add molecule

pages/01_app.ipynb

@@ -2,50 +2,169 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Device with name Apple M1 supports metal minimum requirements\n",
+      "Finsihed opening molecule after 0.22209199999999996 seconds\n",
+      "Adding object to scene.\n",
+      "Added res_id after 0.0002569999999999517 s\n",
+      "Added res_name after 0.002530999999999839 s\n",
+      "Added atomic_number after 0.003058000000000227 s\n",
+      "Added b_factor after 4.500000000007276e-05 s\n",
+      "Added vdw_radii after 0.0031120000000002257 s\n",
+      "Added chain_id after 0.000496000000000052 s\n",
+      "Added entity_id after 0.0002420000000000755 s\n",
+      "Added atom_name after 0.0019409999999999705 s\n",
+      "Added lipophobicity after 0.003919000000000228 s\n",
+      "Added charge after 0.0038169999999997373 s\n",
+      "Added is_backbone after 0.000376000000000154 s\n",
+      "Added is_alpha_carbon after 0.00012599999999984846 s\n",
+      "Added is_solvent after 0.00012699999999998823 s\n",
+      "Added is_nucleic after 0.0005660000000000664 s\n",
+      "Added is_peptide after 0.0008569999999998856 s\n",
+      "Added is_hetero after 0.00010400000000032605 s\n",
+      "Added is_carb after 0.0006049999999997446 s\n",
+      "Added sec_struct after 0.0018339999999996692 s\n",
+      "Finsihed add object after 0.030968000000000107 seconds\n",
+      "METAL API - DETECTED GPU: Apple M1\n",
+      "Fra:1 Mem:58.21M (Peak 62.13M) | Time:00:00.09 | Syncing Light\n",
+      "Fra:1 Mem:58.21M (Peak 62.13M) | Time:00:00.09 | Syncing Camera\n",
+      "Fra:1 Mem:58.21M (Peak 62.13M) | Time:00:00.09 | Syncing 7TYG\n",
+      "Fra:1 Mem:69.90M (Peak 73.03M) | Time:00:00.12 | Rendering 1 / 64 samples\n",
+      "Fra:1 Mem:60.64M (Peak 73.03M) | Time:00:00.21 | Rendering 26 / 64 samples\n",
+      "Fra:1 Mem:60.64M (Peak 73.03M) | Time:00:00.27 | Rendering 51 / 64 samples\n",
+      "Fra:1 Mem:60.64M (Peak 73.03M) | Time:00:00.30 | Rendering 64 / 64 samples\n",
+      "Saved: '/var/folders/c3/3bzrl3qx043bknt1ycn3fcym0000gn/T/tmp6cvuhryo.JPEG'\n",
+      " Time: 00:00.40 (Saving: 00:00.09)\n",
+      "\n"
+     ]
+    },
+    {
+     "data": {
+      "image/jpeg": 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+      "text/plain": [
+       "<IPython.core.display.Image object>"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "import bpy\n",
     "import tempfile\n",
+    "import molecularnodes as mn\n",
+    "\n",
+    "import bpy\n",
+    "import tempfile\n",
+    "from math import pi\n",
+    "\n",
+    "def generate():\n",
     "\n",
-    "def enable_GPUS():\n",
-    "    bpy.data.scenes[0].render.engine = \"CYCLES\" #\"CYCLES\"\n",
-    "    # Set the device_type\n",
-    "    bpy.context.preferences.addons[\"cycles\"].preferences.compute_device_type = \"METAL\" \n",
+    "    for obj in bpy.context.scene.objects:\n",
+    "      if obj.type == 'MESH':\n",
+    "          bpy.data.objects.remove(obj, do_unlink=True)\n",
     "\n",
-    "    # Set the device and feature set\n",
-    "    bpy.context.scene.cycles.device = \"CUDA\" #GPU\n",
     "\n",
-    "    for scene in bpy.data.scenes:\n",
-    "        scene.cycles.device = \"GPU\"\n",
+    "    molecule = mn.load.molecule_rcsb(\"7TYG\", starting_style=\"cartoon\", center_molecule=True)\n",
+    "    molecule.select_set(True)\n",
     "\n",
-    "    bpy.context.preferences.addons[\"cycles\"].preferences.get_devices()\n",
-    "    print(bpy.context.preferences.addons[\"cycles\"].preferences.compute_device_type)\n",
-    "    for d in bpy.context.preferences.addons[\"cycles\"].preferences.devices:\n",
-    "        d[\"use\"] = True  # Using all devices, include GPU and CPU\n",
-    "        print(d[\"name\"])\n",
+    "    bpy.ops.view3d.camera_to_view_selected()\n",
+    "    camera = bpy.data.objects[\"Camera\"]\n",
+    "    camera.data.dof.use_dof = True\n",
+    "    camera.data.dof.focus_distance = 5\n",
+    "    camera.data.dof.aperture_fstop = 4\n",
+    "    camera.data.angle = pi / 3\n",
+    "    camera.data.type = \"PERSP\"\n",
     "\n",
-    "def render_image():\n",
     "    with tempfile.NamedTemporaryFile(suffix=\".JPEG\", delete=False) as f:\n",
-    "        bpy.context.scene.render.resolution_y = 200\n",
-    "        bpy.context.scene.render.resolution_x = 400\n",
+    "        bpy.context.scene.render.resolution_y = 288\n",
+    "        bpy.context.scene.render.resolution_x = 512\n",
     "        bpy.context.scene.render.image_settings.file_format = \"JPEG\"\n",
     "        bpy.context.scene.render.filepath = f.name\n",
-    "        # enable_GPUS()\n",
+    "        bpy.context.scene.frame_set(1)\n",
+    "        bpy.context.scene.frame_current = 1\n",
     "        bpy.ops.render.render(animation=False, write_still=True)\n",
+    "\n",
     "        bpy.data.images[\"Render Result\"].save_render(\n",
     "            filepath=bpy.context.scene.render.filepath\n",
     "        )\n",
     "        bpy.app.handlers.render_stats.clear()\n",
-    "        return f.name\n"
+    "        return f.name\n",
+    "\n",
+    "\n",
+    "from IPython.display import Image\n",
+    "Image(generate())"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "e5740872b66541d18a024ae31b57becf",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "None\n",
+      "Finsihed opening molecule after 0.1597609999999996 seconds\n",
+      "Adding object to scene.\n",
+      "Added res_id after 0.0002570000000003958 s\n",
+      "Added res_name after 0.01812600000000053 s\n",
+      "Added atomic_number after 0.006369999999999543 s\n",
+      "Added b_factor after 5.100000000002325e-05 s\n",
+      "Added vdw_radii after 0.0065309999999998425 s\n",
+      "Added chain_id after 0.000516000000000183 s\n",
+      "Added entity_id after 0.00023499999999998522 s\n",
+      "Added atom_name after 0.005037999999999876 s\n",
+      "Added lipophobicity after 0.007436999999999472 s\n",
+      "Added charge after 0.007236999999999938 s\n",
+      "Added is_backbone after 0.00047999999999959186 s\n",
+      "Added is_alpha_carbon after 0.0001610000000002998 s\n",
+      "Added is_solvent after 0.0001619999999995514 s\n",
+      "Added is_nucleic after 0.0006459999999997024 s\n",
+      "Added is_peptide after 0.0010190000000003252 s\n",
+      "Added is_hetero after 0.0001120000000005561 s\n",
+      "Added is_carb after 0.000656000000000212 s\n",
+      "Added sec_struct after 0.0031799999999995165 s\n",
+      "Finsihed add object after 0.06568800000000063 seconds\n",
+      "Fra:1 Mem:58.97M (Peak 64.78M) | Time:00:00.01 | Syncing Light\n",
+      "Fra:1 Mem:58.97M (Peak 64.78M) | Time:00:00.01 | Syncing Camera\n",
+      "Fra:1 Mem:58.97M (Peak 64.78M) | Time:00:00.01 | Syncing 7TYG\n",
+      "Fra:1 Mem:70.60M (Peak 73.73M) | Time:00:00.01 | Rendering 1 / 64 samples\n",
+      "Fra:1 Mem:61.22M (Peak 73.73M) | Time:00:00.09 | Rendering 26 / 64 samples\n",
+      "Fra:1 Mem:61.28M (Peak 73.73M) | Time:00:00.16 | Rendering 51 / 64 samples\n",
+      "Fra:1 Mem:61.22M (Peak 73.73M) | Time:00:00.19 | Rendering 64 / 64 samples\n",
+      "Saved: '/var/folders/c3/3bzrl3qx043bknt1ycn3fcym0000gn/T/tmp6sh3rfo0.JPEG'\n",
+      " Time: 00:00.20 (Saving: 00:00.00)\n",
+      "\n",
+      "/var/folders/c3/3bzrl3qx043bknt1ycn3fcym0000gn/T/tmp6sh3rfo0.JPEG\n"
+     ]
+    }
+   ],
    "source": [
     "import solara\n",
     "from IPython.display import Image, display\n",
@@ -58,7 +177,7 @@
     "\n",
     "    def render():\n",
     "        if do_render.value:\n",
-    "            return render_image()\n",
+    "            return generate()\n",
     "   \n",
     "    result = solara.use_thread(render, [do_render.value])\n",
     "    if not do_render.value:\n",
@@ -82,7 +201,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [