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