From 905b0081f3aa3404d7ac22174bc25710f9995ff8 Mon Sep 17 00:00:00 2001
From: Justas Dauparas <justas.dauparas@gmail.com>
Date: Thu, 18 Aug 2022 20:45:42 -0700
Subject: [PATCH] updating to work with latest changes

---
 colab_notebooks/quickdemo_wAF2.ipynb | 67 +++++++++++++++++++++++-----
 1 file changed, 56 insertions(+), 11 deletions(-)

diff --git a/colab_notebooks/quickdemo_wAF2.ipynb b/colab_notebooks/quickdemo_wAF2.ipynb
index c7c90b83..cfe99d66 100644
--- 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
-}
+}
\ No newline at end of file