From 95e16b98b75067c44cd8b6427730b32dfedf1962 Mon Sep 17 00:00:00 2001
From: Brady Johnston <brady.johnston@me.com>
Date: Sat, 8 Mar 2025 07:47:41 +0800
Subject: [PATCH] everything except cellpack passing

---
 molecularnodes/entities/molecule/pdbx.py   | 10 +++++++++-
 molecularnodes/entities/molecule/reader.py | 11 +++++++----
 molecularnodes/ui/ops.py                   |  1 +
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/molecularnodes/entities/molecule/pdbx.py b/molecularnodes/entities/molecule/pdbx.py
index 39d1b430..4752de2d 100644
--- a/molecularnodes/entities/molecule/pdbx.py
+++ b/molecularnodes/entities/molecule/pdbx.py
@@ -51,7 +51,15 @@ def _assemblies(self):
         return CIFAssemblyParser(self.file).get_assemblies()
 
     def entity_ids(self):
-        return self.file.block.get("entity").get("pdbx_description").as_array().tolist()
+        try:
+            return (
+                self.file.block.get("entity")
+                .get("pdbx_description")
+                .as_array()
+                .tolist()
+            )
+        except AttributeError:
+            return None
 
     @staticmethod
     def _extract_matrices(category):
diff --git a/molecularnodes/entities/molecule/reader.py b/molecularnodes/entities/molecule/reader.py
index e234229d..2c23aab4 100644
--- a/molecularnodes/entities/molecule/reader.py
+++ b/molecularnodes/entities/molecule/reader.py
@@ -3,7 +3,7 @@
 from io import BytesIO
 from biotite.structure import AtomArray, AtomArrayStack
 from biotite import structure as struc
-from biotite.file import File
+from biotite.file import File, InvalidFileError
 import numpy as np
 import json
 from ...assets import data
@@ -67,9 +67,12 @@ def chain_ids(self) -> list[str] | None:
         return np.unique(self.array.chain_id).tolist()
 
     def assemblies(self, as_json_string: bool = False) -> dict | str:
-        if as_json_string:
-            return json.dumps(self._assemblies())
-        return self._assemblies()
+        try:
+            if as_json_string:
+                return json.dumps(self._assemblies())
+            return self._assemblies()
+        except InvalidFileError:
+            return ""
 
     def _assemblies(self):
         return {}
diff --git a/molecularnodes/ui/ops.py b/molecularnodes/ui/ops.py
index 1db944b0..f8888666 100644
--- a/molecularnodes/ui/ops.py
+++ b/molecularnodes/ui/ops.py
@@ -102,6 +102,7 @@ def execute(self, context):
         if not isinstance(obj, bpy.types.Object):
             self.report({"ERROR"}, "No active object")
             return {"CANCELLED"}
+
         with databpy.nodes.DuplicatePrevention():
             try:
                 if self.inset_node: