Summary

• update OpenFold3 defaults and accept the new PAE key while keeping backward compatibility
• preserve ligand chains in iPAE input preparation
• add RosettaFold3 input conversion, runner, output parsing, PAE/HTML integration, and compact tests

Verification

• Local: uv run --python 3.12 --extra test pytest tests/test_af3_to_rosettafold.py tests/test_run_rosettafold.py tests/test_rosettafold_output.py tests/test_openfold_output.py tests/test_protenix_output.py tests/test_ipsae.py tests/test_argparse.py tests/test_plots.py
• Local: uv run --python 3.12 --extra lint ruff check
• Lobachevsky f4e8205: same pytest subset, 28 passed
• Lobachevsky f4e8205: same ruff subset, all checks passed