Merge branch 'main' into 669-node-modifiers

molecularnodes/__init__.py

@@ -13,7 +13,8 @@
 
 import bpy
 from bpy.app.handlers import frame_change_post, load_post, save_post
-
+from bpy.props import PointerProperty, CollectionProperty
+from .handlers import update_trajectories
 from . import entities, operators, props, session, ui
 from .utils import add_current_module_to_path
 from .ui import pref
@@ -24,8 +25,8 @@
     ui.CLASSES
     + operators.CLASSES
     + entities.CLASSES
+    + props.CLASSES
     + [
-        props.MolecularNodesObjectProperties,
         MN_PT_Scene,
     ]
     + pref.CLASSES
@@ -56,14 +57,13 @@ def register():
 
     save_post.append(session._pickle)
     load_post.append(session._load)
-    frame_change_post.append(entities.trajectory.handlers.update_trajectories)
+    frame_change_post.append(update_trajectories)
 
     bpy.types.Scene.MNSession = session.MNSession()
-    bpy.types.Object.mn = bpy.props.PointerProperty(
-        type=props.MolecularNodesObjectProperties
-    )
-    bpy.types.Object.mn_trajectory_selections = bpy.props.CollectionProperty(
-        type=entities.trajectory.selections.TrajectorySelectionItem
+    bpy.types.Object.mn = PointerProperty(type=props.MolecularNodesObjectProperties)
+    bpy.types.Scene.mn = PointerProperty(type=props.MolecularNodesSceneProperties)
+    bpy.types.Object.mn_trajectory_selections = CollectionProperty(
+        type=entities.trajectory.props.TrajectorySelectionItem
     )
 
 
@@ -81,7 +81,8 @@ def unregister():
 
     save_post.remove(session._pickle)
     load_post.remove(session._load)
-    frame_change_post.remove(entities.trajectory.handlers.update_trajectories)
+    frame_change_post.remove(update_trajectories)
     del bpy.types.Scene.MNSession
+    del bpy.types.Scene.mn
     del bpy.types.Object.mn
     del bpy.types.Object.mn_trajectory_selections

molecularnodes/blender_manifest.toml

@@ -35,16 +35,16 @@ wheels = [
 	"./wheels/biotite-0.41.2-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/biotite-0.41.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
 	"./wheels/biotite-0.41.2-cp311-cp311-win_amd64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-macosx_10_9_x86_64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-win_amd64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-macosx_11_0_arm64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-win_amd64.whl",
 	"./wheels/cycler-0.12.1-py3-none-any.whl",
 	"./wheels/fasteners-0.19-py3-none-any.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-macosx_10_9_universal2.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-win_amd64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-macosx_10_9_universal2.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-macosx_10_9_x86_64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-win_amd64.whl",
 	"./wheels/joblib-1.4.2-py3-none-any.whl",
 	"./wheels/kiwisolver-1.4.7-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/kiwisolver-1.4.7-cp311-cp311-macosx_11_0_arm64.whl",
@@ -62,7 +62,7 @@ wheels = [
 	"./wheels/msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
 	"./wheels/msgpack-1.1.0-cp311-cp311-win_amd64.whl",
 	"./wheels/networkx-3.4.2-py3-none-any.whl",
-	"./wheels/packaging-24.1-py3-none-any.whl",
+	"./wheels/packaging-24.2-py3-none-any.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
@@ -81,7 +81,7 @@ wheels = [
 	"./wheels/six-1.16.0-py2.py3-none-any.whl",
 	"./wheels/starfile-0.5.6-py3-none-any.whl",
 	"./wheels/threadpoolctl-3.5.0-py3-none-any.whl",
-	"./wheels/tqdm-4.66.6-py3-none-any.whl",
+	"./wheels/tqdm-4.67.0-py3-none-any.whl",
 	"./wheels/typing_extensions-4.12.2-py3-none-any.whl",
 	"./wheels/tzdata-2024.2-py2.py3-none-any.whl",
 ]

molecularnodes/entities/ensemble/cif.py

@@ -30,16 +30,15 @@ def _get_structure(self, extra_fields: str = None, sec_struct=True, bonds=True):
         # which can be extracted with the get_component()
         try:
             array = pdbx.get_structure(self.file, extra_fields=extra_fields)
-            try:
-                array.set_annotation(
-                    "sec_struct", _get_secondary_structure(array, self.file)
-                )
-            except KeyError:
-                warnings.warn("No secondary structure information.")
-            try:
-                array.set_annotation("entity_id", _get_entity_id(array, self.file))
-            except KeyError:
-                warnings.warn("Non entity_id information.")
+            annotations = {
+                "sec_struct": _get_secondary_structure,
+                "entity_id": _get_entity_id,
+            }
+            for key, func in annotations.items():
+                try:
+                    array.set_annotation(key, func(array, self.file))
+                except KeyError:
+                    pass
 
         except InvalidFileError:
             array = pdbx.get_component(self.file)

molecularnodes/entities/molecule/ui.py

@@ -14,6 +14,7 @@
 from .pdb import PDB
 from .pdbx import BCIF, CIF
 from .sdf import SDF
+from ...style import STYLE_ITEMS
 
 
 def parse(filepath) -> Molecule:
@@ -103,20 +104,6 @@ def load_local(
     return mol
 
 
-STYLE_ITEMS = (
-    ("spheres", "Spheres", "Space-filling atoms style."),
-    ("cartoon", "Cartoon", "Secondary structure cartoons"),
-    ("surface", "Surface", "Solvent-accsible surface."),
-    ("ribbon", "Ribbon", "Continuous backbone ribbon."),
-    ("sticks", "Sticks", "Sticks for each bond."),
-    ("ball_and_stick", "Ball and Stick", "Spheres for atoms, sticks for bonds"),
-    ("preset_1", "Preset 1", "A pre-made combination of different styles"),
-    ("preset_2", "Preset 2", "A pre-made combination of different styles"),
-    ("preset_3", "Preset 3", "A pre-made combination of different styles"),
-    ("preset_4", "Preset 4", "A pre-made combination of different styles"),
-)
-
-
 class Import_Molecule(bpy.types.Operator):
     style: EnumProperty(  # type: ignore
         name="Style",
@@ -381,7 +368,7 @@ def execute(self, context):
 
         style = None
         if scene.MN_import_node_setup:
-            style = scene.MN_import_style
+            style = scene.mn.import_style
 
         centre = ""
         if scene.MN_import_centre:
@@ -423,7 +410,7 @@ def execute(self, context):
         scene = context.scene
         file_path = scene.MN_import_local_path
 
-        style = scene.MN_import_style
+        style = scene.mn.import_style
         if not scene.MN_import_node_setup:
             style = None
 
@@ -467,7 +454,7 @@ def execute(self, context):
 
         style = None
         if scene.MN_import_node_setup:
-            style = scene.MN_import_style
+            style = scene.mn.import_style
 
         centre = ""
         if scene.MN_import_centre:
@@ -559,7 +546,7 @@ def panel_wwpdb(layout, scene):
     row = options.row()
     row.prop(scene, "MN_import_node_setup", text="")
     col = row.column()
-    col.prop(scene, "MN_import_style")
+    col.prop(scene.mn, "import_style")
     col.enabled = scene.MN_import_node_setup
 
     row_centre = options.row()
@@ -601,7 +588,7 @@ def panel_alphafold(layout, scene):
     row = options.row()
     row.prop(scene, "MN_import_node_setup", text="")
     col = row.column()
-    col.prop(scene, "MN_import_style")
+    col.prop(scene.mn, "import_style")
     col.enabled = scene.MN_import_node_setup
 
     row_centre = options.row()
@@ -638,7 +625,7 @@ def panel_local(layout, scene):
     row = options.row()
     row.prop(scene, "MN_import_node_setup", text="")
     col = row.column()
-    col.prop(scene, "MN_import_style")
+    col.prop(scene.mn, "import_style")
     col.enabled = scene.MN_import_node_setup
 
     row_centre = options.row()

molecularnodes/entities/trajectory/__init__.py

@@ -1,6 +1,7 @@
 from . import selections
 from . import ui
+from . import props
 from .ui import load
 from .trajectory import Trajectory
 
-CLASSES = selections.CLASSSES + ui.CLASSES
+CLASSES = props.CLASSSES + ui.CLASSES