Possible error in receptor_con_hal_idx0 variable in trb file

I think there is a bug in the making of the trb file variable receptor_con_hal_idx0. Perhaps this is not a bug and I misunderstand what this variable is supposed to be.

As an example, I am making a binder using the contig "[A80-598/0 50-70]" (from a pdb containing chain A with residues 80-598).

I upload the (unpickled) trb file.

As expected,

'complex_con_hal_pdb_idx': shows chain and residue ID of residues from chain A in the reference structure, as they appear in the generated model. Because my binder in this case was 69 residues, the first residue appears as (B, 70)

'complex_con_hal_idx0' : shows 0-indexed residues from chain A in the reference structure, as they appear in the generated model. because my binder in this case was 69 residues, the first residue of chain A is numbered 69.

'receptor_con_hal_pdb_idx': shows chain and residue ID of residues non-redesigned chains, as they appear in the generated model. Since my only chain from the reference is chain A, this is identical to complex_con_hal_pdb_idx

Following this logic, 'receptor_con_hal_idx0' should be identical to complex_con_hal_idx0, but it's not. Instead, it starts at 0 (identical to receptor_con_ref_idx0).

Note that this logic does work for the "con_ref" variables. In this example, 'receptor_con_ref_idx0' and 'complex_con_ref_idx0' are identical as I understand they should (because there are no residues taken from the reference structure in designed chains)

I believe what's happening is that the value of 'receptor_con_ref_idx0' is mistakenly being assigned to 'receptor_con_hal_pdb_idx'

trb_file_for_issue.txt

Load the attached trb_file_for_issue.txt and trace the code that creates receptor_con_hal_idx0, receptor_con_hal_pdb_idx, and the related con_ref fields. Reproduce the reported contig "[A80-598/0 50-70]" case and compare the generated arrays; done means the receptor con_hal index values match the stated residue mapping or the issue is explained as intended behavior.