From 185edf6a049505783815561a004ff92ec1bf75d0 Mon Sep 17 00:00:00 2001
From: Kiarash Jamali <kjamali@mrc-lmb.cam.ac.uk>
Date: Thu, 17 Aug 2023 16:11:22 -0700
Subject: [PATCH] Joe dictionary stuff

---
 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 e61ac8d..702ba25 100644
--- a/model_angelo/utils/save_pdb_utils.py
+++ b/model_angelo/utils/save_pdb_utils.py
@@ -2,6 +2,7 @@
 import os
 import pickle
 from typing import List, Union
+from copy import deepcopy
 
 import numpy as np
 import pandas as pd
@@ -69,6 +70,17 @@ 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")
@@ -80,9 +92,7 @@ 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()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def ca_ps_to_pdb(path_to_save, ca_points, p_points):
@@ -118,9 +128,7 @@ def ca_ps_to_pdb(path_to_save, ca_points, p_points):
             element="P",
         )
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def chains_to_pdb(path_to_save, chains):
@@ -135,9 +143,7 @@ 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()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def to_xyz(directory):
@@ -208,9 +214,7 @@ def atom14_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def protein_to_cif(
@@ -280,9 +284,7 @@ def protein_to_cif(
             )
             res_counter += 1
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def chain_atom14_to_cif(
@@ -363,9 +365,7 @@ def chain_atom14_to_cif(
                 res_counter += 1
 
     struct = struct.get_structure()
-    io = MMCIFIO()
-    io.set_structure(struct)
-    io.save(path_to_save)
+    save_structure_to_cif(struct, path_to_save)
 
 
 def write_chain_report(