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Clustering now runs super fast #90

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Merged
NDoering99 merged 1 commit into from
Jul 29, 2025
Merged

Clustering now runs super fast #90

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10 changes: 3 additions & 7 deletions mdpath/src/cluster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,8 @@ def __init__(
self, df_close_res: pd.DataFrame, pathways: list, num_processes: int
) -> None:
self.df = df_close_res
self.close_pairs_set = set(zip(df_close_res['Residue1'], df_close_res['Residue2'])) | \
set(zip(df_close_res['Residue2'], df_close_res['Residue1']))
self.pathways = pathways
self.num_processes = num_processes
self.overlapp_df = self.calculate_overlap_parallel()
Expand All @@ -58,13 +60,7 @@ def calculate_overlap_for_pathway(self, args: tuple) -> list:
overlap_counter = 0
for res1 in path1:
for res2 in path2:
if (
(self.df["Residue1"] == res1)
& (self.df["Residue2"] == res2)
).any() or (
(self.df["Residue1"] == res2)
& (self.df["Residue2"] == res1)
).any():
if (res1, res2) in self.close_pairs_set:
overlap_counter += 1
result.append(
{"Pathway1": i, "Pathway2": j, "Overlap": overlap_counter}
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