Fpocket notebook/ directory restructure

Dockerfile

@@ -4,7 +4,7 @@ WORKDIR /app
 ENV NODE_VERSION=16.13.1
 
 RUN apt-get --allow-releaseinfo-change update && apt-get -y upgrade
-RUN apt-get install -y curl
+RUN apt-get install -y curl build-essential
 
 # Set up jupyter conda environment
 RUN conda update conda

cookbook/00_Template.ipynb

@@ -51,6 +51,8 @@
    "outputs": [],
    "source": [
     "# Load a TYL into your workspace\n",
+    "# Full set of functions for plugin available at \n",
+    "# https://nanome.readthedocs.io/en/latest/nanome.beta.redis_interface.html#module-nanome.beta.redis_interface\n",
     "tyl_pdb = 'test_data/1tyl.pdb'\n",
     "plugin.send_files_to_load([tyl_pdb])\n"
    ]
@@ -180,14 +182,6 @@
     "plugin.update_structures_deep([comp])\n",
     "plugin.apply_color_scheme(enums.ColorScheme.DonorAcceptor, enums.ColorSchemeTarget.All)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14ee53ec-6ae8-4704-be1e-aa56e3de3dfc",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

cookbook/notebooks/01_Basics.ipynb → cookbook/01_Basics.ipynb

@@ -39,7 +39,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "# benzenes contain 12 atoms\n",
@@ -66,7 +66,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "# Write complex to new pdb file\n",
@@ -110,7 +110,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "comp.name = 'Benzene'\n",
     "\n",
@@ -133,7 +133,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "comp.name = 'Benzene'\n",
     "\n",
@@ -167,7 +167,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "comp.new_property = 'blah blah blah'\n",
@@ -191,7 +191,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "atom = next(comp.atoms)\n",
     "\n",
@@ -214,7 +214,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Get list of atoms bonded to selected one\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "atom = next(comp.atoms)\n",
     "\n",
@@ -251,7 +251,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "bond = next(comp.bonds)\n",
     "print(bond.kind)"
@@ -276,7 +276,7 @@
     "from nanome.api.structure import Complex\n",
     "\n",
     "# Read using filepath\n",
-    "input_dir = 'assets/cookbook/1tyl.pdb'\n",
+    "input_dir = 'test_data/1tyl.pdb'\n",
     "comp = Complex.io.from_pdb(path=input_dir)\n",
     "\n",
     "for i, chain in enumerate(comp.chains):\n",
@@ -301,7 +301,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "print(list(comp.bonds))\n"
@@ -322,7 +322,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/benzene_241.sdf'\n",
+    "input_dir = 'test_data/benzene_241.sdf'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "print(list(comp.residues))\n"
@@ -343,7 +343,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/1tyl.pdb'\n",
+    "input_dir = 'test_data/1tyl.pdb'\n",
     "comp = Complex.io.from_sdf(path=input_dir)\n",
     "\n",
     "print(list(comp.molecules))"
@@ -371,7 +371,7 @@
    "source": [
     "from nanome.api.structure import Complex\n",
     "\n",
-    "input_dir = 'assets/cookbook/1tyl.pdb'\n",
+    "input_dir = 'test_data/1tyl.pdb'\n",
     "comp = Complex.io.from_pdb(path=input_dir)\n",
     "\n",
     "atom_count = len(list(comp.atoms))\n",
@@ -402,7 +402,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.5"
+   "version": "3.9.18"
   },
   "toc-autonumbering": false,
   "toc-showcode": false,

cookbook/02_ColorChangerStream.ipynb

@@ -0,0 +1,100 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "381bc757-d397-4a2f-b9ef-74dd0def85ba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from nanome.beta.redis_interface import PluginInstanceRedisInterface\n",
+    "from nanome.util.enums import StreamType\n",
+    "import os\n",
+    "import itertools\n",
+    "\n",
+    "# Set up redis credentials\n",
+    "redis_host = os.environ.get(\"REDIS_HOST\")\n",
+    "redis_port = os.environ.get(\"REDIS_PORT\")\n",
+    "redis_password = os.environ.get(\"REDIS_PASSWORD\")\n",
+    "redis_channel = \"\"  # Use room id code received when activating cookbook plugin\n",
+    "\n",
+    "plugin = PluginInstanceRedisInterface(redis_host, redis_port, redis_password, redis_channel)\n",
+    "plugin.connect()\n",
+    "print('Plugin Connected')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8b82a3ae-c281-4cb9-9435-7dd57b0407ef",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "comps = plugin.request_complex_list()\n",
+    "[comp] = plugin.request_complexes([comps[0].index])\n",
+    "print(comp)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a07c480-b68a-41d0-b60e-ec333f932dd4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "roygbiv = [\n",
+    "    (255, 0, 0),  # Red\n",
+    "    (255, 127, 0),  # Orange\n",
+    "    (255, 255, 0),  # Yellow\n",
+    "    (0, 255, 0),  # Green\n",
+    "    (0, 0, 255),  # Blue\n",
+    "    (75, 0, 130),  # Indigo\n",
+    "    (148, 0, 211),  # Violet\n",
+    "]\n",
+    "\n",
+    "\n",
+    "def set_color_stream_data(atom_indices, color):\n",
+    "    \"\"\"Set the color for every atom in the stream.\"\"\"\n",
+    "    stream_data = [None] * (len(atom_indices) * 3)\n",
+    "    color_vals = itertools.cycle(color)\n",
+    "    for i in range(len(stream_data)):\n",
+    "        stream_data[i] = next(color_vals)\n",
+    "    return stream_data\n",
+    "\n",
+    "\n",
+    "# Create a writing stream to sets color for every atom in the complex.\n",
+    "atom_indices = [atom.index for atom in comp.atoms]\n",
+    "stream_type = StreamType.color\n",
+    "stream = plugin.create_writing_stream(atom_indices, stream_type)\n",
+    "\n",
+    "color_cycle = itertools.cycle(roygbiv)\n",
+    "for color in color_cycle:\n",
+    "    stream_data = set_color_stream_data(atom_indices, color)\n",
+    "    plugin.update_stream(stream, stream_data)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}