Add rfdiffusion3, rosettafold3 and protparadelle-1c

Author: pansapiens

dockerfiles/protparadelle-1c/f4c9c14/Dockerfile

@@ -0,0 +1,84 @@
+# syntax=docker/dockerfile:1.4
+FROM condaforge/miniforge3:25.11.0-0 AS base
+
+LABEL org.opencontainers.image.source https://github.com/Australian-Protein-Design-Initiative/containers
+
+# Build arguments
+ARG DOWNLOAD_MODELS=true
+ARG GIT_REF=f4c9c14
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    CUDA_HOME=/usr/local/cuda \
+    PATH=/opt/conda/bin:$PATH \
+    PROTPARDELLE_OUTPUT_DIR=/tmp \
+    PROJECT_ROOT_DIR=/app/protpardelle-1c \
+    PROTPARDELLE_MODEL_PARAMS=/app/protpardelle-1c/model_params
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    wget \
+    curl \
+    git \
+    aria2 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install huggingface-hub for model downloads
+RUN --mount=type=cache,target=/root/.cache/pip \
+    pip install "huggingface_hub[cli]"
+
+# Install Foldseek
+RUN wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz && \
+    tar -xzf foldseek-linux-gpu.tar.gz && \
+    mv foldseek/bin/foldseek /usr/bin/ && \
+    rm -rf foldseek-linux-gpu.tar.gz foldseek
+
+ENV FOLDSEEK_BIN=/usr/bin/foldseek
+
+WORKDIR /app
+
+# Clone the repository
+RUN git clone https://github.com/ProteinDesignLab/protpardelle-1c.git /app/protpardelle-1c && \
+    cd /app/protpardelle-1c && \
+    git checkout ${GIT_REF}
+
+# Setup Python environment and install dependencies
+RUN --mount=type=cache,target=/root/.cache/pip \
+    cd /app/protpardelle-1c && \
+    pip install torch && \
+    pip install -e .
+
+# Download model weights (conditional)
+RUN --mount=type=cache,target=/models \
+    if [ "$DOWNLOAD_MODELS" = "true" ]; then \
+        cd /app/protpardelle-1c && \
+        # Zenodo seems the be blocking aria2c, so we patch to use wget instead
+        sed -i 's/aria2c \-x16 \-s16 \-o/wget -O/' download_model_params.sh && \
+        echo "Downloading model weights..." && \
+        bash download_model_params.sh && \
+        mkdir -p /models && \
+        ln -s /app/protpardelle-1c/model_params /models/protpardelle-1c && \
+        chmod -R a+r /app/protpardelle-1c/model_params && \
+        find /app/protpardelle-1c/model_params -type d -exec chmod a+x {} \;; \
+    else \
+        echo "Skipping model weights download - to use this container please pre-download models to the host and bind them as a volume at /app/protpardelle-1c/model_params"; \
+    fi
+
+# Create wrapper scripts
+RUN printf '#!/bin/sh\nexec python -m protpardelle.sample "$@"\n' > /usr/local/bin/protpardelle-sample && \
+    printf '#!/bin/sh\nexec python -m protpardelle.train "$@"\n' > /usr/local/bin/protpardelle-train && \
+    printf '#!/bin/sh\nexec python -m protpardelle.likelihood "$@"\n' > /usr/local/bin/protpardelle-likelihood && \
+    chmod +x /usr/local/bin/protpardelle-*
+
+# Create non-root user
+RUN useradd -m -u 1001 protpardelle && \
+    mkdir -p /app && \
+    chown -R protpardelle:protpardelle /app
+
+# Switch back to non-root user for final execution
+USER protpardelle
+
+CMD ["protpardelle-sample", "--help"]

dockerfiles/rfdiffusion3/0.1.9/Dockerfile

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+FROM python:3.12
+
+LABEL org.opencontainers.image.source https://github.com/Australian-Protein-Design-Initiative/containers
+
+#ARG GIT_REPO=https://github.com/RosettaCommons/modelforge.git
+ARG GIT_REF=0.1.9
+
+ARG DOWNLOAD_MODELS=true
+
+ENV FOUNDRY_CHECKPOINT_DIRS=/models/foundry
+ENV DEBIAN_FRONTEND=noninteractive \
+    PIP_NO_CACHE_DIR=1 \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+RUN mkdir -p /models/foundry
+
+RUN pip install "rc-foundry[rfd3]==${GIT_REF}"
+
+RUN if [ "$DOWNLOAD_MODELS" = "true" ]; then \
+        foundry install rfd3 --checkpoint-dir ${FOUNDRY_CHECKPOINT_DIRS}; \
+        chmod -R a+rx ${FOUNDRY_CHECKPOINT_DIRS}; \
+    fi
+
+RUN groupadd -g 1000 rfd3user && \
+    useradd -m -u 1000 -g 1000 -s /bin/bash rfd3user
+
+USER rfd3user
+
+CMD ["rfd3", "--help"]

dockerfiles/rosettafold3/0.1.9/Dockerfile

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+FROM python:3.12
+
+LABEL org.opencontainers.image.source https://github.com/Australian-Protein-Design-Initiative/containers
+
+#ARG GIT_REPO=https://github.com/RosettaCommons/modelforge.git
+ARG GIT_REF=0.1.9
+
+ARG DOWNLOAD_MODELS=true
+
+ENV FOUNDRY_CHECKPOINT_DIRS=/models/foundry
+ENV DEBIAN_FRONTEND=noninteractive \
+    PIP_NO_CACHE_DIR=1 \
+    PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+RUN mkdir -p /models/foundry
+
+RUN pip install "rc-foundry[rf3]==${GIT_REF}"
+
+# RUN git clone https://github.com/RosettaCommons/modelforge.git /apps/rosettafold3 \
+#   && cd /apps/rosettafold3 \
+#   && pip install -e ".[rf3]"
+
+RUN if [ "$DOWNLOAD_MODELS" = "true" ]; then \
+        foundry install rf3 --checkpoint-dir ${FOUNDRY_CHECKPOINT_DIRS}; \
+        chmod -R a+rx ${FOUNDRY_CHECKPOINT_DIRS}; \
+    fi
+
+RUN groupadd -g 1000 rf3user && \
+    useradd -m -u 1000 -g 1000 -s /bin/bash rf3user
+
+USER rf3user
+
+CMD ["rfd3", "--help"]