Merge remote-tracking branch 'origin/main' into bcif

docs/example_animations.qmd

@@ -53,7 +53,7 @@ To morph between 3 conformations of ATP synthase use ChimeraX commands "open 6n2
 ::: callout-caution
 # Requires MDAnalysis Installed
 
-To follow this particular tutorial, ensure you have first [installed Molecular Nodes properly](installation.md), including the optional MDAnalysis python package.
+To follow this particular tutorial, ensure you have first [installed Molecular Nodes properly](installation.qmd), including the optional MDAnalysis python package.
 :::
 
 Download the trajectory files from the the [CHARMM-GUI website](https://charmm-gui.org/?doc=archive&lib=covid19):

docs/generate.py

@@ -35,14 +35,14 @@
         if submenu.description:
             file.write(submenu.description)
             file.write("\n\n")
-        for item in submenu.items:
-            if item.is_break:
+        for menu_item in submenu.items:
+            if menu_item.is_break:
                 continue
-            if item.backup is not None:
-                name = item.backup
+            if menu_item.backup is not None:
+                name = menu_item.backup
             else:
-                name = item.name
-            doc = noodlenotes.MenuItemDocumenter(item)
+                name = menu_item.name
+            documenter = noodlenotes.MenuItemDocummenter(menu_item)
 
-            file.write(doc.as_markdown())
+            file.write(documenter.as_markdown())
             file.write("\n\n")

docs/nodes/index.qmd

@@ -18,4 +18,5 @@ At any point you can view the internals of the node groups that are included wit
 With a node selected, you can <kbd>Tab</kbd> to enter a selected node, and use <kbd>Ctrl</kbd> + <kbd>Tab</kbd> to exit the node group.
 You can also do the same by right clicking.
 Feel free to tweak the internals of node groups, but beware that changing one node group will change that node group for all othe uses of it.
-Starting a new Blender session will ensure that the node groups are fresh and 'factor reset'.
+Starting a new Blender session will ensure that the node groups are fresh and 'factor reset'.
+

docs/noodlenotes/__init__.py

@@ -1 +1 @@
-from .documenter import TreeDocumenter, MenuItemDocumenter
+from .documenter import MenuItemDocummenter, Documenter

docs/noodlenotes/documenter.py

@@ -1,19 +1,24 @@
 import bpy
+import pathlib
+import sys
 
 from .interface import InterfaceGroup, InterfaceItem
 from . import markdown
+from typing import List
 
+TOP_FOLDER = pathlib.Path(__file__).resolve().parent.parent.parent
+sys.path.insert(0, str(TOP_FOLDER))
 
-class TreeDocumenter:
-    def __init__(
-        self, tree: bpy.types.NodeTree, description: str = None, image: str = None
-    ) -> None:
+from molecularnodes.ui.menu import Menu, MenuItem, CustomItem, Item, Break
+
+
+class Documenter:
+    def __init__(self, tree: bpy.types.NodeTree, menu_item: MenuItem = None) -> None:
         self.tree = tree
         self.items = [InterfaceItem(x) for x in tree.interface.items_tree]
         self.inputs = InterfaceGroup([x for x in self.items if x.is_input])
         self.outputs = InterfaceGroup([x for x in self.items if x.is_output])
-        self._description = description
-        self.image = markdown.Video(image)
+        self.menu_item = menu_item
         self.level = 2
 
     @property
@@ -24,20 +29,37 @@ def title(self) -> str:
         return f"## {self.tree.name.removesuffix('_')}"
 
     def description(self) -> str:
-        if self._description:
-            return self._description + "\n\n" + self.tree.description
+        return self.menu_item.description + "\n\n" + self.tree.description
+
+    def videos(self) -> List[str]:
+        links = self.menu_item.videos
+
+        if links is None:
+            return None
+
+        for x in links:
+            if x is None:
+                return None
+
+        if isinstance(links, str):
+            links = [links]
+
+        if not all([isinstance(x, str) for x in links]):
+            raise ValueError(f"All url values must be strings: {links=}")
+
+        videos = "\n\n".join(
+            [markdown.Video(x).as_markdown() for x in links if x is not None]
+        )
 
-        return self.tree.description
+        return "\n\n" + videos + "\n\n"
 
     def collect_items(self):
         items = [
             self.title(),
             self.description(),
-            self.image.as_markdown(),
-            "### Inputs",
-            self.inputs.as_markdown(),
-            "### Outputs",
-            self.outputs.as_markdown(),
+            self.videos(),
+            self.inputs.as_markdown("Inputs"),
+            self.outputs.as_markdown("Outputs"),
         ]
         return [item for item in items if item is not None]
 
@@ -47,14 +69,11 @@ def as_markdown(self) -> str:
         return text
 
 
-def MenuItemDocumenter(menu_item) -> TreeDocumenter:
-    if menu_item.backup:
-        tree = bpy.data.node_groups[menu_item.backup]
-    else:
-        tree = bpy.data.node_groups[menu_item.name]
+class MenuItemDocummenter(Documenter):
+    def __init__(self, menu_item: MenuItem) -> None:
+        super().__init__(tree=menu_item.tree, menu_item=menu_item)
 
-    doc = TreeDocumenter(
-        tree=tree, description=menu_item.description, image=menu_item.video_url
-    )
 
-    return doc
+class TreeDocumenter(Documenter):
+    def __init__(self, tree: bpy.types.NodeTree) -> None:
+        super().__init__(tree=tree)

docs/noodlenotes/interface.py

@@ -33,6 +33,22 @@ def type(self) -> str:
             return "PANEL"
         return "`{}`".format(self.item.socket_type.replace("NodeSocket", ""))
 
+    @property
+    def is_vector(self) -> bool:
+        return self.type in ["Vector", "Color", "Rotation", "Matrix"]
+
+    def __len__(self) -> int:
+        if self.type == "PANEL":
+            return 0
+        elif self.type in ["Vector", "Rotation"]:
+            return 3
+        elif self.type in ["Color"]:
+            return 4
+        elif self.type == "Matrix":
+            return 16
+        else:
+            return 1
+
     @property
     def default(self, round_length: int = 3) -> str:
         try:
@@ -89,19 +105,9 @@ def description(self):
             return ""
 
     def max_length(self):
-        info_to_test = [self.description, self.min, self.max, self.default]
+        info_to_test = [self.description, self.min, self.max, self.default, self.type]
         return max([len(x) for x in info_to_test if x is not None])
 
-    def formatted(self):
-        text = f"Default Value: {self.default}\n"
-        try:
-            text += f"Min: {self.min}\n"
-            text += f"Max: {self.max}\n"
-        except AttributeError:
-            pass
-
-        return text
-
 
 class InterfaceGroup:
     def __init__(self, items: List[InterfaceItem]) -> None:
@@ -144,8 +150,16 @@ def body(self) -> str:
     def tail(self) -> str:
         return '\n\n: {tbl-colwidths="[15, 10, 55, 20]"}\n\n'
 
-    def as_markdown(self):
-        return self.top_line() + self.sep() + self.body() + self.tail() + "\n"
+    def as_markdown(self, title: str = "", level: int = 3):
+        body = self.body()
+        if not body:
+            return ""
+        hashes = "#" * level
+        lines = f"{hashes} {title}\n\n"
+        for x in [self.top_line(), self.sep(), self.body(), self.tail(), "\n"]:
+            lines += x
+
+        return lines
 
     def __repr__(self) -> str:
         return self.as_markdown()

docs/noodlenotes/markdown.py

@@ -5,7 +5,7 @@ def __init__(self, url: str, caption: str = "") -> None:
 
     def as_markdown(self) -> str:
         if not self.url or self.url == "":
-            return None
+            return "![]()"
         return f"![{self.caption}]({self.format_url()})"
 
     def format_url(self) -> str:

molecularnodes/__init__.py

@@ -45,8 +45,8 @@ def register():
     for op in all_classes:
         try:
             bpy.utils.register_class(op)
-        except Exception:
-            # print(e)
+        except Exception as e:
+            print(e)
             pass
 
     bpy.types.NODE_MT_add.append(MN_add_node_menu)

molecularnodes/blender/__init__.py

@@ -10,3 +10,10 @@ def path_resolve(path: Union[str, Path]) -> Path:
         return Path(bpy.path.abspath(str(path)))
     else:
         raise ValueError(f"Unable to resolve path: {path}")
+
+
+def active_object(context: bpy.types.Context = None) -> bpy.types.Object:
+    if context is None:
+        return bpy.context.active_object
+
+    return context.active_object

molecularnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "molecularnodes"
-version = "4.2.6"
+version = "4.2.7"
 name = "Molecular Nodes"
 tagline = "A toolbox for molecular import and animation in Blender"
 maintainer = "Brady Johnston<[email protected]>"
@@ -35,7 +35,6 @@ 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/colorama-0.4.6-py2.py3-none-any.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",
@@ -64,10 +63,10 @@ wheels = [
 	"./wheels/msgpack-1.1.0-cp311-cp311-win_amd64.whl",
 	"./wheels/networkx-3.3-py3-none-any.whl",
 	"./wheels/packaging-24.1-py3-none-any.whl",
-	"./wheels/pandas-2.2.2-cp311-cp311-macosx_10_9_x86_64.whl",
-	"./wheels/pandas-2.2.2-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/pandas-2.2.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/pandas-2.2.2-cp311-cp311-win_amd64.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",
+	"./wheels/pandas-2.2.3-cp311-cp311-win_amd64.whl",
 	"./wheels/pillow-10.4.0-cp311-cp311-macosx_10_10_x86_64.whl",
 	"./wheels/pillow-10.4.0-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/pillow-10.4.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",

molecularnodes/entities/__init__.py

@@ -7,7 +7,7 @@
 from .molecule.pdb import PDB
 from .molecule.pdbx import BCIF, CIF
 from .molecule.sdf import SDF
-from .molecule.ui import MN_OT_Import_wwPDB, fetch, load_local
+from .molecule.ui import fetch, load_local
 from .trajectory.trajectory import Trajectory
 
 CLASSES = (
@@ -16,7 +16,6 @@
         MN_OT_Import_Map,
         MN_OT_Import_OxDNA_Trajectory,
         MN_OT_Import_Star_File,
-        MN_OT_Import_wwPDB,
     ]
     + trajectory.CLASSES
     + molecule.CLASSES

molecularnodes/entities/entity.py

@@ -15,7 +15,7 @@ def __init__(self, message):
 class MolecularEntity(metaclass=ABCMeta):
     def __init__(self) -> None:
         self.uuid: str = str(uuid1())
-        self.object_ref: bpy.types.Object | None
+        self._object: bpy.types.Object | None
         self.type: str = ""
 
     @property
@@ -45,24 +45,27 @@ def object(self) -> bpy.types.Object | None:
             # 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_ref.name
-            return self.object_ref
+            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_ref}, now connected to {obj}"
+                            f"Lost connection to object: {self._object}, now connected to {obj}"
                         )
                     )
-                    self.object_ref = obj
+                    self._object = obj
                     return obj
 
             return None
 
     @object.setter
     def object(self, value):
-        self.object_ref = value
+        if isinstance(value, bpy.types.Object) or value is None:
+            self._object = value
+        else:
+            raise TypeError(f"The `object` must be a Blender object, not {value=}")
 
     def named_attribute(self, name="position", evaluate=False) -> np.ndarray | None:
         """

molecularnodes/entities/trajectory/trajectory.py

@@ -7,7 +7,7 @@
 
 from ... import data
 from ..entity import MolecularEntity, ObjectMissingError
-from ...blender import coll, mesh, nodes
+from ...blender import coll, mesh, nodes, path_resolve
 from ...utils import lerp, correct_periodic_positions
 from .selections import Selection, TrajectorySelectionItem
 
@@ -416,6 +416,13 @@ def _attributes_2_blender(self):
             },
         }
 
+    def save_filepaths_on_object(self) -> None:
+        obj = self.object
+        obj.mn.filepath_topology = str(path_resolve(self.universe.filename))
+        obj.mn.filepath_trajectory = str(
+            path_resolve(self.universe.trajectory.filename)
+        )
+
     def create_object(
         self,
         style: str = "vdw",
@@ -447,6 +454,7 @@ def create_object(
         obj["atom_type_unique"] = self.atom_type_unique
         self.subframes = subframes
         obj.mn.molecule_type = "md"
+        self.save_filepaths_on_object()
 
         if style is not None:
             nodes.create_starting_node_tree(obj, style=style, name=f"MN_{obj.name}")