Converting RFDiffusion Format to Genie2 Format

[ssiddhantsharma]

I've created a utility that addresses the two limitations mentioned in your documentation regarding the motif scaffolding problem definition format:

1. Residue Order Matching: My script automatically reorders residues in the PDB file to match the order specified in the motif scaffolding specification.

2. PDB Name Handling: The script also correctly places the PDB name only in the REMARK 999 PDB line and not in individual motif segment definitions.

Features

• Converts intuitive RFDiffusion-style format to Genie2's column-specific format.
• Validates that specified residues exist in the PDB structure.
• Automatically reorders residues to match motif specifications.
• Supports multi-chain complexes with proper group assignment.

Here's my repository: https://github.com/ssiddhantsharma/RFdiffusion_to_Genie2_Convertor

Would this be useful to reference in your documentation or potentially including in Genie2? I'd be happy add test-cases and validate this further. Thank you for creating and maintaining Genie2!