From 275e036c3815a3e460333409d55db1238e12f48c Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:35:36 +0100
Subject: [PATCH 01/39] Fix to 1. Get canon sites to list only assembly ress
 and 2. Seperate xtalform sites spatially

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 9058b319..317e7d5d 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -915,7 +915,7 @@ def _crystalform_incremental_cluster(
 
     # Get CA positions
     centroid_ca_positions = {
-        observation_id: neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
+        observation_id.join('/'): neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
         for observation_id, centroid_res
         in observation_centroid_residues.items()
     }

From 6b3272ef1a4ad14540f39312d4b4e79435350cce Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:39:44 +0100
Subject: [PATCH 02/39] Fix to 1. Get canon sites to list only assembly ress
 and 2. Seperate xtalform sites spatially

---
 src/ligand_neighbourhood_alignment/cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 317e7d5d..df05a73a 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1343,13 +1343,14 @@ def _update(
 
     # Assign datasets
     for dtag, dataset in new_datasets.items():
-        dataset_assignments[dtag] = _assign_dataset(
+        new_dataset_assignments[dtag] = _assign_dataset(
             dataset,
             assemblies,
             xtalforms,
             structures[dtag],
             structures,
         )
+        dataset_assignments.update(dataset_assignments)
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")
 

From a8deff13cf04274b5c8fa11234388ead33e5a7fd Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:39:53 +0100
Subject: [PATCH 03/39] Fix to 1. Get canon sites to list only assembly ress
 and 2. Seperate xtalform sites spatially

---
 src/ligand_neighbourhood_alignment/cli.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index df05a73a..f5fa3d9d 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1342,6 +1342,7 @@ def _update(
     alignment_heirarchy.save_yaml(fs_model.assembly_transforms, assembly_transforms, lambda x: x)
 
     # Assign datasets
+    new_dataset_assignments = {}
     for dtag, dataset in new_datasets.items():
         new_dataset_assignments[dtag] = _assign_dataset(
             dataset,

From 1269ca0131eb48d877a7215c510c77fbece45f27 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:40:37 +0100
Subject: [PATCH 04/39] Fix to 1. Get canon sites to list only assembly ress
 and 2. Seperate xtalform sites spatially

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index f5fa3d9d..59a0bf9c 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1351,7 +1351,7 @@ def _update(
             structures[dtag],
             structures,
         )
-        dataset_assignments.update(dataset_assignments)
+        dataset_assignments.update(new_dataset_assignments)
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")
 

From 653f183008053f7b7aaebc720414c67a52c4398b Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:45:44 +0100
Subject: [PATCH 05/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 59a0bf9c..9bd9a0ef 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1351,7 +1351,10 @@ def _update(
             structures[dtag],
             structures,
         )
-        dataset_assignments.update(new_dataset_assignments)
+    print(len(dataset_assignments))
+    dataset_assignments.update(new_dataset_assignments)
+    print(len(dataset_assignments))
+
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")
 

From 5ec9e2ee0f57e9acf2538c303a9c476247aab87a Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:45:54 +0100
Subject: [PATCH 06/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 9bd9a0ef..d1a730e6 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1354,7 +1354,7 @@ def _update(
     print(len(dataset_assignments))
     dataset_assignments.update(new_dataset_assignments)
     print(len(dataset_assignments))
-
+    raise Exception
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")
 

From 262369174d856d5eb3b6830e9fe106ce063ca626 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:49:29 +0100
Subject: [PATCH 07/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index d1a730e6..5d3ee2f7 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1883,6 +1883,10 @@ def _load_dataset_assignments(dataset_assignments_yaml):
 
         for dtag, assignment in dic.items():
             dataset_assignments[dtag] = assignment
+
+    print('assignment')
+    print(dataset_assignments)
+    raise Exception
     return dataset_assignments
 
 

From d21cdbd7f4e2e33866d3dd41e2db5c92af27c577 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:55:53 +0100
Subject: [PATCH 08/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 5d3ee2f7..b8625042 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1884,9 +1884,6 @@ def _load_dataset_assignments(dataset_assignments_yaml):
         for dtag, assignment in dic.items():
             dataset_assignments[dtag] = assignment
 
-    print('assignment')
-    print(dataset_assignments)
-    raise Exception
     return dataset_assignments
 
 

From 33d7f026ca5cb75f5818a0f8b4a08aaf0cfdc7c7 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 14:57:55 +0100
Subject: [PATCH 09/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index b8625042..e410e16e 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1351,10 +1351,7 @@ def _update(
             structures[dtag],
             structures,
         )
-    print(len(dataset_assignments))
-    dataset_assignments.update(new_dataset_assignments)
-    print(len(dataset_assignments))
-    raise Exception
+
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")
 

From 60398af00d452aa1271018f3202f0c7506de8be4 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:00:26 +0100
Subject: [PATCH 10/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index e410e16e..fc572cab 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1351,6 +1351,7 @@ def _update(
             structures[dtag],
             structures,
         )
+    dataset_assignments.update(new_dataset_assignments)
 
     _save_assignments(fs_model, dataset_assignments)
     logger.info(f"Assigned {len(dataset_assignments)} xtalform assignments to datasets!")

From a938fc5fbc1e315d1315009506752e95751e8c9d Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:07:00 +0100
Subject: [PATCH 11/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index fc572cab..d6498578 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -915,7 +915,7 @@ def _crystalform_incremental_cluster(
 
     # Get CA positions
     centroid_ca_positions = {
-        observation_id.join('/'): neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
+        '/'.join(observation_id): neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
         for observation_id, centroid_res
         in observation_centroid_residues.items()
     }

From 6945539954d96468f5e80e071a4f82edd237dc60 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:16:45 +0100
Subject: [PATCH 12/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index d6498578..f2786f67 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -915,7 +915,7 @@ def _crystalform_incremental_cluster(
 
     # Get CA positions
     centroid_ca_positions = {
-        '/'.join(observation_id): neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
+        observation_id: neighbourhoods[observation_id].atoms[(centroid_res[0], centroid_res[1], 'CA')]
         for observation_id, centroid_res
         in observation_centroid_residues.items()
     }

From 62756664a7b0e346b3bd566b861b75043b01ee8d Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:21:14 +0100
Subject: [PATCH 13/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index f2786f67..3df3182c 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -922,7 +922,7 @@ def _crystalform_incremental_cluster(
 
     # Identify current xtalform centre residues (for the considered canonical site)
     centre_residues_positions = {
-        xtalform_site_id: centroid_ca_positions[xtalform_site_id]
+        xtalform_site_id: centroid_ca_positions[xtalform_site_id.split('/')]
         for xtalform_site_id in xtalform_sites
     }
 

From 8dc9ff3f59469e1704747ef34af1349f4e223bb2 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:31:26 +0100
Subject: [PATCH 14/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 3df3182c..b23ed997 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -922,7 +922,7 @@ def _crystalform_incremental_cluster(
 
     # Identify current xtalform centre residues (for the considered canonical site)
     centre_residues_positions = {
-        xtalform_site_id: centroid_ca_positions[xtalform_site_id.split('/')]
+        xtalform_site_id: centroid_ca_positions[tuple(xtalform_site_id.split('/'))]
         for xtalform_site_id in xtalform_sites
     }
 

From 633ba4139cc3d14b631a8c3b2c1918f9b7e32de7 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:37:47 +0100
Subject: [PATCH 15/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index b23ed997..6bfc4857 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1556,6 +1556,15 @@ def _update(
     # for canonical_site_id, canonical_site in canonical_sites.items():
     #     for conformer_site_id, conformer_site in canonical_site.conformer_sites.items():
     #         for lid in conformer_site.ligand_ids:
+    for dtag, dataset_alignment_info in fs_model.alignments.items():
+        for chain, chain_alignment_info in dataset_alignment_info.items():
+            for residue, residue_alignment_info in chain_alignment_info.items():
+                for version, ligand_neighbourhood_output in residue_alignment_info.items():
+                    for (
+                            canonical_site_id,
+                            aligned_structure_path,
+                    ) in ligand_neighbourhood_output.aligned_structures.items():
+                        print(aligned_structure_path)
     for dtag, dataset_alignment_info in fs_model.alignments.items():
         for chain, chain_alignment_info in dataset_alignment_info.items():
             for residue, residue_alignment_info in chain_alignment_info.items():

From 050473777eee847b4bc726607651ba6f10d25019 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:38:04 +0100
Subject: [PATCH 16/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 6bfc4857..9886858d 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1565,6 +1565,7 @@ def _update(
                             aligned_structure_path,
                     ) in ligand_neighbourhood_output.aligned_structures.items():
                         print(aligned_structure_path)
+    exit()
     for dtag, dataset_alignment_info in fs_model.alignments.items():
         for chain, chain_alignment_info in dataset_alignment_info.items():
             for residue, residue_alignment_info in chain_alignment_info.items():

From 6917b9f439013fca73574e888164df4be4e06b3d Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:41:37 +0100
Subject: [PATCH 17/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 9886858d..3fad1f66 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1556,17 +1556,10 @@ def _update(
     # for canonical_site_id, canonical_site in canonical_sites.items():
     #     for conformer_site_id, conformer_site in canonical_site.conformer_sites.items():
     #         for lid in conformer_site.ligand_ids:
+
     for dtag, dataset_alignment_info in fs_model.alignments.items():
-        for chain, chain_alignment_info in dataset_alignment_info.items():
-            for residue, residue_alignment_info in chain_alignment_info.items():
-                for version, ligand_neighbourhood_output in residue_alignment_info.items():
-                    for (
-                            canonical_site_id,
-                            aligned_structure_path,
-                    ) in ligand_neighbourhood_output.aligned_structures.items():
-                        print(aligned_structure_path)
-    exit()
-    for dtag, dataset_alignment_info in fs_model.alignments.items():
+        if dtag not in new_datasets:
+            continue
         for chain, chain_alignment_info in dataset_alignment_info.items():
             for residue, residue_alignment_info in chain_alignment_info.items():
                 for version, ligand_neighbourhood_output in residue_alignment_info.items():

From 76c1b7a93be0ca95ff631f445c01de02ed1bcdf8 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:49:58 +0100
Subject: [PATCH 18/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 3fad1f66..3ae1eb61 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1310,6 +1310,7 @@ def _update(
         assembly_landmarks,
         assembly_transforms,
         version,
+        base_dir
 ):
     logger.info(f"Version is: {version}")
     # Get the structures
@@ -1558,8 +1559,6 @@ def _update(
     #         for lid in conformer_site.ligand_ids:
 
     for dtag, dataset_alignment_info in fs_model.alignments.items():
-        if dtag not in new_datasets:
-            continue
         for chain, chain_alignment_info in dataset_alignment_info.items():
             for residue, residue_alignment_info in chain_alignment_info.items():
                 for version, ligand_neighbourhood_output in residue_alignment_info.items():
@@ -1567,7 +1566,7 @@ def _update(
                             canonical_site_id,
                             aligned_structure_path,
                     ) in ligand_neighbourhood_output.aligned_structures.items():
-                        if not Path(aligned_structure_path).exists():
+                        if not ( (fs_model.source_dir / aligned_structure_path).exists() or Path(aligned_structure_path).exists()):
                             # _update_aligned_structures()
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
@@ -1628,7 +1627,7 @@ def _update(
         for canonical_site_id, alignment_info in dataset_alignment_info.items():
             aligned_structure_path = alignment_info["aligned_structures"]
             logger.info(f"Outputting reference structure: {aligned_structure_path}")
-            if not Path(aligned_structure_path).exists():
+            if not ( (fs_model.source_dir / aligned_structure_path).exists() or Path(aligned_structure_path).exists()):
                 _structure = structures[dtag].clone()
                 _align_reference_structure(
                     _structure,
@@ -1658,7 +1657,7 @@ def _update(
                             aligned_event_map_path,
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
-                        if not Path(aligned_event_map_path).exists():
+                        if not ( (fs_model.source_dir / aligned_event_map_path).exists() or Path(aligned_event_map_path).exists()):
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
                             # Check for the matching conformer site

From 2836b14375c93a7736d8d895911829dd85e48451 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:50:39 +0100
Subject: [PATCH 19/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 3ae1eb61..fbd8e28f 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1310,7 +1310,6 @@ def _update(
         assembly_landmarks,
         assembly_transforms,
         version,
-        base_dir
 ):
     logger.info(f"Version is: {version}")
     # Get the structures

From 60d57a6cf96211a2989430b868552a99ecfe2e06 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 15:59:44 +0100
Subject: [PATCH 20/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index fbd8e28f..c48b039e 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1565,7 +1565,20 @@ def _update(
                             canonical_site_id,
                             aligned_structure_path,
                     ) in ligand_neighbourhood_output.aligned_structures.items():
-                        if not ( (fs_model.source_dir / aligned_structure_path).exists() or Path(aligned_structure_path).exists()):
+                        rprint(fs_model.source_dir / aligned_structure_path)
+                        rprint(Path(aligned_structure_path))
+
+    rprint(fs_model.source_dir)
+    exit()
+    for dtag, dataset_alignment_info in fs_model.alignments.items():
+        for chain, chain_alignment_info in dataset_alignment_info.items():
+            for residue, residue_alignment_info in chain_alignment_info.items():
+                for version, ligand_neighbourhood_output in residue_alignment_info.items():
+                    for (
+                            canonical_site_id,
+                            aligned_structure_path,
+                    ) in ligand_neighbourhood_output.aligned_structures.items():
+                        if not ( (fs_model.source_dir / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
                             # _update_aligned_structures()
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
@@ -1626,7 +1639,7 @@ def _update(
         for canonical_site_id, alignment_info in dataset_alignment_info.items():
             aligned_structure_path = alignment_info["aligned_structures"]
             logger.info(f"Outputting reference structure: {aligned_structure_path}")
-            if not ( (fs_model.source_dir / aligned_structure_path).exists() or Path(aligned_structure_path).exists()):
+            if not ( (fs_model.source_dir / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
                 _structure = structures[dtag].clone()
                 _align_reference_structure(
                     _structure,
@@ -1656,7 +1669,7 @@ def _update(
                             aligned_event_map_path,
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
-                        if not ( (fs_model.source_dir / aligned_event_map_path).exists() or Path(aligned_event_map_path).exists()):
+                        if not ( (fs_model.source_dir / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
                             # Check for the matching conformer site

From 18fa4466ce17f0e256752f9476b03707b157adf4 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:06:39 +0100
Subject: [PATCH 21/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 18 +++---------------
 1 file changed, 3 insertions(+), 15 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index c48b039e..f1cbc128 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1557,19 +1557,7 @@ def _update(
     #     for conformer_site_id, conformer_site in canonical_site.conformer_sites.items():
     #         for lid in conformer_site.ligand_ids:
 
-    for dtag, dataset_alignment_info in fs_model.alignments.items():
-        for chain, chain_alignment_info in dataset_alignment_info.items():
-            for residue, residue_alignment_info in chain_alignment_info.items():
-                for version, ligand_neighbourhood_output in residue_alignment_info.items():
-                    for (
-                            canonical_site_id,
-                            aligned_structure_path,
-                    ) in ligand_neighbourhood_output.aligned_structures.items():
-                        rprint(fs_model.source_dir / aligned_structure_path)
-                        rprint(Path(aligned_structure_path))
 
-    rprint(fs_model.source_dir)
-    exit()
     for dtag, dataset_alignment_info in fs_model.alignments.items():
         for chain, chain_alignment_info in dataset_alignment_info.items():
             for residue, residue_alignment_info in chain_alignment_info.items():
@@ -1578,7 +1566,7 @@ def _update(
                             canonical_site_id,
                             aligned_structure_path,
                     ) in ligand_neighbourhood_output.aligned_structures.items():
-                        if not ( (fs_model.source_dir / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
+                        if not ( (fs_model.source_dir.parent / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
                             # _update_aligned_structures()
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
@@ -1639,7 +1627,7 @@ def _update(
         for canonical_site_id, alignment_info in dataset_alignment_info.items():
             aligned_structure_path = alignment_info["aligned_structures"]
             logger.info(f"Outputting reference structure: {aligned_structure_path}")
-            if not ( (fs_model.source_dir / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
+            if not ( (fs_model.source_dir.parent / aligned_structure_path).exists() | Path(aligned_structure_path).exists()):
                 _structure = structures[dtag].clone()
                 _align_reference_structure(
                     _structure,
@@ -1669,7 +1657,7 @@ def _update(
                             aligned_event_map_path,
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
-                        if not ( (fs_model.source_dir / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
+                        if not ( (fs_model.source_dir.parent / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
                             # Check for the matching conformer site

From ef6fc0cbde999f094786db1de937117c791d7351 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:14:55 +0100
Subject: [PATCH 22/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index f1cbc128..0c2ffbda 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1678,6 +1678,9 @@ def _update(
                             xmap_path = datasets[dtag].ligand_binding_events[(dtag, chain, residue)].xmap
 
                             aligned_structure_path = ligand_neighbourhood_output.aligned_structures[canonical_site_id]
+                            st_path = fs_model.source_dir.parent / aligned_structure_path
+                            if not st_path.exists():
+                                st_path = aligned_structure_path
                             aligned_structure = gemmi.read_structure(str(aligned_structure_path))
                             aligned_res = aligned_structure[0][chain][str(residue)][0]
 

From 27367203a64f9d070c9c70f976c033e5121541d0 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:15:00 +0100
Subject: [PATCH 23/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 0c2ffbda..a966fd0f 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1681,7 +1681,7 @@ def _update(
                             st_path = fs_model.source_dir.parent / aligned_structure_path
                             if not st_path.exists():
                                 st_path = aligned_structure_path
-                            aligned_structure = gemmi.read_structure(str(aligned_structure_path))
+                            aligned_structure = gemmi.read_structure(str(st_path))
                             aligned_res = aligned_structure[0][chain][str(residue)][0]
 
                             # logger.info(datasets[dtag].ligand_binding_events[(dtag, chain, residue)].dtag)

From 50ae5d6753077a243263cb476927455256074e12 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:28:45 +0100
Subject: [PATCH 24/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index a966fd0f..f5d0a996 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1658,6 +1658,7 @@ def _update(
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
                         if not ( (fs_model.source_dir.parent / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
+                            print(fs_model.source_dir.parent / aligned_event_map_path)
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
                             # Check for the matching conformer site

From 66ad8187f4791931f0a4ef711a8a3540e3ef123b Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:47:55 +0100
Subject: [PATCH 25/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index f5d0a996..110910e1 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1657,7 +1657,8 @@ def _update(
                             aligned_event_map_path,
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
-                        if not ( (fs_model.source_dir.parent / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
+                        # if not ( (fs_model.source_dir.parent / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
+                        if Path(aligned_event_map_path).is_relative_to(fs_model.source_dir):
                             print(fs_model.source_dir.parent / aligned_event_map_path)
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]

From 67a43cd0ac5619bfdf6a7cda21dd4536b8887858 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Tue, 15 Oct 2024 16:56:57 +0100
Subject: [PATCH 26/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 110910e1..635a6831 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1658,7 +1658,12 @@ def _update(
                     ) in ligand_neighbourhood_output.aligned_event_maps.items():
                         logger.info(f"Writing to: {aligned_event_map_path}")
                         # if not ( (fs_model.source_dir.parent / aligned_event_map_path).exists() | Path(aligned_event_map_path).exists()):
-                        if Path(aligned_event_map_path).is_relative_to(fs_model.source_dir):
+                        rel = True
+                        try:
+                            rel = Path(aligned_event_map_path).is_relative_to(fs_model.source_dir)
+                        except:
+                            rel = False
+                        if rel:
                             print(fs_model.source_dir.parent / aligned_event_map_path)
                             _structure = structures[dtag].clone()
                             canonical_site = canonical_sites[canonical_site_id]
@@ -1686,9 +1691,6 @@ def _update(
                             aligned_structure = gemmi.read_structure(str(st_path))
                             aligned_res = aligned_structure[0][chain][str(residue)][0]
 
-                            # logger.info(datasets[dtag].ligand_binding_events[(dtag, chain, residue)].dtag)
-                            # logger.info(datasets[dtag].ligand_binding_events[(dtag, chain, residue)].chain)
-                            # logger.info(datasets[dtag].ligand_binding_events[(dtag, chain, residue)].residue)   # *
                             if (xmap_path != "None") and (xmap_path is not None):
                                 xmap = read_xmap(xmap_path)
 

From 0890b0262e9a91eee2fecafcba3ef8c6ab55ad2b Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:45:52 +0000
Subject: [PATCH 27/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/alignment_heirarchy.py      | 1 +
 .../generate_sites_from_components.py                          | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/alignment_heirarchy.py b/src/ligand_neighbourhood_alignment/alignment_heirarchy.py
index faa7e027..9b1cddaf 100644
--- a/src/ligand_neighbourhood_alignment/alignment_heirarchy.py
+++ b/src/ligand_neighbourhood_alignment/alignment_heirarchy.py
@@ -75,6 +75,7 @@ def _chain_to_biochain(chain_name, xtalform: dt.XtalForm, assemblies: dict[str,
         for _j, _chain_name in enumerate(_xtal_assembly.chains):
             if chain_name == _chain_name:
                 return assemblies[_xtal_assembly.assembly].generators[_j].biomol
+    raise Exception(f'No biochain found for chain {chain_name}')
 
 
 StructureLandmarks = dict[tuple[str, str, str], tuple[float, float, float]]
diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 431ac26a..37314d5c 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -336,10 +336,11 @@ def _update_reference_structure_transforms(
     # Determine whether the biochain is shared, and if not skip
     reference_structure = structures[key[0]]
     reference_structure_xtalform = xtalforms[dataset_assignments[key[0]]]
+    xtalform_chains = [chain for assembly in reference_structure_xtalform.assemblies.values() for chain in assembly.chains]
     reference_structure_biochains = {
         chain.name: alignment_heirarchy._chain_to_biochain(chain.name, reference_structure_xtalform, assemblies)
         for chain
-        in reference_structure[0]
+        in xtalform_chains
     }
     reference_structure_biochains_inv = {v: k for k, v in reference_structure_biochains.items()}
 

From 94c3e0411c19b244dfdb7a817a2d92a6d8800832 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:49:03 +0000
Subject: [PATCH 28/39] Fix for A71

---
 .../generate_sites_from_components.py                          | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 37314d5c..ecdaebb0 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -351,7 +351,8 @@ def _update_reference_structure_transforms(
     alignment_residues_ref_st = []
     alignment_residues_mov_st = []
     core_chain = reference_structure_biochains_inv[canonical_site_biochain]
-    for rid in canonical_site.residues:
+    canonical_site_residues = canonical_site.residues
+    for rid in canonical_site_residues:
         chain, res = rid[0], rid[1]
         biochain = alignment_heirarchy._chain_to_biochain(
             chain,

From e7de75e1c01514ca94bb9ee5b1b11b9a7633897d Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:50:21 +0000
Subject: [PATCH 29/39] Fix for A71

---
 .../generate_sites_from_components.py                           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index ecdaebb0..317f5c6a 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -338,7 +338,7 @@ def _update_reference_structure_transforms(
     reference_structure_xtalform = xtalforms[dataset_assignments[key[0]]]
     xtalform_chains = [chain for assembly in reference_structure_xtalform.assemblies.values() for chain in assembly.chains]
     reference_structure_biochains = {
-        chain.name: alignment_heirarchy._chain_to_biochain(chain.name, reference_structure_xtalform, assemblies)
+        chain: alignment_heirarchy._chain_to_biochain(chain.name, reference_structure_xtalform, assemblies)
         for chain
         in xtalform_chains
     }

From 2aa62b3d917142a0d49b7a6db9b1aaf409ff72e4 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:52:34 +0000
Subject: [PATCH 30/39] Fix for A71

---
 .../generate_sites_from_components.py                           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 317f5c6a..616c8a3c 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -338,7 +338,7 @@ def _update_reference_structure_transforms(
     reference_structure_xtalform = xtalforms[dataset_assignments[key[0]]]
     xtalform_chains = [chain for assembly in reference_structure_xtalform.assemblies.values() for chain in assembly.chains]
     reference_structure_biochains = {
-        chain: alignment_heirarchy._chain_to_biochain(chain.name, reference_structure_xtalform, assemblies)
+        chain: alignment_heirarchy._chain_to_biochain(chain, reference_structure_xtalform, assemblies)
         for chain
         in xtalform_chains
     }

From 89fc7fc6f4631e0aa7383efbfb9b499368bc9b56 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:09:10 +0000
Subject: [PATCH 31/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py             |  4 +++-
 .../generate_sites_from_components.py                 | 11 +++++++++--
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 635a6831..2fab9b4d 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1534,7 +1534,9 @@ def _update(
                     conformer_sites,
                     assemblies,
                     xtalforms,
-                    dataset_assignments
+                    dataset_assignments,
+                    xtalform_sites,
+                    canonical_site_id
                 )
     logger.info(f"Now have {len(reference_structure_transforms)} reference structure transforms")
     save_reference_structure_transforms(
diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 616c8a3c..3677f484 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -322,13 +322,20 @@ def _update_reference_structure_transforms(
     conformer_sites: dict[str, dt.ConformerSite],
     assemblies,
     xtalforms,
-    dataset_assignments
+    dataset_assignments,
+    xtalform_sites,
+canonical_site_id
 ):
     # Get the biochain of the canonical site
     site_reference_ligand_id = conformer_sites[canonical_site.reference_conformer_site_id].reference_ligand_id
     site_reference_ligand_xtalform = xtalforms[dataset_assignments[site_reference_ligand_id[0]]]
+    for xsid, xtalform_site in xtalform_sites.items():
+        if xtalform_site.xtalform_id == dataset_assignments[site_reference_ligand_id[0]]:
+            if xtalform_site.canonical_site_id == canonical_site_id:
+                break
+    site_chain = xtalform_site.crystallographic_chain
     canonical_site_biochain = alignment_heirarchy._chain_to_biochain(
-        site_reference_ligand_id[1],
+        site_chain,
         site_reference_ligand_xtalform,
         assemblies
     )

From c84c5ffcc552b0cc15c0c50abcfa2f9d97751889 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:17:31 +0000
Subject: [PATCH 32/39] Fix for A71

---
 .../generate_sites_from_components.py                 | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 3677f484..778bbade 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -328,11 +328,12 @@ def _update_reference_structure_transforms(
 ):
     # Get the biochain of the canonical site
     site_reference_ligand_id = conformer_sites[canonical_site.reference_conformer_site_id].reference_ligand_id
-    site_reference_ligand_xtalform = xtalforms[dataset_assignments[site_reference_ligand_id[0]]]
-    for xsid, xtalform_site in xtalform_sites.items():
-        if xtalform_site.xtalform_id == dataset_assignments[site_reference_ligand_id[0]]:
-            if xtalform_site.canonical_site_id == canonical_site_id:
-                break
+    site_reference_ligand_xtalform_id = dataset_assignments[site_reference_ligand_id[0]]
+    site_reference_ligand_xtalform = xtalforms[site_reference_ligand_xtalform_id]
+    for xsid, _xtalform_site in xtalform_sites.items():
+        if _xtalform_site.xtalform_id == site_reference_ligand_xtalform_id:
+            if _xtalform_site.canonical_site_id == canonical_site_id:
+                xtalform_site = _xtalform_site
     site_chain = xtalform_site.crystallographic_chain
     canonical_site_biochain = alignment_heirarchy._chain_to_biochain(
         site_chain,

From 7f1ac4ea13a15d9bbebc2f333d28eb4f23341f16 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:18:49 +0000
Subject: [PATCH 33/39] Fix for A71

---
 .../generate_sites_from_components.py                       | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 778bbade..0c2b2175 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -331,8 +331,10 @@ def _update_reference_structure_transforms(
     site_reference_ligand_xtalform_id = dataset_assignments[site_reference_ligand_id[0]]
     site_reference_ligand_xtalform = xtalforms[site_reference_ligand_xtalform_id]
     for xsid, _xtalform_site in xtalform_sites.items():
-        if _xtalform_site.xtalform_id == site_reference_ligand_xtalform_id:
-            if _xtalform_site.canonical_site_id == canonical_site_id:
+        _xtalform_id = _xtalform_site.xtalform_id
+        if _xtalform_id == site_reference_ligand_xtalform_id:
+            _xtalform_canonical_site_id = _xtalform_site.canonical_site_id
+            if _xtalform_canonical_site_id == canonical_site_id:
                 xtalform_site = _xtalform_site
     site_chain = xtalform_site.crystallographic_chain
     canonical_site_biochain = alignment_heirarchy._chain_to_biochain(

From 65ee3165b98a60a4d1e080d049696645c2d6385b Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:53:28 +0000
Subject: [PATCH 34/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py             | 11 +++++++++--
 .../generate_sites_from_components.py                 |  2 +-
 2 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 2fab9b4d..c780b6aa 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -976,7 +976,8 @@ def _update_xtalform_sites(
         canonical_site_id: str,
         dataset_assignments: dict[str, str],
         conformer_sites: dict[str, dt.ConformerSite],
-        neighbourhoods
+        neighbourhoods,
+        debug=False
 ):
     # Iterate over Canonical Sites, collecting Observations that are in the same crystalform
     # Then get their centroid CA positions,
@@ -1007,6 +1008,8 @@ def _update_xtalform_sites(
         }
         for xtalform_name in crystalform_observations
     }
+    if debug:
+        raise Exception
 
     # Spatially cluster
     crystalform_observation_cluster_assignments = {
@@ -1479,13 +1482,17 @@ def _update(
     for canonical_site_id, canonical_site in canonical_sites.items():
         # If canonical site in a xtalform site, replace with new data, otherwise
         # Check if residues match as usual, otherwise create a new canon site for it
+        debug = False
+        if canonical_site_id == 'LYSRSCPZ-x0426+A+805+1':
+            debug=True
         _update_xtalform_sites(
             xtalform_sites,
             canonical_site,
             canonical_site_id,
             dataset_assignments,
             conformer_sites,
-            ligand_neighbourhoods
+            ligand_neighbourhoods,
+            debug
         )
     logger.info(f"Now have {len(xtalform_sites)} xtalform sites")
     _save_xtalform_sites(fs_model, xtalform_sites)
diff --git a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
index 0c2b2175..f331f7d5 100644
--- a/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
+++ b/src/ligand_neighbourhood_alignment/generate_sites_from_components.py
@@ -324,7 +324,7 @@ def _update_reference_structure_transforms(
     xtalforms,
     dataset_assignments,
     xtalform_sites,
-canonical_site_id
+    canonical_site_id
 ):
     # Get the biochain of the canonical site
     site_reference_ligand_id = conformer_sites[canonical_site.reference_conformer_site_id].reference_ligand_id

From e7e8eddaedc365488600d928a3fb05f83eca285d Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 16:57:32 +0000
Subject: [PATCH 35/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index c780b6aa..3a783970 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1008,8 +1008,7 @@ def _update_xtalform_sites(
         }
         for xtalform_name in crystalform_observations
     }
-    if debug:
-        raise Exception
+
 
     # Spatially cluster
     crystalform_observation_cluster_assignments = {
@@ -1021,6 +1020,9 @@ def _update_xtalform_sites(
         for xtalform_name in crystalform_observations
     }
 
+    if debug:
+        raise Exception
+
     # Create the xtalforms or assign new observations
     for xtalform_name in crystalform_observation_cluster_assignments:
         for centroid_residue, asigned_observation_ids in crystalform_observation_cluster_assignments[

From a52668c19c0b145061a00f34664cda6a4d50357c Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:01:34 +0000
Subject: [PATCH 36/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 3a783970..1b4fc072 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1039,7 +1039,7 @@ def _update_xtalform_sites(
                 xtalform_site_id = "/".join(centroid_residue)
                 xtalform_site = dt.XtalFormSite(
                     xtalform_name,
-                    centroid_residue[1],
+                    crystalform_observation_centroids[centroid_residue][1],
                     canonical_site_id,
                     asigned_observation_ids,
                 )

From 038290ba64a7c15e2c66ce7f81f7b847c62c8f84 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:02:01 +0000
Subject: [PATCH 37/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 1b4fc072..d6d22d3d 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1020,8 +1020,8 @@ def _update_xtalform_sites(
         for xtalform_name in crystalform_observations
     }
 
-    if debug:
-        raise Exception
+    # if debug:
+    #     raise Exception
 
     # Create the xtalforms or assign new observations
     for xtalform_name in crystalform_observation_cluster_assignments:

From 02ce9ae26fb904c6019cbef8484dccc673409397 Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:06:24 +0000
Subject: [PATCH 38/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index d6d22d3d..4088df12 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1039,7 +1039,7 @@ def _update_xtalform_sites(
                 xtalform_site_id = "/".join(centroid_residue)
                 xtalform_site = dt.XtalFormSite(
                     xtalform_name,
-                    crystalform_observation_centroids[centroid_residue][1],
+                    crystalform_observation_centroids[xtalform_name][centroid_residue][1],
                     canonical_site_id,
                     asigned_observation_ids,
                 )

From 6d6d5d88ca38d4e1684fd9168859b24557182ddd Mon Sep 17 00:00:00 2001
From: ConorFWild <41680328+ConorFWild@users.noreply.github.com>
Date: Thu, 31 Oct 2024 17:08:41 +0000
Subject: [PATCH 39/39] Fix for A71

---
 src/ligand_neighbourhood_alignment/cli.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ligand_neighbourhood_alignment/cli.py b/src/ligand_neighbourhood_alignment/cli.py
index 4088df12..36154a03 100644
--- a/src/ligand_neighbourhood_alignment/cli.py
+++ b/src/ligand_neighbourhood_alignment/cli.py
@@ -1039,7 +1039,7 @@ def _update_xtalform_sites(
                 xtalform_site_id = "/".join(centroid_residue)
                 xtalform_site = dt.XtalFormSite(
                     xtalform_name,
-                    crystalform_observation_centroids[xtalform_name][centroid_residue][1],
+                    crystalform_observation_centroids[xtalform_name][centroid_residue][0],
                     canonical_site_id,
                     asigned_observation_ids,
                 )