From 110e2b627adc830b3eeba01ef7f617c78132d25b Mon Sep 17 00:00:00 2001
From: Sergey O <krypton@uw.edu>
Date: Fri, 15 Dec 2023 02:18:17 -0600
Subject: [PATCH] RoseTTFold2 fix - updating dgl to cuda 12

---
 RoseTTAFold2.ipynb | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/RoseTTAFold2.ipynb b/RoseTTAFold2.ipynb
index 5cf1ddc8..db6f0729 100644
--- a/RoseTTAFold2.ipynb
+++ b/RoseTTAFold2.ipynb
@@ -61,7 +61,7 @@
         "  print(\"install RoseTTAFold2\")\n",
         "  os.system(\"git clone https://github.com/sokrypton/RoseTTAFold2.git\")\n",
         "  os.system(\"pip -q install py3Dmol\")\n",
-        "  os.system(\"pip install dgl==1.0.2+cu116 -f https://data.dgl.ai/wheels/cu116/repo.html\")\n",
+        "  os.system(\"pip install dgl -f https://data.dgl.ai/wheels/cu121/repo.html\")\n",
         "  os.system(\"cd RoseTTAFold2/SE3Transformer; pip -q install --no-cache-dir -r requirements.txt; pip -q install .\")\n",
         "  os.system(\"wget https://raw.githubusercontent.com/sokrypton/ColabFold/beta/colabfold/mmseqs/api.py\")\n",
         "\n",
@@ -160,7 +160,7 @@
         "          # expand homooligomeric sequences\n",
         "          xs = ['/'.join([x]*num) for x,num in zip(xs,u_nums)]\n",
         "          msa.append('/'.join(xs))\n",
-        "  \n",
+        "\n",
         "  if len(msa) < max_msa and (mode in [\"unpaired\",\"unpaired_paired\"] or len(u_seqs) == 1):\n",
         "    print(\"getting unpaired MSA\")\n",
         "    out = run_mmseqs2(u_seqs,f\"{path}/\")\n",
@@ -184,7 +184,7 @@
         "            sub_msa[-1].append('/'.join(xs))\n",
         "            sub_msa_num += 1\n",
         "      sub_idx.append(list(range(len(sub_msa[-1]))))\n",
-        "    \n",
+        "\n",
         "    while len(msa) < max_msa and sub_msa_num > 0:\n",
         "      for n in range(len(sub_idx)):\n",
         "        if len(sub_idx[n]) > 0:\n",
@@ -372,8 +372,8 @@
       "source": [
         "#@title Download prediction\n",
         "\n",
-        "#@markdown Once this cell has been executed, a zip-archive with \n",
-        "#@markdown the obtained prediction will be automatically downloaded \n",
+        "#@markdown Once this cell has been executed, a zip-archive with\n",
+        "#@markdown the obtained prediction will be automatically downloaded\n",
         "#@markdown to your computer.\n",
         "\n",
         "# add settings file\n",
@@ -410,7 +410,7 @@
         "---\n",
         "**symmetry settings**\n",
         "\n",
-        "RoseTTAFold2 was finetuned with explicit symmetry information. If the symmetry is known, you can specify using `sym` and `order` options. Supported symmetries include: [C]yclic, [D]ihedral, [T]etrahedral, [I]cosahedral, [O]ctahedral and [X] for unknown. \n",
+        "RoseTTAFold2 was finetuned with explicit symmetry information. If the symmetry is known, you can specify using `sym` and `order` options. Supported symmetries include: [C]yclic, [D]ihedral, [T]etrahedral, [I]cosahedral, [O]ctahedral and [X] for unknown.\n",
         "- `order` define number of copies in X/C/D symmetries.\n",
         "- `msa_concat_mode` defines how the msa is concatenated.\n",
         "```bash\n",
@@ -442,7 +442,7 @@
         "- `max_msa` - if `max_msa * 8` is lower than number of sequences in the input MSA. The number of sequences are subsampled to the max number. Different subsamplings may also results in stochasticity.\n",
         "\n",
         "**I'm running out of memory, what do I do??**\n",
-        "- Try decrease `max_msa` to a smaller number. \n",
+        "- Try decrease `max_msa` to a smaller number.\n",
         "- Get better GPU, on free Google colab max total length ~1600"
       ],
       "metadata": {