From 42c1ec1cf5b33047635f9af7517eec235fc5b43c Mon Sep 17 00:00:00 2001 From: Michael Milton Date: Fri, 12 Aug 2022 15:07:56 +1000 Subject: [PATCH 1/2] Fix bug --- arpeggio/core/protein_reader.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/arpeggio/core/protein_reader.py b/arpeggio/core/protein_reader.py index a2c1a3c..5a4384e 100644 --- a/arpeggio/core/protein_reader.py +++ b/arpeggio/core/protein_reader.py @@ -16,11 +16,7 @@ def _get_res_id(atom_sites, i): - return int( - atom_sites["pdbe_label_seq_id"][i] - if "pdbe_label_seq_id" in atom_sites - else atom_sites["auth_seq_id"][i] - ) + return atom_sites["pdbe_label_seq_id"][i] if "pdbe_label_seq_id" in atom_sites else atom_sites["auth_seq_id"][i] def _get_b_factor(atom_sites, i): @@ -352,7 +348,7 @@ def _init_biopython_atom(builder, atom_sites, i): _get_b_factor(atom_sites, i), float(atom_sites["occupancy"][i]), " " - if atom_sites["label_alt_id"][i] == "." + if atom_sites["label_alt_id"][i] in {".", "?"} else atom_sites["label_alt_id"][i], atom_sites["label_atom_id"][i], int(atom_sites["id"][i]), @@ -371,7 +367,7 @@ def _init_biopython_atom(builder, atom_sites, i): _get_b_factor(atom_sites, i), float(atom_sites["occupancy"][i]), " " - if atom_sites["label_alt_id"][i] == "." + if atom_sites["label_alt_id"][i] in {".", "?"} else atom_sites["label_alt_id"][i], atom_sites["label_atom_id"][i], int(atom_sites["id"][i]), From d57ded6e09ff3af48cbc4f3e7f720bb6ad28327a Mon Sep 17 00:00:00 2001 From: Michael Milton Date: Fri, 12 Aug 2022 15:09:17 +1000 Subject: [PATCH 2/2] Revert old change --- arpeggio/core/protein_reader.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/arpeggio/core/protein_reader.py b/arpeggio/core/protein_reader.py index 5a4384e..03d64aa 100644 --- a/arpeggio/core/protein_reader.py +++ b/arpeggio/core/protein_reader.py @@ -16,7 +16,11 @@ def _get_res_id(atom_sites, i): - return atom_sites["pdbe_label_seq_id"][i] if "pdbe_label_seq_id" in atom_sites else atom_sites["auth_seq_id"][i] + return int( + atom_sites["pdbe_label_seq_id"][i] + if "pdbe_label_seq_id" in atom_sites + else atom_sites["auth_seq_id"][i] + ) def _get_b_factor(atom_sites, i):