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Modify graphs.py to handle insertions when {'insertions': True} #223

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merged 12 commits into from
Dec 8, 2022
Merged

Modify graphs.py to handle insertions when {'insertions': True} #223

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8845e85
update conversion
Oct 18, 2022
f9bfc95
fix coord issues
Oct 18, 2022
b4e150a
update graphs.py to handle insertions
Oct 24, 2022
ade2cb2
Merge branch 'master' into insertion
a-r-j Oct 31, 2022
a75b207
fix affedcted test
a-r-j Nov 2, 2022
d807dd8
accomodate insertion in hbond donor and acceptor
a-r-j Nov 2, 2022
2aeeaa4
update changelog
a-r-j Nov 2, 2022
707e6e5
Merge branch 'master' into insertion
a-r-j Nov 9, 2022
98dbe17
Merge branch 'master' into insertion
a-r-j Dec 7, 2022
cec18d6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
a45316e
Add control flow for insertion labelling
a-r-j Dec 7, 2022
2693ecd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
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update graphs.py to handle insertions
  • Loading branch information
manon Réau committed Oct 24, 2022
commit b4e150a61877ac1fd333082eb0dd920142dc9e9e
8 changes: 6 additions & 2 deletions graphein/protein/graphs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,8 @@ def label_node_id(df: pd.DataFrame, granularity: str) -> pd.DataFrame:
+ df["residue_name"]
+ ":"
+ df["residue_number"].apply(str)
+ ":"
+ df["insertion"].apply(str)
)
df["residue_id"] = df["node_id"]
if granularity == "atom":
Expand Down Expand Up @@ -354,7 +356,7 @@ def sort_dataframe(df: pd.DataFrame) -> pd.DataFrame:
:return: Sorted protein dataframe.
:rtype: pd.DataFrame
"""
return df.sort_values(by=["chain_id", "residue_number", "atom_number"])
return df.sort_values(by=["chain_id", "residue_number", "atom_number", "insertion"])


def assign_node_id_to_dataframe(
Expand All @@ -379,6 +381,8 @@ def assign_node_id_to_dataframe(
+ protein_df["residue_name"]
+ ":"
+ protein_df["residue_number"].apply(str)
+ ":"
+ protein_df["insertion"].apply(str)
)
if granularity in {"atom", "rna_atom"}:
protein_df[
Expand Down Expand Up @@ -546,7 +550,7 @@ def calculate_centroid_positions(
:rtype: pd.DataFrame
"""
centroids = (
atoms.groupby(["residue_number","chain_id","residue_name"])
atoms.groupby(["residue_number","chain_id","residue_name", "insertion"])
.mean()[["x_coord", "y_coord", "z_coord"]]
.reset_index()
)
Expand Down