updating to work with latest changes

dauparas · Aug 19, 2022 · 905b008 · 905b008
1 parent d9af74f
commit 905b008
Showing 1 changed file with 56 additions and 11 deletions.
diff --git a/colab_notebooks/quickdemo_wAF2.ipynb b/colab_notebooks/quickdemo_wAF2.ipynb
@@ -36,8 +36,8 @@
  "if not os.path.isdir(\"ProteinMPNN\"):\n",
  " os.system(\"git clone -q https://github.com/dauparas/ProteinMPNN.git\")\n",
  "\n",
- "if \"ProteinMPNN/vanilla_proteinmpnn\" not in sys.path:\n",
- " sys.path.append('/content/ProteinMPNN/vanilla_proteinmpnn')\n",
+ "if \"ProteinMPNN\" not in sys.path:\n",
+ " sys.path.append('/content/ProteinMPNN')\n",
  "\n",
  "import matplotlib.pyplot as plt\n",
  "import shutil\n",
@@ -61,7 +61,7 @@
  "\n",
  "backbone_noise=0.00 # Standard deviation of Gaussian noise to add to backbone atoms\n",
  "\n",
- "path_to_model_weights='/content/ProteinMPNN/vanilla_proteinmpnn/vanilla_model_weights' \n",
+ "path_to_model_weights='/content/ProteinMPNN/vanilla_model_weights' \n",
  "hidden_dim = 128\n",
  "num_layers = 3 \n",
  "model_folder_path = path_to_model_weights\n",
@@ -105,20 +105,65 @@
  " return f\"{pdb_code}.pdb\""
  ],
  "metadata": {
- "cellView": "form",
- "id": "2nKSlaMlSpcf"
+ "id": "2nKSlaMlSpcf",
+ "outputId": "3ea5b539-aa2b-43e0-ffae-b31cb9526cd3",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ }
  },
- "execution_count": null,
- "outputs": []
+ "execution_count": 1,
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "Number of edges: 48\n",
+ "Training noise level: 0.2A\n",
+ "Model loaded\n"
+ ]
+ }
+ ]
  },
  {
  "cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
  "metadata": {
  "cellView": "form",
- "id": "xMVlYh8Fv2of"
+ "id": "xMVlYh8Fv2of",
+ "outputId": "243ab7cf-187f-45c9-f005-16253f708e0c",
+ "colab": {
+ "base_uri": "https://localhost:8080/"
+ }
  },
- "outputs": [],
+ "outputs": [
+ {
+ "output_type": "stream",
+ "name": "stdout",
+ "text": [
+ "{'6MRR': (['A'], [])}\n",
+ "Length of chain A is 68\n",
+ "Generating sequences...\n",
+ ">6MRR, score=1.4495, fixed_chains=[], designed_chains=['A'], model_name=v_48_020\n",
+ "GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLEKKGYTVDIKIE\n",
+ ">T=0.1, sample=0, score=1.0100, seq_recovery=0.4559\n",
+ "GIDEELEKVVKEIKAFLEKQGITNVEIKVEDGELTIVMKGASKKTIDFLKKTKKRLEAKGYKVNVKIE\n",
+ ">T=0.1, sample=0, score=0.9381, seq_recovery=0.4853\n",
+ "GVDPELEKVVKELEAFLKEKGVTNVKIEVKDGVLTITMKGASKEVKEFLEKLKKELEAKGYTVNVKIE\n",
+ ">T=0.1, sample=0, score=0.9491, seq_recovery=0.4853\n",
+ "GIDPELEKYKEKLEKFLKEQGITNVEIKIENGTLTIKMNGASEEVKNYLKKLKEELEAKGYKVNVEIS\n",
+ ">T=0.1, sample=0, score=0.9319, seq_recovery=0.5000\n",
+ "GIDEELEKYVKKLKEFLKKKGITNVKIEIKDGKLTITMKGASKETKEFLKKLKKELEEKGYEVNIEIK\n",
+ ">T=0.1, sample=0, score=0.9127, seq_recovery=0.4853\n",
+ "GIDEELEKYVKELKKFLKEKGVNNVKIKVEDGELTIEMKGASKEVKEFLEKLKKELEKKGYKVNVKIE\n",
+ ">T=0.1, sample=0, score=0.9532, seq_recovery=0.5735\n",
+ "GMDEELEKVKEELEAFLKKQGITNVEIKIENGKLTIKMKGASEEVKKKLEELEKELKAKGYEVEIKIE\n",
+ ">T=0.1, sample=0, score=0.9198, seq_recovery=0.5294\n",
+ "HMDEELEKYVEKLKAFLKEQGITNVEIEIEDGELTIKMKGASEEVKEFLEKLKKELEAKGYKVNIEIE\n",
+ ">T=0.1, sample=0, score=0.9605, seq_recovery=0.5441\n",
+ "GVDEELEKYVEKLKEFLKKKGINNVEIEIKDGELTIKMNGASKETKEFLEKLKKELEEKGYTVNIEIK\n"
+ ]
+ }
+ ],
  "source": [
  "#@title #Run ProteinMPNN\n",
  "\n",
@@ -606,4 +651,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}