Validate ESM3-VQVAE Scripts

[mahdip72]

Hi,

Thanks to your amazing team for open-sourcing the ESM series. It's been a huge help to the research community!

Could you please validate the correctness of the backbone coordinate conversion scripts in this fork: https://github.com/mahdip72/esm
Specifically, these two:

• pdb_to_tokens.py: Converts protein backbone coordinates to discrete tokens
• tokens_to_pdb.py: Decodes discrete structure tokens back to backbone coordinates

These scripts are being used for benchmarking ESM3's structure tokenization performance against other methods. We want to ensure the coordinate-to-token-to-coordinate roundtrip is accurate.

The scripts use ESM3_structure_encoder_v0 for encoding and ESM3_structure_decoder_v0 for decoding with mixed precision (FP16) and batch processing.

Any feedback or fixes would be super helpful to keep our benchmarks accurate!

Thanks a lot!