Add AYA to constants #387 (#390)

* add AYA to constants #387

* bump changelog

* reset index after handling altlocs #384

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

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---------

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

CHANGELOG.md

@@ -4,6 +4,8 @@
 * Fixes progress bar for `download_pdb_multiprocessing`. [#394](https://github.com/a-r-j/graphein/pull/394)
 * Add support for DSSP >4. Backwards compatibility is still supported. [#355](https://github.com/a-r-j/graphein/pull/355). Fixes [#353](https://github.com/a-r-j/graphein/issues/353).
 * Fixes bug where RSA features are missing from nodes with insertion codes. [#355](https://github.com/a-r-j/graphein/pull/355). Fixes [#354](https://github.com/a-r-j/graphein/issues/353).
+* 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)
+* Add missing modified residue `AYA` to constants [#390](https://github.com/a-r-j/graphein/pull/390)
 * 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)
 * Fix cluster file loading bug in `pdb_data.py` [#396](https://github.com/a-r-j/graphein/pull/396)
 

graphein/protein/graphs.py

@@ -285,7 +285,7 @@ def remove_alt_locs(
     # Unsort
     if keep in ["max_occupancy", "min_occupancy"]:
         df = df.sort_index()
-
+    df = df.reset_index(drop=True)
     return df
 
 

graphein/protein/resi_atoms.py

@@ -463,6 +463,7 @@
     "ABA",
     "ACE",
     "AIB",
+    "AYA",
     "BMT",
     "BOC",
     "CBX",
@@ -535,6 +536,7 @@
     "ABA",
     "ACE",
     "AIB",
+    "AYA",
     "ALA",
     "ARG",
     "ASN",
@@ -639,6 +641,7 @@
     "ASN": "N",
     "ASP": "D",
     "ASX": "B",
+    "AYA": "A",
     "BMT": "T",
     "BOC": "X",
     "CBX": "X",
@@ -795,6 +798,7 @@
     "ABA": "ALA",
     "ACE": "-",
     "AIB": "ALA",
+    "AYA": "ALA",
     "BMT": "THR",
     "BOC": "-",
     "CBX": "-",