From dfea5e301d9eba33a73617c9f7680b093dd3360d Mon Sep 17 00:00:00 2001
From: Kiarash Jamali <kjamali@mrc-lmb.cam.ac.uk>
Date: Mon, 28 Aug 2023 14:41:17 +0100
Subject: [PATCH] Revert "Fix for issue #51"

---
 model_angelo/utils/save_pdb_utils.py | 36 ++++++++++++++--------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/model_angelo/utils/save_pdb_utils.py b/model_angelo/utils/save_pdb_utils.py
index 702ba25..e61ac8d 100644
--- a/model_angelo/utils/save_pdb_utils.py
+++ b/model_angelo/utils/save_pdb_utils.py
@@ -2,7 +2,6 @@
 import os
 import pickle
 from typing import List, Union
-from copy import deepcopy
 
 import numpy as np
 import pandas as pd
@@ -70,17 +69,6 @@ def points_to_xyz(path_to_save, points, zyx_order=False):
                 f.write(f"C {point[2]} {point[1]} {point[0]}\n")
 
 
-def save_structure_to_cif(structure, path_to_save: str):
-    io = MMCIFIO()
-    io.set_structure(structure)
-    # These are switched, as pointed out by Tristan Croll
-    auth_seq_id = deepcopy(io.dic["_atom_site.label_seq_id"])
-    label_seq_id = deepcopy(io.dic["_atom_site.auth_seq_id"])
-    io.dic["_atom_site.label_seq_id"] = label_seq_id
-    io.dic["_atom_site.auth_seq_id"] = auth_seq_id
-    io.save(path_to_save)
-
-
 def points_to_pdb(path_to_save, points):
     struct = StructureBuilder()
     struct.init_structure("1")
@@ -92,7 +80,9 @@ def points_to_pdb(path_to_save, points):
         struct.init_residue(f"ALA", " ", i, " ")
         struct.init_atom("CA", point, 0, 1, " ", "CA", "C")
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def ca_ps_to_pdb(path_to_save, ca_points, p_points):
@@ -128,7 +118,9 @@ def ca_ps_to_pdb(path_to_save, ca_points, p_points):
             element="P",
         )
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def chains_to_pdb(path_to_save, chains):
@@ -143,7 +135,9 @@ def chains_to_pdb(path_to_save, chains):
             struct.init_residue(f"ALA", " ", j, " ")
             struct.init_atom("CA", point, 0, 1, " ", "CA", "C")
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def to_xyz(directory):
@@ -214,7 +208,9 @@ def atom14_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def protein_to_cif(
@@ -284,7 +280,9 @@ def protein_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def chain_atom14_to_cif(
@@ -365,7 +363,9 @@ def chain_atom14_to_cif(
                 res_counter += 1
 
     struct = struct.get_structure()
-    save_structure_to_cif(struct, path_to_save)
+    io = MMCIFIO()
+    io.set_structure(struct)
+    io.save(path_to_save)
 
 
 def write_chain_report(