update readme.md

CAODH · Oct 15, 2024 · 32fbe0b · 32fbe0b
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Showing 1 changed file with 17 additions and 15 deletions.
diff --git a/README.md b/README.md
@@ -28,21 +28,23 @@ If you want to train one of our models with the data then:
 (in CodeOcean we have setuped the environment, youcan run the bash script to use SurfDock)
 Or you can follow the instructions to setup the environment
 
-`conda create -y -n SurfDock python==3.10`
-`source /opt/conda/bin/activate SurfDock`
-`conda install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg mamba && conda clean -ya`
-`mamba install -y pytorch pytorch-cuda=12.1 -c pytorch -c nvidia`
-`mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg numpy==1.20 scipy==1.8.1 pandas==2.1.2 &&conda clean -ya`
-`mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg openff-toolkit==0.15.2 openmm==8.1.1 openmmforcefields==0.12.0 pdbfixer==1.9 && conda clean -ya`
-`mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg babel==2.13.1 biopandas==0.4.1 openbabel==3.1.1 plyfile==1.0.1 prody==2.4.0 torch-ema==0.3 torchmetrics==1.2.1 && conda clean -ya`
-`mamba install -y pyg -c pyg`
-`pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.2.0+cu121.html`
-`pip install -U --no-cache-dir spyrmsd scikit-learn==1.3.2 accelerate==0.15.0 biopython==1.79 e3nn==0.5.1 huggingface-hub==0.17.3 mdanalysis==2.4.0 posebusters==0.2.7 rdkit==2023.3.1 tokenizers==0.13.3 transformers==4.29.2 wandb==0.16.1`
-`pip install pymesh`
-`pip install https://github.com/nuvolos-cloud/PyMesh/releases/download/v0.3.1/pymesh2-0.3.1-cp310-cp310-linux_x86_64.whl`
-`mamba install loguru`
-`pip install dimorphite_dl`
-`pip install prefetch_generator`
+```bash
+conda create -y -n SurfDock python==3.10
+source /opt/conda/bin/activate SurfDock
+conda install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg mamba && conda clean -ya
+mamba install -y pytorch pytorch-cuda=12.1 -c pytorch -c nvidia
+mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg numpy==1.20 scipy==1.8.1 pandas==2.1.2 &&conda clean -ya
+mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg openff-toolkit==0.15.2 openmm==8.1.1 openmmforcefields==0.12.0 pdbfixer==1.9 && conda clean -ya
+mamba install -y --channel=https://conda.anaconda.org/conda-forge --channel=https://conda.anaconda.org/pytorch --channel=https://conda.anaconda.org/pyg babel==2.13.1 biopandas==0.4.1 openbabel==3.1.1 plyfile==1.0.1 prody==2.4.0 torch-ema==0.3 torchmetrics==1.2.1 && conda clean -ya
+mamba install -y pyg -c pyg
+pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.2.0+cu121.html
+pip install -U --no-cache-dir spyrmsd scikit-learn==1.3.2 accelerate==0.15.0 biopython==1.79 e3nn==0.5.1 huggingface-hub==0.17.3 mdanalysis==2.4.0 posebusters==0.2.7 rdkit==2023.3.1 tokenizers==0.13.3 transformers==4.29.2 wandb==0.16.1
+pip install pymesh
+pip install https://github.com/nuvolos-cloud/PyMesh/releases/download/v0.3.1/pymesh2-0.3.1-cp310-cp310-linux_x86_64.whl
+mamba install loguru
+pip install dimorphite_dl
+pip install prefetch_generator
+```
 ### Masif & data processed env dependencies
 mamba install mx::reduce
 mamba install conda-forge::openbabel