Merge pull request #289 from BradyAJohnston/288-enabling-error

fix: enabling error without `biotite` installed

.gitignore

@@ -11,3 +11,4 @@ build/*
 coverage.xml
 .coverage
 *.npz
+*.log

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
         )

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:

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")

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