axmd/2026/2026-03/antibogy/install RFantibody.md

title, date, tags, collections

title	date	tags	collections
install RFantibody	2026-03-12	antibody soft insatll	antibody install

install RFantibody

# dir: /share/nas3/zhushixin/soft/unzip/RFantibody
git clone ssh://git@39.104.92.69:8512/pub_soft/RFantibody.git

# download weight
bash include/download_weights.sh

mamba create -n rfanibody
mamba activate  rfanibody
mamba install python=3.10

pip install --pre torch torchvision torchaudio --index-url https://download.pytorch.org/whl/nightly/cu128
pip install --pre dgl --no-deps -f https://data.dgl.ai/wheels-test/torch-2.4/cu124/repo.html


# 安装依赖
pip install .
pip install omegaconf
# pip install hydra-core==1.3.2
pip install hydra
pip install scipy

# test
python  /home/src/rfantibody/rfdiffusion/rfdiffusion_inference.py \
    --config-name antibody \
    antibody.target_pdb=/home/scripts/examples/example_inputs/rsv_site3.pdb \
    antibody.framework_pdb=/home/scripts/examples/example_inputs/hu-4D5-8_Fv.pdb \
    inference.ckpt_override_path=/home/weights/RFdiffusion_Ab.pt \
    'ppi.hotspot_res=[T305,T456]' \
    'antibody.design_loops=[L1:8-13,L2:7,L3:9-11,H1:7,H2:6,H3:5-13]' \
    inference.num_designs=20 \
    inference.output_prefix=/home/scripts/examples/example_outputs/ab_des
#faild

gpu0

# dir: /share/nas3/zhushixin/soft/gpu0_soft/RFantibody
git clone ssh://git@39.104.92.69:8512/pub_soft/RFantibody.git

# download weight
bash include/download_weights.sh

# test 
docker run --gpus '"device=1"' -it --rm 36d3aa0632ed

gpu0

# dir: /share/nas3/zhushixin/soft/gpu0_soft/RFantibody
git clone ssh://git@39.104.92.69:8512/pub_soft/RFantibody.git

# download weight
bash include/download_weights.sh

mamba activate uv
uv sync

test

# test
 bash scripts/examples/nanobody_full_pipeline.sh

# 查看设计结果
qvls scripts/examples/example_outputs/nb_ha_pipeline/2_proteinmpnn.qv
mkdir check_install
## split结果
qvextract  scripts/examples/example_outputs/nb_ha_pipeline/3_rf2.qv -o check_install/
## 提取分数文件
qvscorefile scripts/examples/example_outputs/nb_ha_pipeline/3_rf2.qv
cp scripts/examples/example_outputs/nb_ha_pipeline/3_rf2.sc check_install/3_rf2.tsv