rfdiffusion

name	rfdiffusion
description	Use when working from the local RFdiffusion repository to generate protein backbones or binder designs through its Docker Compose workflows.
allowed-tools	Bash

rfdiffusion

Workspace-local gateway for /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion. The repo contains a Chinese quickstart, test_rfdiffusion.sh, design_ebola_binder.sh, a populated models/ directory, and Docker/Compose entrypoints for inference.

Quick Start

• Repository: /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion
• Primary smoke test: ./test_rfdiffusion.sh
• Primary build step: docker compose build

When To Use This Tool

• Running RFdiffusion locally from the checked-out workspace repo
• Generating monomer or binder backbones with the repo's inference script
• Reusing the bundled models/ directory and test harness
• Exploring the repo's Ebola binder design example

Common Patterns

# Build the RFdiffusion container stack
cd /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion
docker compose build

# Run the repo's built-in smoke test
cd /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion
./test_rfdiffusion.sh

# Run direct inference through the repo's compose service
docker compose run --rm --entrypoint /bin/bash rfdiffusion -c \
  "python3 scripts/run_inference.py 'contigmap.contigs=[150-150]' inference.output_prefix=outputs/test_run/test inference.num_designs=1 inference.model_directory_path=/app/RFdiffusion/models inference.input_pdb=/app/RFdiffusion/examples/input_pdbs/1qys.pdb"

Recommended Workflow

1. Work from the local RFdiffusion repo rather than stale absolute paths copied from older notes.
2. Build the Docker/Compose environment first.
3. Run ./test_rfdiffusion.sh before attempting custom binder or motif jobs.
4. Only move on to custom scripts like design_ebola_binder.sh after the compose test succeeds.

Guardrails

• Docker images are not prebuilt in this workspace. docker image inspect rfdiffusion failed with No such image: rfdiffusion:latest.
• The quickstart document still references /media/vimalinx/Data/bio_studio/RFdiffusion; the actual workspace repo is under /home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion.
• The quickstart notes GPU memory around 8GB+ for binder design.
• test_rfdiffusion.sh depends on Docker Compose and the repo's models/ directory layout.
• RFdiffusion is a generative structure-design tool, not a drop-in sequence-to-structure predictor.