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AlphaFold3_of3: fix install on Colab's Python 3.13 runtime #849

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AlphaFold3_of3: fix install on Colab's Python 3.13 runtime #849

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17 changes: 15 additions & 2 deletions AlphaFold3_of3.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
"source": [
"#@title Install dependencies (~3 mins)\n",
"%%time\n",
"import os, time, glob\n",
"import os, sys, time, glob, json, urllib.request\n",
"\n",
"use_af3_weights = True #@param {type:\"boolean\"}\n",
"#@markdown - **use_af3_weights**: leave OFF to use the free, open **OpenFold3** weights. Turn ON to\n",
Expand All @@ -59,7 +59,20 @@
" print('Installing packages...')\n",
" os.system(\"pip install -q 'jax[cuda12]==0.10.1' dm-haiku==0.0.16 rdkit==2025.9.4 \\\n",
" zstandard awscli tokamax==0.0.11 py3Dmol py2Dmol\")\n",
" os.system(\"pip install -q --no-deps 'https://github.com/sokrypton/alphafold3/releases/download/v3.1.4/alphafold3_open-3.1.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl'\")\n",
" # Resolve the alphafold3-open wheel for THIS interpreter (Colab bumps its Python\n",
" # version yearly; a hardcoded cp312 filename breaks the day it does).\n",
" AF3_VER, AF3_REPO = '3.1.5', 'sokrypton/alphafold3'\n",
" _pytag = f'cp{sys.version_info.major}{sys.version_info.minor}'\n",
" _whl = (f'https://github.com/{AF3_REPO}/releases/download/v{AF3_VER}/alphafold3_open-'\n",
" f'{AF3_VER}-{_pytag}-{_pytag}-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl')\n",
" try: # prefer the release manifest, so a changed platform tag still resolves\n",
" _rel = json.load(urllib.request.urlopen(\n",
" f'https://api.github.com/repos/{AF3_REPO}/releases/tags/v{AF3_VER}'))\n",
" _whl = next(a['browser_download_url'] for a in _rel['assets']\n",
" if a['name'].endswith('.whl') and f'-{_pytag}-' in a['name'])\n",
" except Exception as _e:\n",
" print(f'(release lookup failed, using default wheel URL: {_e})')\n",
" os.system(f\"pip install -q --no-deps '{_whl}'\")\n",
" base = 'https://raw.githubusercontent.com/sokrypton/alphafold3/refs/heads/main'\n",
" for script in ['run_alphafold', 'convert_of3_weights']:\n",
" os.system(f'wget -q -nc {base}/{script}.py')\n",
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