Error when importing local .CIF and .MOL file formats

[julioarvellos]

I'm getting an error when I try to import a small molecule using the local method using a file format different from PDB.
The CIF and MOL files were created using Open Babel with the following settings:

• Input PDB > Output CIF | custom setting: "Write bonds using _geom_bond_etc fields"
• Input PDB > Output MOL

The error when Importing CIF file:

bpy.ops.object.select_all(action='SELECT')
bpy.ops.object.delete(use_global=False)
Deleted 2 object(s)
bpy.context.space_data.context = 'SCENE'
bpy.context.space_data.system_bookmarks_active = 1
bpy.context.scene.MN_panel_import = 'local'
bpy.context.space_data.system_bookmarks_active = 1
bpy.ops.mn.import_protein_local()

Python: Traceback (most recent call last):
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\ui.py", line 39, in parse
    molecule = parser[suffix](filepath)
               ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\pdbx.py", line 262, in __init__
    self.array = self.get_structure()
                 ^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\pdbx.py", line 43, in get_structure
    array = pdbx.get_structure(self.file, extra_fields=extra_fields)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdbx\convert.py", line 270, in get_structure
    raise InvalidFileError("Missing 'atom_site' category in file")
biotite.InvalidFileError: Missing 'atom_site' category in file

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\ensemble\cif.py", line 32, in _get_structure
    array = pdbx.get_structure(self.file, extra_fields=extra_fields)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdbx\convert.py", line 270, in get_structure
    raise InvalidFileError("Missing 'atom_site' category in file")
biotite.InvalidFileError: Missing 'atom_site' category in file

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdbx\convert.py", line 1128, in get_component
    atom_category = block["chem_comp_atom"]
                    ~~~~~^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdbx\cif.py", line 647, in __getitem__
    category = self._categories[key]
               ~~~~~~~~~~~~~~~~^^^^^
KeyError: 'chem_comp_atom'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\ui.py", line 41, in parse
    molecule = OldCIF(filepath)
               ^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\ensemble\cif.py", line 16, in __init__
    self.array = self._get_structure(
                 ^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\ensemble\cif.py", line 45, in _get_structure
    array = pdbx.get_component(self.file)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\.local\lib\python3.11\site-packages\biotite\structure\io\pdbx\convert.py", line 1130, in get_component
    raise InvalidFileError("Missing 'chem_comp_atom' category in file")
biotite.InvalidFileError: Missing 'chem_comp_atom' category in file

The error when Importing MOL file:

bpy.ops.object.select_all(action='SELECT')
bpy.ops.object.delete(use_global=False)
Deleted 2 object(s)
bpy.context.space_data.context = 'SCENE'
bpy.context.scene.MN_panel_import = 'alphafold'
bpy.context.scene.MN_panel_import = 'local'
bpy.context.space_data.system_bookmarks_active = 1
bpy.ops.mn.import_protein_local()
Python: Traceback (most recent call last):
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\ui.py", line 407, in invoke
    return self.execute(context)
           ^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\ui.py", line 391, in execute
    mol = load_local(
          ^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\ui.py", line 93, in load_local
    mol.create_object(
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\molecule.py", line 201, in create_object
    obj, frames = _create_object(
                  ^^^^^^^^^^^^^^^
  File "C:\Users\Julio Arvellos\AppData\Roaming\Blender Foundation\Blender\4.2\extensions\blender_org\molecularnodes\entities\molecule\molecule.py", line 307, in _create_object
    centre_array(atom_array, centre)
                 ^^^^^^^^^^
UnboundLocalError: cannot access local variable 'atom_array' where it is not associated with a value

To Reproduce

• Convert the PDB file to CIF or MOL using Open Babel and the settings above mentioned;
• Import the files using MN

Desktop (please complete the following information):

• Windows 11
• Blender 4.2.2 LTS
• Molecular Nodes 4.2.7

FILES:
bodipy_ar_opt_v2.zip

[BradyAJohnston]

Thanks for reporting this! I won't have time for another week or so to look into this but should definitely be able to get something working