HETATM Records Not Included in `parsed_pdb["pdb_idx"]`

I encountered an issue where HETATM records (e.g. ligands like IMP, NAD) are not being included in parsed_pdb["pdb_idx"], which causes residue lookups like ('A', 601) to fail during get_idx0().

My .pdb file definitely contains HETATM records, it's like:

...
ATOM   2888  CZ  PHE A 514     192.186 187.688 131.489  1.00 29.38           C  
ATOM   2889  OXT PHE A 514     189.765 192.642 131.230  1.00 29.38           O1-
TER   
HETATM 2890  P   IMP A 601     191.927 170.397 138.491  1.00 17.82           P  
HETATM 2891  O1P IMP A 601     192.083 170.120 137.031  1.00 17.82           O  
HETATM 2892  O2P IMP A 601     190.546 170.479 139.055  1.00 17.82           O1-
...

However, when I inspect parsed_pdb["pdb_idx"], it only contains the entries which are standard protein residues (ATOM lines). No entries beyond residue 514 (the last standard residue) are included.

Use Case

I'm working on a binder design task, where my input includes a contig map like:

contigmap.contigs = [A1-111/A231-423/A435-514/A601-602/0 45-65]

The segment A601-602 refers to two ligands (IMP and NAD) in chain A, which are important for defining the binding interface. However, these residues cannot be resolved in get_idx0() because they are missing from parsed_pdb["pdb_idx"].

It seems that the PDB parsing utility used internally filters only ATOM records and ignores HETATM entries, even when they share the same chain ID.

Could you please confirm whether HETATM lines are intentionally excluded from the parsed PDB file? If this exclusion is intentional, could you point me to the recommended way to include ligands like IMP or NAD in parsed_pdb["pdb_idx"]?

Alternatively, if the issue is due to a misunderstanding on my part — for example, if there is a correct way to handle HETATM entries via the contig map or input specification — I'd really appreciate any clarification or documentation reference.

Trace the PDB parsing utility that builds parsed_pdb["pdb_idx"] and the get_idx0() lookup using the HETATM example and contig map in the issue. Determine whether ligand residues are intentionally excluded or should be represented, then document the supported behavior or identify the parsing change needed.