Hackathon setup

.dockerignore

@@ -0,0 +1,48 @@
+# Git
+.git
+.gitignore
+.github
+
+# Python
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+env/
+venv/
+.venv/
+pip-log.txt
+pip-delete-this-directory.txt
+.tox
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.log
+.idea
+.mypy_cache
+
+# Documentation
+*.md
+docs/
+
+# Development files
+.vscode/
+*.swp
+*.swo
+*~
+
+# Build artifacts (keep minimal)
+predictions/
+submission/
+inputs/
+.tmp_spec.json
+
+# Keep these for the container
+!requirements.txt
+!examples/
+!src/
+!scripts/

.github/workflows/ci.yml

@@ -0,0 +1,30 @@
+name: CI - Build and Test
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test-scaffold:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pyyaml
+        # Install any additional requirements from participants
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Test script help and argument parsing
+      run: |
+        python predict_hackathon.py --help

.gitignore

@@ -161,6 +161,14 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
+# Data files
+hackathon_data/
+
 # Boltz prediction outputs
 #   All result files generated from a boltz prediction call
-boltz_results_*/
+boltz_results_*/
+my_predictions/
+tmp/
+my_results/
+asos_public_evaluation/
+abag_public_evaluation/

Dockerfile

@@ -0,0 +1,71 @@
+# Based on Liana64's contribution https://github.com/jwohlwend/boltz/blob/5ee0e6b9740b85ff24349aacc4d69615f499490b/Dockerfile
+ARG MINIFORGE_NAME=Miniforge3
+ARG MINIFORGE_VERSION=23.3.1-0
+ARG BASE_IMAGE=nvidia/cuda:12.3.0-runtime-ubuntu22.04
+
+FROM ${BASE_IMAGE} AS builder
+ARG MINIFORGE_NAME
+ARG MINIFORGE_VERSION
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  git \
+  build-essential \
+  python3 \
+  python3-venv \
+  python3-dev \
+  wget \
+  && wget --no-check-certificate --no-hsts https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_NAME}-${MINIFORGE_VERSION}-Linux-$(uname -m).sh -O miniforge.sh \
+  && bash miniforge.sh -b -p /opt/conda \
+  && rm miniforge.sh \
+  && /opt/conda/bin/mamba init bash
+
+WORKDIR /app
+COPY environment.yml /app/
+COPY src /app/src
+COPY pyproject.toml /app/pyproject.toml
+
+RUN /opt/conda/bin/mamba env create -f environment.yml --name boltz && \
+    /opt/conda/bin/mamba init bash && \
+    /opt/conda/bin/conda run -n boltz pip install --no-cache-dir --upgrade pip && \
+    /opt/conda/bin/conda run -n boltz pip install --no-cache-dir .[cuda] && \
+    apt-get purge -y git build-essential wget && \
+    apt-get autoremove -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+FROM ${BASE_IMAGE}
+COPY --from=builder /opt/conda /opt/conda
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+  python3 \
+  build-essential \
+  python3-dev \
+  && apt-get autoremove -y \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV PATH="/opt/conda/bin:$PATH" \
+  LANG=C.UTF-8 \
+  PYTHONUNBUFFERED=1
+
+ARG USERNAME=boltz
+ARG UID=900
+ARG GID=900
+RUN groupadd --gid $GID $USERNAME && \
+  useradd --uid $UID --gid $GID --create-home --shell /bin/bash $USERNAME
+
+WORKDIR /app
+
+# Copy everything
+COPY . /app/
+
+RUN chown -R $USERNAME:$USERNAME /app
+
+USER $USERNAME
+
+# Initialize mamba and activate the boltz environment
+SHELL ["/bin/bash", "-c"]
+RUN mamba init bash && \
+    echo "mamba activate boltz" >> ~/.bashrc
+
+CMD ["/bin/bash"]

README.md

@@ -11,6 +11,11 @@
 
 ![](docs/boltz1_pred_figure.png)
 
+## Hackathon Instructions
+
+Please refer to the [hackathon README](hackathon/README_Hackathon.md) for instructions on how to participate in the Boltz hackathon.
+
+**Note:** The hackathon requires at least one CUDA-enabled GPU for running inference.
 
 ## Introduction
 

environment.yml

@@ -0,0 +1,7 @@
+name: boltzplatz
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - pymol-open-source

examples/specs/example_protein_complex.json

@@ -0,0 +1,19 @@
+{
+  "datapoint_id": "complex",
+  "task_type": "protein_complex",
+  "proteins": [
+    {
+      "id": "A",
+      "sequence": "MVTPEGNVSLVDESLLVGV",
+      "msa_path": "examples/msa/seq1.a3m"
+    },
+    {
+      "id": "B",
+      "sequence": "MVTPEGNVSLVDESLLVGK",
+      "msa_path": "examples/msa/seq2.a3m"
+    }
+  ],
+  "ground_truth": {
+    "structure": "examples/ground_truth/complex.pdb"
+  }
+}

examples/specs/example_protein_ligand.json

@@ -0,0 +1,20 @@
+{
+  "datapoint_id": "affinity",
+  "task_type": "protein_ligand",
+  "proteins": [
+    {
+      "id": "A",
+      "sequence": "MVTPEGNVSLVDESLLVGV",
+      "msa_path": "examples/msa/seq1.a3m"
+    }
+  ],
+  "ligands": [
+    {
+      "id": "B",
+      "smiles": "N[C@@H](Cc1ccc(O)cc1)C(=O)O"
+    }
+  ],
+  "ground_truth": {
+    "structure": "examples/ground_truth/affinity.pdb"
+  }
+}

examples/test_dataset.jsonl

@@ -0,0 +1,2 @@
+{"datapoint_id": "affinity", "task_type": "protein_ligand", "proteins": [{"id": "A", "sequence": "MVTPEGNVSLVDESLLVGV", "msa_path": "examples/msa/seq1.a3m"}], "ligands": [{"id": "B", "smiles": "N[C@@H](Cc1ccc(O)cc1)C(=O)O"}], "ground_truth": {"structure": "examples/ground_truth/affinity.pdb"}}
+{"datapoint_id": "complex", "task_type": "protein_complex", "proteins": [{"id": "A", "sequence": "MVTPEGNVSLVDESLLVGV", "msa_path": "examples/msa/seq1.a3m"}, {"id": "B", "sequence": "MVTPEGNVSLVDESLLVGK", "msa_path": "examples/msa/seq2.a3m"}], "ground_truth": {"structure": "examples/ground_truth/complex.pdb"}}