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Merge pull request #182 from gcorso/dev_v1.1
Version 1.1
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‎.dockerignore

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# Ignore hidden files and folders
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**/.*
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.DS_store
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# Ignore git directories (redundant)
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.git
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.gitattributes
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# Ignore generated user results
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results/*
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tmp/
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# Ignore trained models
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workdir/*
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# Do not include PDBBind files
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# (quite likely they are in the same directory)
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**/pdbbind_sequences.fasta
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**/PDBBind_processed/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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.pytest_cache/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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local_config_inference2.yml
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.vscode/
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*.zip
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.idea/

‎.gitignore

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renew.sh
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tmux_renew.sh
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images
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tmp/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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!/data/testset_csv.csv
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!/data/INDEX_general_PL_data.2020
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test_run
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artifacts
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cache
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wandb
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logs
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!/runs/flexible_self_docking
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local_config.yml
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local_config_inference.yml
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local_config_confidence.yml
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local_config_filtering.yml
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temp1.py
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temp5.py
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temp3.py

‎Dockerfile

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# Stage 1: Build Environment Setup
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FROM nvidia/cuda:11.7.1-devel-ubuntu22.04 as builder
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RUN apt-get update -y && apt-get install -y wget curl git tar bzip2 unzip && rm -rf /var/lib/apt/lists/*
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# Create a user
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ENV APPUSER="appuser"
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ENV HOME=/home/$APPUSER
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RUN useradd -m -u 1000 $APPUSER
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USER $APPUSER
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WORKDIR $HOME
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ENV ENV_NAME="diffdock"
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ENV DIR_NAME="ligbind"
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# Install micromamba
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RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xj bin/micromamba
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ENV PATH=$HOME/bin:$HOME/.local/bin:$PATH
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# Copy and create Conda environment
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ENV ENV_FILE_NAME=environment.yml
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COPY --chown=$APPUSER:$APPUSER ./$ENV_FILE_NAME .
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RUN ~/bin/micromamba env create --file $ENV_FILE_NAME && ~/bin/micromamba clean -afy --quiet
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# Copy application code
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COPY --chown=$APPUSER:$APPUSER cuda-ubuntu22.04 $HOME/$DIR_NAME
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# Download models
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# These should download automatically on first inference
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# RUN curl -L -o diffdock_models_v1.1.zip "https://www.dropbox.com/scl/fi/drg90rst8uhd2633tyou0/diffdock_models.zip?rlkey=afzq4kuqor2jb8adah41ro2lz&dl=1" \
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# && mkdir -p $HOME/$DIR_NAME/workdir \
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# && unzip diffdock_models_v1.1.zip -d $HOME/$DIR_NAME/workdir
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# Stage 2: Runtime Environment
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FROM nvidia/cuda:11.7.1-runtime-ubuntu22.04
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# Create user and setup environment
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ENV APPUSER="appuser"
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ENV HOME=/home/$APPUSER
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RUN useradd -m -u 1000 $APPUSER
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USER $APPUSER
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WORKDIR $HOME
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ENV ENV_NAME="diffdock"
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ENV DIR_NAME="ligbind"
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# Copy the Conda environment and application code from the builder stage
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COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/micromamba $HOME/micromamba
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COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/bin $HOME/bin
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COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/$DIR_NAME $HOME/$DIR_NAME
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WORKDIR $HOME/$DIR_NAME
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# Set the environment variables
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ENV MAMBA_ROOT_PREFIX=$HOME/micromamba
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ENV PATH=$HOME/bin:$HOME/.local/bin:$PATH
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RUN micromamba shell init -s bash --root-prefix $MAMBA_ROOT_PREFIX
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# Precompute series for SO(2) and SO(3) groups
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RUN micromamba run -n ${ENV_NAME} python utils/precompute_series.py
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# Expose ports for streamlit and gradio
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EXPOSE 7860 8501
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# Default command
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CMD ["sh", "-c", "micromamba run -n ${ENV_NAME} python utils/print_device.py"]

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