Fix relative filepaths

molecularnodes/bpyd/object.py

@@ -95,7 +95,7 @@ def __init__(self, obj: Object | None):
         """
         if not isinstance(obj, Object):
             raise ValueError(f"{obj} must be a Blender object of type Object")
-        self._object = obj
+        self._object_name = obj.name
 
     @property
     def object(self) -> Object | None:
@@ -107,30 +107,8 @@ def object(self) -> Object | None:
         Object | None
             The Blender object, or None if not found.
         """
-        # If we don't have connection to an object, attempt to re-stablish to a new
-        # object in the scene with the same UUID. This helps if duplicating / deleting
-        # objects in the scene, but sometimes Blender just loses reference to the object
-        # we are working with because we are manually setting the data on the mesh,
-        # which can wreak havoc on the object database. To protect against this,
-        # if we have a broken link we just attempt to find a new suitable object for it
-        try:
-            # if the connection is broken then trying to the name will raise a connection
-            # error. If we are loading from a saved session then the object_ref will be
-            # None and get an AttributeError
-            self._object.name
-            return self._object
-        except (ReferenceError, AttributeError):
-            for obj in bpy.data.objects:
-                if obj.mn.uuid == self.uuid:
-                    print(
-                        Warning(
-                            f"Lost connection to object: {self._object}, now connected to {obj}"
-                        )
-                    )
-                    self._object = obj
-                    return obj
 
-            return None
+        return bpy.data.objects.get(self._object_name)
 
     @object.setter
     def object(self, value: Object) -> None:
@@ -142,7 +120,7 @@ def object(self, value: Object) -> None:
         value : Object
             The Blender object to set.
         """
-        self._object = value
+        self._object_name = value.name
 
     def store_named_attribute(
         self,

molecularnodes/entities/__init__.py

@@ -1,14 +1,19 @@
-from . import molecule, trajectory
+from .molecule import CLASSES as MOL_CLASSES
+from .trajectory import CLASSES as TRAJ_CLASSES
 from .density import MN_OT_Import_Map
 from .trajectory.dna import MN_OT_Import_OxDNA_Trajectory
+from .ensemble.ui import MN_OT_Import_Cell_Pack, MN_OT_Import_Star_File
+
 from .ensemble.cellpack import CellPack
 from .ensemble.star import StarFile
-from .ensemble.ui import MN_OT_Import_Cell_Pack, MN_OT_Import_Star_File
 from .molecule.pdb import PDB
 from .molecule.pdbx import BCIF, CIF
 from .molecule.sdf import SDF
 from .molecule.ui import fetch, load_local
-from .trajectory.trajectory import Trajectory
+from .trajectory import Trajectory
+from .molecule import Molecule
+from .ensemble import Ensemble
+
 
 CLASSES = (
     [
@@ -17,6 +22,6 @@
         MN_OT_Import_OxDNA_Trajectory,
         MN_OT_Import_Star_File,
     ]
-    + trajectory.CLASSES
-    + molecule.CLASSES
+    + TRAJ_CLASSES
+    + MOL_CLASSES
 )

molecularnodes/entities/ensemble/__init__.py

@@ -1 +1,2 @@
 from .ui import load_starfile, load_cellpack
+from .ensemble import Ensemble

molecularnodes/entities/ensemble/ensemble.py

@@ -18,11 +18,9 @@ def __init__(self, file_path: Union[str, Path]):
 
         """
         super().__init__()
-        self.type: str = "ensemble"
         self.file_path: Path = bl.path_resolve(file_path)
         self.instances: bpy.types.Collection = None
         self.frames: bpy.types.Collection = None
-        bpy.context.scene.MNSession.ensembles[self.uuid] = self
 
     @classmethod
     def create_object(

molecularnodes/entities/ensemble/star.py

@@ -15,7 +15,6 @@
 class StarFile(Ensemble):
     def __init__(self, file_path):
         super().__init__(file_path)
-        self.type = "starfile"
 
     @classmethod
     def from_starfile(cls, file_path):

molecularnodes/entities/entity.py

@@ -1,6 +1,7 @@
 from abc import ABCMeta
 import bpy
 from uuid import uuid1
+from bpy.types import Object
 from ..bpyd import (
     BlenderObject,
 )
@@ -12,9 +13,28 @@ class MolecularEntity(
 ):
     def __init__(self) -> None:
         self.uuid: str = str(uuid1())
-        self.type: str = ""
-        self._object: bpy.types.Object | None
+        bpy.context.scene.MNSession.entities[self.uuid] = self
 
     @property
     def bob(self) -> BlenderObject:
         return BlenderObject(self.object)
+
+    @property
+    def object(self) -> Object:
+        try:
+            return bpy.data.objects[self._object_name]
+        except KeyError:
+            # if we can't find a refernce to the object via a name, then we look via the
+            # unique uuids that were assigned to the object and the entity to match up
+            for obj in bpy.data.objects:
+                if obj.mn.uuid == self.uuid:
+                    self._object_name = obj.name
+                    return obj
+
+    @object.setter
+    def object(self, value) -> None:
+        if not isinstance(value, Object):
+            raise ValueError(
+                f"Can only set object to be of type bpy.types.Object, not {type(value)=}"
+            )
+        self._object_name = value.name

molecularnodes/entities/molecule/molecule.py

@@ -4,6 +4,7 @@
 from abc import ABCMeta
 from pathlib import Path
 from typing import Optional, Tuple, Union
+from bpy.types import Collection
 
 import biotite.structure as struc
 import bpy
@@ -71,10 +72,18 @@ def __init__(self, file_path: Union[str, Path, io.BytesIO]):
         self._parse_filepath(file_path=file_path)
         self.file: str
         self.array: np.ndarray
-        self.frames: bpy.types.Collection | None = None
-        self.frames_name: str = ""
+        self._frames_collection_name: str = ""
 
-        bpy.context.scene.MNSession.molecules[self.uuid] = self
+    @property
+    def frames(self) -> Collection:
+        return bpy.data.collections.get(self._frames_collection_name)
+
+    @frames.setter
+    def frames(self, value) -> None:
+        if value is None:
+            self._frames_collection_name = None
+        else:
+            self._frames_collection_name = value.name
 
     @classmethod
     def _read(self, file_path: Union[Path, io.BytesIO]):

molecularnodes/entities/trajectory/trajectory.py

@@ -21,7 +21,6 @@ def __init__(self, universe: mda.Universe, world_scale: float = 0.01):
         self.calculations: Dict[str, Callable] = {}
         self.world_scale = world_scale
         self.frame_mapping: npt.NDArray[np.in64] | None = None
-        bpy.context.scene.MNSession.trajectories[self.uuid] = self
 
     def selection_from_ui(self, ui_item: TrajectorySelectionItem) -> Selection:
         self.selections[ui_item.name] = Selection(

molecularnodes/entities/trajectory/ui.py

@@ -9,7 +9,6 @@
 import MDAnalysis as mda
 
 from ... import blender as bl
-from ...session import get_session
 from .trajectory import Trajectory
 from bpy.props import StringProperty
 
@@ -63,7 +62,7 @@ class MN_OT_Reload_Trajectory(bpy.types.Operator):
     @classmethod
     def poll(cls, context):
         obj = context.active_object
-        traj = get_session(context).trajectories.get(obj.mn.uuid)
+        traj = context.scene.MNSession.trajectories.get(obj.mn.uuid)
         return not traj
 
     def execute(self, context):