Add Singularity support and some fixes

[hegelab]

Summary

This PR introduces a Singularity container definition to facilitate reproducible deployment of RFantibody on HPC and cloud environments. It also includes several fixes encountered while setting up and using the tool.

Key Changes

• Working Dockerfile with active Python environment
• Patched Python scripts for RFdiffusion, ProteinMPNN, RF2
• Added working examples and corrected file paths
• Quiver-based workflows are not tuned
• Container user write permissions fixed with --user $(id -u)
• Preserved original README as README.orig.md
• Singularity definition file (singularity.def) added for HPC-compatible container builds

Motivation

We adapted RFantibody for our use case in a high-performance compute environment where Singularity is preferred over Docker. Along the way, we encountered and fixed several small issues that we believe may affect other users as well.

Notes

We understand that not all changes may be directly aligned with upstream design goals. Please feel free to suggest edits, or let us know if you'd prefer these changes to be split into multiple PRs. We're happy to collaborate further.