This is the new molecular nodes file

tools/blender/3.4.1-cpu-ubuntu18.04/Dockerfile.txt

@@ -0,0 +1,3 @@
+FROM linuxserver/blender:3.4.1
+COPY . .
+CMD [ "bash" ]

tools/blender/3.4.1-cpu-ubuntu18.04/app.py

@@ -1,92 +1,134 @@
 import bpy
 import os
+import subprocess
 import sys
+import mathutils
 from math import radians
-import random
-from mathutils import Vector, Matrix
-
-def get_random_color(pastel_factor=0.4):
-    return [(x + pastel_factor) / (1.0 + pastel_factor) for x in [random.uniform(0, 1.0) for i in [1, 2, 3]]]
-
-def color_distance(c1, c2):
-    return sum([abs(x[0] - x[1]) for x in zip(c1, c2)])
-
-def generate_new_color(existing_colors, pastel_factor=0.5):
-    max_distance = None
-    best_color = None
-    for i in range(0, 100):
-        color = get_random_color(pastel_factor=pastel_factor)
-        if not existing_colors:
-            return color
-        best_distance = min([color_distance(color, c) for c in existing_colors])
-        if not max_distance or best_distance > max_distance:
-            max_distance = best_distance
-            best_color = color
-    return best_color
-
-def main(input_file_path, output_file_path):
-    bpy.ops.preferences.addon_enable(module='io_mesh_atomic')
-
-    pdb_file_path = input_file_path
-
-    if os.path.exists(pdb_file_path):
-        bpy.ops.object.select_all(action='SELECT')
-        bpy.ops.object.delete()
-        bpy.ops.import_mesh.pdb(filepath=pdb_file_path)
-    else:
-        print("PDB file not found:", pdb_file_path)
-        return
-
-    camera_data = bpy.data.cameras.new(name="New_Camera")
-    camera_object = bpy.data.objects.new("New_Camera", camera_data)
-    scene = bpy.context.scene
-    scene.collection.objects.link(camera_object)
-    scene.camera = camera_object
-    camera_object.location = (58.991, -11.855, 30.663)
-    camera_object.rotation_mode = 'ZYX'
-    camera_object.rotation_euler = (radians(24.4), radians(57.9), radians(-291))
-    camera_object.scale = (1.0, 1.0, 1.0)
-    bpy.ops.object.select_all(action='DESELECT')
-    camera_object.select_set(True)
-    bpy.context.view_layer.objects.active = camera_object
-
-    colors = []
-    for material in bpy.data.materials:
-        new_color = generate_new_color(colors, pastel_factor=0.9)
-        if material.use_nodes:
-            for node in material.node_tree.nodes:
-                if node.type == 'BSDF_PRINCIPLED':
-                    node.inputs['Base Color'].default_value = (new_color[0], new_color[1], new_color[2], 1)
-                    node.inputs['Roughness'].default_value = 0
-                    node.inputs['Sheen Tint'].default_value = 0.7
-                    node.inputs['Metallic'].default_value = 0.8
-
-    bpy.context.view_layer.update()
-
-    camera_location = Vector((58.991, -11.855, 30.663))
-    camera_rotation = (radians(24.4), radians(57.9), radians(-291))
-    light_location = camera_location + Vector((0, 0, 3)) - 3 * (Matrix.Rotation(camera_rotation[0], 3, 'X') @ Matrix.Rotation(camera_rotation[1], 3, 'Y') @ Matrix.Rotation(camera_rotation[2], 3, 'Z') @ Vector((0, 1, 0))) + Vector((2, 0, 0))
-
-    light_data = bpy.data.lights.new(name="New_Sun_Light", type='SUN')
-    light_object = bpy.data.objects.new("New_Sun_Light", light_data)
-    scene.collection.objects.link(light_object)
-    light_object.location = light_location
-    light_object.rotation_mode = 'XYZ'
-    light_rotation = Vector(camera_rotation)
-    random_y_rotation_offset = radians(random.uniform(-12, -8))
-    light_rotation.y += random_y_rotation_offset
-    light_object.rotation_euler = light_rotation
-    light_data.energy = 10
-
-    bpy.context.scene.render.image_settings.file_format = 'PNG'
-    bpy.context.scene.render.filepath = output_file_path
+from mathutils import Vector
+
+def install_addon(addon_path):
+    bpy.ops.preferences.addon_install(filepath=addon_path)
+    addon_name = os.path.splitext(os.path.basename(addon_path))[0]
+    bpy.ops.preferences.addon_enable(module=addon_name)
+
+def install_biotite():
+    blender_python_exe = os.path.join(sys.prefix, 'bin', 'python3.10')
+    cmd = [blender_python_exe, "-m", "pip", "install", "biotite"]
+    subprocess.run(cmd, check=True)
+
+def delete_existing_objects():
+    bpy.ops.object.select_all(action='SELECT')
+    bpy.ops.object.delete(use_global=False)
+
+def set_import_properties(local_path, local_name, include_bonds, center, del_solvent, default_style):
+    bpy.context.scene.mol_import_local_path = local_path
+    bpy.context.scene.mol_import_local_name = local_name
+    bpy.context.scene.mol_import_include_bonds = include_bonds
+    bpy.context.scene.mol_import_center = center
+    bpy.context.scene.mol_import_del_solvent = del_solvent
+    bpy.context.scene.mol_import_default_style = default_style
+
+def import_protein_local():
+    bpy.ops.mol.import_protein_local()
+
+def set_render_engine(engine):
+    bpy.context.scene.render.engine = engine
+
+def enable_gpu_rendering():
+    bpy.context.preferences.addons['cycles'].preferences.compute_device_type = 'METAL'
+
+def create_empty_objects():
+    object_evaluated = bpy.context.object.evaluated_get(bpy.context.evaluated_depsgraph_get())
+    bbox_cos_local = [bbox_co[:] for bbox_co in object_evaluated.bound_box[:]]
+    bbox_cos_global = [bpy.context.object.matrix_world @ Vector(bbox_co) for bbox_co in bbox_cos_local]
+    empty_objects = []
+
+    for co in bbox_cos_global:
+        empty = bpy.data.objects.new(name='empty', object_data=None)
+        bpy.context.scene.collection.objects.link(object=empty)
+        empty.location = co
+        empty.empty_display_type = 'CUBE'
+        empty.empty_display_size = 0.6
+        empty_objects.append(empty)
+
+    lowest_empty = min(empty_objects, key=lambda empty: empty.location.z)
+    return lowest_empty, bbox_cos_global
+
+def add_camera(center):
+    bpy.ops.object.camera_add()
+    camera = bpy.context.object
+    camera.location = center + Vector((0, -5, 0))
+    camera.rotation_euler = (1.5708, 0, 0)
+    bpy.context.scene.camera = camera
+    return camera
+
+def set_background_color(color):
+    bpy.context.scene.world.use_nodes = True
+    bpy.context.scene.world.node_tree.nodes["Background"].inputs[0].default_value = color
+
+def add_plane_below(lowest_empty):
+    plane_size = 7.0
+    plane_height = 0.1
+    plane_location = lowest_empty.location - Vector((0, 0, plane_height / 2))
+    bpy.ops.mesh.primitive_plane_add(size=plane_size, enter_editmode=False, location=plane_location)
+    plane = bpy.context.active_object
+    plane.name = 'plane'
+    material = bpy.data.materials.new(name='PlaneMaterial')
+    material.diffuse_color = (0.8, 0.8, 0.8, 1)
+    plane.data.materials.append(material)
+
+def add_point_light(location, energy):
+    light_data = bpy.data.lights.new(name="PointLight", type='POINT')
+    light_object = bpy.data.objects.new(name="PointLight", object_data=light_data)
+    bpy.context.collection.objects.link(light_object)
+    light_object.location = location
+    light_object.data.energy = energy
+
+def set_render_output(output_path, output_filename):
+    render = bpy.context.scene.render
+    render.filepath = os.path.join(output_path, output_filename)
+    render.image_settings.file_format = 'PNG'
+
+def render_scene():
     bpy.ops.render.render(write_still=True)
 
+def main(input_file_path, output_file_name, output_file_path):
+    addon_path = "./MolecularNodes.zip"
+    install_addon(addon_path)
+    install_biotite()
+    delete_existing_objects()
+
+    local_name = 'PROTEIN NAME'
+    include_bonds = True
+    center = False
+    del_solvent = True
+    default_style = 1
+    set_import_properties(input_file_path, local_name, include_bonds, center, del_solvent, default_style)
+
+    import_protein_local()
+    set_render_engine('CYCLES')
+    enable_gpu_rendering()
+
+    lowest_empty, bbox_cos_global = create_empty_objects()
+    camera = add_camera(sum(bbox_cos_global, Vector()) / 8)
+    set_background_color((0, 0, 0, 1))
+    add_plane_below(lowest_empty)
+    add_point_light((0, 0, 0), 15.0)
+
+    set_render_output(output_file_path, output_file_name)
+    render_scene()
+
+    output_filepath = os.path.join(output_file_path, output_file_name)
+    print("Rendered image saved to:", output_filepath)
+
+
 if __name__ == "__main__":
     if "--" not in sys.argv:
         argv = []  # as if no args are passed
     else:
         argv = sys.argv[sys.argv.index("--") + 1:]  # get all args after "--"
     input_file_path = argv[0]
-    output_file_path = argv[1]
-    main(input_file_path, output_file_path)
+    output_file_name = argv[1]
+    output_file_path = argv[2]
+    main(input_file_path, output_file_name, output_file_path)
+