Merge remote-tracking branch 'upstream/main'

molecularnodes/addon.py

@@ -14,7 +14,7 @@
 import bpy
 from bpy.app.handlers import frame_change_pre, load_post, save_post
 from bpy.props import PointerProperty, CollectionProperty
-from .handlers import update_trajectories
+from .handlers import update_entities
 from . import entities, operators, props, session, ui
 from .utils import add_current_module_to_path
 from .ui import pref
@@ -58,7 +58,7 @@ def register():
 
     save_post.append(session._pickle)
     load_post.append(session._load)
-    frame_change_pre.append(update_trajectories)
+    frame_change_pre.append(update_entities)
 
     bpy.types.Scene.MNSession = session.MNSession()  # type: ignore
     bpy.types.Object.uuid = props.uuid_property  # type: ignore
@@ -88,7 +88,7 @@ def unregister():
 
     save_post.remove(session._pickle)
     load_post.remove(session._load)
-    frame_change_pre.remove(update_trajectories)
+    frame_change_pre.remove(update_entities)
     del bpy.types.Scene.MNSession  # type: ignore
     del bpy.types.Scene.mn  # type: ignore
     del bpy.types.Scene.interaction_visualiser  # type: ignore

molecularnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "molecularnodes"
-version = "4.2.10"
+version = "4.2.11"
 name = "Molecular Nodes"
 tagline = "A toolbox for molecular import and animation in Blender"
 maintainer = "Brady Johnston<[email protected]>"
@@ -41,12 +41,12 @@ wheels = [
 	"./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/databpy-0.0.7-py3-none-any.whl",
+	"./wheels/databpy-0.0.8-py3-none-any.whl",
 	"./wheels/fasteners-0.19-py3-none-any.whl",
-	"./wheels/fonttools-4.55.3-cp311-cp311-macosx_10_9_universal2.whl",
-	"./wheels/fonttools-4.55.3-cp311-cp311-macosx_10_9_x86_64.whl",
-	"./wheels/fonttools-4.55.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/fonttools-4.55.3-cp311-cp311-win_amd64.whl",
+	"./wheels/fonttools-4.55.8-cp311-cp311-macosx_10_9_universal2.whl",
+	"./wheels/fonttools-4.55.8-cp311-cp311-macosx_10_9_x86_64.whl",
+	"./wheels/fonttools-4.55.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/fonttools-4.55.8-cp311-cp311-win_amd64.whl",
 	"./wheels/joblib-1.4.2-py3-none-any.whl",
 	"./wheels/kiwisolver-1.4.8-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/kiwisolver-1.4.8-cp311-cp311-macosx_11_0_arm64.whl",
@@ -59,7 +59,7 @@ wheels = [
 	"./wheels/mda_xdrlib-0.2.0-py3-none-any.whl",
 	"./wheels/mdahole2-0.5.0-py3-none-any.whl",
 	"./wheels/mmtf_python-1.1.3-py2.py3-none-any.whl",
-	"./wheels/mrcfile-1.5.3-py2.py3-none-any.whl",
+	"./wheels/mrcfile-1.5.4-py2.py3-none-any.whl",
 	"./wheels/msgpack-1.1.0-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/msgpack-1.1.0-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
@@ -77,17 +77,17 @@ wheels = [
 	"./wheels/pillow-11.1.0-cp311-cp311-win_amd64.whl",
 	"./wheels/pyparsing-3.2.1-py3-none-any.whl",
 	"./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl",
-	"./wheels/pytz-2024.2-py2.py3-none-any.whl",
-	"./wheels/scipy-1.15.0-cp311-cp311-macosx_10_13_x86_64.whl",
-	"./wheels/scipy-1.15.0-cp311-cp311-macosx_12_0_arm64.whl",
-	"./wheels/scipy-1.15.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/scipy-1.15.0-cp311-cp311-win_amd64.whl",
+	"./wheels/pytz-2025.1-py2.py3-none-any.whl",
+	"./wheels/scipy-1.15.1-cp311-cp311-macosx_10_13_x86_64.whl",
+	"./wheels/scipy-1.15.1-cp311-cp311-macosx_12_0_arm64.whl",
+	"./wheels/scipy-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/scipy-1.15.1-cp311-cp311-win_amd64.whl",
 	"./wheels/six-1.17.0-py2.py3-none-any.whl",
-	"./wheels/starfile-0.5.10-py3-none-any.whl",
+	"./wheels/starfile-0.5.11-py3-none-any.whl",
 	"./wheels/threadpoolctl-3.5.0-py3-none-any.whl",
 	"./wheels/tqdm-4.67.1-py3-none-any.whl",
 	"./wheels/typing_extensions-4.12.2-py3-none-any.whl",
-	"./wheels/tzdata-2024.2-py2.py3-none-any.whl",
+	"./wheels/tzdata-2025.1-py2.py3-none-any.whl",
 	"./wheels/waterdynamics-1.2.0-py3-none-any.whl",
 ]
 

molecularnodes/entities/trajectory/dna.py

@@ -56,7 +56,7 @@ def _create_object(self, style: str = "oxdna", name: str = "NewUniverseObject"):
 
         return self.object
 
-    def _update_positions(self, frame: int) -> None:
+    def set_frame(self, frame: int) -> None:
         super()._update_positions(frame)
         self._update_timestep_values()
 

molecularnodes/handlers.py

@@ -1,28 +1,17 @@
 import bpy
 from bpy.app.handlers import persistent
-# from .session import update_trajectories
-
-# from .session import MNSession
 
 
 # this update function requires a self and context input, as funcitons with these inputs
 # have ot be passed to the `update` arguments of UI properties. When the UI is updated,
 # the function is called with the UI element being `self` and the current context being
 # passed into the function
-def _update_trajectories(self, context: bpy.types.Context) -> None:
-    """
-    Function for being called at various points in the updating of the UI, to ensure
-    positions and selections of the trajectories are udpated with the new inputs
-    """
-    update_trajectories(context.scene)
-
-
-def _update_trajectories_on_frame_change(self, context: bpy.types.Context) -> None:
+def _udpate_entities(self, context: bpy.types.Context) -> None:
     """
     Function for being called at various points in the updating of the UI, to ensure
     positions and selections of the trajectories are udpated with the new inputs
     """
-    update_trajectories(context.scene)
+    update_entities(context.scene)
 
 
 def _selection_update_trajectories(self, context: bpy.types.Context) -> None:
@@ -34,7 +23,7 @@ def _selection_update_trajectories(self, context: bpy.types.Context) -> None:
     if self.immutable:
         return
     else:
-        update_trajectories(context.scene)
+        update_entities(context.scene)
 
 
 # this is the 'perisisent' function which can be appended onto the
@@ -43,17 +32,24 @@ def _selection_update_trajectories(self, context: bpy.types.Context) -> None:
 # use the `frame_change_pre` handler as we want the frame to change first, then we update
 # the universe based on the current frame value
 @persistent
-def update_trajectories(scene):
-    "Call the set_frame method of all trajectories in the current session"
+def update_entities(scene):
+    "Call the `set_frame()` method of all entities in the current session"
     session = scene.MNSession
-    for traj in session.trajectories.values():
+    for entity in session.entities.values():
         # use the updated method if it exists but otherwise fallback on the old method
         # of updating the trajectories
-        if hasattr(traj, "update_with_scene"):
-            if traj.update_with_scene:
-                traj.set_frame(scene.frame_current)
+
+        if hasattr(entity, "update_with_scene"):
+            if entity.update_with_scene:
+                frame_to_set = scene.frame_current
             else:
-                traj.set_frame(traj.frame)
+                frame_to_set = entity.frame
+
+            # do the entity setting, if the method isn't implemented, just pass
+            try:
+                entity.set_frame(frame_to_set)
+            except NotImplementedError:
+                pass
 
         else:
             traj._update_positions(scene.frame_current)

molecularnodes/props.py

@@ -1,7 +1,7 @@
 import bpy
 from bpy.types import PropertyGroup
 from bpy.props import IntProperty, BoolProperty, EnumProperty, StringProperty
-from .handlers import _selection_update_trajectories, _update_trajectories
+from .handlers import _selection_update_trajectories, _udpate_entities
 from .style import STYLE_ITEMS
 
 
@@ -117,47 +117,47 @@ class MolecularNodesObjectProperties(PropertyGroup):
         name="Frame",
         description="Frame of the loaded trajectory",
         default=0,
-        update=_update_trajectories,
+        update=_udpate_entities,
         min=0,
     )
     update_with_scene: BoolProperty(  # type: ignore
         name="Update with Scene",
         description="Update the trajectory with the scene frame",
         default=True,
-        update=_update_trajectories,
+        update=_udpate_entities,
     )
     subframes: IntProperty(  # type: ignore
         name="Subframes",
         description="Number of subframes to insert between frames of the loaded trajectory",
         default=0,
-        update=_update_trajectories,
+        update=_udpate_entities,
         min=0,
     )
     offset: IntProperty(  # type: ignore
         name="Offset",
         description="Offset the starting playback for the trajectory on the timeine. Positive starts the playback later than frame 0, negative starts it earlier than frame 0",
         default=0,
-        update=_update_trajectories,
+        update=_udpate_entities,
     )
     interpolate: BoolProperty(  # type: ignore
         name="Interpolate",
         description="Whether to interpolate when using subframes",
         default=True,
-        update=_update_trajectories,
+        update=_udpate_entities,
     )
     average: IntProperty(  # type: ignore
         name="Average",
         description="Average the position this number of frames either side of the current frame",
         default=0,
-        update=_update_trajectories,
+        update=_udpate_entities,
         min=0,
         soft_max=5,
     )
     correct_periodic: BoolProperty(  # type: ignore
         name="Correct",
         description="Correct for periodic boundary crossing when using interpolation or averaging. Assumes cubic dimensions and only works if the unit cell is orthorhombic",
         default=False,
-        update=_update_trajectories,
+        update=_udpate_entities,
     )
     filepath_trajectory: StringProperty(  # type: ignore
         name="Trajectory",
@@ -265,7 +265,7 @@ def execute(self, context):
         i = int(len(obj.mn_trajectory_selections) - 1)
         obj.mn_trajectory_selections[i].name = f"selection_{i + 1}"
         obj.mn["list_index"] = i
-        _update_trajectories(self, context)
+        _udpate_entities(self, context)
 
         return {"FINISHED"}
 
@@ -286,7 +286,7 @@ def execute(self, context):
         sel_list = obj.mn_trajectory_selections
         sel_list.remove(index)
         obj.mn.trajectory_selection_index = len(sel_list) - 1
-        _update_trajectories(self, context)
+        _udpate_entities(self, context)
 
         return {"FINISHED"}
 

molecularnodes/ui/node_info.py

@@ -866,6 +866,23 @@
                     videos="https://imgur.com/FcEXSZx",
                 ),
                 Break(),
+                MenuItem(
+                    name="Falloff Object",
+                    description="Falloff computed from the location on the input object",
+                ),
+                MenuItem(
+                    name="Falloff Geometry",
+                    description="Falloff computed from the proximity of the nearest geometry",
+                ),
+                MenuItem(
+                    name="Noise Vector",
+                    description="Noise that can be evolved over time with `Animate` based on the `Position` attribute",
+                ),
+                MenuItem(
+                    name="Noise Repeat",
+                    description="Noise that repeats ever x period, based on some of the `Position` attribute",
+                ),
+                Break(),
                 MenuItem(
                     label="Noise Position",
                     name="MN_animate_noise_position",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "molecularnodes"
-version = "4.2.10"
+version = "4.2.11"
 description = "Toolbox for molecular animations with Blender and Geometry Nodes."
 readme = "README.md"
 dependencies = ["databpy", "MDAnalysis>=2.7.0", "biotite~=0.40", "mrcfile", "starfile"]