Incorrect bonds after add_hydrogen() for proteins with non-consecutive residue indices

[Grifonek]

When using hydride.add_hydrogen() on a protein structure, the resulting structure contains incorrect bonds between neighboring atoms (see attached image). This issue occurs for both PDB and CIF inputs, suggesting it is not format-specific.

Observed behavior

• The output structure contains incorrect bonds between some atoms.
• These bonds appear between neighboring residues.
• The issue seems to occur specifically when residue indices are not consecutive (e.g. residue 14 followed by 16 instead of 15).
• Visualization shows clearly incorrect connectivity.

Expected behavior

• Hydrogen addition should not introduce incorrect bonds.
• Bond topology should remain chemically valid, even if residue numbering is non-consecutive.

Additional context

• The input structure appears to have a gap in residue numbering (e.g. 14 → 16).
• However, other tools handle this correctly like moleculekit's systemPrepare() function adds hydrogens without introducing incorrect bonds.

Is this a known issue or there any way how to fix it please?

Thank you!

This is minimal example of my code:

import biotite.structure.io as strucio
import hydride

protein = strucio.load_structure(structure_path, model=1, include_bonds=True)

protein_h, _ = hydride.add_hydrogen(protein)

hydride version: 1.2.3