Chai-1

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
 
[root@rockylinux9 ~]# uname -r
5.14.0-503.14.1.el9_5.x86_64
 
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  570.172.08  Tue Jul  8 18:31:33 UTC 2025
GCC version:  gcc version 11.5.0 20240719 (Red Hat 11.5.0-5) (GCC)
 
[root@rockylinux9 ~]#

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
 
pyenv install anaconda3-2024.10-1

[root@rockylinux9 ~]# source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
[root@rockylinux9 ~]# conda create -n Chai-1 pip python=3.12 -c conda-forge -y
 
[root@rockylinux9 ~]# conda activate Chai-1
(Chai-1) [root@rockylinux9 ~]# cd /apps/src/
(Chai-1) [root@rockylinux9 src]# git clone https://github.com/chaidiscovery/chai-lab
(Chai-1) [root@rockylinux9 src]# cd chai-lab/
(Chai-1) [root@rockylinux9 chai-lab]# pip install .
 
(Chai-1) [root@rockylinux9 chai-lab]# conda list
 :
chai-lab                  0.6.1                    pypi_0    pypi
 :
numpy                     1.26.4                   pypi_0    pypi
nvidia-cublas-cu12        12.6.4.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.6.80                  pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.6.77                  pypi_0    pypi
nvidia-cuda-runtime-cu12  12.6.77                  pypi_0    pypi
nvidia-cudnn-cu12         9.5.1.17                 pypi_0    pypi
nvidia-cufft-cu12         11.3.0.4                 pypi_0    pypi
nvidia-cufile-cu12        1.11.1.6                 pypi_0    pypi
nvidia-curand-cu12        10.3.7.77                pypi_0    pypi
nvidia-cusolver-cu12      11.7.1.2                 pypi_0    pypi
nvidia-cusparse-cu12      12.5.4.2                 pypi_0    pypi
nvidia-cusparselt-cu12    0.6.3                    pypi_0    pypi
nvidia-nccl-cu12          2.26.2                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.6.85                  pypi_0    pypi
nvidia-nvtx-cu12          12.6.77                  pypi_0    pypi
 :
python                    3.12.11         h9e4cc4f_0_cpython    conda-forge
 :
rdkit                     2024.9.6                 pypi_0    pypi
 :
torch                     2.7.1                    pypi_0    pypi
 :
typer                     0.16.0                   pypi_0    pypi
 :
(Chai-1) [root@rockylinux9 chai-lab]#
 
(Chai-1) [root@rockylinux9 chai-lab]# conda install kalign3 -c bioconda

(Chai-1) [root@rockylinux9 chai-lab]# mkdir /apps/Chai
 
(Chai-1) [root@rockylinux9 chai-lab]# CHAI_DOWNLOADS_DIR=/apps/Chai  python  ./examples/predict_structure.py
 
(Chai-1) [root@rockylinux9 chai-lab]# conda deactivate
 
[root@rockylinux9 chai-lab]#

[root@rockylinux9 ~]# cd /apps/Chai/
[root@rockylinux9 Chai]# ls -lR
.:
total 119M
-rw-r--r--. 1 root root 119M Jul 21 02:08 conformers_v1.apkl
-rw-r--r--. 1 root root    0 Jul 21 02:08 conformers_v1.download_lock
drwxr-xr-x. 2 root root  107 Jul 21 02:23 esm
drwxr-xr-x. 2 root root 4.0K Jul 21 02:24 models_v2
 
./esm:
total 5.3G
-rw-r--r--. 1 root root    0 Jul 21 02:09 traced_sdpa_esm2_t36_3B_UR50D_fp16.download_lock
-rw-r--r--. 1 root root 5.3G Jul 21 02:23 traced_sdpa_esm2_t36_3B_UR50D_fp16.pt
 
./models_v2:
total 615M
-rw-r--r--. 1 root root    0 Jul 21 02:24 bond_loss_input_proj.download_lock
-rw-r--r--. 1 root root 5.4K Jul 21 02:24 bond_loss_input_proj.pt
-rw-r--r--. 1 root root    0 Jul 21 02:24 feature_embedding.download_lock
-rw-r--r--. 1 root root 4.4M Jul 21 02:24 feature_embedding.pt
-rw-r--r--. 1 root root    0 Jul 21 02:24 token_embedder.download_lock
-rw-r--r--. 1 root root 6.0M Jul 21 02:24 token_embedder.pt
-rw-r--r--. 1 root root    0 Jul 21 02:24 trunk.download_lock
-rw-r--r--. 1 root root 604M Jul 21 02:24 trunk.pt
[root@rockylinux9 Chai]#
 
 
[root@rockylinux9 Chai]# mkdir --mode=1777 /apps/Chai/template_cifs

#%Module1.0
set          root       /apps/pyenv/versions/anaconda3-2024.10-1/envs/Chai-1
prepend-path PATH       $root/bin
 
setenv CHAI_DOWNLOADS_DIR /apps/Chai
setenv DISABLE_PANDERA_IMPORT_WARNING true

[saber@rockylinux9 ~]$ cat query.fasta
>protein|sample-A
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK
 
[saber@rockylinux9 ~]$
 
 
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load Chai
 
[saber@rockylinux9 ~]$ chai-lab fold --use-msa-server --use-templates-server query.fasta out

>protein|name=example-of-long-protein
AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQWMFGCDLGPDGRLLRGYDQSAYDGK（略
>protein|name=example-of-short-protein
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
>protein|name=example-peptide
GAAL
>ligand|name=example-ligand-as-smiles
CCCCCCCCCCCCCC(=O)O