From 015639b270c140a93f1f693adc605292103e2742 Mon Sep 17 00:00:00 2001 From: ZhouGengmo <2015201981@ruc.edu.cn> Date: Mon, 20 May 2024 08:28:31 +0800 Subject: [PATCH] update model weight (#223) Co-authored-by: zhougm --- unimol_docking_v2/README.md | 21 +++++++++++++++++++ unimol_docking_v2/docker/Dockerfile | 2 +- .../{unimol/scripts => }/train.sh | 2 +- 3 files changed, 23 insertions(+), 2 deletions(-) rename unimol_docking_v2/{unimol/scripts => }/train.sh (92%) diff --git a/unimol_docking_v2/README.md b/unimol_docking_v2/README.md index c7120af..acdb3ca 100644 --- a/unimol_docking_v2/README.md +++ b/unimol_docking_v2/README.md @@ -7,3 +7,24 @@ Dependencies - [Uni-Core](https://github.com/dptech-corp/Uni-Core), check its [Installation Documentation](https://github.com/dptech-corp/Uni-Core#installation). - rdkit==2022.9.3, install via `pip install rdkit-pypi==2022.9.3 -i https://pypi.tuna.tsinghua.edu.cn/simple/ --trusted-host pypi.tuna.tsinghua.edu.cn` - biopandas==0.4.1, install via `pip install biopandas` + + +Model weights +---------------------------------- + +| Model | File Size |Update Date | Download Link | +|--------------------------|------------| ------------|--------------------------------------------------------------| +| unimol docking v2 | 464MB | May 17 2024 |https://www.dropbox.com/scl/fi/sfhrtx1tjprce18wbvmdr/unimol_docking_v2_240517.pt?rlkey=5zg7bh150kcinalrqdhzmyyoo&st=n6j0nt6c&dl=0 | + + +Results +---------------------------------- +|< 2.0 Å RMSD(% ) | PoseBusters (N=428) | Astex (N=85) | +|--------|----|----| +| DeepDock | 17.8 | 34.12 | +| DiffDock | 37.9 |71.76 | +| UMol | 45| - | +| Vina | 52.3 | 57.65 | +| Uni-Mol Docking | 58.9 | 82.35 | +| AlphaFold latest | 73.6 | - | +| **Uni-Mol Docking V2** | **77.6** | **95.29**| diff --git a/unimol_docking_v2/docker/Dockerfile b/unimol_docking_v2/docker/Dockerfile index f120935..d9a8f5c 100644 --- a/unimol_docking_v2/docker/Dockerfile +++ b/unimol_docking_v2/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM dptechnology/unicore:0.0.1-pytorch1.11.0-cuda11.3 +FROM dptechnology/unicore:latest-pytorch1.12.1-cuda11.6-rdma RUN pip install rdkit-pypi==2022.9.3 RUN pip install biopandas diff --git a/unimol_docking_v2/unimol/scripts/train.sh b/unimol_docking_v2/train.sh similarity index 92% rename from unimol_docking_v2/unimol/scripts/train.sh rename to unimol_docking_v2/train.sh index 05d1e42..90d2171 100644 --- a/unimol_docking_v2/unimol/scripts/train.sh +++ b/unimol_docking_v2/train.sh @@ -15,7 +15,7 @@ recycling=4 export NCCL_ASYNC_ERROR_HANDLING=1 export OMP_NUM_THREADS=1 -python -m torch.distributed.launch --nproc_per_node=$n_gpu --master_port=$MASTER_PORT $(which unicore-train) --user-dir ../../unimol $data_path --train-subset train --valid-subset valid \ +python -m torch.distributed.launch --nproc_per_node=$n_gpu --master_port=$MASTER_PORT $(which unicore-train) --user-dir ./unimol $data_path --train-subset train --valid-subset valid \ --num-workers 8 --ddp-backend=c10d \ --task docking_pose_v2 --loss docking_pose_v2 --arch docking_pose_v2 \ --optimizer adam --adam-betas '(0.9, 0.99)' --adam-eps 1e-6 --clip-norm 1.0 \