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Add AYA to constants #387 #390

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merged 5 commits into from
Aug 3, 2024
Merged

Add AYA to constants #387 #390

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e11e17a
add AYA to constants #387
Apr 23, 2024
f8b5ef5
bump changelog
Apr 23, 2024
1575ecf
reset index after handling altlocs #384
Apr 23, 2024
6d548fb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 23, 2024
517f2f8
Merge branch 'master' into modified_res
a-r-j Aug 3, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

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2 changes: 1 addition & 1 deletion graphein/protein/graphs.py
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Expand Up @@ -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


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4 changes: 4 additions & 0 deletions graphein/protein/resi_atoms.py
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Expand Up @@ -463,6 +463,7 @@
"ABA",
"ACE",
"AIB",
"AYA",
"BMT",
"BOC",
"CBX",
Expand Down Expand Up @@ -535,6 +536,7 @@
"ABA",
"ACE",
"AIB",
"AYA",
"ALA",
"ARG",
"ASN",
Expand Down Expand Up @@ -639,6 +641,7 @@
"ASN": "N",
"ASP": "D",
"ASX": "B",
"AYA": "A",
"BMT": "T",
"BOC": "X",
"CBX": "X",
Expand Down Expand Up @@ -795,6 +798,7 @@
"ABA": "ALA",
"ACE": "-",
"AIB": "ALA",
"AYA": "ALA",
"BMT": "THR",
"BOC": "-",
"CBX": "-",
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