From d9af74f79899aedc8aed947451b38bf8dd70236d Mon Sep 17 00:00:00 2001 From: Justas Dauparas Date: Thu, 18 Aug 2022 20:35:59 -0700 Subject: [PATCH] update to work with changes --- colab_notebooks/quickdemo.ipynb | 63 ++++++++++++++++++--------------- 1 file changed, 35 insertions(+), 28 deletions(-) diff --git a/colab_notebooks/quickdemo.ipynb b/colab_notebooks/quickdemo.ipynb index 31e23967..873f3a9b 100644 --- a/colab_notebooks/quickdemo.ipynb +++ b/colab_notebooks/quickdemo.ipynb @@ -7,7 +7,7 @@ "colab_type": "text" }, "source": [ - "\"Open" + "\"Open" ] }, { @@ -22,9 +22,8 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 9, "metadata": { - "cellView": "form", "id": "iYDU3ftml2k5" }, "outputs": [], @@ -34,7 +33,7 @@ "\n", "if not os.path.isdir(\"ProteinMPNN\"):\n", " os.system(\"git clone -q https://github.com/dauparas/ProteinMPNN.git\")\n", - "sys.path.append('/content/ProteinMPNN/vanilla_proteinmpnn')" + "sys.path.append('/content/ProteinMPNN')" ] }, { @@ -64,7 +63,7 @@ "\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", @@ -86,11 +85,10 @@ "colab": { "base_uri": "https://localhost:8080/" }, - "cellView": "form", "id": "2nKSlaMlSpcf", - "outputId": "bdbbb9ef-bf1b-43db-ffe1-0bb1d3dba202" + "outputId": "293c6f08-8256-4e08-d8ab-3c2a02ab74b8" }, - "execution_count": 48, + "execution_count": 10, "outputs": [ { "output_type": "stream", @@ -122,10 +120,9 @@ " return my_dict" ], "metadata": { - "cellView": "form", "id": "yjnUkQuZX-de" }, - "execution_count": 49, + "execution_count": 11, "outputs": [] }, { @@ -143,14 +140,13 @@ }, { "cell_type": "code", - "execution_count": 50, + "execution_count": 12, "metadata": { - "cellView": "form", "id": "k4o6w2Y23wxO", "colab": { "base_uri": "https://localhost:8080/" }, - "outputId": "2932cc35-e6d4-4663-bdea-e6a0b9890b24" + "outputId": "58d89f72-5d3c-44a7-c2cb-e26c3c54d43f" }, "outputs": [ { @@ -158,9 +154,9 @@ "name": "stdout", "text": [ "{'1O91': (['A', 'B', 'C'], [])}\n", - "Length of chain A is 131\n", "Length of chain C is 131\n", - "Length of chain B is 131\n" + "Length of chain B is 131\n", + "Length of chain A is 131\n" ] } ], @@ -278,14 +274,14 @@ }, { "cell_type": "code", - "execution_count": 51, + "execution_count": 13, "metadata": { "cellView": "form", "id": "xMVlYh8Fv2of", "colab": { "base_uri": "https://localhost:8080/" }, - "outputId": "e8259379-d4e0-4ef6-b096-d39261249807" + "outputId": "7b3d1839-d872-4f48-f907-775eaf035754" }, "outputs": [ { @@ -293,10 +289,10 @@ "name": "stdout", "text": [ "Generating sequences...\n", - ">1O91, score=1.3063, fixed_chains=[], designed_chains=['A', 'B', 'C'], model_name=v_48_020\n", + ">1O91, score=1.3217, fixed_chains=[], designed_chains=['A', 'B', 'C'], model_name=v_48_020\n", "EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM/EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM/EMPAFTAELTVPFPPVGAPVKFDKLLYNGRQNYNPQTGIFTCEVPGVYYFAYHVHCKGGNVWVALFKNNEPMMYTYDEYKKGFLDQASGSAVLLLRPGDQVFLQMPSEQAAGLYAGQYVHSSFSGYLLYPM\n", - ">T=0.1, sample=0, score=0.6477, seq_recovery=0.4962\n", - "EKEAFTALLTTPHPAVGTPIKFNKVIYNGRNVYDPATGIFTCKTPGIYFFTWVLYVYGNDLHAVLYKNDTPILKTYLQNIPGYINQVSGAAVLELEEGDKVYVKIPSSSANGLYASPDNHSYFSGYLLYEK/EKEAFTALLTTPHPAVGTPIKFNKVIYNGRNVYDPATGIFTCKTPGIYFFTWVLYVYGNDLHAVLYKNDTPILKTYLQNIPGYINQVSGAAVLELEEGDKVYVKIPSSSANGLYASPDNHSYFSGYLLYEK/EKEAFTALLTTPHPAVGTPIKFNKVIYNGRNVYDPATGIFTCKTPGIYFFTWVLYVYGNDLHAVLYKNDTPILKTYLQNIPGYINQVSGAAVLELEEGDKVYVKIPSSSANGLYASPDNHSYFSGYLLYEK\n" + ">T=0.1, sample=0, score=0.6755, seq_recovery=0.4885\n", + "EVEAFTALLTTPHPPVGEPIKFNKLVYNGRNVYDPATGIFTVKTPGVYFFTFVLYVYGADLHAELMKNDTPVIKVYLQTVNGKINQVSGAAVLELEEGDKVYVKIPSASANGLWASADAHSYFSGYLLTEK/EVEAFTALLTTPHPPVGEPIKFNKLVYNGRNVYDPATGIFTVKTPGVYFFTFVLYVYGADLHAELMKNDTPVIKVYLQTVNGKINQVSGAAVLELEEGDKVYVKIPSASANGLWASADAHSYFSGYLLTEK/EVEAFTALLTTPHPPVGEPIKFNKLVYNGRNVYDPATGIFTVKTPGVYFFTFVLYVYGADLHAELMKNDTPVIKVYLQTVNGKINQVSGAAVLELEEGDKVYVKIPSASANGLWASADAHSYFSGYLLTEK\n" ] } ], @@ -410,13 +406,13 @@ "metadata": { "cellView": "form", "id": "xbsaRChNfybM", - "outputId": "710af7b3-1ac9-4026-bf4c-26af1bf6f1c8", + "outputId": "e87c30dc-d960-4878-acae-f67a3b69fc1c", "colab": { "base_uri": "https://localhost:8080/", "height": 542 } }, - "execution_count": 52, + "execution_count": 14, "outputs": [ { "output_type": "display_data", @@ -426,9 +422,9 @@ "\n", "\n", "
\n", - "
\n", - "