From 740d84437002c2ba48653d8fa711cca2905115c0 Mon Sep 17 00:00:00 2001 From: Sergey O Date: Thu, 28 Dec 2023 14:18:56 -0500 Subject: [PATCH] fixing esmfold/openfold to use -std=c++17 (needed for cuda12 and pytorch 2) --- ESMFold.ipynb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/ESMFold.ipynb b/ESMFold.ipynb index 0c798fbf..3a009641 100644 --- a/ESMFold.ipynb +++ b/ESMFold.ipynb @@ -68,15 +68,16 @@ " os.system(f\"aria2c -q -x 16 https://colabfold.steineggerlab.workers.dev/esm/{model_name} &\")\n", "\n", " if not os.path.isfile(\"finished_install\"):\n", - " print(\"installing esmfold...\")\n", " # install libs\n", - " os.system(\"pip install -q omegaconf \\\"pytorch_lightning<2\\\" \\\"torch<2\\\" biopython ml_collections einops py3Dmol\")\n", + " print(\"installing libs...\")\n", + " os.system(\"pip install -q omegaconf pytorch_lightning biopython ml_collections einops py3Dmol modelcif\")\n", " os.system(\"pip install -q git+https://github.com/NVIDIA/dllogger.git\")\n", "\n", + " print(\"installing openfold...\")\n", " # install openfold\n", - " commit = \"6908936b68ae89f67755240e2f588c09ec31d4c8\"\n", - " os.system(f\"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}\")\n", + " os.system(f\"pip install -q git+https://github.com/sokrypton/openfold.git\")\n", "\n", + " print(\"installing esmfold...\")\n", " # install esmfold\n", " os.system(f\"pip install -q git+https://github.com/sokrypton/esm.git\")\n", " os.system(\"touch finished_install\")\n", @@ -341,4 +342,4 @@ "outputs": [] } ] -} +} \ No newline at end of file