Merge pull request #182 from gcorso/dev_v1.1

Version 1.1

.dockerignore

@@ -0,0 +1,128 @@
+# Ignore hidden files and folders
+**/.*
+.DS_store
+
+# Ignore git directories (redundant)
+.git
+.gitattributes
+
+# Ignore generated user results
+results/*
+tmp/
+
+# Ignore trained models
+workdir/*
+
+# Do not include PDBBind files
+# (quite likely they are in the same directory)
+**/pdbbind_sequences.fasta
+**/PDBBind_processed/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+local_config_inference2.yml
+.vscode/
+
+
+*.zip
+
+.idea/

.gitignore

@@ -5,6 +5,8 @@ inference_out_dir_not_specified
 renew.sh
 tmux_renew.sh
 images
+tmp/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -130,7 +132,7 @@ local_config_inference2.yml
 !/data/testset_csv.csv
 !/data/INDEX_general_PL_data.2020
 test_run
-
+artifacts
 cache
 wandb
 logs
@@ -154,7 +156,7 @@ results
 !/runs/flexible_self_docking
 local_config.yml
 local_config_inference.yml
-local_config_confidence.yml
+local_config_filtering.yml
 temp1.py
 temp5.py
 temp3.py

Dockerfile

@@ -0,0 +1,66 @@
+# Stage 1: Build Environment Setup
+FROM nvidia/cuda:11.7.1-devel-ubuntu22.04 as builder
+
+RUN apt-get update -y && apt-get install -y wget curl git tar bzip2 unzip && rm -rf /var/lib/apt/lists/*
+
+# Create a user
+ENV APPUSER="appuser"
+ENV HOME=/home/$APPUSER
+RUN useradd -m -u 1000 $APPUSER
+USER $APPUSER
+WORKDIR $HOME
+
+ENV ENV_NAME="diffdock"
+ENV DIR_NAME="ligbind"
+
+# Install micromamba
+RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xj bin/micromamba
+ENV PATH=$HOME/bin:$HOME/.local/bin:$PATH
+
+# Copy and create Conda environment
+ENV ENV_FILE_NAME=environment.yml
+COPY --chown=$APPUSER:$APPUSER ./$ENV_FILE_NAME .
+RUN ~/bin/micromamba env create --file $ENV_FILE_NAME && ~/bin/micromamba clean -afy --quiet
+
+# Copy application code
+COPY --chown=$APPUSER:$APPUSER cuda-ubuntu22.04 $HOME/$DIR_NAME
+
+# Download models
+# These should download automatically on first inference
+# RUN curl -L -o diffdock_models_v1.1.zip "https://www.dropbox.com/scl/fi/drg90rst8uhd2633tyou0/diffdock_models.zip?rlkey=afzq4kuqor2jb8adah41ro2lz&dl=1" \
+#     && mkdir -p $HOME/$DIR_NAME/workdir \
+#     && unzip diffdock_models_v1.1.zip -d $HOME/$DIR_NAME/workdir
+
+
+# Stage 2: Runtime Environment
+FROM nvidia/cuda:11.7.1-runtime-ubuntu22.04
+
+# Create user and setup environment
+ENV APPUSER="appuser"
+ENV HOME=/home/$APPUSER
+RUN useradd -m -u 1000 $APPUSER
+USER $APPUSER
+WORKDIR $HOME
+
+ENV ENV_NAME="diffdock"
+ENV DIR_NAME="ligbind"
+
+# Copy the Conda environment and application code from the builder stage
+COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/micromamba $HOME/micromamba
+COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/bin $HOME/bin
+COPY --from=builder --chown=$APPUSER:$APPUSER $HOME/$DIR_NAME $HOME/$DIR_NAME
+WORKDIR $HOME/$DIR_NAME
+
+# Set the environment variables
+ENV MAMBA_ROOT_PREFIX=$HOME/micromamba
+ENV PATH=$HOME/bin:$HOME/.local/bin:$PATH
+RUN micromamba shell init -s bash --root-prefix $MAMBA_ROOT_PREFIX
+
+# Precompute series for SO(2) and SO(3) groups
+RUN micromamba run -n ${ENV_NAME} python utils/precompute_series.py
+
+# Expose ports for streamlit and gradio
+EXPOSE 7860 8501
+
+# Default command
+CMD ["sh", "-c", "micromamba run -n ${ENV_NAME} python utils/print_device.py"]