RoseTTAFold-All-Atom の変更点

• 追加された行はこの色です。
• 削除された行はこの色です。
• RoseTTAFold-All-Atom へ行く。
• RoseTTAFold-All-Atom の差分を削除

#author("2024-03-18T15:24:09+00:00","default:sysosa","sysosa")
#author("2025-06-01T07:10:33+00:00","default:sysosa","sysosa")
本家様 [[https://github.com/baker-laboratory/RoseTTAFold-All-Atom>+https://github.com/baker-laboratory/RoseTTAFold-All-Atom]]


インストールにmambaを使ってって書いてあるので

#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH

pyenv install miniforge3-23.11.0-0
source /apps/pyenv/versions/miniforge3-23.11.0-0/etc/profile.d/conda.sh
}}

#code(nonumber){{
cd /apps
git clone https://github.com/baker-laboratory/RoseTTAFold-All-Atom
cd RoseTTAFold-All-Atom
}}


#code(nonumber){{
CONDA_OVERRIDE_CUDA="11.8" mamba env create -f environment.yaml

conda activate RFAA

conda list
 :
tensorflow                2.11.0          cuda112py310he87a039_0    conda-forge
tensorflow-base           2.11.0          cuda112py310h52da4a5_0    conda-forge
tensorflow-estimator      2.11.0          cuda112py310h37add04_0    conda-forge
 :

cd rf2aa/SE3Transformer/
pip3 install --no-cache-dir -r requirements.txt
python3 setup.py install
cd ../../

signalp6-register /tmp/signalp-6.0h.fast.tar.gz
mv /apps/pyenv/versions/miniforge3-23.11.0-0/envs/RFAA/lib/python3.10/site-packages/signalp/model_weights/distilled_model_signalp6.pt \
   /apps/pyenv/versions/miniforge3-23.11.0-0/envs/RFAA/lib/python3.10/site-packages/signalp/model_weights/ensemble_model_signalp6.pt

bash ./install_dependencies.sh

wget http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt

wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
mkdir -p UniRef30_2020_06
tar xfz UniRef30_2020_06_hhsuite.tar.gz -C ./UniRef30_2020_06

wget https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
mkdir -p bfd
tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd

wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
tar xfz pdb100_2021Mar03.tar.gz
}}