AlphaFold 3.0.3

AlphaFold3 のモデルパラメータについては各自で申請、ダウンロードしてください。

ウェブページ

https://github.com/google-deepmind/alphafold3

バージョン

3.0.3

導入環境

  • NVIDIA ドライバ 610.43.02

導入手順(抜粋)

AlphaFold

[user@ccfep4 ~]$ curl -LsSf https://astral.sh/uv/install.sh | sh
[user@ccfep4 ~]$ export UV_PYTHON_INSTALL_DIR=/apl/alphafold/3.0.3/python-uv
[user@ccfep4 ~]$ uv python install 3.12
[user@ccfep4 ~]$ export UV_PYTHON=/apl/alphafold/3.0.3/python-uv/cpython-3.12.13-linux-x86_64-gnu/bin/python
[user@ccfep4 ~]$ export UV_PROJECT_ENVIRONMENT=/apl/alphafold/3.0.3/venv
[user@ccfep4 ~]$ uv venv $UV_PROJECT_ENVIRONMENT

[user@ccfep4 ~]$ cd /apl/alphafold/3.0.3
[user@ccfep4 3.0.3]$ git clone https://github.com/google-deepmind/alphafold3.git -b v3.0.3
[user@ccfep4 3.0.3]$ cd alphafold3/
[user@ccfep4 alphafold3]$ module load gcc-toolset/14
[user@ccfep4 alphafold3]$ uv sync --frozen --all-groups --no-editable

[user@ccfep4 alphafold3]$ . /apl/alphafold/3.0.3/venv/bin/activate
(venv) [user@ccfep4 alphafold3]$ build_data 

hmmer-3.4 (patched)

[user@ccfep1 ~]$ cd /apl/alphafold/3.0.3
[user@ccfep1 3.0.3]$ wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz --directory-prefix hmmer_build
[user@ccfep1 3.0.3]$ cd hmmer_build
[user@ccfep1 hmmer_build]$ echo "ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 hmmer-3.4.tar.gz" | sha256sum --check
hmmer-3.4.tar.gz: OK
[user@ccfep1 hmmer_build]$ echo $?
0
[user@ccfep1 hmmer_build]$ tar xf hmmer-3.4.tar.gz && rm -f hmmer-3.4.tar.gz
[user@ccfep1 hmmer_build]$ patch -p0 < ../alphafold3/docker/jackhmmer_seq_limit.patch
patching file hmmer-3.4/src/jackhmmer.c
[user@ccfep1 hmmer_build]$ cd hmmer-3.4
[user@ccfep1 hmmer-3.4]$ ./configure --prefix /apl/alphafold/3.0.3/hmmer
[user@ccfep1 hmmer-3.4]$ make -j16
[user@ccfep1 hmmer-3.4]$ make install
[user@ccfep1 hmmer-3.4]$ cd easel
[user@ccfep1 easel]$ make install
[user@ccfep1 easel]$ rm -rf /apl/alphafold/3.0.3/hmmer_build

メモ