From 0aab9f4df35911c687dbda789e2e9ba36915592e Mon Sep 17 00:00:00 2001 From: Sam Gelman Date: Fri, 5 Jan 2024 15:50:43 -0600 Subject: [PATCH] Fix for newer versions of Pandas --- code/gen_structure_graph.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/code/gen_structure_graph.py b/code/gen_structure_graph.py index f63f87d..798055d 100644 --- a/code/gen_structure_graph.py +++ b/code/gen_structure_graph.py @@ -102,7 +102,7 @@ def cbeta_distance_matrix(pdb_fn, start=0, end=None): ppdb = PandasPdb().read_pdb(pdb_fn) # group by residue number - grouped = ppdb.df["ATOM"].groupby(["residue_number"]) + grouped = ppdb.df["ATOM"].groupby("residue_number") # a list of coords for the cbeta or calpha of each residue coords = [] @@ -110,11 +110,6 @@ def cbeta_distance_matrix(pdb_fn, start=0, end=None): # loop through each residue and find the coordinates of cbeta for i, (residue_number, values) in enumerate(grouped): - # later versions of biopandas are returning the residue_number - # as a tuple, so convert it to a single integer - if isinstance(residue_number, tuple) and len(residue_number) == 1: - residue_number = residue_number[0] - # skip residues not in the range end_index = (len(grouped) if end is None else end) if i not in range(start, end_index):