pad(
+        coords_trans[: total_num_angles - 1], (0, 0, 0, 0, 1, 0)
+    )  # original
     # coords = F.pad(coords_trans[: total_num_angles - 2], (0, 0, 0, 0, 2, 0))
     # coords = F.pad(coords_trans[: total_num_angles - 3], (0, 0, 0, 0, 3, 0))
     # return coords
-    return coords_trans
+    # return coords_trans
+    return coords
 
 
 def sn_nerf(