How to preserve conformer indices in the XYZ comment line?

[YKikuchi1222]

I am trying to track specific conformations before and after clustering to see which ones are discarded.

I added a conformer index to the comment line of my ensemble XYZ file, but the output file overwrites these comments, leaving only the energy values.

Is there a way to prevent the comment line from being overwritten?

If not, what is the best practice for tracking conformer IDs throughout the workflow?

I need to map the final clustered structures back to their original indices. Any advice would be appreciated.

Thank you

[pprcht]

No, unfortunately you can't pass along information through the sampling.

However, for your specific issue this might be helpful: https://github.com/pprcht/irmsd