package changes

Dockerfile

@@ -9,12 +9,14 @@ COPY . .
 # install dependcies
 # FROM continuumio/miniconda3:4.10.3
 # RUN conda install -y python=3.9 pandas numpy scikit-learn
-RUN conda install -y python=3.9
-# RUN conda install -y pandas numpy scikit-learn
-
+# RUN conda install -y python=3.9
 # RUN pip install --upgrade setuptools
+# RUN pip install --no-cache-dir -r requirements.txt
+
+# Create Conda environment from env.yaml
+RUN conda env create -f env.yaml
+SHELL ["conda", "run", "-n", "dockformer-venv", "/bin/bash", "-c"]
 
-RUN pip install --no-cache-dir -r requirements.txt
 
 #if you need to download executable and run them switch to the default non-root user
 USER user

environment.yml

@@ -0,0 +1,32 @@
+name: dockformer-venv
+channels:
+  - conda-forge
+  - pytorch
+dependencies:
+  - python=3.9
+#  - libgcc=7.2
+  - setuptools=59.5.0
+  - pip
+#  - openmm=7.7
+#  - pdbfixer
+#  - cudatoolkit==11.3.*
+  - lightning=2.*
+  - biopython==1.79
+  - numpy==1.21
+  - PyYAML==5.4.1
+  - requests
+  - scipy==1.7
+  - tqdm==4.62.2
+  - typing-extensions
+  - wandb==0.12.21
+  - modelcif==0.7
+  - awscli
+  - ml-collections
+  - aria2
+  - rdkit==1.21
+  - git
+  - pytorch::pytorch=2.3.0
+  - pip:
+#      - torch==2.3.0 --index-url https://download.pytorch.org/whl/cu118
+      - dm-tree==0.1.6
+      - git+https://github.com/NVIDIA/dllogger.git