Merge branch 'main' into docs-tutorials

.gitignore

@@ -1,7 +1,6 @@
 *.blend1
 __pycache__/*
 .vscode/*
-*.zip
 *.pyc
 .Rproj.user
 /.quarto/

MolecularNodes/__init__.py

@@ -26,15 +26,20 @@
 }
 
 from . import auto_load
-from .ui import mol_add_node_menu
+from .ui import MN_add_node_menu
 import bpy
+import pathlib
+import os
+from . import pref
 
 auto_load.init()
 
 def register():
     auto_load.register()
-    bpy.types.NODE_MT_add.append(mol_add_node_menu)
+    bpy.types.NODE_MT_add.append(MN_add_node_menu)
+    pref.template_install()
 
 def unregister():
-    bpy.types.NODE_MT_add.remove(mol_add_node_menu)
+    bpy.types.NODE_MT_add.remove(MN_add_node_menu)
     auto_load.unregister()
+    pref.template_uninstall()

MolecularNodes/assembly/mesh.py

@@ -81,11 +81,11 @@ def transform_chains(assembly, index = 0):
 
 def rotation_from_matrix(matrix):
     from scipy.spatial.transform import Rotation as R
+    import warnings
 
     # calculate the euler rotation from the rotation matrix
     # Blender is 'xyz' euler rotations. Internally they use matrices / quaternions, but
     # current interfaces for geometry nodes are just eulers
-
-    rotation = R.from_matrix(matrix).as_euler('xyz')
-
-    return rotation
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        return R.from_matrix(matrix).as_euler('xyz')

MolecularNodes/assets/template/Molecular_Nodes/__init__.py

@@ -0,0 +1,28 @@
+# SPDX-License-Identifier: GPL-2.0-or-later
+
+import bpy
+# from bpy.app.handlers import persistent
+
+
+# @persistent
+# def load_handler(_):
+    # import bpy
+    # Apply subdivision modifier on startup
+    # bpy.ops.object.mode_set(mode='OBJECT')
+    # if bpy.app.opensubdiv.supported:
+    #     bpy.ops.object.modifier_apply(modifier="Subdivision")
+    #     bpy.ops.object.mode_set(mode='EDIT')
+    #     bpy.ops.transform.tosphere(value=1.0)
+    # else:
+    #     bpy.ops.object.modifier_remove(modifier="Subdivision")
+    #     bpy.ops.object.mode_set(mode='EDIT')
+    #     bpy.ops.mesh.subdivide(number_cuts=6, smoothness=1.0)
+    # bpy.ops.object.mode_set(mode='SCULPT')
+
+
+def register():
+    # bpy.app.handlers.load_factory_startup_post.append(load_handler)
+
+
+def unregister():
+    # bpy.app.handlers.load_factory_startup_post.remove(load_handler)

MolecularNodes/color.py

@@ -0,0 +1,9 @@
+import random
+import colorsys
+import numpy as np
+
+def random_rgb():
+    """Random Pastel RGB values
+    """
+    r, g, b = colorsys.hls_to_rgb(random.random(), 0.6, 0.6)
+    return np.array((r, g, b, 1))

MolecularNodes/density.py

@@ -1,20 +1,19 @@
 import bpy
-# import pyopenvdb as vdb
 import numpy as np
 from . import nodes
 import os
 
-bpy.types.Scene.mol_import_map_nodes = bpy.props.BoolProperty(
-    name = "mol_import_map_nodes", 
+bpy.types.Scene.MN_import_map_nodes = bpy.props.BoolProperty(
+    name = "MN_import_map_nodes", 
     description = "Creating starting node tree for imported map.",
     default = True
     )
-bpy.types.Scene.mol_import_map_invert = bpy.props.BoolProperty(
-    name = "mol_import_map_invert", 
+bpy.types.Scene.MN_import_map_invert = bpy.props.BoolProperty(
+    name = "MN_import_map_invert", 
     description = "Invert the values in the map. Low becomes high, high becomes low.",
     default = False
     )
-bpy.types.Scene.mol_import_map = bpy.props.StringProperty(
+bpy.types.Scene.MN_import_map = bpy.props.StringProperty(
     name = 'path_map', 
     description = 'File path for the map file.', 
     options = {'TEXTEDIT_UPDATE'}, 
@@ -166,8 +165,8 @@ def load(file: str, name: str = None, invert: bool = False, world_scale: float =
 
     return vol_object
 
-class MOL_OT_Import_Map(bpy.types.Operator):
-    bl_idname = "mol.import_map"
+class MN_OT_Import_Map(bpy.types.Operator):
+    bl_idname = "mn.import_map"
     bl_label = "ImportMap"
     bl_description = "Import a CryoEM map into Blender"
     bl_options = {"REGISTER"}
@@ -177,9 +176,9 @@ def poll(cls, context):
         return True
 
     def execute(self, context):
-        map_file = bpy.context.scene.mol_import_map
-        invert = bpy.context.scene.mol_import_map_invert
-        setup_node_tree = bpy.context.scene.mol_import_map_nodes
+        map_file = bpy.context.scene.MN_import_map
+        invert = bpy.context.scene.MN_import_map_invert
+        setup_node_tree = bpy.context.scene.MN_import_map_nodes
 
         vol = load(
             file = map_file, 
@@ -194,17 +193,17 @@ def panel(layout_function, scene):
     col_main = layout_function.column(heading = '', align = False)
     col_main.label(text = 'Import EM Maps as Volumes')
     row = col_main.row()
-    row.prop(bpy.context.scene, 'mol_import_map_nodes',
+    row.prop(bpy.context.scene, 'MN_import_map_nodes',
                   text = 'Starting Node Tree'
                   )
-    row.prop(bpy.context.scene, 'mol_import_map_invert', 
+    row.prop(bpy.context.scene, 'MN_import_map_invert', 
              text = 'Invert Data', 
              emboss = True
             )
 
-    row.operator('mol.import_map', text = 'Load Map', icon = 'FILE_TICK')
+    row.operator('mn.import_map', text = 'Load Map', icon = 'FILE_TICK')
 
-    col_main.prop(bpy.context.scene, 'mol_import_map', 
+    col_main.prop(bpy.context.scene, 'MN_import_map', 
              text = 'EM Map', 
              emboss = True
             )
@@ -213,7 +212,7 @@ def panel(layout_function, scene):
     box.alignment = "LEFT"
     box.scale_y = 0.4
     box.label(
-        text = f"Intermediate file: {path_to_vdb(bpy.context.scene.mol_import_map)}."
+        text = f"Intermediate file: {path_to_vdb(bpy.context.scene.MN_import_map)}."
         )
     box.label(
         text = "Please do not delete this file or the volume will not render."

MolecularNodes/esmfold.py

@@ -5,16 +5,16 @@
 import requests
 import io
 
-bpy.types.Scene.mol_esmfold_sequence = bpy.props.StringProperty(
+bpy.types.Scene.MN_esmfold_sequence = bpy.props.StringProperty(
     name = 'amino_acid_sequence', 
     description = 'Amino acid sequence of the structure to open', 
     options = {'TEXTEDIT_UPDATE'}, 
     default = '', 
     subtype = 'FILE_PATH', 
     maxlen = 0
     )
-bpy.types.Scene.mol_esmfold_name = bpy.props.StringProperty(
-    name = 'mol_name', 
+bpy.types.Scene.MN_esmfold_name = bpy.props.StringProperty(
+    name = 'MN_name', 
     description = 'Name of the molecule on import', 
     options = {'TEXTEDIT_UPDATE'}, 
     default = 'NewMolecule', 
@@ -24,7 +24,7 @@
 
 def molecule_esmfold(
     amino_acid_sequence,               
-    mol_name = "Name",                   
+    MN_name = "Name",                   
     center_molecule = False,               
     del_solvent = True,               
     include_bonds = True,   
@@ -36,9 +36,9 @@ def molecule_esmfold(
         include_bonds=include_bonds
         )
 
-    mol_object, coll_frames = load.create_molecule(
-        mol_array = mol,
-        mol_name = mol_name,
+    MN_object, coll_frames = load.create_molecule(
+        MN_array = mol,
+        MN_name = MN_name,
         file = file,
         calculate_ss = True,
         center_molecule = center_molecule,
@@ -48,11 +48,11 @@ def molecule_esmfold(
 
     if setup_nodes:
         nodes.create_starting_node_tree(
-            obj = mol_object, 
+            obj = MN_object, 
             coll_frames=coll_frames, 
             starting_style = starting_style
             )    
-    return mol_object
+    return MN_object
 
 def open_structure_esm_fold(amino_acid_sequence, include_bonds=True):
     import biotite.structure.io.pdb as pdb
@@ -89,8 +89,8 @@ def open_structure_esm_fold(amino_acid_sequence, include_bonds=True):
         raise ValueError(f'ESMFold returned an error for the amino acid sequence input. This is the error message: {r.text}')
 
 # operator that calls the function to import the structure from ESMFold
-class MOL_OT_Import_Protein_ESMFold(bpy.types.Operator):
-    bl_idname = "mol.import_protein_esmfold"
+class MN_OT_Import_Protein_ESMFold(bpy.types.Operator):
+    bl_idname = "mn.import_protein_esmfold"
     bl_label = "import_protein_esmfold"
     bl_description = "Generate structure from ESMFold"
     bl_options = {"REGISTER", "UNDO"}
@@ -100,21 +100,21 @@ def poll(cls, context):
         return not False
 
     def execute(self, context):
-        amino_acid_sequence = bpy.context.scene.mol_esmfold_sequence
+        amino_acid_sequence = bpy.context.scene.MN_esmfold_sequence
 
-        mol_object = molecule_esmfold(
+        MN_object = molecule_esmfold(
             amino_acid_sequence=amino_acid_sequence, 
-            mol_name=bpy.context.scene.mol_esmfold_name,
-            include_bonds=bpy.context.scene.mol_import_include_bonds, 
-            center_molecule=bpy.context.scene.mol_import_center, 
-            del_solvent=bpy.context.scene.mol_import_del_solvent, 
-            starting_style=bpy.context.scene.mol_import_default_style, 
+            MN_name=bpy.context.scene.MN_esmfold_name,
+            include_bonds=bpy.context.scene.MN_import_include_bonds, 
+            center_molecule=bpy.context.scene.MN_import_center, 
+            del_solvent=bpy.context.scene.MN_import_del_solvent, 
+            starting_style=bpy.context.scene.MN_import_default_style, 
             setup_nodes=True
             )
 
         # return the good news!
-        bpy.context.view_layer.objects.active = mol_object
-        self.report({'INFO'}, message=f"Generated protein '{amino_acid_sequence}' as {mol_object.name}")
+        bpy.context.view_layer.objects.active = MN_object
+        self.report({'INFO'}, message=f"Generated protein '{amino_acid_sequence}' as {MN_object.name}")
         return {"FINISHED"}
 
     def invoke(self, context, event):
@@ -129,13 +129,13 @@ def panel(layout_function, ):
     col_main.active = True
     col_main.label(text = "Generate Structure from ESMFold")
     row_name = col_main.row(align = False)
-    row_name.prop(bpy.context.scene, 'mol_esmfold_name', 
+    row_name.prop(bpy.context.scene, 'MN_esmfold_name', 
                     text = "Name", icon_value = 0, emboss = True)
-    row_name.operator('mol.import_protein_esmfold', text='Generate', icon='IMPORT')
+    row_name.operator('mn.import_protein_esmfold', text='Generate', icon='IMPORT')
 
     row_seq = col_main.row()
     row_seq.prop(
-        bpy.context.scene, 'mol_esmfold_sequence', 
+        bpy.context.scene, 'MN_esmfold_sequence', 
         text = "Sequence", 
         icon_value = 0, 
         emboss = True