From 76a1be5b6eba7dc2ebf681b4404937f8a279b2ec Mon Sep 17 00:00:00 2001
From: Brady <brady.johnston@me.com>
Date: Sat, 12 Aug 2023 08:20:00 +0800
Subject: [PATCH 1/2] fix: enabling error without packages installed

---
 MolecularNodes/assembly/cif.py  | 5 +++--
 MolecularNodes/assembly/mmtf.py | 5 ++---
 MolecularNodes/assembly/pdb.py  | 5 +++--
 MolecularNodes/load.py          | 6 ++++--
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/MolecularNodes/assembly/cif.py b/MolecularNodes/assembly/cif.py
index 2aac84a18..8022ffee9 100644
--- a/MolecularNodes/assembly/cif.py
+++ b/MolecularNodes/assembly/cif.py
@@ -1,7 +1,6 @@
 import numpy as np
 import itertools
-import biotite.structure.io.pdbx as pdbx
-import biotite
+
 from . import AssemblyParser
 
 
@@ -13,10 +12,12 @@ def __init__(self, mmtf_file):
     
 
     def list_assemblies(self):
+        import biotite.structure.io.pdbx as pdbx    
         return list(pdbx.list_assemblies(self._file).keys())
     
 
     def get_transformations(self, assembly_id):
+        import biotite
         assembly_gen_category = self._file.get_category(
             "pdbx_struct_assembly_gen", expect_looped=True
         )
diff --git a/MolecularNodes/assembly/mmtf.py b/MolecularNodes/assembly/mmtf.py
index fa7ce7262..013453ebb 100644
--- a/MolecularNodes/assembly/mmtf.py
+++ b/MolecularNodes/assembly/mmtf.py
@@ -1,9 +1,6 @@
 import numpy as np
-import biotite.structure.io.mmtf as mmtf
-import biotite
 from . import AssemblyParser
 
-
 class MMTFAssemblyParser(AssemblyParser):
     ### Implementation adapted from ``biotite.structure.io.mmtf.assembly``
 
@@ -12,10 +9,12 @@ def __init__(self, mmtf_file):
     
 
     def list_assemblies(self):
+        import biotite.structure.io.mmtf as mmtf
         return mmtf.list_assemblies(self._file)
     
 
     def get_transformations(self, assembly_id):
+        import biotite
         # Find desired assembly
         selected_assembly = None
         if not "bioAssemblyList" in self._file:
diff --git a/MolecularNodes/assembly/pdb.py b/MolecularNodes/assembly/pdb.py
index e4a3d99d7..8e423d976 100644
--- a/MolecularNodes/assembly/pdb.py
+++ b/MolecularNodes/assembly/pdb.py
@@ -1,6 +1,5 @@
 import numpy as np
-import biotite.structure.io.mmtf as mmtf
-import biotite
+# import biotite.structure.io.mmtf as mmtf
 from . import AssemblyParser
 
 
@@ -16,6 +15,7 @@ def list_assemblies(self):
     
 
     def get_transformations(self, assembly_id):
+        import biotite
         # Get lines containing transformations for assemblies
         remark_lines = self._file.get_remark(350)
         if remark_lines is None:
@@ -102,6 +102,7 @@ def _parse_transformations(lines):
     *REMARK* 290 or 350.
     Return as array of matrices and vectors respectively
     """
+    import biotite
     # Each transformation requires 3 lines for the (x,y,z) components
     if len(lines) % 3 != 0:
         raise biotite.InvalidFileError("Invalid number of transformation vectors")
diff --git a/MolecularNodes/load.py b/MolecularNodes/load.py
index 483fe9993..4bc023dfa 100644
--- a/MolecularNodes/load.py
+++ b/MolecularNodes/load.py
@@ -1,7 +1,7 @@
 import requests
 import io
 from pathlib import Path
-from biotite import InvalidFileError
+
 import bpy
 import numpy as np
 from . import coll
@@ -88,6 +88,7 @@ def molecule_rcsb(
     setup_nodes = True,
     cache_dir = None,      
     ):
+    from biotite import InvalidFileError
     start = time.process_time()
     mol, file = open_structure_rcsb(
         pdb_code = pdb_code, 
@@ -138,7 +139,7 @@ def molecule_local(
     default_style = 0,                    
     setup_nodes = True
     ): 
-    
+    from biotite import InvalidFileError
     import biotite.structure as struc
     import os
     
@@ -221,6 +222,7 @@ def open_structure_rcsb(pdb_code, cache_dir = None, include_bonds = True):
     import biotite.structure.io.mmtf as mmtf
     import biotite.database.rcsb as rcsb
     
+    
     file = mmtf.MMTFFile.read(rcsb.fetch(pdb_code, "mmtf", target_path = cache_dir))
     
     # returns a numpy array stack, where each array in the stack is a model in the 

From a92ba612b6656c422571e0029de550a91e027189 Mon Sep 17 00:00:00 2001
From: Brady <brady.johnston@me.com>
Date: Sat, 12 Aug 2023 08:21:14 +0800
Subject: [PATCH 2/2] Update .gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 1b0b483c5..8980b6ff0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ build/*
 coverage.xml
 .coverage
 *.npz
+*.log